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Sample records for mutation breeding methods

  1. Mutations induced in plant breeding

    Energy Technology Data Exchange (ETDEWEB)

    Barriga B, P. (Universidad Austral de Chile, Valdivia. Inst. de Produccion y Sanidad Vegetal)

    1984-10-01

    The most significant aspects of the use of ionizing radiations in plant breeding are reviewed. Aspects such as basic principles of mutation, expression and selection in obtention of mutants, methods for using induced mutations and sucess achieved with this methodology in plant breeding are reviewed. Results obtained in a program of induced mutation on wheat for high content of protein and lysine at the Universidad Austral de Chile are presented.

  2. Radiation mutation breeding

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hi Sup; Kim, Jae Sung; Kim, Jin Kyu; Shin, In Chul; Lim, Young Taek

    1998-04-01

    In order to develop an advanced technical knowledge for the selection of better mutants, some of the crops were irradiated and the mutation rate, the survival rate and the method for selction of a mutant were studied. Furthermore, this study aimed to obtain basic data applicable to the development of genetic resources by evaluation and analysis the specific character for selection of the superior mutant and its plant breeding. 1. selection of the mutant with a superior resistance against environment in the principal crops 1) New varieties of mutant rices such as Wonpyeongbyeo, Wongwangbyeo, Winmibyeo, and heogseon chalbeyeo (sticky forma) were registered in the national variety list and made an application to crop variety protection right. They are under review now. 2) We also keep on studying on the number of a grain of 8 lines of excellent mutant rice for the purpose of improvement of breeding . 3) We selected 3 lines which have a resistance to pod and stem blight in large soybean, 31 lines with small grain size and higher yield, 112 lines of soybean of cooking, 7 lines of low lipoxygenase content, and 12 lines with decreased phytic acid content by 20 % compared to the previous level. 2. Selection of advanced Mugunwha (Rose of Sharon) mutant 1) Bagseul, a new variety of mutant, was developed and 30 plantlets of it are being proliferated. 2) Fifty-three lines of a mutant having a various morphologies were selected.

  3. [Research on discrimination method of tomato via space mutation breeding based on spectroscopy technology].

    Science.gov (United States)

    Shi, Jia-Hui; Shao, Yong-Ni; He, Yong; Li, Duo; Feng, Pan; Zhu, Jia-Jin

    2009-11-01

    In order to quickly analyze varieties of tomato via space mutation breeding with near infrared spectra, firstly, principal component analysis was used to analyze the clustering of tomato leaf samples, and then abundant spectral data were compressed by wavelet transform and the model was built with radial basis function neural network, which offered a quantitative analysis of tomato varieties discrimination. The model regarded the compressed data as the input of neural network input vectors and the training process speeded up. One hundred and five leaf samples of CK, M1 and M2 were selected randomly to build the training model, and forty five samples formed the prediction set. The discrimination rate of 97.8% was achieved by this method. It offered a new approach to the fast discrimination of varieties of tomato via space mutation breeding.

  4. Plant Breeding by Using Radiation Mutation

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Si Yong; Kim, Dong Sub; Lee, Geung Joo (and others)

    2007-06-15

    A mutation breeding is to use physical or chemical mutagens to induce mutagenesis, followed by individual selections with favorable traits. The mutation breeding has many advantages over other breeding methods, which include the usefulness for improving one or two inferior characteristics, applications to broad species with different reproductive systems or to diverse plant materials, native or plant introduction with narrow genetic background, time and cost-effectiveness, and valuable mutant resources for genomic researches. Recent applications of the radiation breeding techniques to developments of flowering plants or food crops with improved functional constituents heightened the public's interests in agriculture and in our genetic resources and seed industries. The goals of this project, therefore, include achieving advances in domestic seed industries and agricultural productivities by developing and using new radiation mutants with favored traits, protecting an intellectual property right of domestic seeds or germplasm, and sharing the valuable mutants and mutated gene information for the genomic and biotech researches that eventually leads to economic benefits.

  5. Biotechnological approach in crop improvement by mutation breeding in Indonesia

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    Soeranto, H.; Sobrizal; Sutarto, Ismiyati; Manurung, Simon; Mastrizal [National Nuclear Energy Agency, Center for Research and Development of Isotope and Radiation Technology, Jakarta (Indonesia)

    2002-02-01

    Mutation breeding has become a proven method of improving crop varieties. Most research on plant mutation breeding in Indonesia is carried out at the Center for Research and Development of Isotope and Radiation Technology, National Nuclear Energy Agency (BATAN). Nowadays, a biotechnological approach has been incorporated in some mutation breeding researches in order to improve crop cultivars. This approach is simply based on cellular totipotency, or the ability to regenerate whole, flowering plants from isolated organs, pieces of tissue, individual cells, and protoplasts. Tissue culture technique has bee extensively used for micro propagation of disease-free plants. Other usage of this technique involves in various steps of the breeding process such as germplasm preservation, clonal propagation, and distant hybridization. Mutation breeding combined with tissue culture technique has made a significant contribution in inducing plant genetic variation, by improving selection technology, and by accelerating breeding time as for that by using anther or pollen culture. In Indonesia, research on mutation breeding combined with tissue culture techniques has been practiced in different crop species including rice, ginger, banana, sorghum etc. Specially in rice, a research on identification of DNA markers linked to blast disease resistance is now still progressing. A compiled report from some research activities is presented in this paper. (author)

  6. Radiation-induced mutations and plant breeding

    Energy Technology Data Exchange (ETDEWEB)

    Naqvi, S.H.M.

    1985-01-01

    Ionizing radiation could cause genetic changes in an organism and could modify gene linkages. The induction of mutation through radiation is random and the probability of getting the desired genetic change is low but can be increased by manipulating different parameters such as dose rate, physical conditions under which the material has been irradiated, etc. Induced mutations have been used as a supplement to conventional plant breeding, particularly for creating genetic variability for specific characters such as improved plant structure, pest and disease resistance, and desired changes in maturity period; more than 200 varieties of crop plants have been developed by this technique. The Pakistan Atomic Energy Commission has used this technique fruitfully to evolve better germplasm in cotton, rice, chickpea, wheat and mungbean; some of the mutants have become popular commercial varieties. This paper describes some uses of radiation induced mutations and the results achieved in Pakistan so far.

  7. Studies on mutation breeding of hibiscus syriacuse

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hee Sub; Kim, Jin Kyu; Lee, Ki Un; Lim, Yong Taek [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1995-12-01

    Hibiscus has been known as a national flower of Korea. Hibiscus has ahch a characteristic of self-incompatibility that all the plants exist as natural hybrids and have heterogeneous genes. Thirth two domestic varieties were propagated. Radiosensitivity of H. syriacus irradiated with gamma ray was investigated in plant cuttings. The plant height was reduced by 45 percent in 5 kR irradiated group compared to control group. The radiation dose of 5 kR could be rrecommended for mutation breeding of Hibiscus cuttings. Promising mutant lines were selected form the varieties of Hwarang Wolsan 176, I1pyondansim and Emille. 6 tabs., 2 figs., 13 refs., 4 ills. (Author).

  8. Studies on mutation breeding of hibiscus Syriacus

    Energy Technology Data Exchange (ETDEWEB)

    Song, Heui Sub; Lee, Ki Woon; Im, Yong Taek [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1994-12-01

    Hibiscus(Hibiscus syracuse L.) has been know as a national flower of Korea science old times. Although there are some ancient records that the Hibiscus had been planted in large quantities in Korea, Japanese had dug out all the good plants of Hibiscus in this country during their colonial period. But Hibiscus has such a characteristics of self-incompatibility that all the plants exist as a hybrid naturally and have heterogeneous genes. Therefore many good characters can be taken out from the surviving plants. Many domestic 78 varieties of Hibiscus syracuse were collected and propagated 26 varieties cuttings. Radiosensitivity of gamma-ray irradiated Hibiscus syracuse were investigated the germination rate, survival rate, plant height was with the increase of 4 kR better than control. The radiation doses of 10-12 kR are recommended for mutation breeding of Hibiscus. 6 figs, 11 tabs, 41 refs. (Author).

  9. Bee Queen Breeding Methods - Review

    Directory of Open Access Journals (Sweden)

    Silvia Patruica

    2016-05-01

    Full Text Available The biological potential of a bee family is mainly generated by the biological value of the queen. Whether we grow queens widely or just for our own apiaries, we must consider the acquisition of high-quality biological material, and also the creation of optimal feeding and caring conditions, in order to obtain high genetic value queens. Queen breeding technology starts with the setting of hoeing families, nurse families, drone-breeding families – necessary for the pairing of young queens, and also of the families which will provide the bees used to populate the nuclei where the next queens will hatch. The complex of requirements for the breeding of good, high-production queens is sometimes hard to met, under the application of artificial methods. The selection of breeding method must rely on all these requirements and on the beekeeper’s level of training.

  10. Utilization of {gamma}-irradiation technique on plant mutation breeding and plant growth regulation in Tokyo Metropolitan Isotope Research Center

    Energy Technology Data Exchange (ETDEWEB)

    Suda, Hirokatsu [Tokyo Metropolitan Isotope Research Center (Japan)

    1997-03-01

    During about 30-years, we have developed {gamma}-irradiation technique and breeding back pruning method for the study of mutation breeding of ornamental plants. As a result, we have made a wide variety of new mutant lines in chrysanthemum, narcissus, begonia rex, begonia iron cross, winter daphne, zelkova, sweet-scented oleander, abelia, kobus, and have obtained 7 plant patents. By the use of {gamma}-irradiation to plant mutation breeding, we often observed that plants irradiated by low dose of {gamma}-rays showed superior or inferior growth than the of non-irradiated plants. Now, we established the irradiation conditions of {gamma}-rays for mutation breeding and growth of regulation in narcissus, tulip, Enkianthus perulatus Schneid., komatsuna, moyashi, african violet. In most cases, irradiation dose rate is suggested to be a more important factor to induce plant growth regulators than irradiation dose. (author)

  11. Mutation breeding in Dianthus caryophyllus for economic traits

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    Rajib Roychowdhury and Jagatpati Tah

    2011-06-01

    Full Text Available Dianthus caryophyllus is a commercial season based floricultural crop which grows well in temperate climate all over the worldand popular as cut-flowers for its variegated petal’s colour. So, it has terrific market demands in international trading. In thismodern era, an agronomic demand of high yielding cultivar of this crop was noticed. Development of cultivars with moredesirable floral characteristics and higher productivity are also very important in this crop. Keeping this view in our mind, weundertook the venture of mutation breeding programme by selecting chemical mutagens, viz. Colchicine (Col, Ethyl MethaneSulphonate (EMS, and Maleic Hydrazide (MH at different concentrations, which were applied on the seeds and leaves. The firstmutation generation (M1 seeds of the crop were harvested properly and kept in dessicator for its proper restoring. Thereafter, thesecond mutation generation (M2 seeds were grown in the next season for availing M2 populations. Various biometricalcharacters viz. number of tillering per plant, total number of flowers, length (cm of flowers, length (cm of petals and weight (gof 1000 seeds were studied and the obtained raw data were analyzed following the ANOVA model.

  12. Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds.

    Science.gov (United States)

    Vankan, D M; Waine, D R; Fortes, M R S

    2010-04-01

    This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C > A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle.

  13. Not only emerging technologies are at risk: The case of mutation breeding

    DEFF Research Database (Denmark)

    Hagemann, Kit S.; Scholderer, Joachim

    2007-01-01

    plants. Unlike crop cultivars developed by newer techniques such as genetic engineering, mutation-bred cultivars are not subject to special types of horizontal regulation in any UN country. Based on representative survey data (N = 1000), public attitudes towards mutation breeding were compared....... One technology where such a latent crisis potential has often been suspected is mutation breeding. Mutation breeding is a standard technique in the development of new crop cultivars, known since the 1930s, typically involving the use of ionizing radiation to induce alterations in the genomes of crop...... with attitudes towards several other agricultural and food biotechnologies in terms of evaluative extremity, strength, and structure. Among the technologies included in the survey, mutation breeding was by far the most negatively evaluated one (substantially more so than genetic engineering). At the same time...

  14. Investigation of FecB Mutation in Four Romanian Sheep Breeds

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    Sergiu-Emil Georgescu

    2011-05-01

    Full Text Available Hyperprolific phenotype of Booroola sheep was first discovered in the Australian Merino breed. This phenotype is due to the action of a single autosomal gene that influences the number of ovulations per estrogenic cycle. Recent discoveries have revealed that high prolificacy in Booroola Merino sheep is the result of a mutation (FecB in the bone morphogenetic protein receptor 1B (BMPR-1B gene. This mutation is located in the highly conserved kinase domain of the bone morphogenetic protein receptor IB, and is characterized by precocious differentiation of ovarian follicles, leading to the production of large numbers of ovulatory follicles. Our objective was to develop an easy method to identify the FecB mutation in order to screen sheep populations in terms of prolificacy. We designed primers to amplify a 190 bp fragment from the BMPR-1B gene containing or lacking the mutation. The PCR product was cut with AvaII endonuclease and the restriction products were analysed by agarose gel electrophoresis. Using the PCR-RFLP technique, we established an easy and efficient method that can be used to screen the FecB mutation. Therefore, these new methods increase the panel of molecular tools available for sheep breeders to choose the most prolific genotypes for improving artificial selection.

  15. Not only emerging technologies are at risk: The case of mutation breeding

    DEFF Research Database (Denmark)

    Hagemann, Kit S.; Scholderer, Joachim

    2007-01-01

    plants. Unlike crop cultivars developed by newer techniques such as genetic engineering, mutation-bred cultivars are not subject to special types of horizontal regulation in any UN country. Based on representative survey data (N = 1000), public attitudes towards mutation breeding were compared...

  16. The Mutation Breeding and Mutagenic Effect of Air Plasma on Penicillium Chrysogenum

    Institute of Scientific and Technical Information of China (English)

    桂芳; 王辉; 王鹏; 刘会; 蔡晓春; 胡以华; 袁成凌; 郑之明

    2012-01-01

    Low temperature air plasma was used as the mutation tool for penicillin-producing strain Penicillium chrysogenum. The discharge conditions were RF power of 360 W, temperature of 40℃ in a sealed chamber, and pressure of 10 Pa to 30 Pa. The result showed that the kinetics of the survival rate followed a typical saddle-shaped curve. Based on a statistic analysis, at the treating duration of 10 min, the positive mutation rate was as high as 37.5% while the negative mutation rate was low. The colonial morphology changed obviously when the plasma treating duration reached or exceeded 45 min. After both primary and secondary screening, a mutant designated as aPc051310 with high productivity of penicillin was obtained, and a strong mutagenic effect on P. chrysogenurn was observed in the process. It was proved that after five generations, the mutant aPc051310 still exhibits a high productivity. All the results prove that the plasma mutation method could be developed as a convenient and effective tool to breed high-yield strains in the fermentation industry, while expanding the plasm application at the same time.

  17. The Mutation Breeding and Mutagenic Effect of Air Plasma on Penicillium Chrysogenum

    Science.gov (United States)

    Gui, Fang; Wang, Hui; Wang, Peng; Liu, Hui; Cai, Xiaochun; Hu, Yihua; Yuan, Chengling; Zheng, Zhiming

    2012-04-01

    Low temperature air plasma was used as the mutation tool for penicillin-producing strain Penicillium chrysogenum. The discharge conditions were RF power of 360 W, temperature of 40°C in a sealed chamber, and pressure of 10 Pa to 30 Pa. The result showed that the kinetics of the survival rate followed a typical saddle-shaped curve. Based on a statistic analysis, at the treating duration of 10 min, the positive mutation rate was as high as 37.5% while the negative mutation rate was low. The colonial morphology changed obviously when the plasma treating duration reached or exceeded 45 min. After both primary and secondary screening, a mutant designated as aPc051310 with high productivity of penicillin was obtained, and a strong mutagenic effect on P. chrysogenum was observed in the process. It was proved that after five generations, the mutant aPc051310 still exhibits a high productivity. All the results prove that the plasma mutation method could be developed as a convenient and effective tool to breed high-yield strains in the fermentation industry, while expanding the plasm application at the same time.

  18. Induced mutations and marker assisted breeding in soybean

    Energy Technology Data Exchange (ETDEWEB)

    Chotechuen, Somsong [Prachinburi Rice Research Center, Prachinburi (Thailand); Srisombun, Somsak [Department of Agriculture, Field Crops Research Institute, Bangkok (Thailand); Lamseejan, Siranut [Kasetsart Univ., Department of Applied Radiation and Isotopes, Bangkok (Thailand)

    2002-02-01

    Soybean is one of the important crops in Thailand. Constraints to soybean production include low yield potential, susceptibility to diseases and insects, and non-adoption of appropriate management practices. Mutation induction has been used to improve soybean yield and resistance to major diseases such as rust, purple seed, crinkle leaf, anthracnose and green seed. This paper reviews previous work and achievements of induced mutations in soybean. Successful examples are the release of a soybean variety, Doi Kham, and the development of a mutant CM 60-10kr-71; both are resistant to rust disease. The paper also gives example of the use of soybean SSR markers to identify QTL associated with pod shattering, and emphasizes the integration of mutation techniques and marker assisted selection for soybean improvement. (author)

  19. Identification of the GDF9 mutation in two sheep breeds by using ...

    African Journals Online (AJOL)

    ... of the GDF9 mutation in two sheep breeds by using polymerase chain reaction- ... The amplified fragment of Exon 1 was digested with Hin6I restriction enzyme ... With attention to the role of a GDF9 in increasing ovulation rate, it seems that ...

  20. [Monitoring chromosome mutations in large-scale breeding operations].

    Science.gov (United States)

    Rubes, J; Raszyk, J; Horínová, Z; Gajdůsková, V; Masek, J; Docekalová, H; Bartos, J; Neumannová, M

    1988-03-01

    The frequency of chromosomal aberrations and exchanges of sister chromatids (SCEs) in peripheral lymphocytes was studied in 65 pigs from five large breeding herds. Four groups comprised fattened pigs and the fifth group consisted of sows from a large multiplier breeding herd. During the investigation, the dust from the sites was analyzed for the presence of zinc, lead, cadmium, mercury, aflatoxin B1, PCB, DDT, and lindane. The average frequency of aberrant cells (AB.B) in the pigs of group I was 3.85 +/- 1.60%, in group II 2.10 +/- 1.52%, in group III 5.01 +/- 2.1%, in group IV 3.50 +/- 1.58%, and in group V 6.20 +/- 3.21%. The cytogenetic finding corresponded to the differences in the amount of foreign substances found in the dust on the premises where the animals of all groups were kept. The average frequency of the SCEs was 7.00 +/- 1.10 (I), 6.51 +/- 0.89 (II), 6.92 +/- 0.72 (III), 7.10 +/- 0.85 (IV) and 7.06 +/- 1.47 (V) per one cell. Statistically significant differences in the numbers of AB.B. were recorded between groups II and I, II and IV, I and III, IV and V (p less than 0.05) and between groups II and III, II and V (p less than 0.01). There was no statistically significant difference in the frequency of SCEs. The determination of the frequency of chromosomal aberrations can be used for the hygienic control of the degree of exposure of pigs to mutagens.

  1. Plasma mutation breeding of Lactococcus lactis in producing Nisin

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    Shuanli ZHANG

    2015-12-01

    Full Text Available With Nisin-producing Lactococcus lactis as the starting strain, the strain with tolerance to 10 000 IU/mL Nisin is selected on high-concentration Nisin medium. The Nisin titer of the strain is up to 1 680 IU/mL. As the starting strain, the strain is further treated by atmospheric and room temperature plasmas(ARTP and mutant strain for high yield of Nisin is quickly selected with 24 well culture plate. At a survival rate of 3%, the positive mutation rate of the Lactococcus lactis is 273% compared with the starting strain. The results of shake flask culture further confirmed that one positive mutant strains could produce 6 120 IU/mL Nisin.

  2. Erythrocyte Pyruvate Kinase Deficiency mutation identified in multiple breeds of domestic cats

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    Grahn Robert A

    2012-10-01

    Full Text Available Abstract Background Erythrocyte pyruvate kinase deficiency (PK deficiency is an inherited hemolytic anemia that has been documented in the Abyssinian and Somali breeds as well as random bred domestic shorthair cats. The disease results from mutations in PKLR, the gene encoding the regulatory glycolytic enzyme pyruvate kinase (PK. Multiple isozymes are produced by tissue-specific differential processing of PKLR mRNA. Perturbation of PK decreases erythrocyte longevity resulting in anemia. Additional signs include: severe lethargy, weakness, weight loss, jaundice, and abdominal enlargement. In domestic cats, PK deficiency has an autosomal recessive mode of inheritance with high variability in onset and severity of clinical symptoms. Results Sequence analysis of PKLR revealed an intron 5 single nucleotide polymorphism (SNP at position 304 concordant with the disease phenotype in Abyssinian and Somali cats. Located 53 nucleotides upstream of the exon 6 splice site, cats with this SNP produce liver and blood processed mRNA with a 13 bp deletion at the 3’ end of exon 5. The frame-shift mutation creates a stop codon at amino acid position 248 in exon 6. The frequency of the intronic SNP in 14,179 American and European cats representing 38 breeds, 76 western random bred cats and 111 cats of unknown breed is 6.31% and 9.35% when restricted to the 15 groups carrying the concordant SNP. Conclusions PK testing is recommended for Bengals, Egyptian Maus, La Perms, Maine Coon cats, Norwegian Forest cats, Savannahs, Siberians, and Singapuras, in addition to Abyssinians and Somalis as well an any new breeds using the afore mentioned breeds in out crossing or development programs.

  3. A preliminary physiological and biochemical study on He-Ne laser mutation breeding of Erigeron breviscapus

    Science.gov (United States)

    Gao, Bo; Zhang, Canbang; Li, He; Lin, Lifei; Zhang, Rui; Zhou, Tengfei; Tian, Jiajin; Zhang, Jucheng

    2008-12-01

    Erigeron Breviscapus is known as a natural plant medicinal material with special clinical effect. In this work, the seeds of Erigeron Breviscapus were irradiated by He-Ne laser (632.8nm, 6mw) with different doses. Plant physiology and biochemistry index such as total soluble sugar and chlorophyll content were analyzed one month after germination to study the He-Ne laser effect to the Erigeron Breviscapus seeds. This work may provide the experimental basis for good growth vigor and high yield genetic character screening of Erigeron Breviscapus treated by laser mutation breeding.

  4. The search for the mdr1-1Δ mutation of the MDR1 gene in four canine breeds in Uruguay (preliminary study)

    OpenAIRE

    Rosa Gagliardi B; Diana Martínez A.; Beatriz Tellechea H.; Pedro Sitjar Q.; Silvia Llambí D.; María Arruga L.

    2015-01-01

    Objective. The objective of this study is to analyze the frequency of mdr1-1Δ mutation in German Shepherd, Doberman, Border Collie and Greyhound dog breeds in Uruguay. Materials and methods. A total of 95 animals from the four breeds mentioned above were studied. DNA was isolated from blood using potassium acetate with a subsequent degradation from RNA with RNAsaH. The concentration and quality of the DNA obtained was evaluated with a Nanodrop, ND-1000 spectrophotometer. To determine the pres...

  5. Fitness loss and germline mutations in barn swallows breeding in Chernobyl

    Energy Technology Data Exchange (ETDEWEB)

    Ellegren, Hans; Lindgren, Gabriella; Primmer, C.R. [Swedish Univ. of Agricultural Sciences, Animal Breeding and Genetics Dept., Uppsala (Sweden); Moeller, A.P. [Universite Pierre et Marie Curie. Lab. d`Ecologie, Paris, 75 (France)

    1997-10-09

    The severe nuclear accident at Chernobyl in 1986 resulted in the worst reported accidental exposure of radioactive material to free-living organisms. Short-term effects on human populations inhabiting polluted areas include increased incidence of thyroid cancer, infant leukaemia, and congenital malformations in newborns. Two recent studies have reported, although with some controversy, that germline mutation rates were increased in humans and voles living close to Chernobyl, but little is known about the viability of the organisms affected. Here we report an increased frequency of partial albinism, a morphological aberration associated with a loss of fitness, among barn swallows, Hirundo rustica, breeding close to Chernobyl. Heretability estimates indicate that mutations causing albinism were at least partly of germline origin. Furthermore, evidence for an increased germline mutation rate was obtained from segregation analysis at two hypervariable microsatellite loci, indicating that mutation events in barn swallows from Chernobyl were two- to tenfold higher than in birds from control areas in Ukraine and Italy. (author).

  6. Status of biotechnology with emphasis on molecular techniques for mutation breeding in the Philippines

    Energy Technology Data Exchange (ETDEWEB)

    Lapade, A.G.; Nazarea, T.Y.; Veluz, A.M.S.; Marbella, L.J.; Nato, A.Q.; Coloma, C.B. Jr.; Asencion, A.B. [Philippine Nuclear Research Institute, Commonwealth Avenue, Quezon (Philippines)

    2002-02-01

    This paper summarizes the status of biotechnology with emphasis on molecular techniques for plant breeding in the Philippines. Several molecular and in-vitro culture techniques are integrated in plant breeding for crop improvement at PNRI, UPLB, IRRI and PhilRice. At IRRI, PCR techniques, RFLP and RAPD, PCR techniques, RFLP and RAPD were developed to establish high density molecular maps, determine breadth and diversity of germplasm and characterize alien introgression. The molecular maps have identified DNA sequence of resistance genes of HYVs and NPTs to abiotic and biotic stresses, the major achievement is the development of high density molecular maps in rice with at least 2000 markers. The biotechnology program at PhilRice for varietal improvement includes: (1) utilization of molecular marker technology such gene mapping of desired traits in rice, analysis of genetic relationships of germplasm materials and breeding lines through DNA fingerprinting and genetic diversity studies and development and application of marker aided selection for disease resistance (RTD and BLB); (2) application of in-vitro techniques in the development of lines with tolerance to adverse conditions; (3) molecular cloning of important genes for RTD resistance; (4) genetic transformation for male sterility and resistance to sheath blight and stem borers; and (5) transfer of disease resistance from wild species to cultivated varieties. In IPB, molecular markers:microsatellites or SSR, AFLP and RGA are being used for mapping and diversity studies in coconut, mango, banana, mungbean, corn and tomato. Mutation breeding at PNRI using gamma radiation has resulted in the development of crop varieties with desirable traits. The use of AFLP coupled to PCR is being used to study polymorphism in plant variants of radiation-induced mutants of rice, pineapple and ornamentals. (author)

  7. The search for the mdr1-1Δ mutation of the MDR1 gene in four canine breeds in Uruguay (preliminary study

    Directory of Open Access Journals (Sweden)

    Rosa Gagliardi B.

    2015-01-01

    Full Text Available Objective. The objective of this study is to analyze the frequency of mdr1-1Δ mutation in German Shepherd, Doberman, Border Collie and Greyhound dog breeds in Uruguay. Materials and methods. A total of 95 animals from the four breeds mentioned above were studied. DNA was isolated from blood using potassium acetate with a subsequent degradation from RNA with RNAsaH. The concentration and quality of the DNA obtained was evaluated with a Nanodrop, ND-1000 spectrophotometer. To determine the presence or absence of the mdr1-1Δ mutation, DNA samples were sent to Gene Seek, Neogen Corporation of Chicago, United States, for genotyping. Results. In all 95 animals studied, the mdr1-1Δ mutation was not present. Conclusions. Based on the preliminary results obtained, other elements that may cause adverse drug reactions must be considered: unidentified mutations in other regions of the MDR1 gene; mutations in other genes involved in the transport of drugs from the same subfamily or another; mutations in enzymes involved in drug metabolism (e.g. Cytochrome P450. Moreover, especially with Border Collies and Greyhounds, it is advisable to increase the number of animals in the study.

  8. Mutation breeding of lycopene-producing strain Blakeslea trispora by a novel atmospheric and room temperature plasma (ARTP).

    Science.gov (United States)

    Qiang, Wang; Ling-ran, Feng; Luo, Wei; Han-guang, Li; Lin, Wang; Ya, Zhou; Xiao-bin, Yu

    2014-09-01

    To improve the fermentation efficiency of lycopene, a plasma jet, driven by an active helium atom supplied with atmospheric and room temperature plasma (ARTP) biological breeding system, was used as a new method to generate mutations in Blakeslea trispora (-). After several rounds of screening, a mutant A5 with high concentration of lycopene and dry biomass was isolated, which showed a maximum lycopene concentration (26.4 ± 0.2 mg/g dry biomass) which was 55 % higher than the parent strain (16.9 ± 0.3 mg/g dry biomass) in the production of lycopene. Compared with parent strain, B. trispora A5 required less dissolved oxygen (10 % less than that of parent strain) to reach maximum concentration in a 5-L stirred tank reactor batch fermentation.

  9. Methods for detection of ataxia telangiectasia mutations

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Richard A.

    2005-10-04

    The present invention is directed to a method of screening large, complex, polyexonic eukaryotic genes such as the ATM gene for mutations and polymorphisms by an improved version of single strand conformation polymorphism (SSCP) electrophoresis that allows electrophoresis of two or three amplified segments in a single lane. The present invention also is directed to new mutations and polymorphisms in the ATM gene that are useful in performing more accurate screening of human DNA samples for mutations and in distinguishing mutations from polymorphisms, thereby improving the efficiency of automated screening methods.

  10. Molecular methods for the detection of mutations.

    Science.gov (United States)

    Monteiro, C; Marcelino, L A; Conde, A R; Saraiva, C; Giphart-Gassler, M; De Nooij-van Dalen, A G; Van Buuren-van Seggelen, V; Van der Keur, M; May, C A; Cole, J; Lehmann, A R; Steinsgrimsdottir, H; Beare, D; Capulas, E; Armour, J A

    2000-01-01

    We report the results of a collaborative study aimed at developing reliable, direct assays for mutation in human cells. The project used common lymphoblastoid cell lines, both with and without mutagen treatment, as a shared resource to validate the development of new molecular methods for the detection of low-level mutations in the presence of a large excess of normal alleles. As the "gold standard, " hprt mutation frequencies were also measured on the same samples. The methods under development included i) the restriction site mutation (RSM) assay, in which mutations lead to the destruction of a restriction site; ii) minisatellite length-change mutation, in which mutations lead to alleles containing new numbers of tandem repeat units; iii) loss of heterozygosity for HLA epitopes, in which antibodies can be used to direct selection for mutant cells; iv) multiple fluorescence-based long linker arm nucleotides assay (mf-LLA) technology, for the detection of substitutional mutations; v) detection of alterations in the TP53 locus using a (CA) array as the target for the screening; and vi) PCR analysis of lymphocytes for the presence of the BCL2 t(14:18) translocation. The relative merits of these molecular methods are discussed, and a comparison made with more "traditional" methods.

  11. A method for discriminating a Japanese chicken, the Nagoya breed, using microsatellite markers.

    Science.gov (United States)

    Nakamura, A; Kino, K; Minezawa, M; Noda, K; Takahashi, H

    2006-12-01

    The Nagoya breed native to Japan is popular as a dual-purpose breed for eggs and meat. The current study describes a method to discriminate between the Nagoya breed and other breeds and commercial stocks of chicken. Four strains of the Nagoya breed established at the Aichi-ken Agricultural Research Center were analyzed using 25 microsatellite markers. In these strains, 5 of the markers (ABR0015, ABR0257, ABR0417, ABR0495, and ADL0262) had a single allele. Other chicken samples (448) of various breeds and hybrids were analyzed using the same 5 markers. None of these chicken samples had the same allele combination as the Nagoya breed strains. These 5 microsatellite markers provide a practical method to accurately discriminate the Nagoya breed from other chicken breeds.

  12. Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.

    Science.gov (United States)

    Fontanesi, L; Beretti, F; Riggio, V; Gómez González, E; Dall'Olio, S; Davoli, R; Russo, V; Portolano, B

    2009-01-01

    In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val128Gly). Allele and genotype frequencies suggested that these mutations are not associated or not completely associated with coat color in the investigated goat breeds. Moreover, genotyping and sequencing results, deviation from Hardy-Weinberg equilibrium, as well as allele copy number evaluation from semiquantitative fluorescent multiplex PCR, indicated the presence of copy number variation (CNV) in all investigated breeds. To confirm the presence of CNV and evaluate its extension, we applied a bovine-goat cross-species array comparative genome hybridization (aCGH) experiment using a custom tiling array based on bovine chromosome 13. aCGH results obtained for 8 goat DNA samples confirmed the presence of CNV affecting a region of less that 100 kb including the ASIP and AHCY genes. In Girgentana and Saanen breeds, this CNV might cause the A(Wt) allele, as already suggested for a similar structural mutation in sheep affecting the ASIP and AHCY genes, providing evidence for a recurrent interspecies CNV. However, other mechanisms may also be involved in determining coat color in these 2 breeds.

  13. Proceedings of the 8th workshop on plant mutation breeding. Effective use of physical/chemical mutagens

    Energy Technology Data Exchange (ETDEWEB)

    Kume, Tamikazu; Watanabe, Kazuo; Tano, Shigemitsu (eds.) [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

    2001-03-01

    The Workshop on Plant Mutation Breeding of FNCA (Forum for Nuclear Cooperation in Asia), was held on 9-13 October 2000 in Hanoi, Vietnam. The Workshop was co-sponsored by the Science and Technology Agency (STA), the Ministry of Science, Technology and Environment (MOSTE of Vietnam) and the Ministry of Agriculture and Rural Development (MARD of Vietnam) in cooperation with the Ministry of Agriculture, Forestry and Fisheries (MAFF), National Institute of Agrobiological Resources (NIAR of Vietnam), the Japan Atomic Industrial Forum (JAIF) and Japan Atomic Energy Research Institute (JAERI). Two Scientists, a Project Leader and an expert on methodology for plant/crop mutation breeding, participated from each of the member countries, i.e. China, Indonesia, Malaysia, the Philippines, Thailand, Vietnam and Japan. Also attending the Workshop were, one participant from Korea, seven participants from both Japan and Vietnam. The number of the participants in the Workshop totalled about sixty people including guests and observers. Sixteen papers including eight invited papers on the current status of methodology for plant/crop mutation breeding in the participating countries were presented. Discussions were focused on the subject concerning 'Effective Use of Physical/Chemical Mutagens', as well as a detailed report on the current status of research in each participating country. In addition, the topics of developing a mutant breeding database, an information exchange for plant/crop mutation breeding, and more tightly bound international co-operative research in the near future were also high on the agenda. This proceeding compiles the invited and contributed papers that were submitted from the speakers. (author)

  14. Mutation breedings in ornamental plants. Technique used for radiation induced mutant in begonia, chrysanthemum, aberia and winter daphne

    Energy Technology Data Exchange (ETDEWEB)

    Matsubara, Hisao

    1984-03-01

    Several methods of obtaining somatic mutant plants by el-ray irradiation on pieces of tissues as in vitro adventitious bud technique or small cutting methods with repeated pruning are described. The irradiation to the adventitious buds in the small pieces of organ cultured in vitro and to the small cuttings are employed. Culture beds of agar or of Japanese Kanuma soil were used in vitro culture. In these experiments, Japanese Kanuma soil bed in in vitro culture worked well for root development and transplant of the induced mutants. Combination with in vitro culture and repeated pruning technique were used for isolation and fixation of solid somatic mutant from small sectorial mutation induced by irradiation. This method was successful for begonia, chrysanthemum, aberia and winter daphne. These data indicates that most of the induced mutant plants were non-chimeric, while a few others were chimeric. Among the new varieties, ''Gin-Sei'', ''Ryoku-Ha'', ''Big-Cross'', ''Kaede-Iron'', ''Mei-Fu-Hana-Tsukubane-Utsugi'' and ''Daphne-el-3'' are non-chimeric, and ''Mini-Mini-Iron'' and ''Orange-Iron'' are chimeric. Moreover, these new varieties have remarkably differed in size and in color pattern from original variety. From the experimental results of somatic mutation, it is indicated that plant tissue culture have enormous potential in radiation breeding and in rapid propagation of the somatic mutant. (author).

  15. Mutational breeding and genetic engineering in the development of high grain protein content.

    Science.gov (United States)

    Wenefrida, Ida; Utomo, Herry S; Linscombe, Steve D

    2013-12-04

    Cereals are the most important crops in the world for both human consumption and animal feed. Improving their nutritional values, such as high protein content, will have significant implications, from establishing healthy lifestyles to helping remediate malnutrition problems worldwide. Besides providing a source of carbohydrate, grain is also a natural source of dietary fiber, vitamins, minerals, specific oils, and other disease-fighting phytocompounds. Even though cereal grains contain relatively little protein compared to legume seeds, they provide protein for the nutrition of humans and livestock that is about 3 times that of legumes. Most cereal seeds lack a few essential amino acids; therefore, they have imbalanced amino acid profiles. Lysine (Lys), threonine (Thr), methionine (Met), and tryptophan (Trp) are among the most critical and are a limiting factor in many grain crops for human nutrition. Tremendous research has been put into the efforts to improve these essential amino acids. Development of high protein content can be outlined in four different approaches through manipulating seed protein bodies, modulating certain biosynthetic pathways to overproduce essential and limiting amino acids, increasing nitrogen relocation to the grain through the introduction of transgenes, and exploiting new genetic variance. Various technologies have been employed to improve protein content including conventional and mutational breeding, genetic engineering, marker-assisted selection, and genomic analysis. Each approach involves a combination of these technologies. Advancements in nutrigenomics and nutrigenetics continue to improve public knowledge at a rapid pace on the importance of specific aspects of food nutrition for optimum fitness and health. An understanding of the molecular basis for human health and genetic predisposition to certain diseases through human genomes enables individuals to personalize their nutritional requirements. It is critically important

  16. Mutation Breeding of an Organic Phosphorus-Solubilizing Bacterium B3 by Low Energy Ion Beam Implantation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiangsheng; LI Youguo; WU Yuejin; ZHOU Junchu; CHEN Dasong; LEI Lei

    2008-01-01

    A preliminary study on the mutation breeding of an organic phosphorus-solubilizing bacterium B3 by low-energy N+ ion beam was conducted.Analysis of dosage vs.survival rate and mutation rate showed that the dosage of 3×1015 ions/cm2 was optimal for the mutation.Some parameters for determining the efficient phosphorus content were studied to simplify the protocols for screening.Ultimately one reliable mutant was screened out under plating and flask-culturing screening conditions.Importantly,a novel phosphorus-dissolving mechanism is reported for the first time in terms of bio-surfactant production,which indicates that bio-surfactant might play a vital role in phosphorus-dissolving for some phosphobacteria.

  17. METHOD OF SKETCHES IN ARCHAEOGENETICS AND BREEDING OF AGRICULTURAL PLANTS

    Directory of Open Access Journals (Sweden)

    Tsatsenko L. V.

    2015-02-01

    Full Text Available The issues associated with visualization images of the examined object and the method of sketches or visual notes have been discussed in the article. The images of lagenaria (bottle, shape pumpkins or gourds in works of art and agrobotanic illustration as a research tool have been selected, with the aim to conduct a visual analysis of the morphological characteristics of bottle gourd for further application of the knowledge gained in archaeogenetics and plant breeding. The article presents images of plants of lagenaria for the period from 1311 to 2014 years. Visual analysis of the morphological characteristics of lagenaria on the basis of visual notes allowed us to identify several key points: the polymorphism of fruits and different duration of the vegetation period, particularly of the reproductive system, which is characterized by different proportions of male and female flowers, the presence of pollinators, night flowering, fruit pubescence on the first stages of development, polymorphism seeds, features maturation based on the size and weight of the fetus. Understanding the range of individual development allows the breeder to submit a complete selection issue, search for new signs will touch the ancient forms of the object, diseases, pests, images which have remained only on the pictures. In our opinion, the method of visual notes can be successfully used in the educational process because it stimulates creativity and cognitive activity of students to search for information about the studied object and its reflection

  18. A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (Oryctolagus cuniculus) breeds.

    Science.gov (United States)

    Fontanesi, L; Scotti, E; Allain, D; Dall'olio, S

    2014-04-01

    In rabbit, the dilute locus is determined by a recessive mutated allele (d) that causes the dilution of both eumelanic and pheomelanic pigmentations. In mice, similar phenotypes are determined by mutations in the myosin VA, Rab27a and melanophilin (MLPH) genes. In this study, we investigated the rabbit MLPH gene and showed that a mutation in this gene appears responsible for the dilute coat colour in this species. Checkered Giant F1 families segregating for black and grey (diluted or blue) coat colour were first genotyped for a complex indel in intron 1 of the MLPH gene that was completely associated with the coat colour phenotype (θ = 0.00; LOD = 4.82). Then, we sequenced 6357 bp of the MLPH gene in 18 rabbits of different coat colours, including blue animals. A total of 165 polymorphisms were identified: 137 were in non-coding regions and 28 were in coding exons. One of them was a frameshift deletion in exon 5. Genotyping the half-sib families confirmed the complete cosegregation of this mutation with the blue coat colour. The mutation was analysed in 198 rabbits of 23 breeds. All Blue Vienna and all other blue/grey/ash rabbits in other breeds (Californian, Castor Rex, Checkered Giant, English Spot, Fairy Marburg and Fairy Pearly) were homozygous for this deletion. The identification of MLPH as the responsible gene for the dilute locus in rabbit provides a natural animal model for human Griscelli syndrome type 3 and a new mutant to study the role of this gene on pigmentation. © 2013 Stichting International Foundation for Animal Genetics.

  19. Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.).

    Science.gov (United States)

    Breseghello, Flavio; Coelho, Alexandre Siqueira Guedes

    2013-09-01

    Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

  20. A Missense Mutation in SLC45A2 Is Associated with Albinism in Several Small Long Haired Dog Breeds.

    Science.gov (United States)

    Wijesena, Hiruni R; Schmutz, Sheila M

    2015-01-01

    Homozygosity for a large deletion in the solute carrier family 45, member 2 (SLC45A2) gene causes oculocutaneous albinism (OCA) in the Doberman Pinscher breed. An albino Lhasa Apso did not have this g.27141_31223del (CanFam2) deletion in her SLC45A2 sequence. Therefore, SLC45A2 was investigated in this female Lhasa Apso to search for other possible variants that caused her albinism. The albino Lhasa Apso was homozygous for a nonsynonymous substitution in the seventh exon, a c.1478G>A base change that resulted in a glycine to aspartic acid substitution (p.G493D). This mutation was not found in a wolf, a coyote, or any of the 15 other Lhasa Apso dogs or 32 other dogs of breeds related to the Lhasa Apso. However, an albino Pekingese, 2 albino Pomeranians, and an albino mixed breed dog that was small and long haired were also homozygous for the 493D allele. The colored puppies of the albino Lhasa Apso and the colored dam of the 2 albino Pomeranians were heterozygous for this allele. However, an albino Pug was homozygous for the 493G allele and therefore although we suggest the 493D allele causes albinism when homozygous in several small, long haired dog breeds, it does not explain all albinism in dogs. A variant effect prediction for the albino Lhasa Apso confirms that p.G493D is a deleterious substitution, and a topology prediction for SLC45A2 suggests that the 11th transmembrane domain where the 493rd amino acid was located, has an altered structure.

  1. Late-onset progressive retinal atrophy in the Gordon and Irish Setter breeds is associated with a frameshift mutation in C2orf71.

    Science.gov (United States)

    Downs, L M; Bell, J S; Freeman, J; Hartley, C; Hayward, L J; Mellersh, C S

    2013-04-01

    Progressive retinal atrophy (PRA) in dogs is characterised by the degeneration of the photoreceptor cells of the retina, resulting in vision loss and eventually complete blindness. The condition affects more than 100 dog breeds and is known to be genetically heterogeneous between breeds. Around 14 mutations have now been identified that are associated with PRA in around 49 breeds, but for the majority of breeds the mutation(s) responsible have yet to be identified. Using genome-wide association with 16 Gordon Setter PRA cases and 22 controls, we identified a novel PRA locus, termed rod-cone degeneration 4 (rcd4), on CFA17 (Praw  = 2.22 × 10(-8) , Pgenome  = 2.00 × 10(-5) ), where a 3.2-Mb region was homozygous within cases. A frameshift mutation was identified in C2orf71, a gene located within this region. This variant was homozygous in 19 of 21 PRA cases and was at a frequency of approximately 0.37 in the Gordon Setter population. Approximately 10% of cases in our study (2 of 21) are not associated with this C2orf71 mutation, indicating that PRA in this breed is genetically heterogeneous and caused by at least two mutations. This variant is also present in a number of Irish Setter dogs with PRA and has an estimated allele frequency of 0.26 in the breed. The function of C2orf71 remains unknown, but it is important for retinal development and function and has previously been associated with autosomal recessive retinitis pigmentosa in humans.

  2. A recursive method for computing expected kinship and inbreeding in complex and dynamic breeding programmes.

    Science.gov (United States)

    Sitzenstock, F; Ytournel, F; Simianer, H

    2013-02-01

    In many livestock breeding programmes, the development of inbreeding is of critical importance. Thus, the assessment of the expected development of inbreeding should be an essential element in the design of breeding programmes. We propose a new method to deterministically predict the rate of inbreeding based on the gene-flow method in well-defined complex and dynamic breeding programmes. In the suggested approach, a breeding programme has to be structured in homogeneous age-sex-groups, so called cohorts, with a defined origin of genes. Starting from an initial setup (usually an unrelated and non-inbred base population), transition rules to calculate the kinship within and between cohorts originating from reproduction or ageing, respectively, are defined. Using this approach recursively provides the expected development of kinship within and between all cohorts over time, which can be combined into average kinships for the whole population or defined subsets. From these quantities, relevant parameters like the inbreeding rate or the effective population size are easily derived. We illustrate the method with a simple static example breeding programme in sheep. Based on this reference breeding programme, we demonstrate the use of our approach for dynamic breeding programmes, in which cohort sizes or vectors of gene origin change over time: here, we model the situation of exponential population growth and a bottleneck situation, respectively. The suggested approach does not account for the effect of selection on the development of inbreeding, but ideas to overcome this limitation are discussed.

  3. Mutation Breeding of various spray chrysanthemum cultivars by gamma-ray irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Hoon; Chung, Sung Jin; Kim, Dong Sub; Kim, Jin Baek; Kang, Si Yong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Lee, Geung Joo [Mokpo National University, Muan (Korea, Republic of)

    2009-09-15

    This study was carried out to analyze mutation rate and spectrum of chrysanthemum by gamma-ray irradiation. Five flower types, 16 cultivars including 'Geumsu', 'Hwiparam', 'Ilwol', 'Magic', 'Moonlight', 'Noblewine', 'Pinky', 'Progy', 'Sangtte', 'Waterfog', 'Whitneypangpang', 'Yelloweye', 'Yellowpangpang', 'Yesmiso', 'Yesmorning', and 'Yestogether' were irradiated as 30, 50, and 70 Gy dose during 24 hours. As a result, mutation rate was identified as the highest in single type among five flower types, but there was a little difference according to cultivars. Mutation rate was increased in proportion to irradiation dose in anemone, pompon, and spider type cultivars, but there wasn't clear in single and semi-double type cultivars. Mutation spectrum was identified as the highest in the cultivar 'Noblewine'. The most sensitive cultivars to radiation were revealed as 'Noblewine' and 'Yesmorning' and the least were Moonlight', 'Waterfog', and 'Yellowpangpang'. Consequently, there was much difference in radio-sensitivity according to cultivars of chrysanthemum and flower type was correlated a little with mutation rate.

  4. Selection of maintaining, method for keeping of biologial purity, patternship and health, regarding viruses infection of distinguished potato breeding lines

    Directory of Open Access Journals (Sweden)

    Luiza MIKE

    2008-05-01

    Full Text Available A large number of potato varieties and distinguished breeding lines disappeared as an effect of nonfavourable climatically conditions and especially by viruses diseases, as well as other biological and viruses degeneration. To avoid the negative effect of degeneration on potato varieties and distinguished breeding lines, the method of selection for maintaining and multiplication of potato is applying in Romania in the frame of National Center for Maintaining of potato varieties and distinguished breeding lines Apa Rosie, Covasna County, which belong to the Station for Research and Development of Potato, Targu Secuiesc, Covasna County.In this center are maintained and multiplied all distinguished varieties and breeding centers from Romania (National Institute for research and Development of Potato and Sugar beet Brasov, Research and Development Station for Agriculture Suceava, Research and Development Station for Potato Targu Secuiesc, Research and development Station for Potato Miercurea Ciuc.Using the method of selection for maintaining it is possible an early identification of somatic mutations, disease (especially viruses infection by visual elimination or by serological testing.The viruses’ infection of potato leads to disturbed the metabolism of plants and produces anatomical – morphological alters as: mosaic, crinkle, rolling, browning of leaves and plants deformation.The disturbing of plant metabolism has as negative effect the reduction of vegetation period, decreasing the yield capacity, depreciation of physical and chemical quality of tubers.The genetically complex structure of cultivated potato (2n = 4x = 48 and strong segregation of long – expected characters in the obtained future progeny by sexual hybridization, complicated many times by nonfavourable linkage, are the backgrounds for initiation of maintain selection.

  5. A KCNJ10 mutation previously identified in the Russell group of terriers also occurs in Smooth-Haired Fox Terriers with hereditary ataxia and in related breeds.

    Science.gov (United States)

    Rohdin, Cecilia; Gilliam, Douglas; O'Leary, Caroline A; O'Brien, Dennis P; Coates, Joan R; Johnson, Gary S; Jäderlund, Karin Hultin

    2015-05-23

    Hereditary ataxias with similar phenotypes were reported in the Smooth-Haired Fox Terrier, the Jack Russell Terrier and the Parson Russell Terrier. However, segregation analyses showed differing inheritance modes in these breeds. Recently, molecular genetic studies on the Russell group of terriers found independent mutations in KCNJ10 and CAPN1, each associated with a specific clinical subtype of inherited ataxia. The aim of this study was to clarify whether or not Smooth-Haired Fox Terriers with hereditary ataxia and dogs of other related breeds harbor either of the same mutations. A sub goal was to update the results of KCNJ10 genotyping in Russell group terriers. Three Smooth-Haired Fox Terriers with hereditary ataxia and two Toy Fox Terriers with a similar phenotype were all homozygous for the KCNJ10 mutation. The same mutation was also found in a heterozygous state in clinically unaffected Tenterfield Terriers (n = 5) and, in agreement with previous studies, in Jack Russell Terriers, Parson Russell Terriers, and Russell Terriers. A KCNJ10 mutation, previously associated with an autosomal recessive spinocerebellar ataxia in Jack Russell Terriers, Parson Russell Terriers, and Russell Terriers segregates in at least three more breeds descended from British hunting terriers. Ataxic members of two of these breeds, the Smooth-Haired Fox Terrier and the Toy Fox Terrier, were homozygous for the mutation, strengthening the likelihood that this genetic defect is indeed the causative mutation for the disease known as "hereditary ataxia" in Fox Terriers and "spinocerebellar ataxia with myokymia, seizures or both" in the Russell group of terriers.

  6. To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed.

    Directory of Open Access Journals (Sweden)

    Barbara Gandolfi

    Full Text Available The cat (Felis silvestris catus shows significant variation in pelage, morphological, and behavioral phenotypes amongst its over 40 domesticated breeds. The majority of the breed specific phenotypic presentations originated through artificial selection, especially on desired novel phenotypic characteristics that arose only a few hundred years ago. Variations in coat texture and color of hair often delineate breeds amongst domestic animals. Although the genetic basis of several feline coat colors and hair lengths are characterized, less is known about the genes influencing variation in coat growth and texture, especially rexoid - curly coated types. Cornish Rex is a cat breed defined by a fixed recessive curly coat trait. Genome-wide analyses for selection (di, Tajima's D and nucleotide diversity were performed in the Cornish Rex breed and in 11 phenotypically diverse breeds and two random bred populations. Approximately 63K SNPs were used in the analysis that aimed to localize the locus controlling the rexoid hair texture. A region with a strong signature of recent selective sweep was identified in the Cornish Rex breed on chromosome A1, as well as a consensus block of homozygosity that spans approximately 3 Mb. Inspection of the region for candidate genes led to the identification of the lysophosphatidic acid receptor 6 (LPAR6. A 4 bp deletion in exon 5, c.250_253_delTTTG, which induces a premature stop codon in the receptor, was identified via Sanger sequencing. The mutation is fixed in Cornish Rex, absent in all straight haired cats analyzed, and is also segregating in the German Rex breed. LPAR6 encodes a G protein-coupled receptor essential for maintaining the structural integrity of the hair shaft; and has mutations resulting in a wooly hair phenotype in humans.

  7. THE BREED TRACEABILITY OF SHEEP MEAT BY USING MOLECULAR GENETICS METHODS: PRELIMINARY RESULTS

    Directory of Open Access Journals (Sweden)

    A. Bramante

    2011-04-01

    Full Text Available Safety and quality foods of animal origin are extremely important for consumers. The aim of this work was to evaluate the feasibility of a method to track the breed origin of sheep meat all along the production chain using molecular genetics tools. A total of 800 samples evenly distributed among seven Italian sheep breeds have been typed at 19 STR markers, together with 90 samples from both imported sheep animals and local crossbred animals withdrawn at slaughterhouses. A maximum likelihood assignment test was adopted to evaluate STR ability to allocate samples to their true breed of origin. Sarda animals were all correctly allocated, as well as more than 98% of samples from the other breeds. Only slightly worst allocation performances were observed for imported and crossbred animals. Preliminary results seem quite promising, though further analyses will be needed in order to better understand the statistical power of such an assignment test before implementation in the sheep meat production chain.

  8. A rapid detection method for the ryanodine receptor 1 (C7360G) mutation in Quarter Horses.

    Science.gov (United States)

    Nieto, J E; Aleman, M

    2009-01-01

    Anesthetic-induced malignant hyperthermia has been documented in Quarter Horses and is caused by a single-point mutation in the ryanodine receptor 1 gene at nucleotide C7360G generating a R2454G amino acid substitution. An accurate, faster molecular test that is less prone to contamination would facilitate screening for the mutation in horses intended for breeding, in those undergoing surgical procedures, and in those with clinical signs compatible with malignant hyperthermia. To report a rapid and accurate method for the detection of the ryanodine receptor 1 C7360G mutation. Eleven diseased, 10 healthy, and 225 randomly selected Quarter Horses. This study included horses with the ryanodine receptor 1 C7360G mutation as detected by gene sequencing. Available genomic and complementary DNA extracted from whole blood, hair or skeletal muscle was used for genetic analysis. Real-time polymerase chain reaction (RT-PCR) melting curve analysis was performed by equine specific primers and 2 hybridization probes (sensor and anchor probes) that contain the site of the mutation. Results from this method were blinded and compared with nucleic acid sequencing for validation. A rapid genotyping assay with fluorescence resonance energy transfer probes and melting curve analysis was accurate (100% agreement, K= 1) for identification of affected horses. The prevalence of the mutation in a random population of Quarter Horses was 1.3%. Malignant hyperthermia in Quarter Horses can be rapidly and accurately detected by RT-PCR melting curve genotyping with hybridization probes.

  9. Use of an in vitro adventitious bud technique for mutation breeding of Begonia x hiemalis

    Energy Technology Data Exchange (ETDEWEB)

    Roest, S.; van Berkel, M.A.E.; Bokelmann, G.S.; Broertjes, C. (Instituut voor Toepassing van Atoomenergie in de Landbouw, Wageningen (Netherlands))

    1981-06-01

    An in vitro propagation of two genotypes of Begonia x hiemalis was achieved through adventitious shoot formation on (sub) cultured leaf-disc explants and subsequent transplantation to soil of explant-parts with adventitious shoots. After irradiation of detached leaves with different doses of X-rays and two cycles of adventitious shoot formation on in vitro (sub) cultured leaf-disc explants, plantlets were produced. About 30% of these plants was mutated with respect to e.g. the colour, size and form of the leaves and flowers. The great majority of the mutants (98.5%) proved to be solid (non-chimeric).

  10. A sampling method for estimating the accuracy of predicted breeding values in genetic evaluation

    Directory of Open Access Journals (Sweden)

    Laloë Denis

    2001-09-01

    Full Text Available Abstract A sampling-based method for estimating the accuracy of estimated breeding values using an animal model is presented. Empirical variances of true and estimated breeding values were estimated from a simulated n-sample. The method was validated using a small data set from the Parthenaise breed with the estimated coefficient of determination converging to the true values. It was applied to the French Salers data file used for the 2000 on-farm evaluation (IBOVAL of muscle development score. A drawback of the method is its computational demand. Consequently, convergence can not be achieved in a reasonable time for very large data files. Two advantages of the method are that a it is applicable to any model (animal, sire, multivariate, maternal effects... and b it supplies off-diagonal coefficients of the inverse of the mixed model equations and can therefore be the basis of connectedness studies.

  11. The use of induced mutation combined with crossing in high quality rice breeding

    Energy Technology Data Exchange (ETDEWEB)

    Do Huu At; Bui Huy Thuy; Nguyen Van Bich; Tran Duy Quy [Agricultural Genetics Institute, Division of Genetics and Hybrid Rice Technology, Hanoi (Viet Nam); Nguyen Minh Cong [Hanoi No. 1 Teacher Training Univ., Department of Genetics (Viet Nam)

    2001-03-01

    The high quality rice varieties: Tam thom mutant rice Var., DT17 rice Var, DT21 glutinous rice Var were formed by induced mutation combined with crossing. Tam thom mutant rice Var. lost photosensitivity, could be planted 2 crops/year. DT17 rice Var with high yielding capacity, suitable for growth on lowland in summer crop, is replacing step-by-step Moctuyen rice Var. in North Vietnam. DT21 glutinous rice Var. could be planted 2 crops/year and had short growth duration, average yield was 4.0-4.5 tons/ha. These three ones had good quality, soft and scent cooked rice, suitable for customers and export requirements. Tam thom mutant rice Var. DT17 rice Var., DT21 and glutinous rice Var. were adopted for regional production by Ministry of Agriculture and Rural Development and allowed to be in trial production. (author)

  12. Missense and nonsense mutations in melanocortin 1 receptor (MC1R gene of different goat breeds: association with red and black coat colour phenotypes but with unexpected evidences

    Directory of Open Access Journals (Sweden)

    Davoli Roberta

    2009-08-01

    Full Text Available Abstract Background Agouti and Extension loci control the relative amount of eumelanin and pheomelanin production in melanocytes that, in turn, affects pigmentation of skin and hair. The Extension locus encodes the melanocortin 1 receptor (MC1R whose permanent activation, caused by functional mutations, results in black coat colour, whereas other inactivating mutations cause red coat colour in different mammals. Results The whole coding region of the MC1R gene was sequenced in goats of six different breeds showing different coat colours (Girgentana, white cream with usually small red spots in the face; Maltese, white with black cheeks and ears; Derivata di Siria, solid red; Murciano-Granadina, solid black or solid brown; Camosciata delle Alpi, brown with black stripes; Saanen, white; F1 goats and the parental animals. Five single nucleotide polymorphisms (SNPs were identified: one nonsense mutation (p.Q225X, three missense mutations (p.A81V, p.F250V, and p.C267W, and one silent mutation. The stop codon at position 225 should cause the production of a shorter MC1R protein whose functionality may be altered. These SNPs were investigated in a larger sample of animals belonging to the six breeds. The Girgentana breed was almost fixed for the p.225X allele. However, there was not complete association between the presence of red spots in the face and the presence of this allele in homozygous condition. The same allele was identified in the Derivata di Siria breed. However, its frequency was only 33%, despite the fact that these animals are completely red. The p.267W allele was present in all Murciano-Granadina black goats, whereas it was never identified in the brown ones. Moreover, the same substitution was present in almost all Maltese goats providing evidence of association between this mutation and black coat colour. Conclusion According to the results obtained in the investigated goat breeds, MC1R mutations may determine eumelanic and pheomelanic

  13. Detection of heterozygous MDR1 nt230(del4 mutation in a mixed-breed dog: case report of possible doxorubicin toxicosis

    Directory of Open Access Journals (Sweden)

    Monobe MM

    2013-10-01

    Full Text Available Marina Mitie Monobe,1 Kari V Lunsford,2 João Pessoa Araújo Jr,3 Camilo Bulla41Department of Veterinary Clinics, School of Veterinary Medicine and Animal Science, Sao Paulo State University, Botucatu, Brazil; 2Department of Clinical Sciences and Animal Health Center, College of Veterinary Medicine, Mississippi State University, MS, USA; 3Department of Microbiology and Immunology, Biosciences Institute, Sao Paulo State University, Botucatu, Brazil; 4Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, MS, USAAbstract: P-glycoprotein (ABCB1, the product of the Multidrug Resistance Gene (MDR1 (ABCB1 gene, is the major multidrug transporter contributing to the barrier function of several tissues and organs, including the brain. A four base pair deletion mutation in MDR1 results in the absence of a functional form of ABCB1 and loss of its protective function. Severe intoxication with the ABCB1 substrate, such as with anticancer drugs, has been attributed to genetic lack of functional ABCB1. This mutation has been detected in more than 10 dog breeds as well as in mixed-breed dogs living in different countries. In Brazil, evaluation for this mutation is not as widely available and is rarely used by veterinarians, so drug intoxication may be underdiagnosed. This is the first report from Brazil of doxorubicin neurotoxicity in a mixed-breed dog with the MDR1 nt230(del4 mutation.Keywords: canine, toxicology, cancer, P-glycoprotein

  14. Effect of oestrus synchronization methods on oestrus behaviour, timing of ovulation and pregnancy rate during the breeding and low breeding seasons in Nili-Ravi buffaloes.

    Science.gov (United States)

    Warriach, Hassan Mahmood; Channa, Aijaz Ali; Ahmad, Nasim

    2008-08-01

    The objective of this study was to determine the effect of oestrous synchronization methods on oestrous behaviour, timing of ovulation and pregnancy rate during the breeding and low breeding seasons in Nili-Ravi buffaloes. In Experiment 1, oestrous behaviour and timing of ovulation were determined from (n=34) oestruses. The mean (+/- S.E.M.) time of ovulation after the onset of standing oestrus was greater (P0.05) from those which were inseminated during the low breeding season (55.5%) and (30.4%), respectively. This study demonstrates clearly that (1) timing of ovulation in Nili-Ravi buffalo is about 30h after the onset of standing oestrus and (2) buffaloes can be successfully synchronized with optimum fertility using either PGF(2alpha) alone (detected oestrus) or using (Ovsynch protocol) during low breeding season, to calve during the period when milk availability is short.

  15. A Study of Mutation Breeding of High-Yielding Tryptophanase Escherichia coli by Low-Energy N+ Ion Beam Implantation

    Science.gov (United States)

    Pang, Min; Yao, Jianming; Wang, Dongmei

    2009-12-01

    Low energy ion beam has been widely applied in microbe breeding, plant breeding, gene transfer and cell modification. In this study, the Escherichia coli (E.coli) strain producing tryptophanase was irradiated by a low energy nitrogen ion beam with an energy of 10 keV at a fluence of 13 × 1014 N+/cm2 when glycerin at a 15% concentration was used as a protector. The effect on the biomass of E. coli after N+ implantation was analyzed in detail by statistic methods. The screening methods used in this study were proven to be effective. After continuous mutagenicity, a high-yield tryptophanase strain was selected and both its biomass and enzymatic activity were higher than those of the parent strain. The results of scale-up production showed that the biomass could reach wet weight 8.2 g/L and 110 g L-tryptophan could be formed in the volume of the 1l enzymatic reaction system.

  16. Immune clonal selection optimization method with combining mutation strategies

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In artificial immune optimization algorithm, the mutation of immune cells has been considered as the key operator that determines the algorithm performance. Traditional immune optimization algorithms have used a single mutation operator, typically a Gaussian. Using a variety of mutation operators that can be combined during evolution to generate different probability density function could hold the potential for producing better solutions with less computational effort. In view of this, a linear combination mutation operator of Gaussian and Cauchy mutation is presented in this paper, and a novel clonal selection optimization method based on clonal selection principle is proposed also. The simulation results show the combining mutation strategy can obtain the same performance as the best of pure strategies or even better in some cases.

  17. A novel point mutation within the EDA gene causes an exon dropping in mature RNA in Holstein Friesian cattle breed affected by X-linked anhidrotic ectodermal dysplasia

    Directory of Open Access Journals (Sweden)

    Pariset Lorraine

    2011-07-01

    Full Text Available Abstract Background X-linked anhidrotic ectodermal dysplasia is a disorder characterized by abnormal development of tissues and organs of ectodermal origin caused by mutations in the EDA gene. The bovine EDA gene encodes the ectodysplasin A, a membrane protein expressed in keratinocytes, hair follicles and sweat glands, which is involved in the interactions between cell and cell and/or cell and matrix. Four mutations causing ectodermal dysplasia in cattle have been described so far. Results We identified a new single nucleotide polymorphism (SNP at the 9th base of exon 8 in the EDA gene in two calves of Holstein Friesian cattle breed affected by ectodermal dysplasia. This SNP is located in the exonic splicing enhancer (ESEs recognized by SRp40 protein. As a consequence, the spliceosome machinery is no longer able to recognize the sequence as exonic and causes exon skipping. The mutation determines the deletion of the entire exon (131 bp in the RNA processing, causing a severe alteration of the protein structure and thus the disease. Conclusion We identified a mutation, never described before, that changes the regulation of alternative splicing in the EDA gene and causes ectodermal dysplasia in cattle. The analysis of the SNP allows the identification of carriers that can transmit the disease to the offspring. This mutation can thus be exploited for a rational and efficient selection of unequivocally healthy cows for breeding.

  18. Simple method for detection of mutations causing hereditary fructose intolerance.

    Science.gov (United States)

    Kullberg-Lindh, C; Hannoun, C; Lindh, M

    2002-11-01

    Aldolase B is critical for sugar metabolism, and a catalytic deficiency due to mutations in its gene may result in hereditary fructose intolerance (HFI) syndrome, with hypoglycaemia and severe abdominal symptoms. This report describes two cases of HFI, which were identified by intravenous fructose tolerance test and a new RFLP (restriction fragment length polymorphism) test that detects the two most common mutations, A149P and A174D. The method includes PCR of a 224-base-pair segment of exon 5, a subsequent 3 h incubation with Cac8I and agarose electrophoresis, which reveals either or both of the mutations in one single reaction. The method might be useful for screening of these mutations, which may account for more than 70% of the mutations causing HFI.

  19. Twenty year results on application of induced mutation in soybean (Glycine max (L.) Merr.) breeding at Agricultural Genetics Institute (AGI), Hanoi, Vietnam

    Energy Technology Data Exchange (ETDEWEB)

    Mai Quang Vinh; Phan Phai; Ngo Phuong Thinh; Tran Dinh Dong; Tran Thuy Oanh [Agricultural Genetics Institute (AGI), Hanoi (Viet Nam)

    2001-03-01

    Research on application of the induced mutation method combined with crossing in soybean breeding for 20 years (1980-2000) plays an important role in research work at AGI, (Ministry of Agriculture and Rural Development of Vietnam). 23 soybean varieties and hybrid lines (including 6 local cultivars, 14 selected and introduced varieties, 3 hybrid lines) were treated with Roentgen ray irradiation, Gamma Ray {sup 60}Co with doses 7, 10, 12, 15, 18, 20 krad, and with chemical mutagens: EI, NMU, DNMU, DES, EMS, DEU with various concentrations 0.008, 0.02, 0.04, 0.06, 0.08%. As the results, we obtained the important conclusions about the rule of induced mutation process in soybean in the natural conditions of Vietnam. 8 mutant varieties [1 National varieties (DT84) and 6 regional production varieties (DT83, DT90, DT94, DT95, DT99, AK06 (DT-55))]. Several promising varieties were selected and released for farmers to produce in the large areas that occupied 50-90% percentage of soybean cultivated areas in Vietnam. These varieties have high-yield 1.5-3.5 tons/ha, short growth duration 75-100 days, tolerance to cold and hot temperature and can be planted in 3 crops per year (Winter, Spring and Summer season) over 35-40 thousands ha/year. At present, the mutagens are being used for defect-orientated repair of some promising hybrid lines, in order to contribute new good varieties to soybean production in Vietnam. (author)

  20. Missense mutation in CAPN1 is associated with spinocerebellar ataxia in the Parson Russell Terrier dog breed.

    Directory of Open Access Journals (Sweden)

    Oliver P Forman

    Full Text Available Spinocerebellar ataxia (SCA in the Parson Russell Terrier (PRT dog breed is a disease of progressive incoordination of gait and loss of balance. Clinical signs usually become notable between 6 and 12 months of age with affected dogs presenting with symmetric spinocerebellar ataxia particularly evident in the pelvic limbs. The degree of truncal ataxia, pelvic limb hypermetria and impaired balance is progressive, particularly during the initial months of disease. A certain degree of stabilisation as well as intermittent worsening may occur. At the later stages of the disease ambulation often becomes difficult, with owners often electing to euthanise affected dogs on welfare grounds. Using a GWAS approach and target-enriched massively-parallel sequencing, a strongly associated non-synonymous SNP in the CAPN1 gene, encoding the calcium dependent cysteine protease calpain1 (mu-calpain, was identified. The SNP is a missense mutation causing a cysteine to tyrosine substitution at residue 115 of the CAPN1 protein. Cysteine 115 is a highly conserved residue and forms a key part of a catalytic triad of amino acids that are crucial to the enzymatic activity of cysteine proteases. The CAPN1 gene shows high levels of expression in the brain and nervous system and roles for the protein in both neuronal necrosis and maintenance have been suggested. Given the functional implications and high level of conservation observed across species, the CAPN1 variant represents a provocative candidate for the cause of SCA in the PRT and a novel potential cause of ataxia in humans.

  1. A new mutation in MC1R explains a coat color phenotype in 2 "old" breeds: Saluki and Afghan hound.

    Science.gov (United States)

    Dreger, Dayna L; Schmutz, Sheila M

    2010-01-01

    Melanocortin 1 Receptor (MC1R) has been studied in a wide variety of domestic animals (Klungland et al. 1995; Marklund et al. 1996; Våge et al. 1997; Kijas et al. 1998; Newton et al. 2000; Våge et al. 2003), and also several wild animals (Robbins et al. 1993; Ritland et al. 2001; Eizirik et al. 2003; Nachman et al. 2003; McRobie et al. 2009) in relation to coat color variation. A variety of phenotypic changes have been reported including coat colors from pure black to pure red, as well as some phenotypes with hairs with red and black bands. One phenotype, called grizzle in Salukis and domino in Afghan Hounds, appears to be unique to these 2 old dog breeds. This pattern is characterized by a pale face with a widow's peak above the eyes. The body hairs on the dorsal surface of Salukis and Afghan Hounds have both phaeomelanin and eumelanin portions, even though they had an a(t)/a(t) genotype at ASIP. In addition, all had at least one copy of a newly identified mutation in MC1R, g.233G>T, resulting in p.Gly78Val. This new allele, that we suggest be designated as E(G), is dominant to the E and e (p.Arg306ter) alleles at MC1R but recessive to the E(M) (p.Met264Val) allele. The K(B) allele (p.Gly23del) at DEFB103 and the a(y) allele (p.Ala82Ser and p.Arg83His) of ASIP are epistatic to grizzle and domino.

  2. Using the choice experiment method in the design of breeding goals in dairy sheep.

    Science.gov (United States)

    Ragkos, A; Abas, Z

    2015-02-01

    Market failures are the main cause of poor acknowledgement of the true impact of functional sheep traits on the management and economic performance of farms, which results in their omission from the breeding goal or the estimation of non-representative economic weights in the breeding goal. Consequently, stated-preference non-market valuation techniques, which recently emerged to mitigate these problems, are necessary to estimate economic weights for functional traits. The purpose of this paper is to present an example of the use of a choice experiment (CE) in the estimation of economic weights for sheep traits for the design of breeding goals. Through a questionnaire survey the preferences of sheep farmers are recorded and their marginal willingness to pay (MWTP) for 10 production and functional traits is estimated. Data are analysed using random parameter logit models. The results reveal unobserved preference heterogeneity for fertility, adaptability to grazing and resistance to disease, thus highlighting that these traits are appreciated differently by farmers, because their needs are diverse. Positive MWTP is found for Greek breeds, high milk production and lambs with low fat deposition, for which there is high demand in Greek markets. On the other hand, MWTP for the cheese-making ability of milk is negative, stemming from the fact that sheep milk prices in Greece are not formulated according to milk composition. In addition, farmers seem to understand differences between udder shapes and attribute different values to various types. This application of the CE method indicates that communication channels among farmers and breeders should be established in order to enhance market performance and to provide orientation to the design of breeding programmes. Non-market valuation can be used complementarily to market valuation techniques, in order to provide accurate estimates for production and functional traits.

  3. KRAS mutation analysis by PCR: a comparison of two methods.

    Directory of Open Access Journals (Sweden)

    Louise Bolton

    Full Text Available KRAS mutation assays are important companion diagnostic tests to guide anti-EGFR antibody treatment of metastatic colorectal cancer. Direct comparison of newer diagnostic methods with existing methods is an important part of validation of any new technique. In this this study, we have compared the Therascreen (Qiagen ARMS assay with Competitive Allele-Specific TaqMan PCR (castPCR, Life Technologies to determine equivalence for KRAS mutation analysis.DNA was extracted by Maxwell (Promega from 99 colorectal cancers. The ARMS-based Therascreen and a customized castPCR assay were performed according to the manufacturer's instructions. All assays were performed on either an Applied Biosystems 7500 Fast Dx or a ViiA7 real-time PCR machine (both from Life Technologies. The data were collected and discrepant results re-tested with newly extracted DNA from the same blocks in both assay types.Of the 99 tumors included, Therascreen showed 62 tumors to be wild-type (WT for KRAS, while 37 had KRAS mutations on initial testing. CastPCR showed 61 tumors to be wild-type (WT for KRAS, while 38 had KRAS mutations. Thirteen tumors showed BRAF mutation in castPCR and in one of these there was also a KRAS mutation. The custom castPCR plate included several other KRAS mutations and BRAF V600E, not included in Therascreen, explaining the higher number of mutations detected by castPCR. Re-testing of discrepant results was required in three tumors, all of which then achieved concordance for KRAS. CastPCR assay Ct values were on average 2 cycles lower than Therascreen.There was excellent correlation between the two methods. Although castPCR assay shows lower Ct values than Therascreen, this is unlikely to be clinically significant.

  4. UV Breeding by Induced Mutation of Mucor Protease Strain from Sufu%腐乳毛霉蛋白酶菌株紫外线诱变育种

    Institute of Scientific and Technical Information of China (English)

    刘芳; 曹新志; 方春玉; 梁秋菊

    2009-01-01

    Objective:Breeding of Mucor protease strain with high enzyme activity and good high-temperaturre for fermentation experiments or production of sufu.Method: Mucor protease strains were picked out from sufu,its original strain was induced mutation by UV and fostered by temperature control,breeding of excellent mutant strain.Result:One high enzyme vitality and excellent high-temperature mutant strain named SCLG-mucor 16 was selected,the strain can strongly grow at 32℃.Its HE is 1.39,protease vitality is 180.375u/g,which was enhanced by 7.8% and 51.4% more than the original strain respectively.Conclusion: The excellent mutant strain was used for fermentation experiments or production of sufu, it has a certain using value in shortening the fermentation time,enhancing the quality of sufu and extending the season of production.%目的:选育酶活力高、耐热性好的毛霉蛋白酶菌株,用于腐乳发酵实验或生产.方法:从腐乳中分离毛霉蛋白酶菌株.对其出发菌株进行紫外线诱变,并经控温培养,选育优良变株.结果:获得一株酶活力高、耐热性强的优良变株SCIG-毛霉16.该菌株在32℃条件下,生长茂盛,其HE值为1.39、蛋白酶活力为180.375μ/g,分别较出发菌株高出7.8%和51.4%.结论:将此优良变株用于腐乳发酵实验或生产,在缩短发酵时间,提升腐乳质量,延长生产季节等方面具有一定的应用价值.

  5. Prospects for DNA methods to measure human heritable mutation rates

    Energy Technology Data Exchange (ETDEWEB)

    Mendelsohn, M.L.

    1985-06-14

    A workshop cosponsored by ICPEMC and the US Department of Energy was held in Alta, Utah, December 9-13, 1984 to examine the extent to which DNA-oriented methods might provide new approaches to the important but intractable problem of measuring mutation rates in control and exposed human populations. The workshop identified and analyzed six DNA methods for detection of human heritable mutation, including several created at the meeting, and concluded that none of the methods combine sufficient feasibility and efficiency to be recommended for general application. 8 refs.

  6. Studies on Mutation Breeding of High-Yielding Xylanase Strains by Low-Energy Ion Beam Implantation

    Institute of Scientific and Technical Information of China (English)

    LI Shichang; YAO Jianming; YU Zhengling

    2007-01-01

    As a new mutagenetic method,low-energy ion implantation has been used widely in many research areas in recent years.In order to obtain some industrial strains with high xylanase yield,the wild type strain Aspergillus niger A3 was mutated by means of nitrogen ions implantation (10 keV,2.6 × 1014~1.56 × 1015 ions/cm2) and a mutant N212 was isolated subsequently.However,it was found that the initial screening means of the high-yielding xylanase strains such as transparent halos was unfit for first screening.Compared with that of the wild type strain,xylanase production of the mutant N212 was increased from 320 IU/ml to 610 IU/ml,and the optimum fermentation temperature was increased from 28 ℃ to 30 ℃.

  7. Polysaccharide storage myopathy phenotype in quarter horse-related breeds is modified by the presence of an RYR1 mutation.

    Science.gov (United States)

    McCue, M E; Valberg, S J; Jackson, M; Borgia, L; Lucio, M; Mickelson, J R

    2009-01-01

    In this study we examined a family of Quarter Horses with Polysaccharide Storage Myopathy (PSSM) with a dominant mutation in the skeletal muscle glycogen synthase (GYS1) gene. A subset of horses within this family had a more severe and occasionally fatal PSSM phenotype. The purpose of this study was to identify a modifying gene(s) for the severe clinical phenotype. A genetic association analysis was used to identify RYR1 as a candidate modifying gene. A rare, known equine RYR1 mutation, associated with malignant hyperthermia (MH), was found to segregate in this GYS1 PSSM family. Retrospective analysis of patient records (n=179) demonstrated that horses with both the GYS1 and RYR1 mutations had a more severe clinical phenotype than horses with the GYS1 mutation alone. A treadmill trial (n=8) showed that serum creatine kinase activity was higher and exercise intolerance greater in horses with both mutations compared to the GYS1 mutation alone.

  8. A CLN8 nonsense mutation in the whole genome sequence of a mixed breed dog with neuronal ceroid lipofuscinosis and Australian Shepherd ancestry.

    Science.gov (United States)

    Guo, Juyuan; Johnson, Gary S; Brown, Holly A; Provencher, Michele L; da Costa, Ronaldo C; Mhlanga-Mutangadura, Tendai; Taylor, Jeremy F; Schnabel, Robert D; O'Brien, Dennis P; Katz, Martin L

    2014-08-01

    The neuronal ceroid lipofuscinoses (NCLs) are hereditary neurodegenerative diseases characterized by seizures and progressive cognitive decline, motor impairment, and vision loss accompanied by accumulation of autofluorescent lysosomal storage bodies in the central nervous system and elsewhere in the body. Mutations in at least 14 genes underlie the various forms of NCL. One of these genes, CLN8, encodes an intrinsic membrane protein of unknown function that appears to be localized primarily to the endoplasmic reticulum. Most CLN8 mutations in people result in a form of NCL with a late infantile onset and relatively rapid progression. A mixed breed dog with Australian Shepherd and Blue Heeler ancestry developed neurological signs characteristic of NCL starting at about 8months of age. The signs became progressively worse and the dog was euthanized at 21months of age due to seizures of increasing frequency and severity. Postmortem examination of the brain and retinas identified massive accumulations of intracellular autofluorescent inclusions characteristic of the NCLs. Whole genome sequencing of DNA from this dog identified a CLN8:c.585G>A transition that predicts a CLN8:p.Trp195* nonsense mutation. This mutation appears to be rare in both ancestral breeds. All of our 133 archived DNA samples from Blue Heelers, and 1481 of our 1488 archived Australian Shepherd DNA samples tested homozygous for the reference CLN8:c.585G allele. Four of the Australian Shepherd samples tested heterozygous and 3 tested homozygous for the mutant CLN8:c.585A allele. All 3 dogs homozygous for the A allele exhibited clinical signs of NCL and in 2 of them NCL was confirmed by postmortem evaluation of brain tissue. The occurrence of confirmed NCL in 3 of 4 CLN8:c.585A homozygous dogs, plus the occurrence of clinical signs consistent with NCL in the fourth homozygote strongly suggests that this rare truncating mutation causes NCL. Identification of this NCL-causing mutation provides the

  9. Selection of mango rosa genotypes in a breeding population using the multivariate-biplot method

    Directory of Open Access Journals (Sweden)

    Maria Clideana Cabral Maia

    Full Text Available ABSTRACT: Mango ( Mangifera indica L. trees stand out among the main fruit trees cultivated in Brazil. The mango rosa fruit is a very popular local variety (landrace, especially because of their superior technological characteristics such as high contents of Vitamin C and soluble solids (SS, as well as attractive taste and color. The objective of this study was to select a breeding population of mango rosa (polyclonal variety; ≥5 individuals that can simultaneously meet the fresh and processed fruit markets, using the multivariate method of principal components and the biplot graphic. The principal components, biplot graphic, and phenotype correlations were obtained using the R (2012 software. Pulp percentage and the pulp, skin, and seed mass variables can be indirectly selected using the smallest fruit diameter, which allowed an easier measurement. The P23R AREA3, P30R AREA3, and P32R AREA3 genotypes are selection candidates due to the presence of alleles, which are important agro-technological traits for mango breeding. This study showed that the biplot analysis is a valuable tool for decision making and visualization of interrelationships between variables and genotypes, facilitating the mango selection process.

  10. Mutation Breeding of High - Efficiency Bioflocculant - Producing Strain%高效生物絮凝剂产生菌的诱变选育

    Institute of Scientific and Technical Information of China (English)

    田连生; 陈秀清

    2015-01-01

    为得到絮凝活性高的优良菌株,采用紫外线诱变和化学诱变相结合的方法对野生菌株 XN -3进行人工育种,选育出性能优良、遗传稳定的变异菌株 UH -2-4,其絮凝率达到96.8%,比原菌株提高了25.1%。并研究了金属离子、投加量对其絮凝活性的影响。%To obtain a fine strain with high flocculation activity ,variable strain UH - 2 -4 with excellent performance and stable heredity has been obtained from the artificial breeding of a wild strain XN - 3 by the combination of UV induced muta-tion and chemical mutation and its flocculation rate can reach 96 .8% ,25 .1% higher than the original strain .The effects of the metal ion and dose on the flocculating activity are also studied .

  11. Mutation Breeding of Penicillium Glaucum NS3 Yan Shufang et al.%灰绿青霉Penicillium glaucum NS3的诱变育种

    Institute of Scientific and Technical Information of China (English)

    颜淑芳; 郭敏; 韩诚; 许秋香; 龙秀; 何丽

    2011-01-01

    After fermetation conditions optimising of the Penicillium glaucum NS3, a several of synergistic mutation have been carry out for increasing its cellulase - producing capacity. A higher cellulase - producing strain named NS3cl had been gotten, which was breeded through inducing mutation treatmentt of ultraviolet light and sodium nitrite. The optimal dosage of mutant by UV and sodium nitrite was 9 minutes with 15W UV light in 30em distance and 0.3% concentration. Under the repeated synergistic mutations, the CMCase and FPAase produced by mutant Penicillium glaucum NS3cl reached 400.07 IU/ mL and 9.47 IU/mL, which increased 29.47% and 28.35% than that of the original activities 309 IU/mL and 7.37 IU/mL.%以发酵条件优化的菌株Penicilliumglaucum NS3为出发菌,采用紫外线、亚硝酸钠复合诱变,在UV(15W、距30cm辐照9min)、0.3%亚硝酸钠协同诱变条件下,经多轮反复诱变,得到茵株Penicillium glaucum NS3e1,其发酵液CMC酶活和滤纸酶活分别达到400.07IU/mL和9.47IU/mL,比出发茵酶活309Iu/mL和7.37IU/mL分别提高29.47%和28.35%。

  12. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

    NARCIS (Netherlands)

    Mulder, H.A.; Meuwissen, T.H.E.; Calus, M.P.L.; Veerkamp, R.F.

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing geneassisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-as

  13. 高产纤维素酶菌株筛选及诱变选育%Screening and Mutation Breeding of the Strains of High-yielding Celluase

    Institute of Scientific and Technical Information of China (English)

    许志; 曾柏全; 宋睿

    2011-01-01

    为了得到高产纤维素酶的菌株,达到缓解纤维素酶活不高、纤维素酶供不应求现状的目的.从自然界中筛选出较优良的产纤维素酶菌株并对其进行紫外、60Co-射线诱变选育获得高产纤维素酶活的突变株.从自然界筛选出来的菌株通过菌落、菌丝体以及孢子丝的形态初步鉴定为放线菌并命名为XZ-33.对XZ-33进行复合诱变选育并根据致死率和诱变剂量以及正突变率的相互关系,得出合适的诱变剂量即:紫外照射7min,辐照剂量为0.6 KGy的γ射线对产纤维素酶的出发菌进行诱变,得到高产纤维素酶的突变株UV-Co16,其CMCase酶活达到66.15 IU/mL,以及PFAase酶活2.91 IU/mL,分别是出发菌的3.17倍和2.42倍.该突变株的获得为微生物发酵生产乙醇奠定了基础.%In order to get the strains of high-yielding cellulase, to alleviate the present bad situation: the activity of most cellulase is relatively low; the supply of cellulase has failed to keep pace with demand. Some higher cellulase-producing strain were picked from the nature and then carried them on mutation breeding under the UV light and 60 Co-γrays to obtained mutants of those high-produced. The original stains gained by screening had been preliminarily identified as the Actinomycete XZ-33 by observing the form of bacterial colony, mycelium and spores. According to the interrelation between the fatality rate, mutation doses and mutation rate, it could be deduced that the most appropriate conditions of induced mutation was that exposing them under UV-irradiation for 7 minute and γ rays-irradiation up to 0.6 Kgy. After a series of mutation breeding a high cellulase-producing mutant stain have been obtained, named as mutant UV-C016, its CMCase enzyme activity reached at the level of 66.15 IU/mb, and PFAase enzyme 2.91 IU/mL, it was respectively 3.17 times and 2.42 times higher than the original screened strains. The success to get a high cellulase

  14. Model selection for the North American Breeding Bird Survey: A comparison of methods

    Science.gov (United States)

    Link, William; Sauer, John; Niven, Daniel

    2017-01-01

    The North American Breeding Bird Survey (BBS) provides data for >420 bird species at multiple geographic scales over 5 decades. Modern computational methods have facilitated the fitting of complex hierarchical models to these data. It is easy to propose and fit new models, but little attention has been given to model selection. Here, we discuss and illustrate model selection using leave-one-out cross validation, and the Bayesian Predictive Information Criterion (BPIC). Cross-validation is enormously computationally intensive; we thus evaluate the performance of the Watanabe-Akaike Information Criterion (WAIC) as a computationally efficient approximation to the BPIC. Our evaluation is based on analyses of 4 models as applied to 20 species covered by the BBS. Model selection based on BPIC provided no strong evidence of one model being consistently superior to the others; for 14/20 species, none of the models emerged as superior. For the remaining 6 species, a first-difference model of population trajectory was always among the best fitting. Our results show that WAIC is not reliable as a surrogate for BPIC. Development of appropriate model sets and their evaluation using BPIC is an important innovation for the analysis of BBS data.

  15. TILLING in forage grasses for gene discovery and breeding improvement.

    Science.gov (United States)

    Manzanares, Chloe; Yates, Steven; Ruckle, Michael; Nay, Michelle; Studer, Bruno

    2016-09-25

    Mutation breeding has a long-standing history and in some major crop species, many of the most important cultivars have their origin in germplasm generated by mutation induction. For almost two decades, methods for TILLING (Targeting Induced Local Lesions IN Genomes) have been established in model plant species such as Arabidopsis (Arabidopsis thaliana L.), enabling the functional analysis of genes. Recent advances in mutation detection by second generation sequencing technology have brought its utility to major crop species. However, it has remained difficult to apply similar approaches in forage and turf grasses, mainly due to their outbreeding nature maintained by an efficient self-incompatibility system. Starting with a description of the extent to which traditional mutagenesis methods have contributed to crop yield increase in the past, this review focuses on technological approaches to implement TILLING-based strategies for the improvement of forage grass breeding through forward and reverse genetics. We present first results from TILLING in allogamous forage grasses for traits such as stress tolerance and evaluate prospects for rapid implementation of beneficial alleles to forage grass breeding. In conclusion, large-scale induced mutation resources, used for forward genetic screens, constitute a valuable tool to increase the genetic diversity for breeding and can be generated with relatively small investments in forage grasses. Furthermore, large libraries of sequenced mutations can be readily established, providing enhanced opportunities to discover mutations in genes controlling traits of agricultural importance and to study gene functions by reverse genetics.

  16. Isolation breeds naivety: island living robs Australian varanid lizards of toad-toxin immunity via four-base-pair mutation.

    Science.gov (United States)

    Ujvari, Beata; Mun, Hee-chang; Conigrave, Arthur D; Bray, Alessandra; Osterkamp, Jens; Halling, Petter; Madsen, Thomas

    2013-01-01

    Since their introduction to the toad-free Australian continent cane toads (Bufo marinus) have caused a dramatic increase in naïve varanid mortality when these large lizards attempt to feed on this toxic amphibian. In contrast Asian-African varanids, which have coevolved with toads, are resistant to toad toxin. Toad toxins, such as Bufalin target the H1-H2 domain of the α(1) subunit of the sodium-potassium-ATPase enzyme. Sequencing of this domain revealed identical nucleotide sequences in four Asian as well as in three African varanids, and identical sequences in all 11 Australian varanids. However, compared to the Asian-African varanids, the Australian varanids showed four-base-pair substitutions, resulting in the alteration in three of the 12 amino acids representing the H1-H2 domain. The phenotypic effect of the substitutions was investigated in human embryonic kidney (HEK) 293 cells stably transfected with the Australian and the Asian-African H1-H2 domains. The transfections resulted in an approximate 3000-fold reduction in resistance to Bufalin in the Australian HEK293 cells compared to the Asian-African HEK293 cells, demonstrating the critical role of this minor mutation in providing Bufalin resistance. Our study hence presents a clear link between genotype and phenotype, a critical step in understanding the evolution of phenotypic diversity.

  17. Methods for estimation of daily and lactation milk yields from alternative milk recording scheme in Holstein and Simmental cattle breeds

    Directory of Open Access Journals (Sweden)

    Krešimir Kuterovac

    2010-01-01

    Full Text Available The aim of this study was to compare different statistical methods for the estimation of daily and 305-day lactation milk, fat and protein yields of Holstein and Simmental cattle breeds using an alternative milk recording scheme. Data included 6,824 individual test-day milk yield records collected according to the A4 milk recording method on 668 cows reared on 15 family farms. Daily milk, fat and protein yields were estimated using several statistical methods with regard to breed. The 305-day lactation yields were calculated from estimated daily yields using the Test Interval Method. The correlation between estimated and true yields, as well as the mean difference among estimated and true yield were used as the evaluation criteria for estimation methods. The linear regression of daily to partial milk, fat and protein yields while taking into account the interval between successive milkings was shown to be the most accurate model for estimating daily values, either from morning or evening records. The simple doubling of morning or evening records overestimated and underestimated the daily yields, respectively. When 305-day lactation milk, fat and protein yields were compared no difference between evaluated methods were found. Also, a separate estimation of daily and 305-day lactation yields according to breeds did not result in increased estimation accuracy.

  18. The Mutation Breeding of Streptomyces avermilitis%阿维链霉菌的诱变育种

    Institute of Scientific and Technical Information of China (English)

    陈金辉; 郭伟群; 蔡玉娟; 王天科; 王晓芳; 宋渊

    2011-01-01

    Spores and protoplasts of the original strain Streptomyces avermitilis 76 12 were treated with nitrosoguanidine (NTG), acridine orange, ultraviolet radiation (UV) and LiCl respectively. Then a series of high yield avermectin producing and stable mutants were obtained through mutation and rational selection. The avermection productivity of the mutant N 1 2 was 2.47 times of the original strain. Furthermore, several special mutants were obtained. Mutant strain G 32 produced only "a" avermectins; mutant strain Ave8 had higher lever of avermectin B1a content than original strain; and mutant strain UA G developed bluegreen spores.%以阿维链霉菌(Streptomyces avermitilis)76-12为出发菌株,采用亚硝基胍、吖啶橙、紫外线和氯化锂分别对其孢子和原生质体进行诱变,经抗代谢物理性筛选,获得一系列高产突变株,其中N-1-2高产突变株的发酵单位是出发菌株的2.47倍。实验中同时获得了只产阿维菌素a组分的突变株G-32、Bla组分含量高的Ave8菌株和产蓝绿色孢子的突变株UA-G等。

  19. Immune clonal selection optimization method with combining mutation strategies

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In artificial immune optimization algorithm, the mutation of immune cells has been considered as the key operator that determines the algorithm performance. Traditional immune optimization algorithms have used a single mutation operator, typically a Gaussian. Using a variety of mutation operators that can be combined during evolution to generate different probability density function could hold the potential for producing better solutions with less computational effort. In view of this, a linear combination...

  20. Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

    NARCIS (Netherlands)

    Rosenberg, N.A.; Burke, T.; Elo, K.; Feldman, M.W.; Friedlin, P.J.; Groenen, M.A.M.; Hillel, J.; Maki-Tanila, A.; Tixier-Boichard, M.; Vignal, A.; Wimmers, K.

    2001-01-01

    We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus

  1. Establishing Criteria for a Method to Automatically Detect the Onset of Parturition and Dystocia in Breeding Pigs

    OpenAIRE

    Gutierrez, Winson-Montanez; Kim, Dae-Geun; Kim, Dong-Hyeok; Kim, Suk; Le, Seung-Joo; Kim, Byeong-Woo; Hong, Jong-Tae; Yu, Byeong-Ki; Kim, Hyuck-Joo; Oh, Taek-Keun

    2011-01-01

    The aims of the present study were to characterize the farrowing process in gilts and multiparous sows in terms of duration of farrowing, birth intervals, birth weight, piglets born alive, stillbirth, mummified and dystocia by comparing means in terms of parities, and to establish criteria for a method to automatically detect the first birth and dystocia in breeding pigs for a selected farm in South Korea. One hundred nine Yorkshire x Landrace; YL, Landrace x Yorkshire; LY which were mainly r...

  2. The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods.

    Science.gov (United States)

    Mulder, H A; Meuwissen, T H E; Calus, M P L; Veerkamp, R F

    2010-01-01

    In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD-LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD-LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD-LA was larger than when all animals had phenotypes. Missing

  3. Witches' brooms in Siberian stone pine as somatic mutations and initial genetic material for breeding of nut-bearing and ornamental cultivars

    Directory of Open Access Journals (Sweden)

    M. S. Yamburov

    2013-12-01

    identical shoot length, the number of lateral buds in the WBG was 3-4 times more. This superiority was achieved in several ways: a greater shoot number per node, thepresence of one or even two additional nodes (summer shoot on many annual shoots, the formation of lateral long shoots outside any nodes(instead of short shoots. (iii The number of stem units, their length, and annual shoot length in the WBG were 1.5-2 times less compared with the NCG. The first seed cones were initiated in both variants in the year of grafting. However, by the end of 5-7 year period of supervision, the WBG surpassed the NCG in the number of cones by 5-10 times. WB and NC have also been tested on seed progeny (WBP and NCP. In the WBP halfsib families, a clear tendency of splitting into twoclasses was observed: (1 normal seedlings, statistically indistinguishable from the homogenous NCPs and (2 seedlings with growth essentially slowed down and very intensive branching. The ratio of the two classes was about 1:1. Therefore, the studied WB are a dominant somatic mutation. The principles of using of these mutations in breeding programs are discussed.

  4. High Resolution Melting Analysis: A Rapid and Accurate Method to Detect CALR Mutations

    Science.gov (United States)

    Moreno, Melania; Torres, Laura; Santana-Lopez, Gonzalo; Rodriguez-Medina, Carlos; Perera, María; Bellosillo, Beatriz; de la Iglesia, Silvia; Molero, Teresa; Gomez-Casares, Maria Teresa

    2014-01-01

    Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations. PMID:25068507

  5. The $1^{+}\\to n^{+}$ charge breeding method for the production of radioactive and stable continuous /pulsed multi-chargedion beams

    CERN Document Server

    Chauvin, N; Bouly, J L; Curdy, Jean Claude; Geller, R; Lamy, T; Solé, P; Sortais, P

    1999-01-01

    The principle of the 1+ -> n+ charge breeding method by injecting a mono-charged ion beam in an Electron Cyclotron Resonance Ion Source is recalled. Some 1+ ->n+ breeding efficiencies in continuous mode are given, like 9% for Ar1+ ->Ar8+ and 5% for Rb1+->Rb15+. The global capture efficiency is deduced from the whole charge state distribution spectrum. The ECRIT (ECR Ion Trap) mode that allows to produce a pulsed multi-charged beam is explained. The n+ ions are extracted in a 20 ms pulse. The breeding-bunching efficiencies are measured for Rb1+->Rb15+ (2.2%) and Pb1+->Pb22+ (1.3 %). Ion trapping time in the ECRIT plasma is evaluated to some hundreds of ms. A new application of the 1+->n+ method is developed: the production of multi-charged natural metallic ions. First experiments have been done on uranium: a 500 nA continuous current of U26+ has been measured. Finally, the future developments on the 1+->n+ experiment are discussed. A description of a 1+ ->n+ dedicated high performance ECRIS named PHOENIX (Prod...

  6. Effect of lateral boundary perturbations on the breeding method and the local ensemble transform Kalman filter for mesoscale ensemble prediction

    Directory of Open Access Journals (Sweden)

    Kazuo Saito

    2012-01-01

    Full Text Available The effect of lateral boundary perturbations (LBPs on the mesoscale breeding (MBD method and the local ensemble transform Kalman filter (LETKF as the initial perturbations generators for mesoscale ensemble prediction systems (EPSs was examined. A LBPs method using the Japan Meteorological Agency's (JMA's operational one-week global ensemble prediction was developed and applied to the mesoscale EPS of the Meteorological Research Institute for the World Weather Research Programme, Beijing 2008 Olympics Research and Development Project. The amplitude of the LBPs was adjusted based on the ensemble spread statistics considering the difference of the forecast times of the JMA's one-week EPS and the associated breeding/ensemble Kalman filter (EnKF cycles. LBPs in the ensemble forecast increase the ensemble spread and improve the accuracy of the ensemble mean forecast. In the MBD method, if LBPs were introduced in its breeding cycles, the growth rate of the generated bred vectors is increased, and the ensemble spread and the root mean square errors (RMSEs of the ensemble mean are further improved in the ensemble forecast. With LBPs in the breeding cycles, positional correspondences to the meteorological disturbances and the orthogonality of the bred vectors are improved. Brier Skill Scores (BSSs also showed a remarkable effect of LBPs in the breeding cycles. LBPs showed a similar effect with the LETKF. If LBPs were introduced in the EnKF data assimilation cycles, the ensemble spread, ensemble mean accuracy, and BSSs for precipitation were improved, although the relative advantage of LETKF as the initial perturbations generator against MDB was not necessarily clear. LBPs in the EnKF cycles contribute not to the orthogonalisation but to prevent the underestimation of the forecast error near the lateral boundary.The accuracy of the LETKF analyses was compared with that of the mesoscale 4D-VAR analyses. With LBPs in the LETKF cycles, the RMSEs of the

  7. High resolution melting analysis: a rapid and accurate method to detect CALR mutations.

    Directory of Open Access Journals (Sweden)

    Cristina Bilbao-Sieyro

    Full Text Available The recent discovery of CALR mutations in essential thrombocythemia (ET and primary myelofibrosis (PMF patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN. We tested the feasibility of high-resolution melting (HRM as a screening method for rapid detection of CALR mutations.CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET.Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34, 14% of persistent thrombocytosis suggestive of MPN (3/21 and none of the secondary thrombocytosis (0/98. Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%.This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.

  8. The method for breeding and genetic assessment of Scotch pine clones at forest seed orchards

    Directory of Open Access Journals (Sweden)

    B. V. Raevsky

    2016-10-01

    Full Text Available Fast height growth selection usually considered as the basic type of Scotch pine breeding strategy. Due to this fact height growth of pine clones usually is taken as the first key feature. In the view of good seed production there is only one indicator that could be adopted as having summarized effect reflecting the real contribution of a clone to the whole seed orchard yield. This is an average number of full seeds per tree (ramet. This trait is the second most important one after the height growth ability feature. The way of two-trait breeding program with the aforesaid features seemed to be the most suitable for Scotch pine. Main theses of 4-stages complex assessment procedure have been formulated concerning Scotch pine vegetative progenies grown at seed orchards. It was stated that this system of breeding and genetic assessment is based on correlations found for habitus and reproductive features of Scotch pine clones along with the height growth ability of their seed progenies. In the first stage pine clones meeting the criteria (≥ X + 0.5σx regarding height growth are to be selected. In the second stage, clones with hard tapering stem and crown formed by long and thick branches have to be discarded. At this stage, such feature as «mean diameter of three thickest limbs at the height of 1.5–2.0 m» became the key factor. Its mean value for selected clones must not be by 1–2 % higher than for general clone set. In the third stage a complex of reproductive features for clones that have passed the previous stages are taken into account. The trait «average number of full seeds per ramet» is the key feature in this stage according to the criteria (≥ X . The fourth stage implies that progeny trials with open-pollinated progenies ought to be laid down to calculate the general and specific combining ability. It has been concluded that high intensive selection of clones grown at the I-stage seed orchards promotes a substantial genetic gain

  9. Recent progress on atmospheric and room temperature plasma mutation breeding technology and its applications%常压室温等离子体生物诱变育种及其应用研究进展

    Institute of Scientific and Technical Information of China (English)

    张雪; 张晓菲; 王立言; 张翀; 陈韵亿; 常海波; 李和平; 邢新会

    2014-01-01

    Radio-frequency atmospheric pressure glow discharge (RF APGD) plasmas have outstanding features of no need of expensive and complicated vacuum system, low gas temperatures, high concentrations of reactive species, good discharge uniformity, strong controllability and diverse interactions with various biomolecules, which have attracted more and more attentions for their applications in biotechnology. Our research group introduced the RF APGD plasma jet into the mutation breeding field. Based on the study on the physical characteristics of RF APGD plasmas and their interaction mechanisms with bio-macromolecules and whole cells, a novel mutation breeding system, named as atmospheric and room temperature plasma (ARTP) mutation breeding machine was invented. The ARTP mutation breeding system has the features of high safety for the operators and environment, easy operation, rapid mutation capability, high mutation rate and genetic stability of targeted mutants,as demonstrated by successful mutation for more than 40 different microbes including bacteria, fungi and algae. This paper reviews the recent research progress of ARTP mutation breeding technology, hopefully contributing to the development of the life evolution study and the industrial strain modification as a powerful mutation tool.%大气压射频辉光放电(RF APGD)等离子体具有大气压下操作不需要真空系统、气体温度低、活性粒子浓度高、放电均匀性好、可控性强等特点,能够与各类生物分子发生作用,在生物技术中的应用受到广泛的关注。本研究团队将RF APGD等离子体射流引入生物诱变育种领域,对其物理特性及其与生物大分子和整细胞的作用机制进行了系统研究,并将其开发成新一代高效诱变育种仪,命名为常压室温等离子体(ARTP)诱变育种仪。实践证明,ARTP 诱变育种仪具有对操作者安全、环境友好、操作简便、突变快速、突变率高、获得的

  10. Consensus methods for breeding low methane emitting : Breeding ruminants that emit less methane - development of consensus methods for measurements of methane (white paper)

    NARCIS (Netherlands)

    Pickering, N.K.; Haas, de Y.; Basarab, J.; Cammack, K.; Hayes, B.; Hegarty, R.; Lassen, J.; McEwan, J.; Miller, S.; Pinares-Patino, C.; Shackell, G.; Vercoe, P.; Oddy, Hutton

    2013-01-01

    This report was prepared by a working group of the Animal Selection, Genetics and Genomics Network (ASGGN) of the Global Research Alliance for reducing greenhouse gases from agriculture. It is a summary of published and yet to be published work. The purpose is to evaluate methods that are

  11. Indirect exclusion of four candidate genes for generalized progressive retinal atrophy in several breeds of dogs

    Directory of Open Access Journals (Sweden)

    Kraczyk Britta

    2006-11-01

    Full Text Available Abstract Background Generalized progressive retinal atrophy (gPRA is a hereditary ocular disorder with progressive photoreceptor degeneration in dogs. Four retina-specific genes, ATP binding cassette transporter retina (ABCA4, connexin 36 (CX36, c-mer tyrosin kinase receptor (MERTK and photoreceptor cell retinol dehydrogenase (RDH12 were investigated in order to identify mutations leading to autosomal recessive (ar gPRA in 29 breeds of dogs. Results Mutation screening was performed initially by PCR and single strand conformation polymorphism (SSCP analysis, representing a simple method with comparatively high reliability for identification of sequence variations in many samples. Conspicuous banding patterns were analyzed via sequence analyses in order to detect the underlying nucleotide variations. No pathogenetically relevant mutations were detected in the genes ABCA4, CX36, MERTK and RDH12 in 71 affected dogs of 29 breeds. Yet 30 new sequence variations were identified, both, in the coding regions and intronic sequences. Many of the sequence variations were in heterozygous state in affected dogs. Conclusion Based on the ar transmittance of gPRA in the breeds investigated, informative sequence variations provide evidence allowing indirect exclusion of pathogenetic mutations in the genes ABCA4 (for 9 breeds, CX36 (for 12 breeds, MERTK (for all 29 breeds and RDH12 (for 9 breeds.

  12. Methods for the identification of mutations in the human phenylalanine hydroxylase gene using DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Woo, S.L.C.; Dilella, A.G.

    1990-10-23

    This patent describes a method of detecting a mutation in a phenylalanine hydroxylase gene of human genomic DNA. Also described is an automated method of detecting PKU affected, PKU helerozgotes and normals in fetal to adult human samples.

  13. Reverse breeding: a novel breeding approach based on engineered meiosis

    NARCIS (Netherlands)

    Dirks, R.; Dun, van K.P.M.; Snoo, de B.; Berg, van den M.; Lelivelt, C.L.C.; Voermans, W.; Woudenberg, L.; Wit, de J.P.C.; Reinink, K.; Schut, J.W.; Jong, de J.H.S.G.M.; Wijnker, T.G.

    2009-01-01

    Reverse breeding (RB) is a novel plant breeding technique designed to directly produce parental lines for any heterozygous plant, one of the most sought after goals in plant breeding. RB generates perfectly complementing homozygous parental lines through engineered meiosis. The method is based on re

  14. Prospects for advanced electron cyclotron resonance and electron beam ion source charge breeding methods for EURISOL

    Energy Technology Data Exchange (ETDEWEB)

    Delahaye, P.; Jardin, P.; Maunoury, L.; Traykov, E.; Varenne, F. [GANIL, CEA/DSM-CNRS/IN2P3, Bd. Becquerel, BP 55027, 14076 Caen Cedex 05 (France); Galata, A.; Porcellato, A. M.; Prete, G. F. [INFN-Laboratori Nazionali di Legnaro, Viale dell' Universita 2, 35020 Legnaro, Padova (Italy); Angot, J.; Lamy, T.; Sortais, P.; Thuillier, T. [LPSC Grenoble, 53, rue des Martyrs, 38026 Grenoble Cedex (France); Ban, G. [LPC Caen, 6 bd Marechal Juin, 14050 Caen Cedex (France); Celona, L.; Lunney, D. [INFN-Laboratori Nazionali del Sud, via S.Sofia 62, 95125 Catania (Italy); Choinski, J.; Gmaj, P.; Jakubowski, A.; Steckiewicz, O. [Heavy Ion Laboratory, University of Warsaw, ul. Pasteura 5a, 02 093 Warsaw (Poland); Kalvas, T. [Department of Physics, University of Jyvaeskylae, PB 35 (YFL) 40351 Jyvaeskylae (Finland); and others

    2012-02-15

    As the most ambitious concept of isotope separation on line (ISOL) facility, EURISOL aims at producing unprecedented intensities of post-accelerated radioactive isotopes. Charge breeding, which transforms the charge state of radioactive beams from 1+ to an n+ charge state prior to post-acceleration, is a key technology which has to overcome the following challenges: high charge states for high energies, efficiency, rapidity and purity. On the roadmap to EURISOL, a dedicated R and D is being undertaken to push forward the frontiers of the present state-of-the-art techniques which use either electron cyclotron resonance or electron beam ion sources. We describe here the guidelines of this R and D.

  15. Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations.

    Science.gov (United States)

    Muir, William M; Cheng, Heng-Wei; Croney, Candace

    2014-01-01

    As consumers and society in general become more aware of ethical and moral dilemmas associated with intensive rearing systems, pressure is put on the animal and poultry industries to adopt alternative forms of housing. This presents challenges especially regarding managing competitive social interactions between animals. However, selective breeding programs are rapidly advancing, enhanced by both genomics and new quantitative genetic theory that offer potential solutions by improving adaptation of the bird to existing and proposed production environments. The outcomes of adaptation could lead to improvement of animal welfare by increasing fitness of the animal for the given environments, which might lead to increased contentment and decreased distress of birds in those systems. Genomic selection, based on dense genetic markers, will allow for more rapid improvement of traits that are expensive or difficult to measure, or have a low heritability, such as pecking, cannibalism, robustness, mortality, leg score, bone strength, disease resistance, and thus has the potential to address many poultry welfare concerns. Recently selection programs to include social effects, known as associative or indirect genetic effects (IGEs), have received much attention. Group, kin, multi-level, and multi-trait selection including IGEs have all been shown to be highly effective in reducing mortality while increasing productivity of poultry layers and reduce or eliminate the need for beak trimming. Multi-level selection was shown to increases robustness as indicated by the greater ability of birds to cope with stressors. Kin selection has been shown to be easy to implement and improve both productivity and animal well-being. Management practices and rearing conditions employed for domestic animal production will continue to change based on ethical and scientific results. However, the animal breeding tools necessary to provide an animal that is best adapted to these changing conditions

  16. Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Waterfowl breeding population surveys have been completed annually on the Arctic Coastal Plain of Alaska since 1986. Methods for the 2011 Arctic Coastal Plain...

  17. Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Waterfowl breeding population surveys have been completed annually on the Arctic Coastal Plain of Alaska since 1986. Methods for the 2010 Arctic Coastal Plain...

  18. Garlic breeding system innovations

    NARCIS (Netherlands)

    Zheng, S.J.; Kamenetsky, R.; Féréol, L.; Barandiaran, X.; Rabinowitch, H.D.; Chovelon, V.; Kik, C.

    2007-01-01

    This review outlines innovative methods for garlic breeding improvement and discusses the techniques used to increase variation like mutagenesis and in vitro techniques, as well as the current developments in florogenesis, sexual hybridization, genetic transformation and mass propagation. Sexual ste

  19. Comparison of Milk Fat Globule Membrane (MFGM Proteins of Chianina and Holstein Cattle Breed Milk Samples Through Proteomics Methods

    Directory of Open Access Journals (Sweden)

    Lorraine Pariset

    2009-12-01

    Full Text Available Identification of proteins involved in milk production is important to understand the biology of lactation. Many studies have advanced the understanding of mammary function and milk secretion, but the critical molecular mechanisms implicated in milk fat secretion is still incomplete. Milk Fat Globules are secreted from the apical surface of the mammary cells, surrounded by a thin membrane bilayer, the Milk Fat Globule Membrane (MFGM, formed by proteins which have been suggested to be cholesterolemia-lowering factors, inhibitors of cancer cell growth, vitamin binders, bactericidal, suppressors of multiple sclerosis. Using a proteomic approach, we compared MFGM from milk samples of individuals belonging to two different cattle breeds, Chianina and Holstein, representative of selection for milk and meat traits, respectively. We were able to isolate some of the major MFGM proteins in the examined samples and to identify differences between the protein fractions of the two breeds. We detected differences in the amount of proteins linked to mammary gland development and lipid droplets formation, as well as host defence mechanisms. We have shown that proteomics is a suitable, unbiased method for the study of milk fractions proteins and a powerful tool in nutritional genomics.

  20. Breeding L-arginine-producing strains by a novel mutagenesis method: Atmospheric and room temperature plasma (ARTP).

    Science.gov (United States)

    Cheng, Gong; Xu, Jianzhong; Xia, Xiuhua; Guo, Yanfeng; Xu, Kai; Su, Cunsheng; Zhang, Weiguo

    2016-07-03

    A plasma jet, driven by an active helium atom supplied with an atmospheric and room temperature plasma (ARTP) biological breeding system, was used as a novel method to breed L-arginine high-yielding strains. A mutant with resistance to L-homoarginine and 8-azaguaine, ARG 3-15 (L-HA(r), 8-AG(r), L-His(-)), was screened after several rounds of screening. The L-arginine production of these mutants was more than that of the original strain, increased by 43.79% for ARG 3-15. Moreover, N-acetyl-L-glutamate synthase activity of these mutants was also increased. After a series of passages, the hereditary properties of these mutants were found to be stable. Interestingly, beet molasses was utilized in a co-feeding fermentation and benefited to increase the productivity by 5.88%. Moreover, the fermentation with 1.0 g/L betaine could produce 9.33% more L-arginine than without betaine. In fed-batch fermentation, C. glutamicum ARG 3-15 began to produce L-arginine at the initial of logarithmic phase, and continuously increased over 24 hr to a final titer of 45.36 ± 0.42 g/L. The L-arginine productivity was 0.571 g/L/hr and the conversion of glucose (α) was 32.4% after 96 hr. These results indicated that C. glutamicum ARG 3-15 is a promising industrial producer.

  1. KRAS mutation: comparison of testing methods and tissue sampling techniques in colon cancer.

    Science.gov (United States)

    Franklin, Wilbur A; Haney, Jerry; Sugita, Michio; Bemis, Lynne; Jimeno, Antonio; Messersmith, Wells A

    2010-01-01

    Treatment of colon carcinoma with the anti-epidermal growth factor receptor antibody Cetuximab is reported to be ineffective in KRAS-mutant tumors. Mutation testing techniques have therefore become an urgent concern. We have compared three methods for detecting KRAS mutations in 59 cases of colon carcinoma: 1) high resolution melting, 2) the amplification refractory mutation system using a bifunctional self-probing primer (ARMS/Scorpion, ARMS/S), and 3) direct sequencing. We also evaluated the effects of the methods of sectioning and coring of paraffin blocks to obtain tumor DNA on assay sensitivity and specificity. The most sensitive and specific combination of block sampling and mutational analysis was ARMS/S performed on DNA derived from 1-mm paraffin cores. This combination of tissue sampling and testing method detected KRAS mutations in 46% of colon tumors. Four samples were positive by ARMS/S, but initially negative by direct sequencing. Cloned DNA samples were retested by direct sequencing, and in all four cases KRAS mutations were identified in the DNA. In six cases, high resolution melting abnormalities could not be confirmed as specific mutations either by ARMS/S or direct sequencing. We conclude that coring of the paraffin blocks and testing by ARMS/S is a sensitive, specific, and efficient method for KRAS testing.

  2. 高产黄色素红曲霉菌株的诱变选育%Mutation Breeding of Monascus with High-yielding Yellow Pigment

    Institute of Scientific and Technical Information of China (English)

    赵建博; 王伟平; 李改; 曾乐平; 杨建

    2014-01-01

    To obtain the strain with high-yielding yellow pigment,Monascus SE0 1 is treated by UV mutagenesis,different concentration of hydrogen peroxide and LiCl complex mutation methods.The results show that,under the complex mutation conditions of UV radiation of 60 s and 0.12% LiCl, Monascus SE1 9 is found to be high-yielding yellow pigment producer,and its yellow pigment reaches 57.1 U/mL through liquid-state fermentation,which is 5.54 times higher than that of the start strain SE01,and the stable heritability of selected strain is still well after inoculated for 5 generations.%以红曲霉菌株Monascus SE01为出发菌株,利用紫外线诱变、双氧水筛选和氯化锂复合诱变的方法,选育得到高产黄色素的红曲霉突变株。实验结果表明:在紫外线照射60 s、氯化锂质量分数为0.12%的复合诱变条件下得到的菌株 SE19,经液态发酵后黄色素高达57.1 U/mL,与出发菌株相比,黄色素色价提高了5.54倍。该菌株5代接种后,其黄色素产量相对稳定。

  3. Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations.

    Directory of Open Access Journals (Sweden)

    William eMuir

    2014-11-01

    Full Text Available As consumers and society in general become more aware of ethical and moral dilemmas associated with confined rearing systems, pressure is put on the animal and poultry industries to adopt alternative forms of housing. This presents challenges especially regarding managing competitive social interactions between animals. However, selective breeding programs are rapidly advancing, enhanced by both genomics and new quantitative genetic theory and offer potential solutions by improving adaptation of the bird to existing and proposed production environments. The outcomes of adaptation could lead to improvement of animal welfare by increasing fitness of the animal for the given environments, which might lead to increased contentment and decreased distress in those systems. Genomic selection, based on dense genetic markers, will allow for more rapid improvement of traits that are expensive or difficult to measure, or have a low heritability, such as pecking, cannibalism, robustness, mortality, leg score, bone strength, disease resistance, and thus has the potential to address many poultry welfare concerns. Recently selection programs to include social effects, known as associative or indirect genetic effects (IGE, have received much attention. Group, kin, multi-level and multi-trait selection have all been shown to be highly effective in reducing mortality while increasing productivity of poultry layers and reduce or eliminate the need for beak trimming. Also, multi-level selection was shown to increases robustness as indicated by l greater ability of birds to cope with stressors. Kin selection has been shown to be easy to implement and improve both productivity and animal well-being . Because social effects are improved with such programs, it might be possible to increase stocking density, increase light levels, and use larger groups in floor pens. However, such changes raise ethical concerns that may constrain making these choices.

  4. KRAS Mutations in Lung Adenocarcinoma: Molecular and Epidemiological Characteristics, Methods for Detection, and Therapeutic Strategy Perspectives.

    Science.gov (United States)

    Guibert, N; Ilie, M; Long, E; Hofman, V; Bouhlel, L; Brest, P; Mograbi, B; Marquette, C H; Didier, A; Mazieres, J; Hofman, P

    2015-01-01

    KRAS mutations are detected in over one third of lung adenocarcinomas, most frequently in Caucasian and smoker patients. The impact of KRAS mutations on lung adenocarcinoma prognosis is currently subject to debate, as is their impact on the response to chemotherapy and EGFR tyrosine kinase inhibitors. The different methods for KRAS status assessment, based on histological and cytological samples or biological fluids, offer varying sensitivities. Since no treatments are available in clinical routine for KRAS-mutated lung cancer patients, one of the current major challenges in thoracic oncology is developing new dedicated strategic therapies. Different molecules can be developed that act on a post-transcriptional KRAS protein level, blocking its cytoplasmic membrane recruitment. The efficacy of these molecules' targeting of the different signaling pathways activated by the KRAS mutation (such as the MEK and BRAF pathways) is related to the particular KRAS mutation subtype. New therapeutic strategies are currently focused on certain genes linked with KRAS inducing a synthetic lethal interaction. The purpose of this work is to provide an overview of i) the recent epidemiological and molecular findings concerning KRASmutated lung adenocarcinoma, ii) the prognostic impact of KRAS mutations, in particular during response to treatment, iii) the available methods for detecting this mutation, and iv) the current molecules under development for new therapeutic strategies and the clinical trials targeting this genomic alteration.

  5. Pyrosequencing-based methods reveal marked inter-individual differences in oncogene mutation burden in human colorectal tumours.

    Science.gov (United States)

    Weidlich, S; Walsh, K; Crowther, D; Burczynski, M E; Feuerstein, G; Carey, F A; Steele, R J C; Wolf, C R; Miele, G; Smith, G

    2011-07-12

    The epidermal growth factor receptor-targeted monoclonal antibody cetuximab (Erbitux) was recently introduced for the treatment of metastatic colorectal cancer. Treatment response is dependent on Kirsten-Ras (K-Ras) mutation status, in which the majority of patients with tumour-specific K-Ras mutations fail to respond to treatment. Mutations in the oncogenes B-Raf and PIK3CA (phosphoinositide-3-kinase) may also influence cetuximab response, highlighting the need for a sensitive, accurate and quantitative assessment of tumour mutation burden. Mutations in K-Ras, B-Raf and PIK3CA were identified by both dideoxy and quantitative pyrosequencing-based methods in a cohort of unselected colorectal tumours (n=102), and pyrosequencing-based mutation calls correlated with various clinico-pathological parameters. The use of quantitative pyrosequencing-based methods allowed us to report a 13.7% increase in mutation burden, and to identify low-frequency (<30% mutation burden) mutations not routinely detected by dideoxy sequencing. K-Ras and B-Raf mutations were mutually exclusive and independently associated with a more advanced tumour phenotype. Pyrosequencing-based methods facilitate the identification of low-frequency tumour mutations and allow more accurate assessment of tumour mutation burden. Quantitative assessment of mutation burden may permit a more detailed evaluation of the role of specific tumour mutations in the pathogenesis and progression of colorectal cancer and may improve future patient selection for targeted drug therapies.

  6. A novel coding method for gene mutation correction during protein translation process.

    Science.gov (United States)

    Zhang, Lei; Tian, Fengchun; Wang, Shiyuan; Liu, Xiao

    2012-03-07

    In gene expression, gene mutations often lead to negative effect of protein translation in prokaryotic organisms. With consideration of the influences produced by gene mutation, a novel method based on error-correction coding theory is proposed for modeling and detection of translation initiation in this paper. In the proposed method, combined with a one-dimensional codebook from block coding, a decoding method based on the minimum hamming distance is designed for analysis of translation efficiency. The results show that the proposed method can recognize the biologically significant regions such as Shine-Dalgarno region within the mRNA leader sequences effectively. Also, a global analysis of single base and multiple bases mutations of the Shine-Dalgarno sequences are established. Compared with other published experimental methods for mutation analysis, the translation initiation can not be disturbed by multiple bases mutations using the proposed method, which shows the effectiveness of this method in improving the translation efficiency and its biological relevance for genetic regulatory system.

  7. New Quantitative Method to Identify NPM1 Mutations in Acute Myeloid Leukaemia

    Directory of Open Access Journals (Sweden)

    Sarah Huet

    2013-01-01

    Full Text Available Somatic mutations in the NPM1 gene, which encodes for nucleophosmin, have been reported to be the most frequent genetic abnormalities found in acute myeloid leukaemia (AML. Their identification and quantification remain crucial for the patients’ residual disease monitoring. We investigated a new method that could represent a novel reliable alternative to sequencing for its identification. This method was based on high-resolution melting analysis in order to detect mutated patients and on an allele-specific oligonucleotide real-time quantitative polymerase chain reaction (ASO-RQ-PCR for the identification and quantification of the transcripts carrying NPM1 mutations (NPM1m. Few patients carrying known NPM1m enabled us to set up a table with the different primers’ ΔCT values, identifying a profile for each mutation type. We then analysed a series of 337 AML patients' samples for NPM1 mutational status characterization and confirmed the ASO-RQ-PCR results by direct sequencing. We identified some mutations in 86 samples, and the results were fully correlated in 100% of the 36 sequenced samples. We also detected other rare NPM1m in two samples, that we confirmed by direct sequencing. This highly specific method provides a novel quick, useful, and costless tool, easy to use in routine practice.

  8. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads.

    Science.gov (United States)

    Moriyama, Takuya; Shiraishi, Yuichi; Chiba, Kenichi; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

    2017-03-01

    Detection of somatic mutations from tumor and matched normal sequencing data has become a standard approach in cancer research. Although a number of mutation callers have been developed, it is still difficult to detect mutations with low allele frequency even in exome sequencing. We expect that overlapping paired-end read information is effective for this purpose, but no mutation caller has modeled overlapping information statistically in a proper form in exome sequence data. Here, we develop a Bayesian hierarchical method, OVar- Call (https://github.com/takumorizo/OVarCall), where overlapping paired-end read information improves the accuracy of low allele frequency mutation detection. Firstly, we construct two generative models: one is for reads with somatic variants generated from tumor cells and the other is for reads that does not have somatic variants but potentially includes sequence errors. Secondly, we calculate marginal likelihood for each model using a variational Bayesian algorithm to compute Bayes factor for the detection of somatic mutations. We empirically evaluated the performance of OVarCall and confirmed its better performance than other existing methods.

  9. Methods for Embryos Sexing and Their Applications in Animal Breeding: A Review

    Directory of Open Access Journals (Sweden)

    Rajesh Wakchaure

    2015-12-01

    Full Text Available Identification of the sex at the time of conception necessary and efficient so that all offspring would be of the desired sex. Sexing of embryos before transfer and has great potential for the livestock industry. The genetic sex of an individual is set at fertilization and depends on whether the X-bearing ovum is fertilized by a Y or X- bearing spermatozoa. The perfect method for controlling the sex ratio is by separation of X- bearing and Y- bearing spermatozoa. Many method have been evolved for sexing the embryos, but practical methods of sex diagnosis should have reliable result, simple and time saving, non harmful for embryos, efficient and accurate.

  10. Development Of Space Breeding In China

    Institute of Scientific and Technical Information of China (English)

    Liu Luxiang

    2009-01-01

    @@ Space breeding provides a new technical platform for Chinese agricaltural scientists to explore the mechanism of crop mutation induced during spaceflight and breeds new varieties of crops. It is important for China to develop the space breeding industry,maintain China's lead position in this field,serve agricultural production better,promote China's sustainable and healthy agricultural development,and ensure national food safety.

  11. Introduction of a PCR-RFLP method for the detection of two mutations in VHL gene

    Directory of Open Access Journals (Sweden)

    Antonio Alejandro Esperón

    2013-07-01

    Full Text Available Background: Von Hippel-Lindau disease is an inherited neoplastic disorder caused by germline mutations in the VHL gene. In Cuba, molecular diagnosis is performed by the method of single-strand conformation polymorphism of DNA of the three exons of the gene followed by sequencing. This method is expensive, complicated and time-consuming. Objective: to describe the introduction of the molecular diagnosis of mutations c.362A>G and c.481C> in the VHL gene by PCR-RFLP. Methods: computer software CLC Sequence viewer 6.5.1 was used to identify restriction enzymes with cleavage sites modified by mutation c.362A>G in the exon 2 and c.481C>T in exon 3 in the VHL gene. DNA samples of patients already diagnosed through SSCP-sequencing were used. Such samples were amplified by PCR method followed by the enzymatic digestion with SfaNI and BtgZI restriction enzymes. Amplified fragments were analyzed by agarose gel electrophoresis. Results obtained using both methods were compared. Results: effectiveness of the PRC-RFLP method for the diagnosis of c.362A>G and c.481C>T mutations in the VHL gene was standardized and proved. Conclusions: PCR-RFLP method has advantages over SSCP-sequencing strategy for establishing a fast, reproducible and reliable diagnosis of VHL disease in family cases molecularly characterized.

  12. The elementary level science methods course: Breeding ground of an apprehension toward science? a case study

    Science.gov (United States)

    Duschl, Richard A.

    Ethnographic research methodologies were used to examine the training of elementary education majors in science in an attempt to gain insight on whether or not their training in science contributes to the apprehension elementary teachers have toward science. The field study consisted of 14 weeks of weekly observations in the elementary education majors science methods class. Interviews with the students and the instructors as well as survey instruments to assess students' preparation in science were used. Two different approaches to the study of science, one content oriented, the other process oriented, may contribute to the students' confusion, insecurity, and avoidance of science. The students' perception that science is learning content, an objective of introductory level science courses, and the science methods class's objectives of teaching science as a process sets up an antagonistic dilemma between the two. Such antagonistic dilemma may be manifest in the lack of instructional time accorded to science by elementary educators. The type of science experiences an individual encounters influences their perceptions. To offset student perceptions developed in science courses which stress principally content, the students need science experiences which truly represent science as inquiry. New strategies for the training of elementary education majors in science need to be examined.

  13. Measuring genetic distances between breeds: use of some distances in various short term evolution models

    Directory of Open Access Journals (Sweden)

    SanCristobal Magali

    2002-07-01

    Full Text Available Abstract Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main distances encountered in the literature in various divergence models. In the first part, we consider that breeds are populations in which the assumption of equilibrium between drift and mutation is verified. In this case some interesting distances can be expressed as a function of divergence time, t, and therefore can be used to construct phylogenies. Distances based on allele size distribution (such as (δμ2 and derived distances, taking a mutation model of microsatellites, the Stepwise Mutation Model, specifically into account, exhibit large variance and therefore should not be used to accurately infer phylogeny of closely related breeds. In the last section, we will consider that breeds are small populations and that the divergence times between them are too small to consider that the observed diversity is due to mutations: divergence is mainly due to genetic drift. Expectation and variance of distances were calculated as a function of the Wright-Malécot inbreeding coefficient, F. Computer simulations performed under this divergence model show that the Reynolds distance [57]is the best method for very closely related breeds.

  14. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds.

    Science.gov (United States)

    Colombani, C; Legarra, A; Fritz, S; Guillaume, F; Croiseau, P; Ducrocq, V; Robert-Granié, C

    2013-01-01

    Recently, the amount of available single nucleotide polymorphism (SNP) marker data has considerably increased in dairy cattle breeds, both for research purposes and for application in commercial breeding and selection programs. Bayesian methods are currently used in the genomic evaluation of dairy cattle to handle very large sets of explanatory variables with a limited number of observations. In this study, we applied 2 bayesian methods, BayesCπ and bayesian least absolute shrinkage and selection operator (LASSO), to 2 genotyped and phenotyped reference populations consisting of 3,940 Holstein bulls and 1,172 Montbéliarde bulls with approximately 40,000 polymorphic SNP. We compared the accuracy of the bayesian methods for the prediction of 3 traits (milk yield, fat content, and conception rate) with pedigree-based BLUP, genomic BLUP, partial least squares (PLS) regression, and sparse PLS regression, a variable selection PLS variant. The results showed that the correlations between observed and predicted phenotypes were similar in BayesCπ (including or not pedigree information) and bayesian LASSO for most of the traits and whatever the breed. In the Holstein breed, bayesian methods led to higher correlations than other approaches for fat content and were similar to genomic BLUP for milk yield and to genomic BLUP and PLS regression for the conception rate. In the Montbéliarde breed, no method dominated the others, except BayesCπ for fat content. The better performances of the bayesian methods for fat content in Holstein and Montbéliarde breeds are probably due to the effect of the DGAT1 gene. The SNP identified by the BayesCπ, bayesian LASSO, and sparse PLS regression methods, based on their effect on the different traits of interest, were located at almost the same position on the genome. As the bayesian methods resulted in regressions of direct genomic values on daughter trait deviations closer to 1 than for the other methods tested in this study, bayesian

  15. New real-time-PCR method to identify single point mutations in hepatitis C virus

    Science.gov (United States)

    Chen, Qian; Belmonte, Irene; Buti, Maria; Nieto, Leonardo; Garcia-Cehic, Damir; Gregori, Josep; Perales, Celia; Ordeig, Laura; Llorens, Meritxell; Soria, Maria Eugenia; Esteban, Rafael; Esteban, Juan Ignacio; Rodriguez-Frias, Francisco; Quer, Josep

    2016-01-01

    AIM To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV). METHODS In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. LightCycler methods, based on real-time PCR with sequence-specific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest. RESULTS Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10% (mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80K was detected in 14.6% of G1a patients and 0% of G1b in our setting. CONCLUSION A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This

  16. Improvement of Bacillus circulans beta-amylase activity attained using the ancestral mutation method.

    Science.gov (United States)

    Yamashiro, Kan; Yokobori, Shin-ichi; Koikeda, Satoshi; Yamagishi, Akihiko

    2010-07-01

    Thermostabilization of enzymes is one of the greatest challenges of protein engineering. The ancestral mutation method, which introduces ancestral residues into a target enzyme, has previously been developed and used to improve the thermostabilities of thermophilic enzymes. Herein, we report a study that used the ancestral mutation method to improve the thermostability of Bacillus circulans beta-amylase, a mesophilic enzyme. A bacterial, common-ancestral beta-amylase sequence was inferred using a phylogenetic tree composed of higher plant and bacterial amylase sequences. Eighteen mutants containing ancestral residues were designed, expressed in Escherichia coli and purified. Several of these mutants were more thermostable than that of the wild-type amylase. Notably, one mutant had both greater activity and greater thermostability. The relationship between the extent to which the amino acid residues within 5 A of the mutation site were evolutionarily conserved and the extent to which thermostability was improved was examined. Apparently, it is necessary to conserve the residues surrounding an ancestral residue if thermostability is to be improved by the ancestral mutation method.

  17. A rapid method for detection of five known mutations associated with aminoglycoside-induced deafness

    Directory of Open Access Journals (Sweden)

    Greinwald John H

    2009-01-01

    Full Text Available Abstract Background South Africa has one of the highest incidences of multidrug-resistant tuberculosis (MDR-TB in the world. Concomitantly, aminoglycosides are commonly used in this country as a treatment against MDR-TB. To date, at least five mutations are known to confer susceptibility to aminoglycoside-induced hearing loss. The aim of the present study was to develop a rapid screening method to determine whether these mutations are present in the South African population. Methods A multiplex method using the SNaPshot technique was used to screen for five mutations in the MT-RNR1 gene: A1555G, C1494T, T1095C, 961delT+C(n and A827G. A total of 204 South African control samples, comprising 98 Mixed ancestry and 106 Black individuals were screened for the presence of the five mutations. Results A robust, cost-effective method was developed that detected the presence of all five sequence variants simultaneously. In this pilot study, the A1555G mutation was identified at a frequency of 0.9% in the Black control samples. The 961delT+C(n variant was present in 6.6% of the Black controls and 2% of the Mixed ancestry controls. The T1095C, C1494T and A827G variants were not identified in any of the study participants. Conclusion The frequency of 0.9% for the A1555G mutation in the Black population in South Africa is of concern given the high incidence of MDR-TB in this particular ethnic group. Future larger studies are warranted to determine the true frequencies of the aminoglycoside deafness mutations in the general South African population. The high frequencies of the 961delT+C(n variant observed in the controls suggest that this change is a common non-pathogenic polymorphism. This genetic method facilitates the identification of individuals at high risk of developing hearing loss prior to the start of aminoglycoside therapy. This is important in a low-resource country like South Africa where, despite their adverse side-effects, aminoglycosides will

  18. Welfare in horse breeding

    DEFF Research Database (Denmark)

    Campbell, M.L.H.; Sandøe, Peter

    2015-01-01

    Welfare problems related to the way horses are bred, whether by coitus or by the application of artificial reproduction techniques (ARTs), have been given no discrete consideration within the academic literature. This paper reviews the existing knowledge base about welfare issues in horse breeding...... and identifies areas in which data is lacking. We suggest that all methods of horse breeding are associated with potential welfare problems, but also that the judicious use of ARTs can sometimes help to address those problems. We discuss how negative welfare effects could be identified and limited and how...

  19. Welfare in horse breeding

    DEFF Research Database (Denmark)

    Campbell, M.L.H.; Sandøe, Peter

    2015-01-01

    Welfare problems related to the way horses are bred, whether by coitus or by the application of artificial reproduction techniques (ARTs), have been given no discrete consideration within the academic literature. This paper reviews the existing knowledge base about welfare issues in horse breeding...... and identifies areas in which data is lacking. We suggest that all methods of horse breeding are associated with potential welfare problems, but also that the judicious use of ARTs can sometimes help to address those problems. We discuss how negative welfare effects could be identified and limited and how...

  20. [Somatic hypermutagenesis in immunoglobulin genes. I. Connection of somatic mutations with repeats. A statistical weighting method].

    Science.gov (United States)

    Solov'ev, V V; Rogozin, I V; Kolchanov, N A

    1989-01-01

    Based on the analysis of a number of immunoglobulin genes' nucleotide sequences, it has been suggested, that somatic mutations emerge by means of imperfect duplexes correction, formed by mispairing of complementary regions of direct and inverted repeats. In the present work provides new data, confirming this mechanism of somatic hypermutagenesis. It has been shown that the presented sample of V- and J-segments of immunoglobulin genes is abundant in nonrandom imperfect direct repeats and complementary palindromes. To prove the connection of somatic mutations with the correction of imperfect duplexes, made up by the regions of these repeats, we have developed the method of statistical weights, permitting us to analyse the samples of mutations and repeats and to reveal the reliability of the connection between them. Using this method we have investigated the collection of 203 nucleotide substitutions in V- and J-segments and have shown a statistically reliable (P less than 10(-4) connection of these mutation positions with imperfect repeats.

  1. "Indoor" method of composting and genetic breeding of the strains to improve yield and quality of the almond mushroom Agaricus subrufescens

    OpenAIRE

    Zied, Diego C.; Pardo-Gimenez, A.; Savoie, Jean-Michel; Pardo-Gonzalez, J.E.; Callac, Philippe

    2011-01-01

    The aim of the present work was to evaluate the potential efficiency of an indoor composting method and the genetic breeding of strains on the agronomic performance (yield, number and weight of basidiocarps, precociousness and earliness) and quality of A. subrufescens mushrooms. The experiment followed a factorial combination (3 composts types * 4 strains) with five replicates per treatment. One strain was a hybrid between French and Brazilian isolates. Strains and composts affected a...

  2. Recent trends on crop genetic improvement using mutation techniques

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Siyong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2008-04-15

    The radiation breeding technology has been significantly achieved on creation of mutation genetic resources of plants for commercial cultivation and genomic study since 1920s. According to the FAO-IAEA Mutant Variety Database, more than 2600 varieties have been released in the world. Induction of mutations with radiation has been the most frequently used by sources of X-ray and gamma ray, but in recent Japanese scientist have been used the heavy ion beam as a new radiation sources. And China has been made remarkable outcomes in the mutant creation using new space breeding technology since 1990s. In Korea, more about 40 varieties have been developed by using the mutation breeding method since the mid-1960s. Most of the released mutant varieties in Korea were food and oil seed crops, especially for improving agronomic traits such as yield, lodging tolerance, maturity, and functional compounds. Currently the mutation breeding program in Korea has assigned more resources to develop high functional crops and ornamental plants. These functional and ornamental plants are ideal systems for a mutation breeding. A research program for the development of potential varieties of flowering and ornamental crops as rose, chrysanthemum, lily, carnation, orchids, and wild flowers was started with financial support from the Bio green 21 project of Korean government. The potential outcomes from the program will be new highly valued-added varieties which will provide greater money gains to Korean farmers and lots of valued mutants used for a gene isolation of interest and reverse genetics or functional genomic. Scientific interest in mutation breeding has drastically be ed focused to the field of functional genomic. Scientific interest in mutation breeding has drastically be ed focused to the field of functional genomic after a completion of genome sequencing of some model plant species. A direct approach of discovering the function of a novel gene is to use a mutant which has altered

  3. Genomic breeding value estimation using nonparametric additive regression models

    Directory of Open Access Journals (Sweden)

    Solberg Trygve

    2009-01-01

    Full Text Available Abstract Genomic selection refers to the use of genomewide dense markers for breeding value estimation and subsequently for selection. The main challenge of genomic breeding value estimation is the estimation of many effects from a limited number of observations. Bayesian methods have been proposed to successfully cope with these challenges. As an alternative class of models, non- and semiparametric models were recently introduced. The present study investigated the ability of nonparametric additive regression models to predict genomic breeding values. The genotypes were modelled for each marker or pair of flanking markers (i.e. the predictors separately. The nonparametric functions for the predictors were estimated simultaneously using additive model theory, applying a binomial kernel. The optimal degree of smoothing was determined by bootstrapping. A mutation-drift-balance simulation was carried out. The breeding values of the last generation (genotyped was predicted using data from the next last generation (genotyped and phenotyped. The results show moderate to high accuracies of the predicted breeding values. A determination of predictor specific degree of smoothing increased the accuracy.

  4. Highly sensitive ECL-PCR method for detection of K-ras point mutation

    Institute of Scientific and Technical Information of China (English)

    De Bin Zhu; Da Xing; Ya Bing Tang

    2007-01-01

    A highly sensitive electrochemiluminescence-polymerase chain reaction (ECL-PCR) method for K-ras point mutation detection is developed. Briefly, K-ras oncogene was amplified by a Ru(bpy)32+ (TBR)-labeled forward and a biotin-labeled reverse primer,and followed by digestion with MvaI restriction enzyme, which only cut the wild-type amplicon containing its cutting site. The digested product was then adsorbed to the streptavidin-coated microbead through the biotin label and detected by ECL assay. The experiment results showed that the different genotypes can be clearly discriminated by ECL-PCR method. It is useful in point mutation detection, due to its sensitivity, safety, and simplicity.

  5. Comparison of two methods of breeding Holstein heifers, grazing and stabling In the villa maria farm, in firavitoba – Boyacá

    Directory of Open Access Journals (Sweden)

    Jorge Eliécer Plazas Real

    2012-06-01

    Full Text Available The breeding of replacement heifers constitutes one of the biggest challenges of competitive modern farming, especially in the dairy industry, where profitability is given a priority attention. This study compared two rearing systems for Holstein heifers on the “villa María” farm in Firavitoba (Boyacá - Colombia. This town is located in the highland tropic. For the study, 20 years old calves were randomly chosen. They were divided into two equal groups with the same food conditions and under the same study standards. This was done for a period of six months. Two methods of breeding were tested: grazing and stabling. In order to do a respective testing, the calves were weighed with an electric scale and a cattle tape measure for an interval of fifteen days. The data obtained were compared and analyzed to know which breeding method was the most effective. The results showed that the use of the stabling system produced a gain weight increase in the tested subjects, as well as maintenance of management and health conditions that were not observed in other types of rearing systems. Therefore, this system represents a better response in terms of animal wellbeing

  6. Mutation breeding of antibiotics-production strain Chaetomium cupreum CH21%产抗生素角毛壳菌CH21的诱变育种

    Institute of Scientific and Technical Information of China (English)

    王俊; 谭红; 钟娟; 周金燕; 舒丹; 杨杰

    2011-01-01

    In order to obtain mutants with higher antibiotics yield, the germinating spores of the wild strain Chaetomium cupreum CH21 were mutated by two mutagens, microwave and UV, and screened by PDA double-plate and bioassay both using Colletotrichum capsici as indicator. The optimal mutagen dosages were determined: 500W 2450MHz under microwave irradiation for 15s, and 15W, 30cm under ultraviolet ray irradiation for 300s. CH21, the diameter of inhibiting ring of which was 12.50mm, was mutated by microwave and UV each for once. Five mutants with high yield of antibiotics were isolated. The diameter of inhibiting ring of CH21-2-20 was 20.20 mm, which was the largest and increased by 62% in comparison to CH21. Cultivated for five continuous generations, the diameter of inhibiting ring of CH21-2-20 stabilized between 19.40 mm and 20.38 mm.%以角毛壳菌(Chaetomium cupreum)CH21的萌发孢子作为诱变材料,采用微波辐照和紫外线照射进行诱变处理,用辣椒炭疽菌(Colletotrichum capsici)作为测试菌株,结合PDA双层平板法初筛和管碟法复筛,选育高产抗生素的突变株.结果表明:最佳微波诱变条件为500W、2450MHz、15s,紫外诱变条件为15W、30cm、300s.对出发菌株CH21进行一轮微波诱变和一轮紫外诱变,筛选得到5株高产菌株,其中CH21-2-20抑菌圈直径最大,为20.20mm,较抑菌圈直径为12.50mm的出发菌株增大了62%.连续传代5次,CH21-2-20抑菌圈直径稳定在19.40~20.38mm.

  7. 角蛋白降解菌的筛选及其UV诱变选育%Screening of keratin-degrading strain and its UV mutational breeding

    Institute of Scientific and Technical Information of China (English)

    刘国庆; 宗凯; 余晓峰; 张黎利; 凌庆枝

    2011-01-01

    One keratin-degrading bacterium named C-1 was isolted from the abandoned feather soil piled for long years and the mud from both pool and poultry keeping yard. Its keratinase activity reached 35.6 U. Through the morphological observation, physiological and biochemical experiments, the strain was preliminarily identified as Bacillus sp. In addition, the strain C-1 was dealed with UV mutation and the strain C-1-4 with higher enzyme activity was obtained by 100 s UV irradiation. The enzyme activity of C-1-4 was 122% more than that of the original strain.%从长年堆积废羽毛的土壤,屠鸡场下水道、池塘底污泥中分离出一株角蛋白降解菌C-1,摇瓶发酵测得其角蛋白酶活达35.6U,经形态观察和生理生化鉴定该菌株属于芽孢杆菌属.对菌株进行Uv诱变,在照射时间为100 s下得到一株产角蛋白酶活较高突变株C-1-4,其酶活比原始出发菌株提高了122%,且遗传性状稳定.

  8. Development of pyrosequencing methods for the rapid detection of RAS mutations in clinical samples.

    Science.gov (United States)

    Cortes, Ulrich; Guilloteau, Karline; Rouvreau, Mélanie; Archaimbault, Céline; Villalva, Claire; Karayan-Tapon, Lucie

    2015-10-01

    In advanced colorectal carcinoma (CRC) patients, extended RAS mutations testing (KRAS exons 2 to 4 and NRAS exons 2 to 4) is a prerequisite for patient stratification to anti-EGFr therapy. Accurately distinguishing mutant patients from potential responders has a clinically critical impact, and thus effective and low cost methods are needed for identification of the mutation status. We have developed quantitative pyrosequencing assays for sensitive and rapid detection of mutant RAS alleles in formalin-fixed, paraffin-embedded tissues. Exons 2 to 4 of KRAS and NRAS genes were PCR amplified and analyzed by pyrosequencing. For validation, PCR products were sequenced by conventional Sanger sequencing. Analytical sensitivity of these assays was determined by calculating the limit of detection. The results showed that low levels of mutant RAS alleles (2-13%) can be detected with pyrosequencing assays.

  9. Coupled mutation finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations

    NARCIS (Netherlands)

    M. Gültas (Mehmet); M. Haubrock (Martin); N. Tüysüz (Nesrin); S. Waack (Stephan)

    2012-01-01

    textabstractBackground: The detection of significant compensatory mutation signals in multiple sequence alignments (MSAs) is often complicated by noise. A challenging problem in bioinformatics is remains the separation of significant signals between two or more non-conserved residue sites from the p

  10. 辅酶Q10高产菌株的诱变选育%Induced Mutation Breeding and Screening of a Coenzyme QlO-Producing Strain

    Institute of Scientific and Technical Information of China (English)

    曹燕妮; 岳田利; 袁亚红; 高振鹏

    2012-01-01

    以豌豆根瘤菌(Rhizobium leguminosarum 11723)为出发菌株,利用紫外-LiCl和超声波进行诱变,以期获得高产辅酶Q10菌株。结果表明:lg/LLiCl诱变能显著提高菌株的正突变率,超声波诱变会引起细胞壁结构与构成发生改变。通过罗红霉素初筛和摇床复筛,获得辅酶Q10突变株C40-05,胞内辅酶QlO产量为1.198mg/g干菌,比出发菌株(0.389mg/g)提高了208%。菌株经5次传代培养,胞内辅酶Q10产量下降了2.67%,突变株遗传形状稳定,可作为辅酶Q10生产菌株。%Rhizobium leguminosarum 1.1723 was mutagenized by means of LiCl treatment followed by UV irradiation or ultrasonic treatment alone to yield coenzyme Q10-producing strains. The results showed that 1 g/L LiCl could obviously increase the positive mutation rate and that ultrasonic treatment could change cell wall structure of Rhizobium leguminosarum. A mutant C40-05 with high productivity of coenzyme Q10 was obtained through preliminary screening with roxithromycin and secondary screening by means of shake flask cultivation. Its coenzyme Q10 yield was up to 1.198 mg/g, which revealed a 208% increase compared with the original stain. Only 2.67% reduction in coenzyme Q10 yield of the mutant was observed after the fifth passage. Therefore, the obtained mutant is a stable strain that deserves to be studied further.

  11. Pyrosequencing, a method approved to detect the two major EGFR mutations for anti EGFR therapy in NSCLC

    Directory of Open Access Journals (Sweden)

    Richard Marie-Jeanne

    2011-05-01

    Full Text Available Abstract Background Epidermal Growth Factor Receptor (EGFR mutations, especially in-frame deletions in exon 19 (ΔLRE and a point mutation in exon 21 (L858R predict gefitinib sensitivity in patients with non-small cell lung cancer. Several methods are currently described for their detection but the gold standard for tissue samples remains direct DNA sequencing, which requires samples containing at least 50% of tumor cells. Methods We designed a pyrosequencing assay based on nested PCR for the characterization of theses mutations on formalin-fixed and paraffin-embedded tumor tissue. Results This method is highly specific and permits precise characterization of all the exon 19 deletions. Its sensitivity is higher than that of "BigDye terminator" sequencing and enabled detection of 3 additional mutations in the 58 NSCLC tested. The concordance between the two methods was very good (97.4%. In the prospective analysis of 213 samples, 7 (3.3% samples were not analyzed and EGFR mutations were detected in 18 (8.7% patients. However, we observed a deficit of mutation detection when the samples were very poor in tumor cells. Conclusions pyrosequencing is then a highly accurate method for detecting ΔLRE and L858R EGFR mutations in patients with NSCLC when the samples contain at least 20% of tumor cells.

  12. PCR-SSCP-DNA sequencing method in detecting PTEN gene mutation and its significance in human gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Chuan-Yong Guo; Xuan-Fu Xu; Jian-Ye Wu; Shu-Fang Liu

    2008-01-01

    AIM: To discuss the possible effect of PTEN gene mutations on occurrence and development of gastric cancer.METHODS: Fifty-three gastric cancer specimens were selected to probe PTEN gene mutations in genome of gastric cancer and paracancerous tissues using PCR-SSCP-DNA sequencing method based on microdissection and to observe the protein expression by immunohistochemistry technique.RESULTS: PCR-SSCP-DNA sequencing indicated that 4 kinds of mutation sites were found in 5 of 53 gastric cancer specimens.One kind of mutation was found in exons.AA-TCC mutation was located at 40bp upstream of 3' lateral exert 7 (115946 AA-TCC).Such mutations led to terminator formation in the 297th codon of the PTEN gene.The other 3 kinds of mutation were found in introns,including a G-C point mutation at 91 bp upstream of 5' lateral exon 5(90896 G-C),a T-G point mutation at 24 bp upstream of 5' lateral exon 5 (90963 T-G),and a single base A mutation at 7 bp upstream of 5' lateral exon 5 (90980 A del).The PTEN protein expression in gastric cancer and paracancerous tissues detected using immunohistochemistry technique indicated that the total positive rate of PTEN protein expression was 66% in gastric cancer tissue,which was significantly lower than that (100%) in paracancerous tissues (P<0.005).CONCLUSION: PTEN gene mutation and expression may play an important role in the occurrence and development of gastric cancer.(C)2008 The WJG Press.All rights reserved.

  13. Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

    Institute of Scientific and Technical Information of China (English)

    Hong-Xia Tian; Xu-Chao Zhang; Zhen Wang; Jian-Guang Chen; Shi-Liang Chen; Wei-Bang Guo; Yi-Long Wu

    2016-01-01

    Objective:This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena iPLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on MassARRAY mass spectrometry platform. Methods:We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of 99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a LungCartaTM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencingEGFR andKRAS genes in 100 lung cancer cases. Results:The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with LungCartaTM kit. However, anFGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively. Conclusions:The proposed MassARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.

  14. [Analysis of polymorphisms in exon 14 in porcine Mx1 gene and identification of new mutation points].

    Science.gov (United States)

    Wu, Sheng-Long; Bao, Wen-Bin; Ju, Hui-Ping; Chen, Guo-Hong; Li, Bi-Chun; Cheng, Jin-Hua; Zhu, Guo-Qiang

    2007-06-01

    By the PCR-RFLP method, the polymorphisms of exon 14 of Mx1 gene were detected in 7 native and foreign pig breeds. Taken together with the analysis of restriction enzyme Hin6 I digestion, there were 6 genotypes and 3 alleles. And, all individuals of Duroc exhibited the AA genotype but the Sutai pigs exhibited all three kinds of genotypes. The BB genotype was detected only in Meishan pigs and their derivate Sutai pigs. Among all pig breeds, the allele B only appeared in Chinese indigenous pig breeds and developed pig breed in this study, and the allele A was dominant allele in all pig breeds except for Songliao black pig. The results of Chi Square test showed that there were abundant polymorphisms in all pig breeds. The gene frequency of Meishan pig and Songliao black pig showed greatly significant difference to other pig breeds (P0.05). Three new mutation points in three genotypes were identified by sequencing comparison analysis of PCR products, two of which resulted in Thr-->Ala and Glu-->Arg respectively, the last one was a silence mutation, the Glu-->Arg mutation point and this silence mutation point only appeared in the individuals with the BB genotype.

  15. Accurate and fast methods to estimate the population mutation rate from error prone sequences

    Directory of Open Access Journals (Sweden)

    Miyamoto Michael M

    2009-08-01

    Full Text Available Abstract Background The population mutation rate (θ remains one of the most fundamental parameters in genetics, ecology, and evolutionary biology. However, its accurate estimation can be seriously compromised when working with error prone data such as expressed sequence tags, low coverage draft sequences, and other such unfinished products. This study is premised on the simple idea that a random sequence error due to a chance accident during data collection or recording will be distributed within a population dataset as a singleton (i.e., as a polymorphic site where one sampled sequence exhibits a unique base relative to the common nucleotide of the others. Thus, one can avoid these random errors by ignoring the singletons within a dataset. Results This strategy is implemented under an infinite sites model that focuses on only the internal branches of the sample genealogy where a shared polymorphism can arise (i.e., a variable site where each alternative base is represented by at least two sequences. This approach is first used to derive independently the same new Watterson and Tajima estimators of θ, as recently reported by Achaz 1 for error prone sequences. It is then used to modify the recent, full, maximum-likelihood model of Knudsen and Miyamoto 2, which incorporates various factors for experimental error and design with those for coalescence and mutation. These new methods are all accurate and fast according to evolutionary simulations and analyses of a real complex population dataset for the California seahare. Conclusion In light of these results, we recommend the use of these three new methods for the determination of θ from error prone sequences. In particular, we advocate the new maximum likelihood model as a starting point for the further development of more complex coalescent/mutation models that also account for experimental error and design.

  16. A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing

    Science.gov (United States)

    Fu, Liezhen; Wen, Luan; Luu, Nga; Shi, Yun-Bo

    2016-01-01

    Genome editing with designer nucleases such as TALEN and CRISPR/Cas enzymes has broad applications. Delivery of these designer nucleases into organisms induces various genetic mutations including deletions, insertions and nucleotide substitutions. Characterizing those mutations is critical for evaluating the efficacy and specificity of targeted genome editing. While a number of methods have been developed to identify the mutations, none other than sequencing allows the identification of the most desired mutations, i.e., out-of-frame insertions/deletions that disrupt genes. Here we report a simple and efficient method to visualize and quantify the efficiency of genomic mutations induced by genome-editing. Our approach is based on the expression of a two-color fusion protein in a vector that allows the insertion of the edited region in the genome in between the two color moieties. We show that our approach not only easily identifies developing animals with desired mutations but also efficiently quantifies the mutation rate in vivo. Furthermore, by using LacZα and GFP as the color moieties, our approach can even eliminate the need for a fluorescent microscope, allowing the analysis with simple bright field visualization. Such an approach will greatly simplify the screen for effective genome-editing enzymes and identify the desired mutant cells/animals. PMID:27748423

  17. Growth hormone genotyping by MspI restriction enzyme and PCR-RFLP method in Aceh cattle breed at Indrapuri District, Aceh Province, Indonesia

    Directory of Open Access Journals (Sweden)

    WIDYA PINTAKA BAYU PUTRA

    2014-04-01

    Full Text Available Putra WPB, Hartatik T, Sumadi. 2014. Growth hormone genotyping by MspI restriction enzyme and PCR-RFLP method in Aceh cattle breed at Indrapuri District, Aceh Province, Indonesia. Biodiversitas 15: 1-5. The objective of this research was to identify growth hormone (GH gene in Aceh cattle at Indrapuri’s Breeding and Forage Centre (IBFC of Aceh Cattle. Fourty one cattle consisting of 21 male and 20 female cattle were used in this study. Polymerase Chain Reaction (PCR - Restriction Fragment Length Polymorphism (RFLP and sequencing method was used to detect MspI site on GH gene. Based on the sequencing, it can be concluded that all cattle were monomorphic. The frequency of TT genotype and T allele were 1.00 relatively. The transition of C (cytosine into T (thymine on 1549 position caused the lost of restriction site. The insertion of T and G (guanine on 1542 and 1552 position caused the length of GH gene were 329 bp in Aceh cattle.

  18. Novel methods to enhance single strand conformation polymorphism (SSCP) senstivity and efficiency: Application to mutation detection in cystic fibrosis (CF)

    Energy Technology Data Exchange (ETDEWEB)

    Hagstrom, D.J.; Snow, K.; Yuan, Z.; Thibodeau, S.N. [Mayo Clinic, Rochester, MN (United States)

    1994-09-01

    For single gene defects in which there are a variety of mutations with significant frequencies, it is a challenge to find an efficient and sensitive method for mutation detection. For example, although 70% to 75% of CF chromosomes in a North American Caucasian population have the mutation {delta}F508, more than 400 mutations (mostly single base pair substitutions) are represented on the remaining chromosomes. SSCP analysis is a relatively straightforward procedure and therefore suitable for routine use in a clinical laboratory. However, previous reports have demonstrated suboptimal sensitivity rates in screening for mutations. We have developed a novel set of conditions which greatly enhances sensitivity and efficiency of SSCP. Our protocol incorporates multiplex PCR, stepping of wattages during electrophoresis and increased salt concentration at the anode relative to the gel. To screen for mutations in the CFTR gene, three multiplex PCR reactions are performed using identical thermocycler parameters. Sizes of PCR products range from 441 bp to 196 bp: size differences of > 30 bp are necessary to ensure separation during electrophoresis. All PCR products are separated by electrophoresis at room temperature on a single gel containing 8% (37.5:1) polyacrylamide, 5% glycerol and 1x TBE. Using an anode buffer with increased salt (2x TBE) sharpens smaller sized bands, and stepping watts from 5W to 20W during electrophoresis enhances sensitivity. Positive controls were used to demonstrate that mutations could be detected. Other mutations or polymorphisms were verified by cycle sequencing of PCR products or by alternative PCR-based assays for the more common mutations. Thus, using 3 PCR reactions per patient and one gel condition, we are able to achieve a CF mutation detection rate of approximately 90% in a North American Caucasian population.

  19. A method distinguishing expressed vs. null mutations of the Col1A1 gene in osteogenesis imperfecta

    Energy Technology Data Exchange (ETDEWEB)

    Redford-Badwal, D.A.; Stover, M.L.; McKinstry, M. [and others

    1994-09-01

    Osteogenesis imperfecta (OI) is a heterogeneous group of heritable disorders of bone characterized by increased susceptibility to fracture. Most of the causative mutations were identified in patients with the lethal form of the disease. Attention is now shifting to the milder forms of OI where glycine substitutions and null producing mutations have been found. Single amino acid substitutions can be identified by RT/PCR of total cellular RNA, but this approach does not work well for null mutations since the defective transcript does not accumulate in the cytoplasm. We have altered our RNA extraction method to separate RNA from the nuclear and cytoplasmic compartments of cultured fibroblasts. Standard methods of mutation identification (RT/PCR followed by SSCP) is applied to each RNA fraction. DNA from an abnormal band on the SSCP gel is eluted and amplified by PCR for cloning and sequencing. Using this approach we have identified an Asp to Asn change in exon 50 (type II OI) and a Gly to Arg in exon 11 (type I OI) of the COL1A1 gene. These changes were found in both nuclear and cytoplasmic compartments. These putative mutations are currently being confirmed by protein studies. In contrast, three patients with mild OI associated with reduced {proportional_to}(I)mRNA, had distinguishing SSCP bands present in the nuclear but not the cytoplasmic compartment. In one case a frame shift mutation was observed, while the other two revealed polymorphisms. The compartmentalization of the mutant allele has directed us to look elsewhere in the transcript for the causative mutation. This approach to mutation identification is capable of distinguishing these fundamentally different types of mutations and allows for preferential cloning and sequencing of the abnormal allele.

  20. Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods.

    Science.gov (United States)

    Sollero, Bruna P; Junqueira, Vinícius S; Gomes, Cláudia C G; Caetano, Alexandre R; Cardoso, Fernando F

    2017-06-15

    Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil. To estimate the combined effect of a genomic region that is potentially associated with quantitative trait loci (QTL), 2519 non-overlapping 1-Mb windows that varied in SNP number were defined, with the top 48 windows including 914 SNPs and explaining more than 20% of the estimated genetic variance for tick resistance. Subsequently, the most informative SNPs were selected based on Bayesian parameters (model frequency and t-like statistics), linkage disequilibrium and minor allele frequency to propose a very low-density 58-SNP panel. Some of these tag SNPs mapped close to or within genes and pseudogenes that are functionally related to tick resistance. Prediction ability of this SNP panel was investigated by cross-validation using K-means and random clustering and a BayesA model to predict direct genomic values. Accuracies from these cross-validations were 0.27 ± 0.09 and 0.30 ± 0.09 for the K-means and random clustering groups, respectively, compared to respective values of 0.37 ± 0.08 and 0.43 ± 0.08 when using all 41,045 SNPs and BayesB with π = 0.99, or of 0.28 ± 0.07 and 0.40 ± 0.08 with π = 0.999. Bayesian GWAS model parameters can be used to select tag SNPs for a very low-density panel, which will include SNPs that are potentially linked to functional genes. It can be useful for cost

  1. Plant breeding by using radiation mutation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Il; Song, Hi Sup; Kim, Jin Kyu; Shin, In Chul; Lee, Sang Jae; Lim, Yong Tack; Lee, In Suk; Kim, Dong Sub; Lee, Yong Su; Yang, Seung Gyun; Choi, Soon Ho; Sim, Dong Bo; Kim, Bong Kyu; Lee, Jang Ha [and others

    2000-04-01

    To improve the crop varieties by using variation, various mutant lines were selected from the materials irradiated with gamma ray due to in vivo and in vitro mutagenesis. The selected mutant lines were evaluated in the agronomic characteristics by field observation and analysis of related DNA patterns in laboratory. the results are summarized as follow; 1. Registered new mutant varieties such as Wonpyeongbyeo, Wonkwangbyeo, Wonmibyeo and Heogseonchalbyeo in the national variety list. 2. Advanced 800 mutant lines of rice soybean perilla and sweet potatoes were selected for radiation genetic resources. 3. Promising rice mutants were evaluated in several district regions for releasing. 4. Bagseul, a new mutant variety of Mugungwha (Hibiscus) were developed. 5. Promising soybean mutant lines were selected for improvement of soybean disease resistant, and soybean seed quality. 6. NaCl resistant cell lines were selected in in vitro and analysed the DNA banks. 7. 5-MT and Cysteine resistant cell lines were obtained from in vitro mutagenesis for improvement of rice quality. 8. Other related researches were carried out with coordinated projects. (author)

  2. Mutation breeding in sorghum in Indonesia

    Energy Technology Data Exchange (ETDEWEB)

    Soeranto, H.; Razzak, M.T. [Center for Research and Development of Isotope and Radiation Technology, Batan (Indonesia); Nakanishi, Tomoko M.

    2001-05-01

    Sorghum has a big potential to be grown and developed in Indonesia. The objective of this research is to produce new sorghum variety to improve sorghum production for supporting the development of sorghum agroindustry in Indonesia. The lethal dose 50% (LD-50) value for sorghum was found to be 0.73 kGy. The dose of 0.4 kGy gave the highest variance for plant height and harvest index. Selection in the generating M2, M3 and M4 populations resulted to some promising lines, especially ET20-B, with desirable agronomic characteristics, big and condense head, high yielding, white and clean color of seeds, and good nutrition values. (author)

  3. The Laboratory Breeding Methods of Zebrafish (Danio rerio)%斑马鱼实验室繁育方法研究进展

    Institute of Scientific and Technical Information of China (English)

    邵潘柱; 林金杏; 胡建华

    2013-01-01

    In recent years,because of unique biological characteristics and advantages,zebrafish (Danio rerio) has become a new type of vertebrate model organisms and is beginning to attract the attention of the world scientific researchers.However,there is little information about laboratory breeding and farming methods of zebrafish in our country.A detailed description for the laboratory captivity and breeding of zebrafish was conducted on the basis of the experimental experience,so as to provide basis feeding information for the zebrafish research.%近年来,斑马鱼因其独特的生物学特性及优势已成为一种新型的脊椎动物模式生物,并渐渐引起世界各国科研人员的重视.但目前在我国斑马鱼实验室养殖及繁育等方面的文献、资料并不多见.笔者对斑马鱼实验室人工饲养及繁育等方面做了较为详细的介绍,旨在为斑马鱼这种重要模式生物的研究提供基础的参考资料.

  4. A computational method for clinically relevant cancer stratification and driver mutation module discovery using personal genomics profiles.

    Science.gov (United States)

    Wang, Lin; Li, Fuhai; Sheng, Jianting; Wong, Stephen T C

    2015-01-01

    Personalized genomics instability, e.g., somatic mutations, is believed to contribute to the heterogeneous drug responses in patient cohorts. However, it is difficult to discover personalized driver mutations that are predictive of drug sensitivity owing to diverse and complex mutations of individual patients. To circumvent this problem, a novel computational method is presented to discover potential drug sensitivity relevant cancer subtypes and identify driver mutation modules of individual subtypes by coupling differentially expressed genes (DEGs) based subtyping analysis with the driver mutation network analysis. The proposed method was applied to breast cancer and lung cancer samples available from The Cancer Genome Atlas (TCGA). Cancer subtypes were uncovered with significantly different survival rates, and more interestingly, distinct driver mutation modules were also discovered among different subtypes, indicating the potential mechanism of heterogeneous drug sensitivity. The research findings can be used to help guide the repurposing of known drugs and their combinations in order to target these dysfunctional modules and their downstream signaling effectively for achieving personalized or precision medicine treatment.

  5. ARTP 技术选育吩嗪-1-甲酰胺高产菌株及发酵优化%Breeding of a Phenazine-1-carboxamid-producing Strain by ARTP Mutation and Its Optimization of Fermentation

    Institute of Scientific and Technical Information of China (English)

    谭剑; 熊欣; 梁万利; 彭华松; 张雪洪

    2016-01-01

    Using an atmospheric and room temperature plasma(ARTP)jet to mutagenize a phenazine-1-carboxamide-producting strain Pseudomonas Chlororaphis P3, the mutant strain P3-9 with the highest phenazine-1-carboxamide(PCN)yield of more than 2 093 mg/L was obtained from the primary-screened 20 mutant ones, and it was 125% that by the original strain. Furthermore, single factor experiment was used to investigate the effects of varied nutrient factors on the PCN synthesis of P3-9. The results showed that the best carbon source and nitrogen source were glycerol and tryptone respectively. Adding Fe3+ or Fe2+ had a significant effect on PCN production, and no measurable effect while adding aromatic amino acids of phenylalanine, tryptophan and tyrosine. After the optimization, the PCN yield of strain P3-9 reached 2 810 mg/L, which was the highest yield of PCN by mutation breeding in the world so far.%从一株高产吩嗪-1-甲酰胺(PCN)的绿针假单胞菌 P3株出发,利用常压室温等离子体诱变技术进行诱变育种,从初筛的20株突变株中获得了一株 PCN 产量达到2093 mg/L 的突变株 P3-9,为出发菌株的125%。随后通过单因素实验考察了各种营养因子对该高产菌株合成 PCN 的影响,结果表明发酵培养基的最佳碳源、氮源分别为甘油和蛋白胨,外源添加 Fe3+或 Fe2+对于积累 PCN 有显著促进作用,而添加苯丙氨酸、色氨酸和酪氨酸对 PCN 产量无明显影响。优化后,该突变株的 PCN 产量高达2810 mg/L,是目前国际上通过诱变育种获得的较高 PCN 产量。

  6. Breeding of speciality maize for industrial purposes

    OpenAIRE

    2010-01-01

    The breeding programme on speciality maize with specific traits was established at the Maize Research Institute, Zemun Polje, several decades ago. The initial material was collected, new methods applying to breeding of speciality maize, i.e. popping maize, sweet maize and white-seeded maize, were introduced. The aim was to enhance and improve variability of the initial material for breeding these three types of maize. Then, inbred lines of good combining abilities were developed and used as c...

  7. GROWTH HORMONE GENE GENOTYPING BY Msp I RESTRICTION ENZYME AND PCR-RFLP METHODS IN ACEH CATTLE BREED AT INDRAPURI DISTRICT OF ACEH PROVINCE

    Directory of Open Access Journals (Sweden)

    W.P.B. Putra

    2014-10-01

    Full Text Available The objective of this research was to identify growth hormone (GH genes genotype in selectedAceh cattle at Indrapuri’s Breeding and Forage Centre (IBFC of Aceh Cattle. Fourty one cattleconsisting of 21 male and 20 female cattle were used in this study. The genomic DNA was extractedfrom blood using Sambrook et al. (1989 methods. Polymerase Chain Reaction - Restriction FragmentLength Polymorphism (PCR-RFLP and mehod of sequencing was used to detect MspI site on GH gene.Based on sequencing results, it can be concluded that all cattle were monomorphism. The frequency ofTT genotype were 1.00 and same as T allele frequency. The transition of C (cytosine into T (thymineon 1548 bp caused the lost of restriction site.

  8. High resolution melting curve analysis, a rapid and affordable method for mutation analysis in childhood acute myeloid leukemia

    Directory of Open Access Journals (Sweden)

    Yin eLiu

    2014-09-01

    Full Text Available Background: Molecular genetic alterations with prognostic significance have been described in childhood acute myeloid leukemia (AML. The aim of this study was to establish cost-effective techniques to detect mutations of FMS-like tyrosine kinase 3 (FLT3, Nucleophosmin 1 (NPM1, and a partial tandem duplication within the mixed lineage leukemia (MLL-PTD genes in childhood AML. Procedure: Ninety-nine children with newly diagnosed AML were included in this study. We developed a fluoresent dye SYTO-82 based high resolution melting curve (HRM anaylsis to detect FLT3 internal tandem duplication (FLT3-ITD, FLT3 tyrosine kinase domain (FLT3-TKD and NPM1 mutations. MLL-PTD was screened by real-time quantitative PCR. Results: The HRM methodology correlated well with gold standard Sanger sequencing with less cost. Among the 99 patients studied, the FLT3-ITD mutation was associated with significantly worse event free survival (EFS. Patients with the NPM1 mutation had significantly better EFS and overall survival. However, HRM was not sensitive enough for minimal residual disease monitoring. Conclusions: HRM was a rapid and efficient method for screening of FLT3 and NPM1 gene mutations. It was both affordable and accurate, especially in resource underprivileged regions. Our results indicated that HRM could be a useful clinical tool for rapid and cost effective screening of the FLT3 and NPM1 mutations in AML patients.

  9. Comparative Methods to Improve the Detection of BRAF V600 Mutations in Highly Pigmented Melanoma Specimens.

    Science.gov (United States)

    Frouin, Eric; Maudelonde, Thierry; Senal, Romain; Larrieux, Marion; Costes, Valérie; Godreuil, Sylvain; Vendrell, Julie A; Solassol, Jérôme

    2016-01-01

    Genotyping BRAF in melanoma samples is often challenging. The presence of melanin greatly interferes with thermostable DNA polymerases and/or nucleic acids in traditional polymerase chain reaction (PCR)-based methods. In the present work, we evaluated three easy-to-use strategies to improve the detection of pigmented DNA refractory to PCR amplification. These pre-PCR processing methods include the addition of bovine serum albumin (BSA), the dilution of DNA, and the purification of DNA using the NucleoSpin® gDNA Clean-up XS Kit. We found that BRAF genotyping in weakly and moderately pigmented samples was more efficient when the sample was processed with BSA or purified with a NucleoSpin® gDNA Clean-up XS Kit prior to PCR amplification. In addition, the combination of both methods resulted in successful detection of BRAF mutation in pigmented specimens, including highly pigmented samples, thereby increasing the chance of patients being elicited for anti-BRAF treatment. These solutions to overcome melanin-induced PCR inhibition are of tremendous value and provide a simple solution for clinical chemistry and routine laboratory medicine.

  10. Use of radiation for plant breeding in Japan: results and future

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, I. [National Institute of Agricultural Resource, Tsukuba, Ibaraki (Japan)

    1998-12-31

    In 1966, as the first breeds by radiation mutation in Japan, `Reimei`, a rice variety with increased lodging resistance by short culm mutation and Raiden`, an early variety by mutation of soybean obtained by extreme late variety with nematoda resistance were bred and registered in the Ministry of Agriculture and Forestry. Since these characteristics of `short culm` and early maturing` have a comparatively high mutation rate and ease of selection, among seed propagation crops many kinds of those varieties improved to have either of these characteristics or both of them at the same time by mutation breeding are bred. In Japan, varieties bred by use of mutation breeding count 107 (as of April 1998). Among crops, that with the most varieties is chrysanthemum, which has 20 varieties and the next is rice with 15 varieties. The other 38 varieties of crops such as grains, beans, industrial crops, vegetables, flowering plants, flowering trees and fruit trees, mutation breeding varieties are widely bred. Among mutagens used, gamma ray holds 80%. The recent development in the research of DNA recombination is amazing and plant bodies which have introduced useful genes which other plants have are being obtained. Radiation mutation breeding, however, has the advantages of breeding new varieties by improving only one or two characteristics of excellent races. Radiation mutation breeding and DNA recombination technologies, therefore, may need to be utilized separately according to respective purposes. In the future, for radiation mutation breeding, mutants with quality characteristics which others do not have, corresponding to the diverse demand on agricultural products must come to be required. On the other hand, by the crops like banana for which ordinary breeding is almost impossible, the expectation for radiation mutation breeding will be more and more heightened. In addition, the accumulation of studies on controlling the direction of mutation which has been regarded

  11. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome.

    Directory of Open Access Journals (Sweden)

    Timothy J Dahlem

    Full Text Available The zebrafish is a powerful experimental system for uncovering gene function in vertebrate organisms. Nevertheless, studies in the zebrafish have been limited by the approaches available for eliminating gene function. Here we present simple and efficient methods for inducing, detecting, and recovering mutations at virtually any locus in the zebrafish. Briefly, double-strand DNA breaks are induced at a locus of interest by synthetic nucleases, called TALENs. Subsequent host repair of the DNA lesions leads to the generation of insertion and deletion mutations at the targeted locus. To detect the induced DNA sequence alterations at targeted loci, genomes are examined using High Resolution Melt Analysis, an efficient and sensitive method for detecting the presence of newly arising sequence polymorphisms. As the DNA binding specificity of a TALEN is determined by a custom designed array of DNA recognition modules, each of which interacts with a single target nucleotide, TALENs with very high target sequence specificities can be easily generated. Using freely accessible reagents and Web-based software, and a very simple cloning strategy, a TALEN that uniquely recognizes a specific pre-determined locus in the zebrafish genome can be generated within days. Here we develop and test the activity of four TALENs directed at different target genes. Using the experimental approach described here, every embryo injected with RNA encoding a TALEN will acquire targeted mutations. Multiple independently arising mutations are produced in each growing embryo, and up to 50% of the host genomes may acquire a targeted mutation. Upon reaching adulthood, approximately 90% of these animals transmit targeted mutations to their progeny. Results presented here indicate the TALENs are highly sequence-specific and produce minimal off-target effects. In all, it takes about two weeks to create a target-specific TALEN and generate growing embryos that harbor an array of germ line

  12. Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions

    Science.gov (United States)

    Moretti, Rocco; Fleishman, Sarel J.; Agius, Rudi; Torchala, Mieczyslaw; Bates, Paul A.; Kastritis, Panagiotis L.; Rodrigues, João P. G. L. M.; Trellet, Mikaël; Bonvin, Alexandre M. J. J.; Cui, Meng; Rooman, Marianne; Gillis, Dimitri; Dehouck, Yves; Moal, Iain; Romero-Durana, Miguel; Perez-Cano, Laura; Pallara, Chiara; Jimenez, Brian; Fernandez-Recio, Juan; Flores, Samuel; Pacella, Michael; Kilambi, Krishna Praneeth; Gray, Jeffrey J.; Popov, Petr; Grudinin, Sergei; Esquivel-Rodríguez, Juan; Kihara, Daisuke; Zhao, Nan; Korkin, Dmitry; Zhu, Xiaolei; Demerdash, Omar N. A.; Mitchell, Julie C.; Kanamori, Eiji; Tsuchiya, Yuko; Nakamura, Haruki; Lee, Hasup; Park, Hahnbeom; Seok, Chaok; Sarmiento, Jamica; Liang, Shide; Teraguchi, Shusuke; Standley, Daron M.; Shimoyama, Hiromitsu; Terashi, Genki; Takeda-Shitaka, Mayuko; Iwadate, Mitsuo; Umeyama, Hideaki; Beglov, Dmitri; Hall, David R.; Kozakov, Dima; Vajda, Sandor; Pierce, Brian G.; Hwang, Howook; Vreven, Thom; Weng, Zhiping; Huang, Yangyu; Li, Haotian; Yang, Xiufeng; Ji, Xiaofeng; Liu, Shiyong; Xiao, Yi; Zacharias, Martin; Qin, Sanbo; Zhou, Huan-Xiang; Huang, Sheng-You; Zou, Xiaoqin; Velankar, Sameer; Janin, Joël; Wodak, Shoshana J.; Baker, David

    2014-01-01

    Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side chain sampling and backbone relaxation, and evaluated packing, electrostatic and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of methodological improvement. PMID:23843247

  13. New trends in plant breeding - example of soybean

    Directory of Open Access Journals (Sweden)

    Miladinović Jegor

    2015-01-01

    Full Text Available Soybean breeding and selection is a continual process designed to increase yield levels and improve resistance to biotic and abiotic stresses. Soybean breeders have been successful in producing a large number of varieties using conventional breeding methods, the Single Seed Descent method in particular. In recent decades, with the increased use of genetic transformations, backcrossing is more frequent though the only trait that has been commercialized is glyphosate tolerance. Physiological breeding poses a particular challenge, as well as phenotyping and development of useful criteria and techniques suitable for plant breeding. Using modern remote sensing techniques provides great opportunity for collecting a large amount of physiological data in real environment, which is necessary for physiological breeding. Molecular based plant breeding methods and techniques are a conceptual part of any serious breeding program. Among those methods, the most extensively used is marker-assisted selection, as a supplement to conventional breeding methods. [Projekat Ministarstva nauke Republike Srbije, br. TR-31022

  14. Cryopreservation of turkey semen: effects of breeding line and freezing method on post-thaw sperm quality, fertilization, and hatching

    NARCIS (Netherlands)

    Long, J.A.; Purdy, P.H.; Zuidberg, C.A.; Hiemstra, S.J.; Velleman, S.G.; Woelders, H.

    2014-01-01

    Cryopreservation methods for poultry semen are not reliable for germplasm preservation, especially for turkeys, where fertility rates from frozen/thawed semen are particularly low. The objective was to evaluate cryopreservation methods for effectiveness in promoting cryosurvival and post-thaw functi

  15. Cryopreservation of turkey semen: effects of breeding line and freezing method on post-thaw sperm quality, fertilization, and hatching

    NARCIS (Netherlands)

    Long, J.A.; Purdy, P.H.; Zuidberg, C.A.; Hiemstra, S.J.; Velleman, S.G.; Woelders, H.

    2014-01-01

    Cryopreservation methods for poultry semen are not reliable for germplasm preservation, especially for turkeys, where fertility rates from frozen/thawed semen are particularly low. The objective was to evaluate cryopreservation methods for effectiveness in promoting cryosurvival and post-thaw

  16. Indigenous knowledge of animal breeding and breeds

    OpenAIRE

    I. Kohler-Rollefson

    2004-01-01

    Indigenous knowledge of animal breeding (IK-AB) includes concepts and practices used to influence the genetic composition of herds. Indigenous selection is often based on preferences based on physical characteristics, vigor, social and economic insurance. This issue paper summarizes the value of indigenous knowledge and local breeds to achieve agricultural sustainability. Links to IK-AB information are also provided. Available in SANREM office, ES

  17. Breeding of xylanase producing strain with chaetomium globosum by ultraviolet mutation%紫外诱变球毛壳霉选育木聚糖酶高产菌株

    Institute of Scientific and Technical Information of China (English)

    杨健; 姚色笛; 王颖; 王月; 张丽媛

    2011-01-01

    Xylanase has important potential applications value. In order to gain the strain which has stable genetic traits to produce xylanase, we took the xylanase activity as evaluation index, used ultraviolet mutation method, determined the time of ultraviolet irradiation by single factor experiment. By preliminary screening of Ultraviolet mutation strains in the medium containing xylan, the xylanase activity was measured by DNS methods. Screen was then repeated in the mutation strains. The highest xylanase activity mutant strains were selected to determine their activity and the genetic stability. The results of this experiment showed that the power of ultraviolet lamp was 20W, exposure distance was 30cm and exposure time was 120s. The fatality rate of chaetomium globosum was 92. 35%. Under these conditions, 15 mutant strains with higher yield of xylanase was selected. The strain Z30 - 56 had the highest xylanase activity and highest yield was 9850IU/mL, increasing 53.7% compared with the original strain. The genetics of the strain was also very stable.%木聚糖酶具有重要的潜在应用价值,为获得一株遗传性状稳定的木聚糖酶高产菌株,以木聚糖酶的酶活为评价指标,采用紫外线诱变的方法,利用单因素试验确定紫外线照射时间,通过含木聚糖的初筛培养基对紫外诱变后的菌株进行初筛,然后采用DNS法测定木聚糖酶活性对诱变菌株进行复筛.将筛选出的木聚糖酶活力最高的诱变菌株进行传代培养,测定其酶活,探讨其遗传稳定性.试验结果表明:紫外灯功率20W,照射距离30cm,照射时间120s,球毛壳霉致死率为92.35%.在此条件下进行菌株的紫外诱变获得高产木聚糖酶的正突变株15株,其中1株高产菌株Z30 - 56的酶活为9850IU/mL,比出发菌株提高53.7%,并且遗传性能稳定.

  18. Breeding monkeys for biomedical research

    Science.gov (United States)

    Bourne, G. H.; Golarzdebourne, M. N.; Keeling, M. E.

    1973-01-01

    Captive bred rhesus monkeys show much less pathology than wild born animals. The monkeys may be bred in cages or in an outdoor compound. Cage bred animals are not psychologically normal which makes then unsuited for some types of space related research. Compound breeding provides contact between mother and infant and an opportunity for the infants to play with their peers which are important requirements to help maintain their behavioral integrity. Offspring harvested after a year in the compound appear behaviorally normal and show little histopathology. Compound breeding is also an economical method for the rapid production of young animals. The colony can double its size about every two and a half years.

  19. A sensitive method to detect the hepatitis B virus mutations by using solid phase PCR on oligonucleotide array

    Institute of Scientific and Technical Information of China (English)

    YAN QIN LU; JIN XIANG HAN; ZHONG LIN SHEN; CHUAN XI WANG

    2006-01-01

    A sensitive method based on solid phase PCR on oligonucleotide array was established to detect two point mutations 1896G-A and 1901G-A in hepatitis B virus (HBV) DNA, in which 6 probes including these two point mutations were immobilized on modified glass slides through 5' terminal linker,while the 3' terminal was made to be free. The mutated loci were designed to locate on the last nucleotides of 3' terminal respectively, and the positive control probes lacked the last nucleotide of 3' terminal in comparison with the probes used for detection. Probes fixed on oligonucleotide array were also the solid phase amplification primers. One pair of liquid primers was used to amplify the short template product from whole HBV DNA. Using target DNA as template, the solid primers were extended under the action of Taq DNA polymerase and incorporated with Cy-3dCTP as marker. During the thermal cycling reaction,probes served as solid phase amplification primers and amplification products bound to the oligonucleotide array, which could be visualized by incorporation with fluorescent dyes. After amplification, the oligonucleotide array was washed, performed with laser scanning, and then used for quantitative analysis to obtain the information for mutations. The hybridization results were compared with DNA sequencing. It was demonstrated that in case of sample A, the ratios of fluorescence intensities in wide type and in the muin these two loci. These results correlated to those obtained from DNA sequencing analysis in which the fluorescence intensity ratios in wide type and in the mutated types of 1996G-A and 1901D-A mutations in using solid phase PCR based on oligonucleotide array appears to be a sensitive and promising way to detect mutations with low-density.

  20. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes.

    Science.gov (United States)

    Geng, Cunliang; Vangone, Anna; Bonvin, Alexandre M J J

    2016-08-01

    Reliable prediction of binding affinity changes (ΔΔG) upon mutations in protein complexes relies not only on the performance of computational methods but also on the availability and quality of experimental data. Binding affinity changes can be measured by various experimental methods with different accuracies and limitations. To understand the impact of these on the prediction of binding affinity change, we present the Database of binding Affinity Change Upon Mutation (DACUM), a database of 1872 binding affinity changes upon single-point mutations, a subset of the SKEMPI database (Moal,I.H. and Fernández-Recio,J. Bioinformatics, 2012;28:2600-2607) extended with information on the experimental methods used for ΔΔG measurements. The ΔΔG data were classified into different data sets based on the experimental method used and the position of the mutation (interface and non-interface). We tested the prediction performance of the original HADDOCK score, a newly trained version of it and mutation Cutoff Scanning Matrix (Pires,D.E.V., Ascher,D.B. and Blundell,T.L. Bioinformatics 2014;30:335-342), one of the best reported ΔΔG predictors so far, on these various data sets. Our results demonstrate a strong impact of the experimental methods on the performance of binding affinity change predictors for protein complexes. This underscores the importance of properly considering and carefully choosing experimental methods in the development of novel binding affinity change predictors. The DACUM database is available online at https://github.com/haddocking/DACUM.

  1. Genomics-assisted breeding in fruit trees.

    Science.gov (United States)

    Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

  2. Comparison of three methods for detecting epidermal growth factor receptor mutations in plasma DNA samples of Chinese patients with advanced non-small cell lung cancer

    Institute of Scientific and Technical Information of China (English)

    QIN Ling; ZHONG Wei; ZHANG Li; LI Long-yun; WANG Meng-zhao

    2011-01-01

    Background Epidermal growth factor receptor (EGFR) mutations can predict tumor response to tyrosine kinase inhibitors (TKIs). Detecting EGFR mutations in plasma DNA samples in patients with advanced non-small cell lung cancer is challenging and promising. We compared three methods for detecting plasma EGFR mutations, including direct DNA sequencing, denaturing high-performance liquid chromatography (DHPLC) and Scorpions Amplification Refractory Mutation System (Scorpions ARMS).Methods Plasma DNA samples from 73 patients with stage ⅢB to Ⅳ adenocarcinoma were analyzed for EGFR mutations in exons 19 (deletion mutation) and 21(L858R mutation) using direct DNA sequencing, DHPLC and Scorpions ARMS. Sensitivities of the three methods were compared and the relationship between EGFR mutations and patients'survival was analyzed.Results In 73 patients, we detected EGFR mutations in 5 samples (6.9%) by direct DNA sequencing, in 22 samples (30.1%) by DHPLC, and in 28 samples (38.4%) by Scorpions ARMS. EGFR mutations were found in 13 samples in exon 19 and in 9 samples in exon 21 by DHPLC, while we found mutations in 15 samples in exon 19 and in 13 samples in exon 21 by Scorpions ARMS. Among the 73 patients, there was 90.4% concordance between DHPLC and Scorpions ARMS (66/73, K=0.79, P=0.07). Of the 73 patients, 46 patients were treated with gefitinib, including 18 patients with mutations and 28 patients without mutations as determined by Scorpions ARMS. The 18 patients with mutations had a significantly longer progression-free survival (PFS) time (median PFS was 21.0 months) than the 28 patients without mutations (median PFS was 7.0 months) (P=0.022).Conclusions Among the three methods for detecting EGFR mutations in plasma DNA samples of patients with advanced lung adenocarcinoma, direct gene sequencing had the lowest sensitivity, while Scorpion ARMS showed the highest mutation detecting capability. DHPLC is slightly less sensitive than Scorpion ARMS. EGFR

  3. BRaf signaling principles unveiled by large-scale human mutation analysis with a rapid lentivirus-based gene replacement method.

    Science.gov (United States)

    Lim, Chae-Seok; Kang, Xi; Mirabella, Vincent; Zhang, Huaye; Bu, Qian; Araki, Yoichi; Hoang, Elizabeth T; Wang, Shiqiang; Shen, Ying; Choi, Sukwoo; Kaang, Bong-Kiun; Chang, Qiang; Pang, Zhiping P; Huganir, Richard L; Zhu, J Julius

    2017-03-15

    Rapid advances in genetics are linking mutations on genes to diseases at an exponential rate, yet characterizing the gene mutation-cell behavior relationships essential for precision medicine remains a daunting task. More than 350 mutations on small GTPase BRaf are associated with various tumors, and ∼40 mutations are associated with the neurodevelopmental disorder cardio-facio-cutaneous syndrome (CFC). We developed a fast cost-effective lentivirus-based rapid gene replacement method to interrogate the physiopathology of BRaf and ∼50 disease-linked BRaf mutants, including all CFC-linked mutants. Analysis of simultaneous multiple patch-clamp recordings from 6068 pairs of rat neurons with validation in additional mouse and human neurons and multiple learning tests from 1486 rats identified BRaf as the key missing signaling effector in the common synaptic NMDA-R-CaMKII-SynGap-Ras-BRaf-MEK-ERK transduction cascade. Moreover, the analysis creates the original big data unveiling three general features of BRaf signaling. This study establishes the first efficient procedure that permits large-scale functional analysis of human disease-linked mutations essential for precision medicine. © 2017 Lim et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Cryopreservation of turkey semen: effect of breeding line and freezing method on post-thaw sperm quality, fertilization, and hatching.

    Science.gov (United States)

    Long, Julie A; Purdy, Phillip H; Zuidberg, Kees; Hiemstra, Sipke-Joost; Velleman, Sandra G; Woelders, Henri

    2014-06-01

    Cryopreservation methods for poultry semen are not reliable for germplasm preservation, especially for turkeys, where fertility rates from frozen/thawed semen are particularly low. The objective was to evaluate cryopreservation methods for effectiveness in promoting cryosurvival and post-thaw function of sperm from five turkey lines: one commercial line and four research (RBC1; E; RBC2; F) lines from Ohio State University (OSU). The model for cryopreservation was set up as a 2×2×2×5 design for cryoprotectant (glycerol or dimethylacetamide (DMA)), cryopreservation medium (Lake or ASG), method of dilution (fixed dilution volume versus fixed sperm concentration) and turkey line, respectively. The final cryoprotectant concentrations were 11% glycerol or 6% DMA. Thawed sperm were evaluated for plasma membrane integrity and quality, motility, acrosome integrity and, after artificial insemination, for egg fertility and hatchability. Commercial turkey hens were used for all fertility trials, regardless of semen source. Turkey sperm frozen with glycerol exhibited higher membrane integrity and membrane quality upon thawing than turkey sperm frozen with DMA although no differences in total motility, and only minimal differences in progressive motility, were detected among the eight cryopreservation treatments. Within line, fertility was affected by cryoprotectant, medium and dilution method, where the overall highest percentages of fertile, viable embryos (Day 7) occurred for the DMA/ASG/fixed sperm concentration method, while high percentages (15.8-31.5%) of fertile, non-viable embryos (Day 1-6) were observed for multiple cryopreservation methods, including two glycerol treatments. From a single insemination, the duration of true and viable fertility in all lines was 10-13 weeks and 9-10 weeks, respectively. The duration of hatchability was 4-6 weeks after insemination for four of the turkey lines. The highest percentage of viable embryos was observed for the commercial

  5. Detection of the MYD88 mutation by the combination of the allele-specific PCR and quenching probe methods.

    Science.gov (United States)

    Nogami, S; Kawaguchi-Ihara, N; Shiratori, E; Ohtaka, M; Itoh, M; Tohda, S

    2017-04-01

    The MYD88 missense mutation c.794T>C, p.Leu265Pro, is found in patients with Waldenstörm's macroglobulinemia and lymphoma. Direct sequencing, allele-specific PCR (AS-PCR), PCR-restriction fragment length polymorphism (PCR-RFLP), and high-resolution melting analysis (HRM) are currently used to detect the mutation; however, they are either time-consuming or have low detection sensitivity. Here, we developed a novel highly sensitive and rapid detection method based on the quenching probe (QP) technique and AS-PCR. A lymphoma cell line heterozygous for the MYD88 mutation, two wild-type cell lines, and two samples from Waldenstörm's macroglobulinemia patients were analyzed by AS-PCR, PCR-RFLP, HRM, and QP, and their detection sensitivity was examined using the mixtures of the mutant and wild-type DNA. For mutation-carrying heterozygous samples, the QP method produced W-shaped melting profiles presenting curves derived from the wild-type and mutant alleles. The QP analysis was performed in 2 h and demonstrated the detection limit of 5%, which was similar to that of the other methods. However, the combination of AS-PCR and QP (AS-QP) improved the sensitivity to 0.62% of the mutant allele. The AS-QP analysis is rapid and minimally improves detection sensitivity compared to the AS-PCR. © 2016 John Wiley & Sons Ltd.

  6. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2015-07-01

    Full Text Available A new methodology termed Single Amino Acid Mutation based change in Binding free Energy (SAAMBE was developed to predict the changes of the binding free energy caused by mutations. The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and structure-based methods. The method has two components: a MM/PBSA-based component, and an additional set of statistical terms delivered from statistical investigation of physico-chemical properties of protein complexes. While the approach is rigid body approach and does not explicitly consider plausible conformational changes caused by the binding, the effect of conformational changes, including changes away from binding interface, on electrostatics are mimicked with amino acid specific dielectric constants. This provides significant improvement of SAAMBE predictions as indicated by better match against experimentally determined binding free energy changes over 1300 mutations in 43 proteins. The final benchmarking resulted in a very good agreement with experimental data (correlation coefficient 0.624 while the algorithm being fast enough to allow for large-scale calculations (the average time is less than a minute per mutation.

  7. Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding.

    Science.gov (United States)

    Ohnuki, Shinsuke; Okada, Hiroki; Friedrich, Anne; Kanno, Yoichiro; Goshima, Tetsuya; Hasuda, Hirokazu; Inahashi, Masaaki; Okazaki, Naoto; Tamura, Hiroyasu; Nakamura, Ryo; Hirata, Dai; Fukuda, Hisashi; Shimoi, Hitoshi; Kitamoto, Katsuhiko; Watanabe, Daisuke; Schacherer, Joseph; Akao, Takeshi; Ohya, Yoshikazu

    2017-08-07

    Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies. Copyright © 2017 Ohnuki et al.

  8. Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

    Institute of Scientific and Technical Information of China (English)

    Bao-Rong Lu; Xingxing Cai; Xin Jin

    2009-01-01

    An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the "InDel molecular index" that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.

  9. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

    Directory of Open Access Journals (Sweden)

    Alexov Emil G

    2006-11-01

    Full Text Available Abstract Background Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. Results Here we report a new implementation of the CM method with an added set of selection rules (filters. The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchmarking resulted in a TPR of 0.07 for the CM without filters and to a TPR of 0.09 for the CM with filters. Conclusion Thus, the inclusion of selection rules resulted to an overall improvement of 30%. In addition, the pair-wise comparison of TPR for each protein without and with filters resulted in an average improvement of 1.7. The methodology was implemented into a web server http://www.ces.clemson.edu/compbio/recon that is freely available to the public. The purpose of this implementation is to provide the 3D structure predictors with a tool that can help with ranking alternative models by satisfying the largest number of predicted contacts, as well as it can provide a confidence score for contacts in cases where structure is known.

  10. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  11. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  12. On the Teaching Method of Fruit Tree Breeding%“果树育种学”教学实践与探索

    Institute of Scientific and Technical Information of China (English)

    张剑侠

    2012-01-01

    In view of existing problems in the teaching of Fruit Tree Breeding, the teaching method was reformed through optimizing course content and adopting comprehensive teaching techniques including multimedia, case teaching, heuristic teaching, inductive and the comparative method with the purpose of stimulating and maintaining students' learning interest. In addition, previous teaching experience was summarized on a regular basis. The aim of this study is to improve undergraduates' achievement on the course and form a reasonable teaching model for teachers.%在“果树育种学”课程教学过程中,针对存在的问题,从培养和激发学生的学习兴趣入手。通过优化教学内容。采用多媒体教学、案例教学、启发式教学、归纳与比较等综合教学方法,以及总结前期的教学成败等,进行了教学实践与探索,旨在形成一种较为合理和有效的教学模式,以提高学生对本课程的学习效果。

  13. 《茶树育种学》课程教学方法探索%Researching on Teaching Method of Tea Breeding Course

    Institute of Scientific and Technical Information of China (English)

    卢莉

    2014-01-01

    为了提高教学质量,针对《茶树育种学》课程教学中存在的问题,从课堂教学和实验教学两个方面,对教学方法进行了探索。通过教学方法的改进,激发学生的学习兴趣和热情,培养学生的团队意识、合作精神和实验技能,全面提高课程教学质量。%In order to improve the teaching quality, according to the problems in the teaching practice of Tea Breeding course,the teaching methods were explored from two aspects of class teaching and experiment teaching.Through the improvement of teaching methods, students, learning interests and enthusiasm were inspired, collaborative awareness,teamwork sprit and good experiment skills were cul¯ tured,teaching quality was improved fully.

  14. 新疆建立绵羊分子育种和繁育体系的研究分析%Feasibility Analysis of Established Sheep Molecular Breeding Methods and Varieties Extended System in Xinjiang

    Institute of Scientific and Technical Information of China (English)

    张云生; 靳勇

    2014-01-01

    为了提高新疆羊肉生产的效率和产量,满足新疆消费市场对羊肉的强烈需求。本文就新疆养羊业现状、品种培育和多胎品种羊引进等问题进行总结和分析。依据新疆绵羊生产实际情况,提出绵羊育种和改良技术措施:绵羊新品种培育的分子育种方法(基因锚定育种法和基因连续聚合育种法)能够有效减少品种选育的世代数,准确、快速实现针对目的基因的分子育种目标;绵羊分子繁育体系建立方法可准确、高效完成绵羊新品种的示范、推广和应用;将绵羊分子育种与繁育体系应用于新疆多胎羊引种、改良、育种和生产等实践中,组建多胎导入群、多胎生产群和多胎育种群,实现新疆绵羊新品种选育与推广同步进行。绵羊分子繁育技术能够快速增加新疆绵羊繁育率和羊肉产量,推动新疆养羊业向更好、更高水平发展。%In order to improve the efficiency and yield of Xinjiang mutton production, this paper was summarized and analyzed the Xinjiang mutton production, breeding and multi-fetal sheep introduction. In accordance with the current situation of Xinjiang mutton sheep industry,we given the suggestion as follows: We need to carry out the sheep molecular breeding methods (major gene anchoring breeding method and major gene continuous polymerization breeding method), which can reduce of breeding gen⁃erations, rapidly completed the new sheep varieties breeding.We should constuct the sheep molecular breeding system, which can accuratly and efficiently complete application, demonstration and promotion of the new sheep varieties.All of these methods above could be used in Xinjiang multi-fetal sheep in⁃troduction, improvement, breeding and production. We also need to established import group, produc⁃tion group and nucleus group for multi-fetal sheep breeding, which could achieve sheep varieties breed⁃ing and application synchronously in

  15. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

    Science.gov (United States)

    Rahimi-Mianji, G; Nejati-Javaremi, A; Farhadi, A

    2015-09-01

    The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

  16. PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

    Directory of Open Access Journals (Sweden)

    Dash Aditya P

    2009-07-01

    Full Text Available Abstract Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR, an Amplification Refractory Mutation System (ARMS and Primer Introduced Restriction Analysis-PCR (PIRA-PCR were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method

  17. Implementation in breeding programmes

    NARCIS (Netherlands)

    Coffey, M.P.; McParland, S.; Bastin, C.; Wall, E.; Berry, D.P.; Veerkamp, R.F.

    2013-01-01

    Genetic improvement is easy when selecting for one heritable and well-recorded trait at a time. Many industrialised national dairy herds have overall breeding indices that incorporate a range of traits balanced by their known or estimated economic value. Future breeding goals will contain more non-p

  18. Implementation in breeding programmes

    NARCIS (Netherlands)

    Coffey, M.P.; McParland, S.; Bastin, C.; Wall, E.; Berry, D.P.; Veerkamp, R.F.

    2013-01-01

    Genetic improvement is easy when selecting for one heritable and well-recorded trait at a time. Many industrialised national dairy herds have overall breeding indices that incorporate a range of traits balanced by their known or estimated economic value. Future breeding goals will contain more non-p

  19. A simple method to generate chromosomal mutations in Lactobacillus plantarum strain TF103 to eliminate undesired fermentation products.

    Science.gov (United States)

    Liu, Siqing

    2006-01-01

    Gram-positive bacteria have been explored to convert lignocellulosic biomass to biofuel and bioproducts. Our long-term goal is to create genetically engineered lactic acid bacteria (LAB) strains that convert agricultural biomass into ethanol and other value-added products. The immediate approaches toward this goal involve genetic manipulations by either introducing ethanol production pathway genes or inactivating pathways genes that lead to production of undesired byproducts. The widely studied species Lactobacillus plantarum is now considered a model for genetic manipulations of LAB. In this study, L. plantarum TF103 strain, in which two of the chromosomal L-ldh and D-ldh genes are inactivated, was used to introduce additional mutations on the chromosome to eliminate undesired fermentation products. We targeted the acetolactate synthase gene (als) that converts pyruvate to acetolactate, to eliminate the production of acetoin and 2,3-butanodial. A pBluescript derivative containing sections of the als coding region and an erythromycin resistance gene was directly introduced into L. plantarum TF103 cells to create mutations under selection pressure. The resulting erythromycin resistant (Emr) TF103 strain appears to have chromosomal mutations of both the als and the adjacent lysP genes as revealed by polymerase chain reaction and Southern blot analyses. Mutations were thus generated via targeted homologous recombination using a Gram-negative cloning vector, eliminating the use of a shuttle vector. This method should facilitate research in targeted inactivation of other genes in LAB.

  20. PCR-heteroduplex by grouping: Rapid screening carrier method for cystic fibrosis F508del mutation in Colombia.

    Directory of Open Access Journals (Sweden)

    Lina Manuela Jay

    2009-11-01

    Full Text Available Background: Cystic fibrosis (CF is the most frequent autosomal recessive disorder in the Caucasian population with an incidence of 1 in 2,500 newborns. More than 1,300 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR gene that causes CF have been described. However, mutation F508del is the most common mutation in different populations around the world. Objective: To develop a fast, reliable and low-cost technique to screen carriers and affected individuals for the F508del mutation. This kind of analysis will have an impact on genetic counselling to decrease the incidence of new cases, in the early diagnosis and instauration of appropriate treatment to decrease morbidity and mortality associated to CF in Colombia. Methods: The reliability of the PCR-heteroduplex by grouping technique by analysis of 400 blood spot samples from asymptomatic CF patients was defined. Results: Using PCR-heteroduplex by grouping technique 100% efficiency, reproducibility and specificity and 92%sensitivity were found. Conclusions: The sensitivity and reproducibility of the PCR-heteroduplex by grouping technique up to pooling of 10 samples were demonstrated. This kind of analysis could be used in heterozygotes and affected screening programs.

  1. Biotechnology in maize breeding

    Directory of Open Access Journals (Sweden)

    Mladenović-Drinić Snežana

    2004-01-01

    Full Text Available Maize is one of the most important economic crops and the best studied and most tractable genetic system among monocots. The development of biotechnology has led to a great increase in our knowledge of maize genetics and understanding of the structure and behaviour of maize genomes. Conventional breeding practices can now be complemented by a number of new and powerful techniques. Some of these often referred to as molecular methods, enable scientists to see the layout of the entire genome of any organism and to select plants with preferred characteristics by "reading" at the molecular level, saving precious time and resources. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. Application of molecular markers for genetic studies of maize include: assessment of genetic variability and characterization of germ plasm, identification and fingerprinting of genotypes, estimation of genetic distance, detection of monogamic and quantitative trait loci, marker assisted selection, identification of sequence of useful candidate genes, etc. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible and serve as bases for marker assisted selection. Sequencing of maize genomes would help to elucidate gene function, gene regulation and their expression. Modern biotechnology also includes an array of tools for introducing or deieting a particular gene or genes to produce plants with novel traits. Development of informatics and biotechnology are resulted in bioinformatic as well as in expansion of microarrey technique. Modern biotechnologies could complement and improve the efficiency of traditional selection and breeding techniques to enhance agricultural productivity.

  2. Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations.

    Science.gov (United States)

    Chaudhary, Priyashree; Naganathan, Athi N; Gromiha, M Michael

    2015-07-01

    Protein engineering methods are commonly employed to decipher the folding mechanism of proteins and enzymes. However, such experiments are exceedingly time and resource intensive. It would therefore be advantageous to develop a simple computational tool to predict changes in folding rates upon mutations. Such a method should be able to rapidly provide the sequence position and chemical nature to modulate through mutation, to effect a particular change in rate. This can be of importance in protein folding, function or mechanistic studies. We have developed a robust knowledge-based methodology to predict the changes in folding rates upon mutations formulated from amino and acid properties using multiple linear regression approach. We benchmarked this method against an experimental database of 790 point mutations from 26 two-state proteins. Mutants were first classified according to secondary structure, accessible surface area and position along the primary sequence. Three prime amino acid features eliciting the best relationship with folding rates change were then shortlisted for each class along with an optimized window length. We obtained a self-consistent mean absolute error of 0.36 s(-1) and a mean Pearson correlation coefficient (PCC) of 0.81. Jack-knife test resulted in a MAE of 0.42 s(-1) and a PCC of 0.73. Moreover, our method highlights the importance of outlier(s) detection and studying their implications in the folding mechanism. A web server 'Folding RaCe' has been developed and is available at http://www.iitm.ac.in/bioinfo/proteinfolding/foldingrace.html. gromiha@iitm.ac.in Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Identification of spontaneous mutations within the long-range limb-specific Sonic Hedgehog enhancer (ZRS) that alter Sonic Hedgehog expression in the chicken limb mutants oligozeugodactly and Silkie Breed

    OpenAIRE

    2011-01-01

    The evolutionarily conserved, non-coding ~800 base-pair zone of polarizing activity (ZPA) regulatory sequence (ZRS) controls Shh expression in the posterior limb. We report that the chicken mutant oligozeugodactly (ozd), which lacks limb Shh expression, has a large deletion within the ZRS. Furthermore, the preaxial polydactylous, Silkie Breed chicken, which develops ectopic anterior limb Shh expression, has a single base-pair change within the ZRS. Using an in vivo reporter assay to examine e...

  4. PRINCIPLES OF ANIMAL BREEDING

    Directory of Open Access Journals (Sweden)

    Sonja Jovanovac

    2014-06-01

    Full Text Available University textbook Principles of Animal Breeding is intended for students of agriculture and veterinary medicine. The material is the adapted curricula of undergraduate and graduate level studies in the framework of which the modules Principles of animal breeding as well as Basics of genetics and selection of animals attended are listened. The textbook contains 14 chapters and a glossary of terms. Its concept enables combining fundamental and modern knowledge in the breeding and selection of animals based on balanced and quality manner. The textbook material can be divided into several thematic sections. The first one relates to the classical notions of domestic animals breeding such as the history of breeding, domestication, breed, hereditary and non-hereditary variability and description of general and production traits. The second section focuses on the basic concepts in population and quantitative genetics, as well as biometrics. The third unit is dedicated to the principles of selection and domestic animals improving. The fourth unit relates to the current concepts and objectives of the molecular markers use in domestic animals selection and breeding. The above material has been submitted to the Croatian universities, but so far it has not been published as a textbook. The Ministry of Science, Education and Sports of Republic of Croatia approved financial support for the textbook publication.

  5. An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

    Directory of Open Access Journals (Sweden)

    Barash Danny

    2008-04-01

    Full Text Available Abstract Background RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best examined using the dot plot representation for RNA secondary structure. Results Using RNAsubopt, the suboptimal solutions for a given wild-type sequence are calculated once. Then, specific mutations are selected that are most likely to cause a conformational rearrangement. For an RNA sequence of about 100 nts and 3-point mutations (n = 100, m = 3, for example, the proposed method reduces the running time from several hours or even days to several minutes, thus enabling the practical application of RNAmute to the analysis of multiple-point mutations. Conclusion A highly efficient addition to RNAmute that is as user friendly as the original application but that facilitates the practical analysis of multiple-point mutations is presented. Such an extension can now be exploited prior to site-directed mutagenesis experiments by virologists, for example, who investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary

  6. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.

    Science.gov (United States)

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-03-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.

  7. Transfer method among water content detection models for different breeds of pork by hyperspectral imaging technique%不同品种间的猪肉含水率高光谱模型传递方法研究

    Institute of Scientific and Technical Information of China (English)

    刘娇; 李小昱; 郭小许; 金瑞; 徐森淼; 库静

    2014-01-01

    At present, most studies on model transfer were based on different spectrometers, and models were established using the near infrared spectroscopy. In this study, a hyperspectral detection model of water content of fresh pork was established by partial least squares regression (PLSR) method. In order to enhance model prediction applicability to different breeds of pork samples, a new model transfer method, piecewise direct standardization combined with linear interpolation (PDS-LI) was processed. In this method, the spectra of slave breed were corrected according to the spectra difference between master breed and slave breed, and then the corrected spectra of slave breed were predicted by master model. A function based on the prediction and reference values of slave breed samples was established. This function would be used to correct the prediction values of unknown test samples of slave breed. The specific steps were as followed: 1) Samples of master breed were divided into the calibration set and the test set, and the master model was built based on the calibration set by PLSR method. 2) Samples of slave breed were partitioned into standard sample selection set C2, standard sample set C2std and unknown test set T2un, and C2 was used for the selection of C2std and T2un was used to verify the transferred model. 3) Transfer matrix F was calculated by PDS algorithm according to the spectra difference between calibration set in master breed and C2std in slave breed, and then C2std and T2un were respectively corrected by transfer matrix F. 4) In order to improve the prediction accuracy of master model to the corrected spectrum of slave breed, the prediction value of T2un need to be corrected. For sample i in unknown test set T2un, symbiosis distance D(i) between sample i and every sample else in standard sample set C2std was calculated successively. D(i) was the sum of Euclidean distances between converted spectrum and absolute deviation of the prediction values. Two

  8. Value of Immunohistochemical Methods in Detecting EML4-ALK Fusion Mutations: 
A Meta-analysis

    Directory of Open Access Journals (Sweden)

    Chang LIU

    2016-01-01

    Full Text Available Background and objective The fusion between echinoderm microtubule-associated protein 4 (EML4 and anaplastic lymphatic tumor kinase (ALK rearrangement is present in approximately 5% of non-small cell lung cancer (NSCLC patients. It has been regarded as another new target gene after epidermal growth factor receptor (EGFR and K-ras. Figures showed that the disease control rate could reach up to 80% in NSCLC patients with EML4-ALK fusion gene after treated with ALK inhibitors. Thus, exploring an accurate and rapid detecting method is the key in screening NSCLC patients with EML4-ALK expressions. The aim of this study is to analyze the specificity and sensitivity of IHC in detecting EML4-ALK fusion mutations. To evaluate the accuracy and clinical value of this method, and then provide basis for individual molecular therapy of NSCLC patients. Methods Using Pubmed database to search all documents required. The deadline of retrieval was February 25, 2015. Then further screening the articles according to the inclusion and exclusion criteria. Using diagnostic test meta-analysis methods to analyze the sensitivity and specificity of the immunohistochemistry (IHC method compared with fluorescence in situ hybridization (FISH method. Results Eleven literatures were added into the meta analysis, there were 3,234 of total cases. The diagnositic odds ratio (DOR was 1,135.00 (95%CI: 337.10-3,821.46; the area under curve (AUC of summary receiver operating characteristic curve (SROC curve was 0.992,3 (SEAUC=0.003,2, the Q* was 0.964,4 (SEQ*=0.008,7. Conclusion Immunohistochemical detection of EML4-ALK fusion gene mutation with specific antibody is feasible. It has high sensitivity and specificity. IHC can be a simple and rapid way in screening EML4-ALK fusion gene mutation and exhibits important clinical values.

  9. Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease.

    Science.gov (United States)

    Tan, Ying-Cai; Blumenfeld, Jon D; Anghel, Raluca; Donahue, Stephanie; Belenkaya, Rimma; Balina, Marina; Parker, Thomas; Levine, Daniel; Leonard, Debra G B; Rennert, Hanna

    2009-02-01

    Genetic testing of PKD1 and PKD2 is useful for diagnosis and prognosis of autosomal dominant polycystic kidney disease (ADPKD), particularly in asymptomatic individuals or those without a family history. PKD1 testing is complicated by the large transcript size, complexity of the gene region, and the extent of gene variations. A molecular assay was developed using Transgenomic's SURVEYOR Nuclease and WAVE Nucleic Acid High Sensitivity Fragment Analysis System to screen for PKD1 and PKD2 variants, followed by sequencing of variant gene segments, thereby reducing the sequencing reactions by 80%. This method was compared to complete DNA sequencing performed by a reference laboratory for 25 ADPKD patients from 22 families. The pathogenic potential of gene variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice-site alterations. A total of 90 variations were identified, including all 82 reported by the reference laboratory (100% sensitivity). A total of 76 variations (84.4%) were in PKD1 and 14 (15.6%) in PKD2. Definite pathogenic mutations (seven nonsense, four truncation, and three splicing defects) were detected in 64% (14/22) of families. The remaining 76 variants included 26 missense, 33 silent, and 17 intronic changes. Two heterozygous nonsense mutations were incorrectly determined by the reference laboratory as homozygous. "Probably pathogenic" mutations were identified in an additional five families (overall detection rate 86%). In conclusion, the SURVEYOR nuclease method was comparable to direct sequencing for detecting ADPKD mutations, achieving high sensitivity with lower cost, providing an important tool for genetic analysis of complex genes.

  10. CEBPA-double-mutated acute myeloid leukemia displays a unique phenotypic profile: a reliable screening method and insight into biological features.

    Science.gov (United States)

    Mannelli, Francesco; Ponziani, Vanessa; Bencini, Sara; Bonetti, Maria Ida; Benelli, Matteo; Cutini, Ilaria; Gianfaldoni, Giacomo; Scappini, Barbara; Pancani, Fabiana; Piccini, Matteo; Rondelli, Tommaso; Caporale, Roberto; Gelli, Anna Maria Grazia; Peruzzi, Benedetta; Chiarini, Marco; Borlenghi, Erika; Spinelli, Orietta; Giupponi, Damiano; Zanghì, Pamela; Bassan, Renato; Rambaldi, Alessandro; Rossi, Giuseppe; Bosi, Alberto

    2017-03-01

    Mutations in CCAAT/enhancer binding protein α (CEBPA) occur in 5-10% of cases of acute myeloid leukemia. CEBPA-double-mutated cases usually bear biallelic N- and C-terminal mutations and are associated with a favorable clinical outcome. Identification of CEBPA mutants is challenging because of the variety of mutations, intrinsic characteristics of the gene and technical issues. Several screening methods (fragment-length analysis, gene expression array) have been proposed especially for large-scale clinical use; although efficient, they are limited by specific concerns. We investigated the phenotypic profile of blast and maturing bone marrow cell compartments at diagnosis in 251 cases of acute myeloid leukemia. In this cohort, 16 (6.4%) patients had two CEBPA mutations, whereas ten (4.0%) had a single mutation. First, we highlighted that the CEBPA-double-mutated subset displays recurrent phenotypic abnormalities in all cell compartments. By mutational analysis after cell sorting, we demonstrated that this common phenotypic signature depends on CEBPA-double-mutated multi-lineage involvement. From a multidimensional study of phenotypic data, we developed a classifier including ten core and widely available parameters. The selected markers on blasts (CD34, CD117, CD7, CD15, CD65), neutrophil (SSC, CD64), monocytic (CD14, CD64) and erythroid (CD117) compartments were able to cluster CEBPA-double-mutated cases. In a validation set of 259 AML cases from three independent centers, our classifier showed excellent performance with 100% specificity and 100% sensitivity. We have, therefore, established a reliable screening method, based upon multidimensional analysis of widely available phenotypic parameters. This method provides early results and is suitable for large-scale detection of CEBPA-double-mutated status, allowing gene sequencing to be focused in selected cases. Copyright© Ferrata Storti Foundation.

  11. Birds - Breeding [ds60

    Data.gov (United States)

    California Department of Resources — This data set provides access to information gathered on annual breeding bird surveys in California using a map layer developed by the Department. This data layer...

  12. Genetic analysis of the Saimiri breeding colony of the Pasteur Institute (French Guiana): development of a molecular typing method using a combination of nuclear and mitochondrial DNA markers.

    Science.gov (United States)

    Lavergne, Anne; Catzeflis, François; Lacôte, Sandra; Barnaud, Antoine; Bordier, Marion; Mercereau-Puijalon, Odile; Contamin, Hugues

    2003-12-01

    Saimiri (Cebidae) groups a complex of species and subspecies, which present a large morphological plasticity. Genetic analysis is complicated by the absence of consensus on classification criteria and the paucity of molecular tools available for the genus. As the squirrel monkey is widely used in biomedical research, breeding centers have been established, but the genetic make up and diversity of many of the existing colonies is unknown precluding a rationale breeding policy. To develop a genetic typing strategy for the Saimiri breeding colony of Pasteur Institute of French Guiana, we have used Cytochrome b, a mitochondrial marker, and nuclear microsatellites. Cytochrome b sequences from wild-caught Saimiri boliviensis, Saimiri sciureus sciureus and S. s. collinsi reference specimens and captive animals identified 11 haplotypes, grouped into three distinct clades. An estimate of genetic variability within each captive morphotype, and of the extent of molecular divergence between the Bolivian, Guyanese and Brazilian breeds was obtained from the analysis of three nuclear microsatellites. Taxon-specific microsatellites enabled typing of F0-F3 animals, but did not differentiate Brazilian from Guyanese animals. Three locus microsatellite analysis of a representative sample from each generation showed no trend for loss of heterozygosity, and identified hybrid animals between Bolivian and the two others sub-species. These data provide novel evidence for taxonomic classification and a rationale strategy to further type the whole colony.

  13. Mitochondrial DNA A1555G mutation screening using a testing kit method and its significance in preventing aminoglycoside-related hearing loss

    Institute of Scientific and Technical Information of China (English)

    LIU Xin; YANG Weiyan; HAN Dongyi; JIN Zhengce; GUAN Minxin; DAI Pu; HUANG Deliang; YUAN Huijun; LI Weiming; YU Fei; ZHANG Xin; KANG Dongyang; CAO Juyang

    2006-01-01

    To report a new screening method for mitochondrial DNA 1555A→G mutation and the results of genotype analysis in 19 maternal inherited deafness pedigrees. Method Five hundred and forty-six non-syndromic neuro-sensory hearing loss patients were tested for 1555A→G mutation using a new compact testing kit, which allows clear distinction between wild type and 1555 A→G mutated mtDNAs. Results Nineteen subjects among the 546 patients (3.48%) were found to carry mtDNA A1555G mutation. The results were confirmed by sequencing in an ABI 3100 Avant sequencer. Conclusions Maternal inherited deafness families are a frequently seen in outpatient group. The detection ofmtDNA 1555 A→G mutation with a low cost, ready to use detection kit is needed and suitable in China for large scale screening and preventive testing before usage of aminoglycoside antibiotics.

  14. PRINCIPLES OF ANIMAL BREEDING

    OpenAIRE

    2014-01-01

    University textbook Principles of Animal Breeding is intended for students of agriculture and veterinary medicine. The material is the adapted curricula of undergraduate and graduate level studies in the framework of which the modules Principles of animal breeding as well as Basics of genetics and selection of animals attended are listened. The textbook contains 14 chapters and a glossary of terms. Its concept enables combining fundamental and modern knowledge in the ...

  15. An effective method, composed of LAMP and dCAPS, to detect different mutations in fenoxaprop-P-ethyl-resistant American sloughgrass (Beckmannia syzigachne Steud.) populations.

    Science.gov (United States)

    Pan, Lang; Li, Jun; Xia, Wenwen; Zhang, Di; Dong, Liyao

    2015-01-01

    The decreased susceptibility of Beckmannia syzigachne to fenoxaprop-P-ethyl is due to the reliance on it to control grass weeds since the 1990s. Loop-mediated isothermal amplification (LAMP), which is a proven simple, rapid, specific, sensitive and inexpensive assay method, has been used to detect the I1781L mutation in B. syzigachne. In the present study, four sets of primers detected four mutations in B. syzigachne, W2027C, I2041A, D2078G and G2096A, using the LAMP method. Additionally, five newly derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to detect five different mutations. With a method composed of LAMP and dCAPS, 19 fenoxaprop-P-ethyl-resistant B. syzigachne populations collected in 2013 were studied. An effective method, composed of LAMP and dCAPS, to detect five mutations, I1781L, W2027C, I2041A, D2078G and G2096A, in B. syzigachne populations was developed. With this method, a B. syzigachne population resistant to fenoxaprop-P-ethyl can be studied to confirm its constitution. And we determined that the resistance level might be relevant to the mutation type and mutation frequency. The type of mutation and its frequency in fenoxaprop-P-ethyl-resistant B. syzigachne populations can be confirmed to provide appropriate herbicide management.

  16. Breeding without breeding: is a complete pedigree necessary for efficient breeding?

    Directory of Open Access Journals (Sweden)

    Yousry A El-Kassaby

    Full Text Available Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called "Breeding without Breeding" (BwB that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS and incomplete (half-sib: HS analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors, growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP or complete (FS pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB.

  17. 鲑鳟鱼类育种中常用策略、方法及其应用概述%An Overview of Common Strategies, Methods and Applications in Salmon and Trout Breeding

    Institute of Scientific and Technical Information of China (English)

    户国; 谷伟; 白庆利; 王炳谦

    2014-01-01

    鲑鳟鱼类是世界上最早采用现代数量遗传学理论指导育种实践的水产动物之一,在近50年育种实践中积累了大量经验,形成了一整套行之有效的育种策略、选择方法,为其他水产动物的遗传选育提供借鉴。育种者为满足消费市场和养殖者对鱼肉品质、鱼体规格、高抗病力、高饲料转化率等需求,利用多种育种策略和选择方法来开发相应的养殖品种和品系。本文从育种策略、选择方法等概括介绍目前我国鲑鳟鱼遗传育种领域的主要支撑技术,以期为其他水产动物育种提供参考。%Modern quantitative genetics theory was firstly used to guide breeding practice in salmon&trout in aquatic animals in the world. Many experiences and a set of effective breeding strategies, selection method have been accumulated by fish breeders in the past 50 years, which can provide a reference to genetics and breeding of other aquatic animals. Breeders need to use a variety of strate-gies and selection breeding methods to develop appropriate strains to meet different needs including meat quality, fish size, and high resistance to disease, high feed conversion rate and other requirements from consumption market and fish farmers. This paper attempts to introduce the main support technologies in salmon&trout selective breeding fields in China, and provide references to other aquatic animal genetic breeding.

  18. Breeding of Lactic Acid High Producing Bacillus UZ-3-15 by UV Mutation%芽孢杆菌乳酸高产菌株UZ3-15的紫外线诱变选育

    Institute of Scientific and Technical Information of China (English)

    李红亚; 李术娜; 王全; 朱宝成

    2011-01-01

    为了获得乳酸的高产菌株,以实验室前期筛选获得的产乳酸芽孢杆菌Z-3-1为出发菌株,通过紫外线诱变来选育乳酸高产菌株,紫外线诱变条件为30 W紫外灯,30 cm辐照距离,诱变时间为150 s.采用溶钙圈法对诱变后的菌株进行初步筛选,得到在MRS-CaCO3培养基上产生透明圈直径较大的菌株19株.通过对菌株的发酵液进行乳酸含量滴定对初筛到的19株菌进行复筛,得到了一株乳酸高产菌株UZ-3-15.在NB培养基中,该菌株产乳酸的能力较出发菌株提高了7倍多.%In order to obtain lactic acid high producing strains, the study used Bacillus Z-3-1 which was obtained before as original strain for stepwise mutation by UV irradiation was carried out. Conditions for mutagenesis were 30 W UV lamp, 30 cm irradiation distance and irradiation dose of 150 s. In the experiment, the preliminary screening of mutant strains was implemented first through calcium-dissolving, and 19 strains with bigger transparent circle diameters in the MRS-CaCO3 medium were obtained in the preliminary screening. Then the secondary screening of 19 strains was done, and one lactic acid high producing strain named UZ-3-15 was obtained by the titration method for determination of lactic acid in the fermented broth, which produced 7 times more lactic acid than its parent strain in the NB medium.

  19. 磷脂酶D高产菌株的原生质体紫外诱变选育%Breeding of high phospholipase D-producing strain through mutation of protoplasts induced by UV radiation

    Institute of Scientific and Technical Information of China (English)

    杨兰兰; 张小里; 封娟娟; 朱南南; 赵彬侠

    2016-01-01

    In order to screen a high⁃yielding phospholipase D strain from Streptomyces sp. LD0501, we studied the conditions for its protoplasts′preparation and regeneration, and mutagenized its protoplasts by UV radiation as well. The protoplasts were prepared by enzyme and mutagenized with UV irradiation. The mutation result was determined by TLC. The optimum conditions for the preparation of the protoplasts were as follows:the Streptomyces LD0501 was inoculated into mycelia medium with 0�5% glycine and cultured for 72 h�The mycelia were processed with 3 mg/mL lysozyme at 30℃ for 75 min. Protoplasts of Streptomyces sp. LD0501 were induced by UV radiation to obtain a high phospholipase D⁃producing strain,whose phospholipase D′s enzyme activity reached 4�29 U/mL, increased by 180�4% compared with the initial strain. The method improved the preparation effect of protoplasts from Streptomyces LD 0501 effectively and enhanced phospholipase D strain′s vitality greatly by UV irradiation of the protoplasts,the production of the high⁃yielding mutant strain was verified to be genetically stable.%为了获得磷脂酶D高产菌株,由链霉菌野生菌株LD0501出发研究原生质体的制备和再生条件,建立原生质体紫外诱变筛选方案。采用酶解法制备原生质体,用紫外线对原生质体诱变,TLC检测突变株产磷脂酶D活力。原生质体的适宜条件:种子培养基中甘氨酸质量浓度5 g/L,菌龄72 h,用3 mg/mL的溶菌酶在30℃下酶解75 min。通过原生质体诱变筛选,得到1株高产菌株,磷脂酶D水解活力达4�29 U/mL,提高幅度为180�4%。该方法有效改善了链霉菌野生菌株原生质体的制备效果,紫外诱变筛选显著提高了磷脂酶D的活力,高产突变株具有较好的稳定性。

  20. New approaches for effective mutation induction in gamma field

    Energy Technology Data Exchange (ETDEWEB)

    Nagatomi, Shigeki [National Institute of Agrobiological Resources, Institute of Radiation Breeding, Omiya, Ibaraki (Japan)

    2001-03-01

    The purpose of the report is to clarify the effects of chronic irradiation using in vitro culture on inducing the mutation of two model plants. Culture technique combined with irradiation can overcome the problem of chimera formation and provided 10 times greater mutation efficiency than conventional method. Proper mutagenic treatment using cultured materials is indispensable to effective mutation induction. The chronic culture method showed the widest color spectrum in chrysanthemum and extended toward not only the negative but positive direction. However, the acute culture methods indicated a relatively low mutation rate and a very limited flower color spectrum. Flower color mutation of the regenerations could be induced more from petals and buds than from leaves. These facts is supposed that the gene loci fully expressed on floral organs may be unstable for mutation by mutagenesis or culture. It may be likely to control a direction of desired mutation. One possible reason why the chronic culture methods showed higher frequencies is that most of the cells composing the tissue and organs continually irradiated into a cell division which was highly sensitive and more mutable to irradiation. Under these conditions, many mutated sectors may accumulate in the cells of the growing organs. Regenerated mutant lines show remarkable decrease of chromosome numbers by irradiation. It is a proper indicator to monitor radiation damage. In this study, the six flower color mutant varieties registered were derived from chronic irradiation. The combined method of chronic irradiation with floral organ cultures proved to be of particularly great practical use in mutation breeding for not only flower species but any other species. (author)

  1. Broiler breeding : breeding goals, selection schemes and the usefulness of local breeds for China

    NARCIS (Netherlands)

    Jiang, X.

    1999-01-01

    This dissertation considers three aspects of broiler breeding: definition of breeding goals, selection schemes for specialized lines, and the usefulness of local breeds for China. Economic values in broiler breeding were derived based on a deterministic model. A systematic design for the application

  2. Prospects for Hybrid Breeding in Bioenergy Grasses

    DEFF Research Database (Denmark)

    Aguirre, Andrea Arias; Studer, Bruno; Frei, Ursula

    2012-01-01

    of different hybrid breeding schemes to optimally exploit heterosis for biomass yield in perennial ryegrass (Lolium perenne L.) and switchgrass (Panicum virgatum), two perennial model grass species for bioenergy production. Starting with a careful evaluation of current population and synthetic breeding methods......, we address crucial topics to implement hybrid breeding, such as the availability and development of heterotic groups, as well as biological mechanisms for hybridization control such as self-incompatibility (SI) and male sterility (MS). Finally, we present potential hybrid breeding schemes based on SI...... and MS for the two bioenergy grass species, and discuss how molecular tools and synteny can be used to transfer relevant information for genes controlling these biological mechanisms across grass species...

  3. Bioanalytical methods for the metalloproteomics study of bovine longissimus thoracis muscle tissue with different grades of meat tenderness in the Nellore breed (Bos indicus).

    Science.gov (United States)

    Baldassini, Welder Angelo; Braga, Camila Pereira; Chardulo, Luis Artur Loyola; Vasconcelos Silva, Josineudson Augusto; Malheiros, Jessica Moraes; de Albuquerque, Lúcia Galvão; Fernandes, Talita Tanaka; Padilha, Pedro de Magalhães

    2015-02-15

    The work describes a metalloproteomics study of bovine muscle tissue with different grades of meat tenderness from animals of the Nellore breed (Bos indicus) based on protein separation by two-dimensional gel electrophoresis, the identification of calcium ions in protein spots by X-ray fluorescence (SR-XRF) and the characterisation of proteins by electrospray ionisation mass spectrometry. Forty (40) specimens were selected and divided into two experimental groups: animals with tough meat (TO) and animals with tender meat (TE). A third group (P) of Piedmontese breed animals (Bos taurus) was included to serve as a comparative model for the level of meat tenderness. The procedures were efficient and preserved the metal-protein structure, enabling calcium detection in protein spots by SR-XRF at a given molecular weight range of 14-97kDa. Two proteins (pyruvate kinase and albumin) were inferred to be related to the phenotypical differences in animals from the different groups.

  4. Short communication: the beta-casein (CSN2) silent allele C1 is highly spread in goat breeds.

    Science.gov (United States)

    Chessa, S; Rignanese, D; Küpper, J; Pagnacco, G; Erhardt, G; Caroli, A

    2008-11-01

    Several single nucleotide polymorphisms have been identified in the goat milk casein genes, most of them modifying the amino acid sequence of the coded protein. At least 9 variants have been found in goat beta-CN (CSN2); 6 of them were characterized at the DNA level (A, A1, C, E, 0, and 0'), whereas the other 3 variants were described only at the protein level. The recently identified silent A1 allele is characterized by a C-->T transition at the 180th nucleotide of the ninth exon. In the present work, typing results from different breeds (3 Italian, 3 German, and a composite of African breeds for a total of 335 samples) demonstrated that the same mutation is carried by the CSN2*C allele. In addition, the T nucleotide at the 180th nucleotide of the ninth exon was always associated with CSN2*C in all the breeds analyzed. Thus, another silent allele occurs at goat CSN2 and can be named CSN2*C1. The much wider distribution of C1 with respect to the A1 allele indicates that the single nucleotide polymorphisms characterizing the silent mutation originated from CSN2*C. A method for the identification of this allele simultaneously with 5 of the 6 DNA-characterized alleles is also proposed. The mutation involved codifies for the same protein of the C allele; nevertheless, its location in the 3' untranslated region of the gene might affect the specific casein expression.

  5. Charge Breeding of Radioactive Ions

    CERN Document Server

    Wenander, F J C

    2013-01-01

    Charge breeding is a technique to increase the charge state of ions, in many cases radioactive ions. The singly charged radioactive ions, produced in an isotope separator on-line facility, and extracted with a low kinetic energy of some tens of keV, are injected into a charge breeder, where the charge state is increased to Q. The transformed ions are either directed towards a dedicated experiment requiring highly charged ions, or post-accelerated to higher beam energies. In this paper the physics processes involved in the production of highly charged ions will be introduced, and the injection and extraction beam parameters of the charge breeder defined. A description of the three main charge-breeding methods is given, namely: electron stripping in gas jet or foil; external ion injection into an electron-beam ion source/trap (EBIS/T); and external ion injection into an electron cyclotron resonance ion source (ECRIS). In addition, some preparatory devices for charge breeding and practical beam delivery aspects ...

  6. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  7. Citrus breeding, genetics and genomics in Japan

    Science.gov (United States)

    Omura, Mitsuo; Shimada, Takehiko

    2016-01-01

    Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering. PMID:27069387

  8. Citrus breeding, genetics and genomics in Japan.

    Science.gov (United States)

    Omura, Mitsuo; Shimada, Takehiko

    2016-01-01

    Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering.

  9. A three-step programmed method for the identification of causative gene mutations of maturity onset diabetes of the young (MODY).

    Science.gov (United States)

    Li, Qian; Cao, Xi; Qiu, Hai-Yan; Lu, Jing; Gao, Rui; Liu, Chao; Yuan, Ming-Xia; Yang, Guang-Ran; Yang, Jin-Kui

    2016-08-22

    To establish a three-step programmed method to find gene mutations related to maturity onset diabetes of the young (MODY). Target region capture and next-generation sequencing (NGS) were performed using customized oligonucleotide probes designed to capture suspected genes for MODY in 11 probands with clinically diagnosed MODY. The suspected associations of certain genes with MODY were then confirmed by Sanger sequencing in the probands and their family members. Finally, to validate variants of one of the genes of interest (glucokinase, GCK) as pathogenic mutations, protein function editing by the variant genes was assessed. In the target region capture and NGS phase, a total of nine variants of seven genes (GCK, WFS1, SLC19A2, SH2B1, SERPINB4, RFX6, and GATA6) were identified in eight probands. Two heterozygous GCK mutations located on the same allele (p.Leu77Arg and p.Val101Met) were identified in a MODY family. Sanger sequencing was used to confirm the variants identified by NGS to be present in probands and their diabetic family members, but not in non-diabetic family members. Finally, enzyme kinetic and thermal stability analyses revealed that the p.Leu77Arg mutation or the p.Leu77Arg mutation in combination with the p.Val101Met mutation inactivates GCK function and stability, while mutation of p.Val101Met alone does not. The p.Leu77Arg but not p.Val101Met GCK mutation is therefore considered a pathogenic mutation associated with MODY. Genetic screening coupled with gene-editing protein function testing is an effective and reliable method by which causative gene mutations of MODY can be identified.

  10. Applications of the method of high resolution melting analysis for diagnosis of Leber's disease and the three primary mutation spectrum of LHON in the Han Chinese population.

    Science.gov (United States)

    Cui, Guanglin; Ding, Hu; Xu, Yujun; Li, Bin; Wang, Dao Wen

    2013-01-01

    Current screening methods, such as single strand conformational polymorphism (SSCP), denaturing high performance liquid chromatography (dHPLC) and direct DNA sequencing that are used for detecting mutation in Leber's hereditary optic neuropathy (LHON) subjects are time consuming and costly. Here we tested high-resolution melt (HRM) analysis for mtDNA primary mutations in LHON patients. In this study, we applied the high resolution melting (HRM) technology to screen mtDNA primary mutations in 50 LHON patients from their peripheral blood. In order to evaluate the reliability of this technique, we compared the results obtained by HRM and direct mtDNA sequencing. We also investigated the spectrum of three most common mtDNA mutations implicated in LHON in the Han Chinese population. The results showed HRM analysis differentiated all of the mtDNA primary mutations and identified 4 additional mtDNA mutations from 50 patients in the blind study. The prevalence of three primary mutations were 11778G>A (87.9%), 14484T>C (6.5%) and 3460G>A (1.7%) in the Han Chinese population. In conclusion, HRM analysis is a rapid, reliable, and low-cost tool for detecting mtDNA primary mutations and has practical applications in molecular genetics.

  11. Discriminative detection of low-abundance point mutations using a PCR/ligase detection reaction/capillary gel electrophoresis method and fluorescence dual-channel monitoring.

    Science.gov (United States)

    Hamada, Mariko; Shimase, Koji; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2014-04-01

    We applied a facile LIF dual-channel monitoring system recently developed and reported by our group to the polymerase chain reaction/ligase detection reaction/CGE method for detecting low-abundance point mutations present in a wild-type sequence-dominated population. Mutation discrimination limits and signaling fidelity of the analytical system were evaluated using three mutant variations in codon 12 of the K-ras oncogene that have high diagnostic value for colorectal cancer. We demonstrated the high sensitivity of the present method by detecting rare mutations present among an excess of wild-type alleles (one mutation among ~100 normal sequences). This method also simultaneously interrogated the allelic compositions of the test samples with high specificity through spectral discrimination of the dye-tagged ligase detection reaction products using the dual-channel monitoring system. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Neuroglobin mutation associated with hypoxia adaptation in Tibet chicken

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Globin protein family plays an important role in storing and transporting oxygen.As a newly reported globin,the revealed function of neuroglobin includes binding and storing oxygen as well as facilitating the utilization of oxygen in neuronal cells.In the Dresent study,mutations in exons of chicken Ngb gene were identified with the method of sequencing and created restriction site PCR in Tibet chicken and other four lowland chicken breeds.The mutations of Lys-2224(E4)-Asn and Ser-2279(E4)-Gly were identified in exon 4 of the gene.The Lys-2224(E4)-Asn mutation existed only in Tibet chicken and the mutation frequencies increased with increasing altitude.Analysis of the haplotype and diplotype of the two mutations in Tibet chicken populations of different altitudes showed that the frequencies of TG haplotype and TTGG diplotype also increased with increasing altitude,while the reverse tendency was found on GGAA diplotype.Under the hypoxic simulation incubation,the main haplotype was TG in living embryos and GA in dead embryos.The results showed that the Lys-2224(E4)-Asn mutation may be a specific mutation associated with hypoxia adaptation in Tibet chicken.

  13. 隔离器饲育SPF鸡微生物质量控制方法的建立%Establishment of microbiological quality control methods on breeding SPF chickens raised in the isolators

    Institute of Scientific and Technical Information of China (English)

    吴韬奋; 张瑞忠; 孙凤萍; 王佳乐

    2013-01-01

    Objective To establish production management and the methods of microbiological quality control on breeding SPF chickens raised in the isolator. Methods The chickens were bred in the isolator after the eggs from introduced SPF chickens were hatched out. The sera obtained from 10 ,20,40-week-old SPF chickens were used to monitor microbiological quality in order to detect the effectiveness of the current production management and the methods of microbiological quality control on SPF chickens. Results Because the hatching process was not strickly controlled during the early stage of breeding SPF chickens in the isolator,there were the emergence of microbiological contamination. Microbiological condition of the isolator breeding SPF chickens was effectively controlled after improving the operation management during the hatching process. Conclusion If the disinfection during all breeding stages is strengthened ,the microbiological quality of SPF chickens in the isolator could be ensured. The appropriate control on the density of SPF chickens in the isolator is not only beneficial to the breeding of SPF chickens and the recycling of hatching eggs ,but also helpful to the control of environmental microbiology.%目的 建立隔离器饲育SPF鸡生产管理方式,探讨并建立其微生物质量控制方法.方法 对引进的SPF鸡种蛋进行孵化后,将种鸡置于隔离器中进行饲养,在种鸡10、20、40周龄时采取鸡血清进行微生物质量监测,检验当前SPF鸡生产管理和微生物质量控制方法的有效性.结果 隔离器饲育SPF鸡初期由于对孵化环节控制不严出现了微生物污染现象.在对孵化环节操作管理改进后,隔离器饲育SPF鸡的微生物状况得到控制.结论通过加强各个环节消毒,隔离器饲育环境能够保证SPF鸡的微生物质量.适当控制隔离器内SPF鸡的密度不仅有利于SPF鸡的繁育和种蛋回收,而且有利于环境微生物的控制.

  14. Detection of BRAF V600 mutations in melanoma: evaluation of concordance between the Cobas® 4800 BRAF V600 mutation test and the methods used in French National Cancer Institute (INCa) platforms in a real-life setting.

    Science.gov (United States)

    Mourah, Samia; Denis, Marc G; Narducci, Fabienne Escande; Solassol, Jérôme; Merlin, Jean-Louis; Sabourin, Jean-Christophe; Scoazec, Jean-Yves; Ouafik, L'Houcine; Emile, Jean-François; Heller, Remy; Souvignet, Claude; Bergougnoux, Loïc; Merlio, Jean-Philippe

    2015-01-01

    Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs) of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa). For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86) in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively). Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]). Out of the 420 samples tested, 28 (6.7%) showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations.

  15. Detection of BRAF V600 mutations in melanoma: evaluation of concordance between the Cobas® 4800 BRAF V600 mutation test and the methods used in French National Cancer Institute (INCa platforms in a real-life setting.

    Directory of Open Access Journals (Sweden)

    Samia Mourah

    Full Text Available Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa. For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86 in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively. Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]. Out of the 420 samples tested, 28 (6.7% showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations.

  16. Targeted ultradeep next-generation sequencing as a method for KIT D816V mutation analysis in mastocytosis

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Broesby-Olsen, Sigurd; Vestergaard, Hanne;

    2016-01-01

    mutation levels. In this study, we established an NGS-based KIT mutation analysis and analyzed the sensitivity of D816V detection using the Ion Torrent platform. Eighty-two individual NGS analyses were included in the study. All samples were also analyzed using highly sensitive KIT D816V mutation...

  17. 规模化猪场种猪猪瘟免疫方式和剂量的探讨%Immunity Method and Dose of Breeding Pigs against Classical Swine Fever Virus (CSFV) on Large-scale Pig Farms

    Institute of Scientific and Technical Information of China (English)

    罗才庆

    2012-01-01

      对福建某公司2010年、2011年“一刀切”免疫(一年春、秋各免疫1次,每头每次免疫剂量1.5头份猪瘟兔化弱毒脾淋苗)的4561份种猪血清样品采用 HerdChek 猪瘟抗体检测试剂盒进行抗体检测,评价种猪猪瘟免疫效果,保证猪瘟免疫合格率达到80%以上,为规模化猪场种猪进行猪瘟免疫提供科学依据.结果显示:2010年、2011年种猪抗体检测合格率为86.70%、84.32%,对抗体不合格种猪再一次加强免疫后抗体检测总合格率91.28%、89.74%.由此表明:种猪猪瘟全群采用“一刀切”免疫猪瘟兔化弱毒脾淋苗,可以起到良好的免疫效果%  To evaluate the status of the immunity in breeding pigs against classical swine fever virus (CSFV), en-sure that the satisfactory levels of immunity was higher than 80% and provide a scientific basis for the immunity in breeding pigs against CSFV on the large-scale pig farms, 4561 serum samples from a large-scale pig farms in Fu-jian were collected and tested by HerdChek ELISA , which were immunized by "impose uniformity" method. The breeding pigs immunized with the HCLV bovine testis Lymph tissue origin vaccine at dose of 1.5ml/sow/time, ev-ery year twice on spring and autumn respectively. The results showed that the satisfactory levels of antibodies a-gainst CSFV in 2011 and 2012 were 86.70% and 84.32%, respectively. After immunizing once again to the unsat-isfactory levels of antibodies of breeding pigs, the total satisfactory levels of antibodies were 91.28% and 89.74%, respectively. The primary result reveals that the breeding herd immunized with the HCLV bovine testis Lymph tis-sue origin vaccine by "impose uniformity" method could play a good immune effect.

  18. Breeding kennel management.

    Science.gov (United States)

    Mullen, S

    1992-09-01

    Veterinarians and dog breeders should work together to establish protocols for health care and breeding management that are based on sound scientific principles as well as practical systems. These protocols should involve bitches, stud dogs, and puppies. Tantamount importance must be placed on record keeping so that problems may be identified and solved before they are irreversible.

  19. Plant breeding and genetics

    Science.gov (United States)

    The ultimate goal of plant breeding is to develop improved crops. Improvements can be made in crop productivity, crop processing and marketing, and/or consumer quality. The process of developing an improved cultivar begins with intercrossing lines with high performance for the traits of interest, th...

  20. Travelling to breed

    NARCIS (Netherlands)

    Drent, RJ; Fox, AD; Stahl, J

    2006-01-01

    Traditionally, investigation of the dynamics of avian migration has been heavily biased towards the autumn return trip to the wintering quarters. Since the migratory prelude to breeding has direct fitness consequences, the European Science Foundation recently redressed the balance and sponsored a wo

  1. Penguin breeding in Edinburgh

    NARCIS (Netherlands)

    Gillespie, T.H.; F.R.S.E.,; F.Z.S.,

    1939-01-01

    The Scottish National Zoological Park at Edinburgh has been notably successful in keeping and breeding penguins. It is happy in possessing as a friend and benefactor, Mr Theodore E. Salvesen, head of the firm of Christian Salvesen & Co., Leith, to whose interest and generosity it owes the great numb

  2. Characterization of the genetic profile of five Danish dog breeds

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Kristensen, Torsten Nygaard; Loeschcke, Volker

    2013-01-01

    was determined by means of principal component analysis (PCA) and through a Bayesian clustering method. Both the PCA and the Bayesian clustering method revealed a clear genetic separation of the 5 breeds. The level of genetic variation within the breeds varied. The expected heterozygosity (H) as well......This investigation presents results from a genetic characterization of 5 Danish dog breeds genotyped on the CanineHD BeadChip microarray with 170,000 SNP. The breeds investigated were 1) Danish Spitz (DS; n = 8), 2) Danish-Swedish Farm Dog (DSF; n = 18), 3) Broholmer (BR; n = 22), 4) Old Danish...... Pointing Dog (ODP; n = 24), and 5) Greenland Dog (GD; n = 23). The aims of the investigation were to characterize the genetic profile of the abovementioned dog breeds by quantifying the genetic differentiation among them and the degree of genetic homogeneity within breeds. The genetic profile...

  3. Effects on milk production in F1 crossbred of Alpine goat breed (♂ and Albanian goat breed (♀

    Directory of Open Access Journals (Sweden)

    Luan Hajno

    2012-07-01

    Full Text Available About 950,000 goats, farmed mostly in hilly and mountainous areas of Albania, contribute about 8% of the country’s total milk production. In order to increase milk production, farmers are currently using crosses of the local goat breed with exotic breeds, mainly the Alpine breed from France. This study examines milk production data of first lactation from 45 goats of the local breed, 82 goats of the Alpine breed and 58 F1 crosses (♂Alpine breed x ♀local breed. The goats were kept on small-scale farms according to the traditional Albanian system. Milking was carried out in the morning and evening. Kids were weaned at 65 days of age after which milking started. Milk yield was recorded twice with a 15-day interval between the two readings. Total milk yield was calculated using the Fleischmann method. The F1 goats produced 37.8 kg more milk than local breed goats although the lactation length (P<0.05 of F1 goats was six days shorter compared to that of local breed goats (P<0.05. Analysis of variance showed a highly significant effect (P<0.01 of the genotype factor on milk production. The average Cappio-Borlino curves of three genotypes indicated that the lactation curves of local breed and F1 crosses were similar. Although the F1 cross goats had 50% of their genomes from a genetically improved breed they were still able to deal with the difficult conditions that characterize the traditional extensive farming systems in Albania. Breeding pure Alpine breed or its crosses with the local goat breed improved milk production in an extensive traditional system.

  4. PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement.

    Science.gov (United States)

    Matsuda, Kazuyuki

    Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings. © 2017 Elsevier Inc. All rights reserved.

  5. Comparison of PCR-based mutation detection methods and application for identification of mouse Sult1a1 mutant embryonic stem cell clones using pooled templates.

    Science.gov (United States)

    Greber, Boris; Tandara, Helena; Lehrach, Hans; Himmelbauer, Heinz

    2005-05-01

    Reverse genetic approaches to generate mutants of model species are useful tools to assess functions of unknown genes. Recent work has demonstrated the feasibility of such strategies in several organisms, exploiting the power of chemical mutagenesis to disrupt genes randomly throughout the genome. To increase the throughput of gene-driven mutant identification, efficient mutation screening protocols are needed. Given the availability of sequence information for large numbers of unknown genes in many species, mutation detection protocols are preferably based on PCR. Using a set of defined mutations in the Hprt1 gene of mouse embryonic stem (ES) cells, we have systematically compared several PCR-based point mutation and deletion detection methods available for their ability to identify lesions in pooled samples, which is a major criterion for an efficient large-scale mutation screening assay. Results indicate that point mutations are most effectively identified by heteroduplex cleavage using CEL I endonuclease. Small deletions can most effectively be detected employing the recently described "poison" primer PCR technique. Further, we employed the CEL I assay followed by conventional agarose gel electrophoresis analysis for screening a library of chemically mutagenized ES cell clones. This resulted in the isolation of several clones harboring mutations in the mouse Sult1a1 locus, demonstrating the high-throughput compatibility of this approach using simple and inexpensive laboratory equipment.

  6. Identification of spontaneous mutations within the long-range limb-specific Sonic Hedgehog enhancer (ZRS) that alter Sonic Hedgehog expression in the chicken limb mutants oligozeugodactly and Silkie Breed

    Science.gov (United States)

    Maas, Sarah A.; Suzuki, Takayuki; Fallon, John F.

    2011-01-01

    The evolutionarily conserved, non-coding ~800 base-pair zone of polarizing activity (ZPA) regulatory sequence (ZRS) controls Shh expression in the posterior limb. We report that the chicken mutant oligozeugodactly (ozd), which lacks limb Shh expression, has a large deletion within the ZRS. Furthermore, the preaxial polydactylous, Silkie Breed chicken, which develops ectopic anterior limb Shh expression, has a single base-pair change within the ZRS. Using an in vivo reporter assay to examine enhancer function in the chick limb, we demonstrate that the wild-type ZRS drives β-galactosidase reporter expression in the ZPA of both wild-type and ozd limbs. The Silkie ZRS drives β-galactosidase in both posterior and anterior Shh domains in wild-type limb buds. These results support the hypothesis that the ZRS integrates positive and negative prepatterned regulatory inputs in the chicken model system and demonstrate the utility of the chicken limb as an efficient genetic system for gene regulatory studies. PMID:21509895

  7. Breeding without Breeding: Is a Complete Pedigree Necessary for Efficient Breeding?

    Science.gov (United States)

    El-Kassaby, Yousry A.; Cappa, Eduardo P.; Liewlaksaneeyanawin, Cherdsak; Klápště, Jaroslav; Lstibůrek, Milan

    2011-01-01

    Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called “Breeding without Breeding” (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB. PMID:21991342

  8. Simulation Modeling in Plant Breeding: Principles and Applications

    Institute of Scientific and Technical Information of China (English)

    WANG Jian-kang; Wolfgang H Pfeiffer

    2007-01-01

    Conventional plant breeding largely depends on phenotypic selection and breeder's experience, therefore the breeding efficiency is low and the predictions are inaccurate. Along with the fast development in molecular biology and biotechnology, a large amount of biological data is available for genetic studies of important breeding traits in plants,which in turn allows the conduction of genotypic selection in the breeding process. However, gene information has not been effectively used in crop improvement because of the lack of appropriate tools. The simulation approach can utilize the vast and diverse genetic information, predict the cross performance, and compare different selection methods. Thus,the best performing crosses and effective breeding strategies can be identified. QuLine is a computer tool capable of defining a range, from simple to complex genetic models, and simulating breeding processes for developing final advanced lines. On the basis of the results from simulation experiments, breeders can optimize their breeding methodology and greatly improve the breeding efficiency. In this article, the underlying principles of simulation modeling in crop enhancement is initially introduced, following which several applications of QuLine are summarized, by comparing the different selection strategies, the precision parental selection, using known gene information, and the design approach in breeding. Breeding simulation allows the definition of complicated genetic models consisting of multiple alleles, pleiotropy, epistasis, and genes, by environment interaction, and provides a useful tool for breeders, to efficiently use the wide spectrum of genetic data and information available.

  9. Comparative Methods to Improve the Detection of BRAF V600 Mutations in Highly Pigmented Melanoma Specimens

    OpenAIRE

    Frouin, Eric; Maudelonde, Thierry; Senal, Romain; Larrieux, Marion; Costes, Valérie; Godreuil, Sylvain; Vendrell, Julie A.; Solassol, Jérôme

    2016-01-01

    Genotyping BRAF in melanoma samples is often challenging. The presence of melanin greatly interferes with thermostable DNA polymerases and/or nucleic acids in traditional polymerase chain reaction (PCR)-based methods. In the present work, we evaluated three easy-to-use strategies to improve the detection of pigmented DNA refractory to PCR amplification. These pre-PCR processing methods include the addition of bovine serum albumin (BSA), the dilution of DNA, and the purification of DNA using t...

  10. indigenous cattle breeds

    African Journals Online (AJOL)

    the mitochondrial DNA cleavage patterns of the Brahman (zebu) and the Jersey ... that bottlenecks have played in the evolution of the species. ..... Length mutations in human mitochondrial DNA: direct sequencing of enzymatically amplified.

  11. A simple two-step, 'hit and fix' method to generate subtle mutations in BACs using short denatured PCR fragments.

    Science.gov (United States)

    Yang, Yongping; Sharan, Shyam K

    2003-08-01

    The bacteriophage lambda recombination system has proven to be a valuable tool for engineering bacterial artificial chromosomes (BAC). Due to its high efficiency, subtle alterations in the BACs can be generated using oligonucleotides as targeting vectors. Since no selection marker is used, recombinant clones are identified utilizing a selective PCR screening method. However, occasionally the selective PCR screening is not feasible. We describe here a two-step 'hit and fix' method that can be reliably used for generating any subtle alteration in BACs using short denatured PCR fragments as targeting vectors. In the first step of this method, 6-20 nucleotides are changed around the base where the mutation has to be generated. In the second step, these altered nucleotides are reverted to the original sequence and simultaneously a subtle alteration is introduced. Since in each step several nucleotides are changed, PCR primers specific for such alterations can be designed. This two-step method provides a simple and efficient tool for generating subtle alterations in BACs that can be very valuable for functional analysis of genes.

  12. SOE-LRed: a simple and time-efficient method to localize genes with point mutations onto the Escherichia coli chromosome

    Science.gov (United States)

    Benson, Ryan W.; Cafarelli, Tiziana M.; Godoy, Veronica G.

    2011-01-01

    We report a powerful method to replace wild type genes on the chromosome of Escherichia coli. Employing a unique form of PCR, we generate easily constructible gene fusions bearing single point mutations. Used in conjunction with homologous recombination, this method eliminates cloning procedures previously used for this purpose. PMID:21185880

  13. 蛹虫草高产胞外虫草素和虫草多糖的诱变育种%Enhanced production of extracellular cordycepin and polysaccharide in Cordyceps militaris by mutation breeding

    Institute of Scientific and Technical Information of China (English)

    孟泽彬; 文庭池; 康冀川; 康超; 王永江

    2012-01-01

    通过诱变获得高产胞外虫草素和虫草多糖的蛹虫草菌株.采用紫外线诱变(UV)、化学诱变(LiCl)、复合诱变(UV-LiCl) 3种方式对蛹虫草孢子进行诱变;发酵检测存活菌株的胞外虫草素和虫草多糖的含量.结果:以胞外虫草素为指标,3种诱变方式的最大正突变率分别为化学突变(29.2%)>紫外突变(28.6%)>复合诱变(26.5%);以胞外多糖为指标,最大正突变率分别为紫外诱变(35.7%)>复合诱变(33.3%)>化学诱变(27.0%).紫外诱变突变株Z-5-1胞外虫草素产量达0.842g/L,比出发菌株高311%;紫外诱变突变株Z-4-7胞外虫草多糖产量达5.250g/L,比出发菌株高148%.在连续培养5代后,仍具有较好的遗传稳定性.紫外诱变能获得较高的蛹虫草正突变率,同时能获得高产虫草素、虫草多糖的突变株.%The aim was to obtain high-yield strains of extracellular cordycepin and polysaccharide of Cordyceps mititaris. Three kind of mutation way, ultraviolet radiation (UV)、lithium chloride (LiCl) and compound mutagenesis (UV-LiCl) were used to deal with the spores of Cordyceps militaris. Fermenting the survival strains and detecting their content of extracellular cordycepin and cordyceps polysaccharide. The results showed: the maximum positive mutation rate order of extracellular cordycepin was LiCl (29.2%)>UV(28.6%)>UV-LiCl(26.5%) respectively, and that of extracellular polysaccharide was UV(35.7%)>UV-LiCl(33.3%)>LiCl(27.0%). The UV-induced mutant strain Z-5-1 had the highest extracellular cordycepin yield of 0.842g/L, which was 311% higher than that of the original strain. And the UV-induced mutant strain Z-4-7 had the highest extracellular Cordyceps polysaccharide production of 5.250g/L, which was 148% higher than that of the original strain. UV mutagenesis could obtain a higher positive mutation rate for Cordyceps militaris, while could produce good mutant strains with high-yield of extracellular cordycepin and

  14. Optimization of Fermentation Medium and Mutation Breeding of A Glycopeptide Antibiotic A40926 B Producing Strain%糖肽类抗生素A40926B产生菌的培养基优化及菌种选育

    Institute of Scientific and Technical Information of China (English)

    黄灵丽; 沈晓放; 陈少欣

    2012-01-01

    以A40926 B产生菌野野村放线菌SIPI-D-30为出发菌株,通过UV诱变及乙酸钠和甘氨酸抗性平板筛选,获得A40926 B产量提高的突变株SIPI-U- 157.经优化,确定摇瓶发酵培养基(g/L)为;葡萄糖5.0、麦芽糊精30.0、可溶性淀粉10.0、玉米淀粉30.0、大豆蛋白胨5.0、肉蛋白胨10.0、酵母浸粉5.0、冷榨黄豆饼粉10.0、棉籽饼粉5.0、L-缬氢酸1.0,发酵培养7d,突变株的A40926 B发酵单位为893mg/L.该突变株在5L发酵罐中培养180 h,A40926 B的产量最高为583 mg/L.%A medium for Nonomuraea sp. SIPI-D-30 fermentation was developed and the productivity of glycopeptide A40926 B was improved by strain breeding. After SIPI-D-30 was treated with UV and screened in the resistant plate of sodium acetate and glycin, a mutant SIPI-U-157 with higher production of A40926 B was obtained. The effects of carbon and nitrogen sources on the antibiotic production in shake-flask culture were investigated. The optimized medium compositions (g/L) were glucose 5.0, maltodextrin 30.0, soluble starch 10.0, com starch 30.0, soy peptone 5.0, meat peptone 10.0, yeast extract 5.0, soybean meal 10.0, cotton seed meal 5.0 and L-valine 1.0, in which the production of A40926 B by strain SIPI-U-157 reached 893 mg/L after 7 days' cultivation. In addition, a fed-batch culture of SIPI-U-157 in a 5 L fermentator also conducted. The yield of A40926 B was 583 mg/L at 180 h.

  15. Two novel methods for rapid detection and quantification of DNMT3A R882 mutations in acute myeloid leukemia.

    Science.gov (United States)

    Mancini, Melissa; Hasan, Syed Khizer; Ottone, Tiziana; Lavorgna, Serena; Ciardi, Claudia; Angelini, Daniela F; Agostini, Francesca; Venditti, Adriano; Lo-Coco, Francesco

    2015-03-01

    DNMT3A mutations represent one of the most frequent gene alterations detectable in acute myeloid leukemia with normal karyotype. Although various recurrent somatic mutations of DNMT3A have been described, the most common mutation is located at amino acid R882 in the methyltransferase domain of the gene. DNMT3A mutations have been reported to be stable during disease progression and are associated with unfavorable outcome in acute myeloid leukemia patients with normal karyotype. Because of their prognostic significance and high stability during disease evolution, DNMT3A mutations might represent highly informative biomarkers for minimal residual disease monitoring. We describe a new rapid diagnostic RT-PCR assay based on TauI restriction enzyme reaction to identify DNMT3A R882 mutations at diagnosis. In addition, we developed a sensitive and specific test based on peptide nucleic acid real-time PCR technology to monitor DNMT3A R882H mutation. We identified 24 DNMT3A R882H mutated patients out of 134 acute myeloid leukemia screened samples and we analyzed in these patients the kinetics of minimal residual disease after induction and consolidation therapy. This assay may be useful to better assess response to therapy in patients with acute myeloid leukemia bearing the DNMT3A R882H mutation.

  16. Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA from Patients with Non-Small Cell Lung Cancer (NSCLC.

    Directory of Open Access Journals (Sweden)

    James L Sherwood

    Full Text Available Non-invasive mutation testing using circulating tumour DNA (ctDNA is an attractive premise. This could enable patients without available tumour sample to access more treatment options.Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits.2 hr incubation time and double plasma centrifugation (2000 x g reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA. Reduced "contamination" and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT (Streck, after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield.This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous.

  17. 高产腈水解酶Alcaligenes faecalis ULA4菌株的诱变筛选%Mutation Breeding of Nitrilase High-Yielding Alcaligenes faecalis Strain UL44

    Institute of Scientific and Technical Information of China (English)

    徐建明; 柳志强; 徐建妙; 张金峰; 郑裕国

    2011-01-01

    A nitrilase producer Alcaligenes faecalis strain ZJBO9133 screened and preserved in the lab was carried out composite mutation with UV-LiCl and low-energy ion. A high yielding mutant UL44 was screened with the nitrilase activity as high as 74.6 U/g, increased by 124.5% higher than the starter strain. The obtained UL44 strain proclaimed genetically stable after passing five rounds of generation.%应用紫外-氯化锂和低能离子束复合诱变的方法,对1株本实验室筛选得到并保藏的腈水解酶产生菌Alcaligenes faecalis ZJB09133进行诱变育种,筛选到高产菌株UL44,其腈水解酶酶活达到74.6 U/g,较出发.菌株酶活提高124.5%.得到的高产菌株UL44经过5次传代,其遗传稳定性良好.

  18. UNUSUAL SPECTRUM OF GENETIC PATHOLOGIES AND NOVEL MUTATIONS IN PWS AND AS PATIENTS DETECTED BY A WIDE CLUSTER OF METHODS

    Directory of Open Access Journals (Sweden)

    Livia Kotysova

    2014-01-01

    Full Text Available Prader-Willi and Angelman syndromes are clinically distinct neurodevelopmental genetic disorders that map to 15q11.2-q13 locus. The common phenotypes are attributable to loss of expression of parentally specific imprinted genes inside this region, where the gene function is dependent on parental origin. Initial diagnosis was proved for the years by methylation pattern analyses of the SNRPN exon 1/promoter region within the PWS/AS critical domain. Apart from unifying methylation-specific PCR and allele specific real-time PCR with melt-curve analysis as the fundamental methods for suspected diagnosis confirmation, we combined several specifically methods used to clarify the molecular cause. In our study we had identified and genotyped 24 PWS and AS patients from 450 suspected. Applied cluster of methods-microsatellite analysis of SNPs within the chromosome 15, Methylation-specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA and UBE3A gene sequence analysis, enable us to determined atypical deletion that does not include common breakpoints, novel highly likely to be pathologic UBE3A mutation, uniparental heterodisomy together with partial isodisomy and epimutation without any deletions in the imprinting centre. We present genotype-phenotype correlation of all positive cases. In addition, we estimate the incidence for Slovakian population at 1 in 20,000 for PWS and 1 in 40,000 for AS.

  19. Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)

    NARCIS (Netherlands)

    Trong, T.Q.

    2013-01-01

      The aim of this thesis was to optimise the selective breeding program for Nile tilapia in the Mekong Delta region of Vietnam. Two breeding schemes, the “classic” BLUP scheme following the GIFT method (with pair mating) and a rotational mating scheme with own performance selection

  20. Development of Circular Economy of Characteristic Breeding Industry in Guangxi

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    In order to achieve characteristic,high-quality,high-efficiency,low-consumption,healthy and intensive breeding,we use the ecology method to analyze the status quo of development of characteristic breeding industry in Guangxi,from advantages in resources,industrial development,characteristic breeding,and standardized construction.There are some problems existing in the development of characteristic breeding industry in Guangxi:prominent contradiction among human,land and grain;outdated breeding mode;low comprehensive utilization rate of resources;increasingly deteriorating ecological environment.We put forth the following recommendations:based on the ecological and economic principles,introducing"reduce,reuse,recycle"idea of circular economy;striving to choose the development pattern of circular economy adapting to local resource characteristics,planting and breeding habits;in terms of realization path,paying close attention to construction of standardized breeding farm,cultivation of organic fertilizer industry,infrastructure construction,environmental law enforcement,and other parts;reinforcing the policy guidance,adjusting and optimizing industrial structure,strengthening scientific and technological innovation,and advancing industrialization management,to promote steady development of circular economy of characteristic breeding industry in Guangxi,and accelerate the process of rejuvenating province by breeding industry,enriching the people and building up Guangxi.

  1. Impact of two myostatin (MSTN mutations on weight gain and lamb carcass classification in Norwegian White Sheep (Ovis aries

    Directory of Open Access Journals (Sweden)

    Blichfeldt Thor

    2010-01-01

    Full Text Available Abstract Background Our aim was to estimate the effect of two myostatin (MSTN mutations in Norwegian White Sheep, one of which is close to fixation in the Texel breed. Methods The impact of two known MSTN mutations was examined in a field experiment with Norwegian White Sheep. The joint effect of the two MSTN mutations on live weight gain and weaning weight was studied on 644 lambs. Carcass weight gain from birth to slaughter, carcass weight, carcass conformation and carcass fat classes were calculated in a subset of 508 lambs. All analyses were carried out with a univariate linear animal model. Results The most significant impact of both mutations was on conformation and fat classes. The largest difference between the genotype groups was between the wild type for both mutations and the homozygotes for the c.960delG mutation. Compared to the wild types, these mutants obtained a conformation score 5.1 classes higher and a fat score 3.0 classes lower, both on a 15-point scale. Conclusions Both mutations reduced fatness and increased muscle mass, although the effect of the frameshift mutation (c.960delG was more important as compared to the 3'-UTR mutation (c.2360G>A. Lambs homozygous for the c.960delG mutation grew more slowly than those with other MSTN genotypes, but had the least fat and the largest muscle mass. Only c.960delG showed dominance effects.

  2. Correlation between the Insertion/Deletion Mutations of Prion Protein Gene and BSE Susceptibility and Milk Performance in Dairy Cows

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

    Objective To investigate the 23 bp and 12 bp insertion/deletion (indel) mutations within the bovine prion protein (PRNP) gene in Chinese dairy cows, and to detect the associations of two indel mutations with BSE susceptibility and milk performance. Methods Based on bovine PRNP gene sequence, two pairs of primers for testing the 23 bp and 12 bp indel mutations were designed. The PCR ampliifcation and agarose electrophoresis were carried out to distinguish the different genotypes within the mutations. Moreover, based on previous data from other cattle breeds and present genotypic and allelic frequencies of two indels mutations in this study, the corrections between the two indel mutations and BSE susceptibility were tested, as well as the relationships between the mutations and milk performance traits were analyzed in this study based on the statistical analyses. Results In the analyzed Chinese Holstein population, the frequencies of two“del”alleles in 23 bp and 12 bp indel muations were more frequent. The frequency of haplotype of 23del-12del was higher than those of 23del-12ins and 23ins-12del. From the estimated r2 and D’ values, two indel polymorphisms were linked strongly in the Holstein population (D’=57.5%, r2=0.257). Compared with the BSE-affected cattle populations from the reported data, the signiifcant differences of genotypic and allelic frequencies were found among present Holstein and some BSE-affected populations (P0.05). Conclusions These observations revealed that the inlfuence of two indel mutations within the bovine PRNP gene on BSE depended on the breed and they did not affect the milk production traits, which layed the foundation for future selection of resistant animals, and for improving health conditions for dairy breeding against BSE in China.

  3. Rapid and cost-effective method for the detection of the c.533G>A mutation in the HEXA gene.

    Science.gov (United States)

    Ribeiro, Diogo; Duarte, Ana Joana; Amaral, Olga

    2011-03-01

    Tay-Sachs disease is a rare autosomal recessive neurodegenerative disorder that results from mutations in the HEXA gene, leading to β-hexosaminidase A (HexA) α subunit deficiency. An unusual variant of Tay-Sachs disease is known as the B1 variant. Previous studies indicated that, in northern Portugal, this is not only the most common variant but also one of the most prevalent lysosomal storage diseases. Additionally, this variant might also show a higher prevalence in populations of Portuguese and Spanish ancestry. A single mutation is invariably present in at least one of the alleles of B1 variant patients, HEXA mutation c.533G >A. To implement a method for c.533G >A testing in individuals and populations, we have optimized two distinct mutation analysis techniques, one based on restriction fragment length polymorphism analysis and the other based on allelic discrimination. We present the comparison of both methods and their advantages. Mutation screening by allelic discrimination proved to be particularly useful for the studying of large samples of individuals. It is time saving and highly reproducible, and under the conditions used, its cost is lower than the cost of polymerase chain reaction-based restriction fragment length polymorphism analysis.

  4. NEW METHOD FOR DETERMINING HEPATITIS B VIRUS RESISTANCE MUTATIONS M204I/V TO NUCLEOS(TIDE ANALOGUES IN PATIENTS WITH CHRONIC HEPATITIS B

    Directory of Open Access Journals (Sweden)

    E. A. Elpaeva

    2015-01-01

    Full Text Available Аnalogues of nucleos(tides (AN such as lamivudine (LAM, telbivudine (TBV, adefovir (ADP, entecavir (ENT are widely used for the treatment of chronic hepatitis B (CHB. However, the prolonged treatment using these drugs often leads to the development of drug resistance. The most common substitutions in the reverse transcriptase are methionine for valine (rtM204V, or methionine for isoleucine (rtM204I at position 204. Early AN-resistant mutations detection is of great importance to determine the treatment strategy of patients with CHB. Currently there are many highly sensitive methods for detection of drug resistance mutations, such as next-generation sequencing, reverse hybridizationbased line probe assay (LiPA, mass spectrometry. However, these methods require expensive equipment and reagents, and they are not widely used in clinical laboratories. The aim of this study was to develop a simple and accurate real-time PCR method for detection of rtM204I/V mutation. This method showed high specificity and sensitivity (1000 copies/ml, it is less laborious and does not require additional equipment, fast and cost effective compared to other methods. HBV mutations of resistance to AN were determined in 5 groups of patients with CHB. Patients of the first group received monotherapy with pegylated interferon (n = 12, the second group — lamivudine (n = 10, the third group — telbivudine (n = 7, the fourth group — entecavir (n = 15. The fifth group consisted of patients who did not receive antiviral therapy (n = 3. The frequency of mutations in HBV polymerase YMDD-motif was determined among 47 patients with CHB: it was 10% for lamivudine treated patients, 20% — for entecavir, 28% — for telbivudine. YIDD/YVDD motifs were identified in two patients and YMDD/YIDD — in one patient. Real-time PCR method for the detection of AN-resistant rtM204I/V mutations in HBV polymerase can be used in routine diagnostics for primary screening of patients not

  5. Candidate genes for idiopathic epilepsy in four dog breeds

    Directory of Open Access Journals (Sweden)

    Mickelson James R

    2011-04-01

    Full Text Available Abstract Background Idiopathic epilepsy (IE is a naturally occurring and significant seizure disorder affecting all dog breeds. Because dog breeds are genetically isolated populations, it is possible that IE is attributable to common founders and is genetically homogenous within breeds. In humans, a number of mutations, the majority of which are genes encoding ion channels, neurotransmitters, or their regulatory subunits, have been discovered to cause rare, specific types of IE. It was hypothesized that there are simple genetic bases for IE in some purebred dog breeds, specifically in Vizslas, English Springer Spaniels (ESS, Greater Swiss Mountain Dogs (GSMD, and Beagles, and that the gene(s responsible may, in some cases, be the same as those already discovered in humans. Results Candidate genes known to be involved in human epilepsy, along with selected additional genes in the same gene families that are involved in murine epilepsy or are expressed in neural tissue, were examined in populations of affected and unaffected dogs. Microsatellite markers in close proximity to each candidate gene were genotyped and subjected to two-point linkage in Vizslas, and association analysis in ESS, GSMD and Beagles. Conclusions Most of these candidate genes were not significantly associated with IE in these four dog breeds, while a few genes remained inconclusive. Other genes not included in this study may still be causing monogenic IE in these breeds or, like many cases of human IE, the disease in dogs may be likewise polygenic.

  6. Beyond breeding area management

    DEFF Research Database (Denmark)

    Pedersen, Lykke; Thorup, Kasper; Tøttrup, Anders P.

    Every year, billions of songbirds migrate thousands of kilometres between their European breeding grounds and African overwintering area. As migratory birds are dependent on resources at a number of sites varying in both space and time, they are likely to be more vulnerable to environmental change...... technological advances are currently enabling us to track yet smaller songbirds throughout their migration cycle providing valuable insight into the life cycle of individual birds. However, direct tracking of migratory birds has so far mainly been conducted on single populations and our understanding of entire...... and provide important information for conservation management of migratory birds....

  7. Breeding tropical forages

    Directory of Open Access Journals (Sweden)

    L Jank

    2011-01-01

    Full Text Available Brazil has the largest commercial beef cattle herd and is the main beef exporter in the world. Cultivated pastures arethe basis for the Brazilian beef production, and occupy an area of 101.4 million hectares. However, very few forage cultivars arecommercially available, and the majority of these are of apomictic reproduction, thus genetically homogeneous. Tropical foragebreeding is at its infancy, but much investment and efforts have been applied in the last three decades and some new cultivars havebeen released. In this paper, origin of different species, modes of reproduction, breeding programs and targets are discussed andthe resulting new cultivars released are presented.

  8. Ultra-deep sequencing confirms immunohistochemistry as a highly sensitive and specific method for detecting BRAF V600E mutations in colorectal carcinoma.

    Science.gov (United States)

    Rössle, Matthias; Sigg, Michèle; Rüschoff, Jan H; Wild, Peter J; Moch, Holger; Weber, Achim; Rechsteiner, Markus P

    2013-11-01

    The activating BRAF (V600) mutation is a well-established negative prognostic biomarker in metastatic colorectal carcinoma (CRC). A recently developed monoclonal mouse antibody (clone VE1) has been shown to detect reliably BRAF (V600E) mutated protein by immunohistochemistry (IHC). In this study, we aimed to compare the detection of BRAF (V600E) mutations by IHC, Sanger sequencing (SaS), and ultra-deep sequencing (UDS) in CRC. VE1-IHC was established in a cohort of 68 KRAS wild-type CRCs. The VE1-IHC was only positive in the three patients with a known BRAF (V600E) mutation as assessed by SaS and UDS. The test cohort consisted of 265 non-selected, consecutive CRC samples. Thirty-nine out of 265 cases (14.7%) were positive by VE1-IHC. SaS of 20 randomly selected IHC negative tumors showed BRAF wild-type (20/20). Twenty-four IHC-positive cases were confirmed by SaS (24/39; 61.5%) and 15 IHC-positive cases (15/39; 38.5%) showed a BRAF wild-type by SaS. UDS detected a BRAF (V600E) mutation in 13 of these 15 discordant cases. In one tumor, the mutation frequency was below our threshold for UDS positivity, while in another case, UDS could not be performed due to low DNA amount. Statistical analysis showed sensitivities of 100% and 63% and specificities of 95 and 100% for VE1-IHC and SaS, respectively, compared to combined results of SaS and UDS. Our data suggests that there is high concordance between UDS and IHC using the anti-BRAF(V600E) (VE1) antibody. Thus, VE1 immunohistochemistry is a highly sensitive and specific method in detecting BRAF (V600E) mutations in colorectal carcinoma.

  9. Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

    Science.gov (United States)

    Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

    2016-07-01

    Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

  10. 产木聚糖酶海洋微生物的筛选与诱变育种%Screening and breeding by induced mutation of xylanase-producing marine microorganism

    Institute of Scientific and Technical Information of China (English)

    黄小云; 林娟; 林小洪; 王国增; 叶秀云

    2015-01-01

    With self-made xylan as the only carbon source of primary screening medium , totally 60 strains which showed transparent zones and different morphology were screened from different marine samples .The shake flask fermentation results showed that 38 strains had xylanase-producing capabil-ities and strain B659 had the highest xylanase activity of 525.3 U· mL-1 .Via morphological charac-teristics and 16S rDNA sequence analysis , strain B659 was identified as Bacillus.The stable mutant strain G3-17 with 13.9%enhancement of xylanase activity was screened from the UV mutagenesis of strain B659.A stable mutant strain W1-40 with 11.6% xylanase activity increase was obtained by microwave mutation and screening from strain G 3-17.In 72 h fermentation of strain B659 and strain W1-40, the xylanase activity of latter (645.2 U· mL-1 ) achieved 24.6%elevation than the former (517.9 U· mL-1).%以自制木聚糖为初筛培养基的唯一碳源,从多个海洋来源样品中一共筛到60株有透明圈且形态各异的菌株,摇瓶发酵结果显示,38株具有产木聚糖酶能力,其中B659菌株产酶能力最高,酶活力为525.3 U· mL-1.结合B659菌株的形态特征和16S rDNA序列分析鉴定该菌株属于Bacillus属.对B659菌株进行紫外诱变,筛选得到酶活提高13.9%且稳定遗传的突变菌株G3-17;对G3-17菌株进一步进行微波诱变得到酶活较G3-17菌株高出11.6%且稳定遗传的突变菌株W1-40.对B659菌株和W1-40突变菌株进行发酵试验,72 h时W1-40菌株的酶活力达到645.2 U· mL-1,比B659菌株(517.9 U· mL-1)提高24.6%.

  11. A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia.

    Science.gov (United States)

    Ong, Edison; Szedlak, Anthony; Kang, Yunyi; Smith, Peyton; Smith, Nicholas; McBride, Madison; Finlay, Darren; Vuori, Kristiina; Mason, James; Ball, Edward D; Piermarocchi, Carlo; Paternostro, Giovanni

    2015-04-01

    A key aim of systems biology is the reconstruction of molecular networks. We do not yet, however, have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited scalability, in terms of required computational time and power, of existing algorithms. Network reconstruction methods should also be scalable in the sense of allowing scientists from different backgrounds to efficiently integrate additional data. We present a network model of acute myeloid leukemia (AML). In the current version (AML 2.1), we have used gene expression data (both microarray and RNA-seq) from 5 different studies comprising a total of 771 AML samples and a protein-protein interactions dataset. Our scalable network reconstruction method is in part based on the well-known property of gene expression correlation among interacting molecules. The difficulty of distinguishing between direct and indirect interactions is addressed by optimizing the coefficient of variation of gene expression, using a validated gold-standard dataset of direct interactions. Computational time is much reduced compared to other network reconstruction methods. A key feature is the study of the reproducibility of interactions found in independent clinical datasets. An analysis of the most significant clusters, and of the network properties (intraset efficiency, degree, betweenness centrality, and PageRank) of common AML mutations demonstrated the biological significance of the network. A statistical analysis of the response of blast cells from 11 AML patients to a library of kinase inhibitors provided an experimental validation of the network. A combination of network and experimental data identified CDK1, CDK2, CDK4, and CDK6 and other kinases as potential therapeutic targets in AML.

  12. Selkirk Rex: morphological and genetic characterization of a new cat breed.

    Science.gov (United States)

    Filler, Serina; Alhaddad, Hasan; Gandolfi, Barbara; Kurushima, Jennifer D; Cortes, Alejandro; Veit, Christine; Lyons, Leslie A; Brem, Gottfried

    2012-01-01

    Rexoid, curly hair mutations have been selected to develop new domestic cat breeds. The Selkirk Rex is the most recently established curly-coated cat breed originating from a spontaneous mutation that was discovered in the United States in 1987. Unlike the earlier and well-established Cornish and Devon Rex breeds with curly-coat mutations, the Selkirk Rex mutation is suggested as autosomal dominant and has a different curl phenotype. This study provides a genetic analysis of the Selkirk Rex breed. An informal segregation analysis of genetically proven matings supported an autosomal, incomplete dominant expression of the curly trait in the Selkirk Rex. Homozygous curl cats can be distinguished from heterozygous cats by head and body type, as well as the presentation of the hair curl. Bayesian clustering of short tandem repeat (STR) genotypes from 31 cats that represent the future breeding stock supported the close relationship of the Selkirk Rex to the British Shorthair, Scottish Fold, Persian, and Exotic Shorthair, suggesting the Selkirk as part of the Persian breed family. The high heterozygosity of 0.630 and the low mean inbreeding coefficient of 0.057 suggest that Selkirk Rex has a diverse genetic foundation. A new locus for Selkirk autosomal dominant Rex, SADRE, is suggested for the curly trait.

  13. BRAF mutations in conjunctival melanoma

    DEFF Research Database (Denmark)

    Larsen, Ann-Cathrine; Dahl, Christina; Dahmcke, Christina M.

    2016-01-01

    Purpose: To investigate incidence, clinicopathological features and prognosis of BRAF-mutated conjunctival melanoma in Denmark. Furthermore, to determine BRAF mutations in paired premalignant lesions and evaluate immunohistochemical BRAF V600E oncoprotein detection. Methods: Data from 139 patients...

  14. qPCR-HRM法检测NSCLC组织EGFR突变%Detect EGFR mutation in NSCLC with qPCR-HRM method

    Institute of Scientific and Technical Information of China (English)

    郭惠琴; 窦亚玲; 赵宇; 李晓光; 刘巍; 李泽坚

    2012-01-01

    Objective To compare the difference between qPCR-HRM method and sequence method in detecting EG-FR mutation in NSCLC tissue. Methods EGFR mutation of tumor tissue was detected with qPCR-HRM method and sequence method in the 42 paraffin embedded samples selected from PUMCH thoracic department from June, 2010 to July, 2011. Results EGFR mutation rate was 33.3% (14/42) and 28.6% (13/42) with qPCR-HRM method and sequence method, respectively. There is no significant difference in these 2 results ( McNemar Test, P = 0. 5 ) . Conclusion qPCR-HRM method is sensitive and reliable in screening EGFR mutation.%目的 比较qPCR-HRM法和测序法检测非小细胞肺癌(NSCLC)组织表皮生长因子受体(EGFR)基因突变的差异.方法 收集北京协和医院胸外科2010年6月至2011年7月收治的42例非小细胞肺癌患者的石蜡标本,分别用qPCR-HRM法和测序法检测肿瘤组织EGFR基因突变,使用McNemar检验比较其差别.结果 42例标本qPCR-HRM法检测EGFR突变率为33.3% (14/42),测序法为28.6% (13/42),统计学计算未见差异(P=0.5).结论 qPCR-HRM法检测NSCLC组织EGFR基因突变是一种灵敏、可靠的检测方法,可用于体细胞EGFR突变的检测和测序前突变的筛选.

  15. Breed differences in natriuretic peptides in healthy dogs

    DEFF Research Database (Denmark)

    Sjöstrand, K.; Wess, G.; Ljungvall, I.

    2014-01-01

    BACKGROUND: Measurement of plasma concentration of natriuretic peptides (NPs) is suggested to be of value in diagnosis of cardiac disease in dogs, but many factors other than cardiac status may influence their concentrations. Dog breed potentially is 1 such factor. OBJECTIVE: To investigate breed...... variation in plasma concentrations of pro-atrial natriuretic peptide 31-67 (proANP 31-67) and N-terminal B-type natriuretic peptide (NT-proBNP) in healthy dogs. ANIMALS: 535 healthy, privately owned dogs of 9 breeds were examined at 5 centers as part of the European Union (EU) LUPA project. METHODS: Absence...... the median concentration in Doberman Pinschers. CONCLUSIONS AND CLINICAL IMPORTANCE: Considerable interbreed variation in plasma NP concentrations was found in healthy dogs. Intrabreed variation was large in several breeds, especially for NT-proBNP. Additional studies are needed to establish breed...

  16. Next generation breeding.

    Science.gov (United States)

    Barabaschi, Delfina; Tondelli, Alessandro; Desiderio, Francesca; Volante, Andrea; Vaccino, Patrizia; Valè, Giampiero; Cattivelli, Luigi

    2016-01-01

    The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. Breed risk of pyometra in insured dogs in Sweden.

    Science.gov (United States)

    Egenvall, A; Hagman, R; Bonnett, B N; Hedhammar, A; Olson, P; Lagerstedt, A S

    2001-01-01

    An animal insurance database containing data on over 200,000 dogs was used to study the occurrence of pyometra with respect to breed and age during 1995 and 1996 in Swedish bitches pyometra. Thirty breeds with at least 800 bitches insured each year were studied using univariate and multivariate methods. The crude 12-month risk of pyometra for females pyometra differed with age, breed, and geographic location. The risk of developing pyometra was increased (identified using multivariate models) in rough Collies, Rottweilers, Cavalier King Charles Spaniels, Golden Retrievers, Bernese Mountain Dogs, and English Cocker Spaniels compared with baseline (all other breeds, including mixed breed dogs). Breeds with a low risk of developing the disease were Drevers, German Shepherd Dogs, Miniature Dachshunds, Dachshunds (normal size), and Swedish Hounds. Survival rates indicate that on average 23-24% of the bitches in the databases will have experienced pyometra by 10 years of age. In the studied breeds, this proportion ranged between 10 and 54%. Pyometra is a clinically relevant problem in intact bitches, and differences related to breed and age should be taken into account in studies of this disease.

  18. Potato breeding in the Netherlands

    NARCIS (Netherlands)

    Haan, de H.

    1953-01-01

    A remarkable feature of potato breeding in the Netherlands is the great number of private breeders who have concentrated their efforts on the improvement of the potato. The author calls attention to some circumstances and measures that have made potato breeding attractive in the Netherlands

  19. Assessment of caspofungin susceptibility of Candida glabrata by the Etest®, CLSI, and EUCAST methods, and detection of FKS1 and FKS2 mutations.

    Science.gov (United States)

    Bourgeois, N; Laurens, C; Bertout, S; Balard, Y; Krasteva, D; Rispail, P; Lachaud, L

    2014-07-01

    Candida glabrata has emerged as a major pathogen in invasive candidiasis in recent years. Currently, guidelines for invasive candidiasis treatment recommend fluconazole or an echinocandin as the first-line therapy. Nevertheless, the resistance of Candida glabrata to echinocandin is an emerging problem and has been partly associated with mutations in the FKS1 and FKS2 genes. The Etest® is an appropriate method for determining antifungal susceptibility in emergency routine diagnosis. In this work, we evaluated the reliability of the Etest® in comparison with the two reference broth microdilution methods, Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST), to assess the caspofungin resistance of 193 isolates of Candida glabrata. The interpretation of minimum inhibitory concentration (MIC) values was also discussed according to different breakpoints. Moreover, FKS1 and FKS2 mutations were investigated for isolates with high MICs. Our results showed that the MIC50 value was similar to the MIC90 value for each method. The Etest® method showed the lowest MIC values, whereas EUCAST presented the highest. Categorical agreement between the Etest® and CLSI methods was 100 % and 36 % using the breakpoints proposed by Arendrup et al. (Antimicrob Agents Chemother 56(7):3965-3968, 2012) and Pfaller et al. (Int J Antimicrob Agents 38(1):65-69, 2011), respectively. Two isolates showed high MIC values with the three methods and both presented FKS2 mutations. A novel FKS2 mutation was also reported for one isolate. Future epidemiological studies should also evaluate the reliability of the Etest® to detect echinocandin resistance, as it remains a routine method.

  20. Molecular breeding of allergy vaccines and antiallergic cytokines.

    Science.gov (United States)

    Punnonen, J

    2000-03-01

    Molecular breeding, also called DNA shuffling, is a technology that enables the generation of large libraries of novel genes and vectors, from which improved variants can be selected based on functional properties. In a common format, it involves recursive recombination and mutation, performed by random fragmentation of related DNA sequences, followed by reassembly of the fragments in a self-priming polymerase chain reaction. As in natural evolution, the technique takes advantage of crossovers, deletions, insertions, inversions and point mutations of genes to generate large pools of related sequences. Molecular breeding can be used to generate improved variants of proteins used as therapeutics, such as vaccine antigens, growth factors and immunomodulatory molecules. Moreover, the technology can be applied to evolve entire viruses or vectors, including DNA vaccines. Cytokines downregulating allergic immune responses and allergens are attractive targets for evolution by molecular breeding. This review describes approaches to generate chimeric allergens with T cell epitopes from multiple allergen homologues, while reducing the recognition by preexisting IgE. In addition, the results and applications of molecular breeding in the evolution of improved antiallergic cytokines are discussed.

  1. A simple and rapid quantitative method of detection of the common achondroplasia mutation: Analysis in mismatch repair deficient cells

    Directory of Open Access Journals (Sweden)

    Grewal Raji

    2004-01-01

    Full Text Available Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7,500. In more than 97% of cases, it is caused by a recurrent point mutation, a G to A substitution at nucleotide position 1138 (G1138A of the fibroblast growth factor receptor 3 gene. Although this is an autosomal dominant condition, more than 90% of all mutations occur sporadically making this one of the most mutagenic sites in the human genome. The reasons for the high spontaneous G1138A mutation rate are not known. This investigation was performed by developing a simple and rapid semi-quantitative allele specific PCR based assay capable of reliably detecting more than 25 mutant G1138A copies in a pool of 300,000 wild type molecules. Using this assay, the G1138A mutation frequency was measured in cell lines deficient in mismatch repair (LoVo, SW48 and comparing it with controls. No differences were found in the frequency of this point mutation between the mismatch repair deficient and wild type cell lines.

  2. 我国芦笋育种研究进展%Research Progress in Asparagus Breeding in China

    Institute of Scientific and Technical Information of China (English)

    张天翔; 林宗铿; 蔡坤秀; 杨俊杰

    2011-01-01

    概述了近年来我国芦笋育种中取得的主要研究进展,介绍了芦笋在选择育种、杂交育种、多倍体育种、全雄育种、航天诱变育种等方面的研究成果,并提出了我国芦笋育种的前景和发展方向.%This paper summarized the main research progresses of asparagus breeding in China in recent years, including the research achievements in selective breeding, hybrid breeding, polyploid breeding, supermale breeding and space mutation breeding of asparagus.In addition, the author discussed the prospects and developmental direction of asparagus breeding in China in the future.

  3. Genotyping of β-Lactoglobulin gene by PCR-RFLP in Sahiwal and Tharparkar cattle breeds

    Directory of Open Access Journals (Sweden)

    Gupta Neelam

    2006-05-01

    Full Text Available Abstract Background Improvement of efficiency and economic returns is an important goal in dairy farming, as in any agricultural enterprise. The primary goal of dairy industry has been to identify an efficient and economical way of increasing milk production and its constituents without increasing the size of the dairy herd. Selection of animals with desirable genotypes and mating them to produce the next generation has been the basis of livestock improvement and this would continue to remain the same in the coming years. The use of polymorphic genes as detectable molecular markers is a promising alternative to the current methods of trait selection once these genes are proven to be associated with traits of interest in animals. The point mutations in exon IV of bovine β-Lactoglobulin gene determine two allelic variants A and B. These variants were distinguished by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP analysis in two indigenous Bos indicus breeds viz. Sahiwal and Tharparkar cattle. DNA samples (228 in Sahiwal and 86 in Tharparkar were analyzed for allelic variants of β-Lactoglobulin gene. Polymorphism was detected by digestion of PCR amplified products with Hae III enzyme, and separation on 12% non-denaturing gels and resolved by silver staining. Results The allele B of β-Lactoglobulin occurred at a higher frequency than the allele A in both Sahiwal and Tharparkar breeds. The genotypic frequencies of AA, AB, and BB in Sahiwal and Tharparkar breeds were 0.031, 0.276, 0.693 and 0.023, 0.733, 0.244 respectively. Frequencies of A and B alleles were 0.17 and 0.83, and 0.39 and 0.61 in Sahiwal and Tharparkar breeds respectively. The Chi-square test results (at one degree of freedom at one per cent level revealed that the Tharparkar population was not in Hardy-Weinberg equilibrium as there was a continuous migration of animals in the herd studied, where as, the results are not significant for the Sahiwal

  4. Precision breeding for novel starch variants in potato.

    Science.gov (United States)

    Muth, Jost; Hartje, Stefanie; Twyman, Richard M; Hofferbert, Hans-Reinhard; Tacke, Eckhard; Prüfer, Dirk

    2008-08-01

    Potato can be used as a source of modified starches for culinary and industrial processes, but its allelic diversity and tetraploid genome make the identification of novel alleles a challenge, and breeding such alleles into elite lines is a slow and difficult process. An efficient and reliable strategy has been developed for the rapid introduction and identification of new alleles in elite potato breeding lines, based on the ethylmethanesulphonate mutagenesis of dihaploid seeds. Using the granule-bound starch synthase I gene (waxy) as a model, a series of point mutations that potentially affect gene expression or enzyme function was identified. The most promising loss-of-function allele (waxy(E1100)) carried a mutation in the 5'-splice donor site of intron 1 that caused mis-splicing and protein truncation. This was used to establish elite breeding lineages lacking granule-bound starch synthase I protein activity and producing high-amylopectin starch. This is the first report of rapid and efficient mutation analysis in potato, a genetically complex and vegetatively propagated crop.

  5. TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

    DEFF Research Database (Denmark)

    Marquard, Andrea Marion; Birkbak, Nicolai Juul; Thomas, Cecilia Engel

    2015-01-01

    A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations...... detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2...... %/75 % of tumors with/without copy numbers) from those that were less certain. Accuracy in the independent data sets was 46 %, 53 % and 89 % respectively, similar to the accuracy expected from the training data. Identification of primary site from point mutation and/or copy number data may be accurate enough...

  6. RosBREED: Enabling Marker-Assisted Breeding in Rosaceae

    Science.gov (United States)

    Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including ES...

  7. RosBREED: Enabling marker-assisted breeding in Rosaceae

    NARCIS (Netherlands)

    Iezzoni, A.F.; Weebadde, C.; Luby, J.; Yue, C.; Weg, van de W.E.; Fazio, G.; Main, D.; Peace, C.P.; Bassil, N.V.; McFerson, J.

    2010-01-01

    Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including EST

  8. Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle.

    Science.gov (United States)

    Bolormaa, S; Pryce, J E; Kemper, K; Savin, K; Hayes, B J; Barendse, W; Zhang, Y; Reich, C M; Mason, B A; Bunch, R J; Harrison, B E; Reverter, A; Herd, R M; Tier, B; Graser, H-U; Goddard, M E

    2013-07-01

    The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction [BayesR and genomic BLUP (GBLUP)] either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identified many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.

  9. qPCR-HRM法检测NSCLC血清循环EGFR突变%Detect serum circulating EGFR mutation with qPCR-HRM method

    Institute of Scientific and Technical Information of China (English)

    赵宇; 窦亚玲; 郭惠琴; 李晓光; 刘巍; 李泽坚

    2012-01-01

    Objective To investigate the possibility of detecting serum circulating EGFR mutations using qPCR-HRM method and compare the result with that of tumor tissue. Methods Serum circulating and tumor tissue EGFR mutation was detected by qPCR-HRM method in the 42 patients from PUMCH thoracic department from June, 2010 to July, 2011. Results EGFR mutation rate was 35.7% and 33.3% in blood and tissue, respectively. There is no significant difference in these 2 results (McNemar Test, P > 0. 05 ). Κ is 0. 842 (P < 0. 001). Conclusion The detection of EGFR mutation is highly consistent in serum and in tissue DNA samples by qPCR-HRM method.%目的 探讨利用qPCR-HRM法检测血清循环EGFR突变的可能性并与组织检测结果比较.方法 收集北京协和医院胸外科2010年6月至2011年7月收治的42例非小细胞肺癌(NSCLC)患者的石蜡标本及术前静脉血样,用qPCR-HRM法分别检测其EGFR突变情况.结果 42例血样中EGFR突变率35.7% (15/42),肿瘤组织则为33.3% (14/42).统计表明血浆和组织中的EGFR突变的检测结果未见差别(P>0.05).k值为0.842 (P<0.001).结论 使用qPCR-HRM法检测NSCLC患者血清与肿瘤组织的EGFR突变具有极好的一致性.

  10. Efficient selective breeding of live oil-rich Euglena gracilis with fluorescence-activated cell sorting.

    Science.gov (United States)

    Yamada, Koji; Suzuki, Hideyuki; Takeuchi, Takuto; Kazama, Yusuke; Mitra, Sharbanee; Abe, Tomoko; Goda, Keisuke; Suzuki, Kengo; Iwata, Osamu

    2016-05-23

    Euglena gracilis, a microalgal species of unicellular flagellate protists, has attracted much attention in both the industrial and academic sectors due to recent advances in the mass cultivation of E. gracilis that have enabled the cost-effective production of nutritional food and cosmetic commodities. In addition, it is known to produce paramylon (β-1,3-glucan in a crystalline form) as reserve polysaccharide and convert it to wax ester in hypoxic and anaerobic conditions-a promising feedstock for biodiesel and aviation biofuel. However, there remain a number of technical challenges to be solved before it can be deployed in the competitive fuel market. Here we present a method for efficient selective breeding of live oil-rich E. gracilis with fluorescence-activated cell sorting (FACS). Specifically, the selective breeding method is a repetitive procedure for one-week heterotrophic cultivation, staining intracellular lipids with BODIPY(505/515), and FACS-based isolation of top 0.5% lipid-rich E. gracilis cells with high viability, after inducing mutation with Fe-ion irradiation to the wild type (WT). Consequently, we acquire a live, stable, lipid-rich E. gracilis mutant strain, named B1ZFeL, with 40% more lipid content on average than the WT. Our method paves the way for rapid, cost-effective, energy-efficient production of biofuel.

  11. Efficient selective breeding of live oil-rich Euglena gracilis with fluorescence-activated cell sorting

    Science.gov (United States)

    Yamada, Koji; Suzuki, Hideyuki; Takeuchi, Takuto; Kazama, Yusuke; Mitra, Sharbanee; Abe, Tomoko; Goda, Keisuke; Suzuki, Kengo; Iwata, Osamu

    2016-01-01

    Euglena gracilis, a microalgal species of unicellular flagellate protists, has attracted much attention in both the industrial and academic sectors due to recent advances in the mass cultivation of E. gracilis that have enabled the cost-effective production of nutritional food and cosmetic commodities. In addition, it is known to produce paramylon (β-1,3-glucan in a crystalline form) as reserve polysaccharide and convert it to wax ester in hypoxic and anaerobic conditions–a promising feedstock for biodiesel and aviation biofuel. However, there remain a number of technical challenges to be solved before it can be deployed in the competitive fuel market. Here we present a method for efficient selective breeding of live oil-rich E. gracilis with fluorescence-activated cell sorting (FACS). Specifically, the selective breeding method is a repetitive procedure for one-week heterotrophic cultivation, staining intracellular lipids with BODIPY505/515, and FACS-based isolation of top 0.5% lipid-rich E. gracilis cells with high viability, after inducing mutation with Fe-ion irradiation to the wild type (WT). Consequently, we acquire a live, stable, lipid-rich E. gracilis mutant strain, named B1ZFeL, with 40% more lipid content on average than the WT. Our method paves the way for rapid, cost-effective, energy-efficient production of biofuel. PMID:27212384

  12. Meristem cultures in garlic (Allium sativum) breeding

    OpenAIRE

    ŠVEHLOVÁ, Eva

    2017-01-01

    The diploma thesis deals with the use of meristem cultures in garlic (Allium sativum) breeding. The source material was used variety Tantalum of garlic. The using material, before the isolation of meristem, was tested for the occurrence of viral diseases by immunological tests ELISA (Enzyme-Linked Immuno-Sorbent Assay), also known as EIA (Enzyme Immunoassay). The method used to detect antibodies and antigens. The material was tested for viruses onion yellow dwarf (OYDV - Onion Yellow Dwarf Vi...

  13. Structural and functional characterization of pathogenic non- synonymous genetic mutations of human insulin-degrading enzyme by in silico methods.

    Science.gov (United States)

    Shaik, Noor A; Kaleemuddin, Mohammed; Banaganapalli, Babajan; Khan, Fazal; Shaik, Nazia S; Ajabnoor, Ghada; Al-Harthi, Sameer E; Bondagji, Nabeel; Al-Aama, Jumana Y; Elango, Ramu

    2014-04-01

    Insulin-degrading enzyme (IDE) is a key protease involved in degrading insulin and amyloid peptides in human body. Several non-synonymous genetic mutations of IDE gene have been recently associated with susceptibility to both diabetes and Alzheimer's diseases. However, the consequence of these mutations on the structure of IDE protein and its substrate binding characteristics is not well elucidated. The computational investigation of genetic mutation consequences on structural level of protein is recently found to be an effective alternate to traditional in vivo and in vitro approaches. Hence, by using a combination of empirical rule and support vector machine based in silico algorithms, this study was able to identify that the pathogenic nonsynonymous genetic mutations corresponding to p.I54F, p.P122T, p.T533R, p.P581A and p.Y609A have more potential role in structural and functional deviations of IDE activity. Moreover, molecular modeling and secondary structure analysis have also confirmed their impact on the stability and secondary properties of IDE protein. The molecular docking analysis of IDE with combinational substrates has revealed that peptide inhibitors compared to small non-peptide inhibitor molecules possess good inhibitory activity towards mutant IDE. This finding may pave a way to design novel potential small peptide inhibitors for mutant IDE. Additionally by un-translated region (UTR) scanning analysis, two regulatory pathogenic genetic mutations i.e., rs5786997 (3' UTR) and rs4646954 (5' UTR), which can influence the translation pattern of IDE gene through sequence alteration of upstream-Open Reading Frame and Internal Ribosome Entry Site elements were identified. Our findings are expected to help in narrowing down the number of IDE genetic variants to be screened for disease association studies and also to select better competitive inhibitors for IDE related diseases.

  14. Mutation breeding in sunflower for resistance to alternaria leaf spot

    OpenAIRE

    de Marcelo Oliveira F.; Tulmann Augusto Neto; Regina Leite M.V.B.C.; Vania Castiglioni B.R.; Arias C.A.A.

    2004-01-01

    Genetic variability for resistance to Alternarla leaf spot disease (Alternaria helianthi) can be induced by radiation or chemical mutagens. The objectives of this study were to create genetic variability in cultivated sunflower and to select lines resistant to Alternaria leaf spot. In the first experiment, sunflower seeds of the genotype HA BR 104 were irradiated with 150 and 165 Gy of gamma rays. Seeds were sown in the field at the Embrapa Soybean experimental station, in Londrina, PR, Brazi...

  15. Molecular testing for familial hypercholesterolaemia-associated mutations in a UK-based cohort: development of an NGS-based method and comparison with multiplex polymerase chain reaction and oligonucleotide arrays.

    Science.gov (United States)

    Reiman, Anne; Pandey, Sarojini; Lloyd, Kate L; Dyer, Nigel; Khan, Mike; Crockard, Martin; Latten, Mark J; Watson, Tracey L; Cree, Ian A; Grammatopoulos, Dimitris K

    2016-11-01

    Background Detection of disease-associated mutations in patients with familial hypercholesterolaemia is crucial for early interventions to reduce risk of cardiovascular disease. Screening for these mutations represents a methodological challenge since more than 1200 different causal mutations in the low-density lipoprotein receptor has been identified. A number of methodological approaches have been developed for screening by clinical diagnostic laboratories. Methods Using primers targeting, the low-density lipoprotein receptor, apolipoprotein B, and proprotein convertase subtilisin/kexin type 9, we developed a novel Ion Torrent-based targeted re-sequencing method. We validated this in a West Midlands-UK small cohort of 58 patients screened in parallel with other mutation-targeting methods, such as multiplex polymerase chain reaction (Elucigene FH20), oligonucleotide arrays (Randox familial hypercholesterolaemia array) or the Illumina next-generation sequencing platform. Results In this small cohort, the next-generation sequencing method achieved excellent analytical performance characteristics and showed 100% and 89% concordance with the Randox array and the Elucigene FH20 assay. Investigation of the discrepant results identified two cases of mutation misclassification of the Elucigene FH20 multiplex polymerase chain reaction assay. A number of novel mutations not previously reported were also identified by the next-generation sequencing method. Conclusions Ion Torrent-based next-generation sequencing can deliver a suitable alternative for the molecular investigation of familial hypercholesterolaemia patients, especially when comprehensive mutation screening for rare or unknown mutations is required.

  16. Use of a MAMA-PCR Method to detect gyrA Mutations in Nalidixic Acid-Resistant Clinical Isolates of Escherichia coli

    Directory of Open Access Journals (Sweden)

    A Karami

    2008-05-01

    Full Text Available Background: Enterobacteriaceae are a large group of bacteria widely distributed in nature. Escherichia coli is the most com­mon cause of urinary tract infection. Two amino acid substitutions, in GyrA, are commonly responsible for quinolone re­sistance in E. coli. The aim of this study was molecular survey of nalidixic acid resistance E.coli isolated from patients in the codones of 83 and 87 gyrA genes.Methods: During 5 months (January to June 2005 of Molecular Survey of Nalidixic Acid Resistance, one hundred and twenty-one E. coli isolates from urine samples of patients referred to clinical laboratory of Baqiyatallah Hospital were cul­tured. Differential tests were done for diagnosis of E.coli. An economical and time-efficient mismatch amplification muta­tion assay (MAMA PCR was developed to detect mutations in the chromosomal gyrA gene causing these substitutions.Results: In nalidixic acid antibiogram test, 55 cases (45.5% were sensitive, 63 cases (52% were resistant and 3 cases (2.5% were intermediate. Results of PCR and MIC were similar to antibiogram. There was not any mutation in the sensi­tive samples but there were performed five mutations on the 85, 81, 107, 97 and 87 codones of resistance samples. The codone number 87s mutation is one of the main mutations of nalidixic acid resistance.Conclusion: Depending on results of this study and comparison with other studies, trend of resistance of E.coli is increas­ing. Therefore, we recommend control of antibiotic misusage and application of MIC and PCR tests (if possible prior to treat­ment for suitable selection of antibiotic and prevention of microbial resistance.

  17. Seleção genômica ampla e novos métodos de melhoramento do milho Genome wide selection and new methods of maize breeding

    Directory of Open Access Journals (Sweden)

    Roberto Fritsche-Neto

    2012-12-01

    Full Text Available Os objetivos deste trabalho foram verificar a acurácia do método da Seleção Genômica Ampla (GWS no melhoramento de milho nas condições de estresse nutricional e propor novos métodos de melhoramento baseados em GWS. Foram estimados os dois componentes da eficiência no uso de nitrogênio e de fósforo (eficiência de absorção e de utilização em 41 combinações híbridas, em dois experimentos, sob baixa e alta disponibilidades de N e P. Para a genotipagem da população de estimação, foram utilizados 80 marcadores microssatélites. As estimativas dos parâmetros genéticos foram obtidas via REML/BLUP, e a predição dos valores genéticos genômicos, via regressão aleatória (Random Regression - RR aplicada à seleção genômica ampla (RR-BLUP/GWS. Para os caracteres em que a GWS apresentou altos valores de acurácia, essa foi comparada com os métodos de Seleção Recorrente Intra e Interpopulacional. Com o uso da GWS houve aumento significativo na acurácia seletiva e nos ganhos genéticos por unidade de tempo.The objectives of this work were to verify the accuracy of the Genome Wide Selection method (GWS in the maize breeding for nutritional stress conditions and propose new breeding methods based on GWS. The efficiency of two components of use of nitrogen and phosphorus (absorption and utilization was estimated in 41 single-cross hybrids assessed in two experiments under low and high availability of N and P. Eighty microsatellite markers were used to genotype the base population. The estimates of genetic parameters were obtained by REML/BLUP and the predictions of genetic genomic values were obtained by random regression (RR, applied to genome wide selection (RR-BLUP/GWS. GWS showed high values of accuracy for the traits; it was comparable to the methods of Recurrent Intra and Interpopulational Selection. It was concluded that there is a significant increase in selective accuracy and in the genetic gains per unit of time with

  18. Illinois’ 2000 breeding season report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the 2000 breeding season for grassland birds in Illinois. The report begins by summarizing weather conditions throughout the season and...

  19. Atlantic Flyway Breeding Waterfowl Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Atlantic Flyway Technical Section initiated this breeding waterfowl survey in 11 northeast states ranging from New Hampshire to Virginia.

  20. Tricolored Blackbird - Breeding [ds20

    Data.gov (United States)

    California Department of Resources — These data come from observations of breeding tricolored blackbirds throughout their range in California. NAD27 coordinates are given in the data for each record....

  1. Mutational Changes In Delphinium malabaricum (Huth. Munz.: A Potential Ornamental Plant

    Directory of Open Access Journals (Sweden)

    Kolar Firdose R.

    2015-12-01

    Full Text Available Mutation breeding is an established method used for crop improvement and has played a major role in the development of many new flower color/shape mutant cultivars in ornamentals. The present study is aimed at inducing mutations in Delphinium malabaricum using chemical mutagens ethyl methane sulfonate (EMS, sodium azide (SA and physical mutagen (gamma rays. It was observed that D. malabaricum manifested specific reactions to the treatments with EMS, SA and gamma rays. Identification and selection of mutations were carried out in the second generation (M2. A variety of chlorophyll deficient mutants and high percentage of the flower color and morphological mutants were recorded. The maximum frequency of chlorophyll and flower color and morphological mutations were recorded in EMS treated plants when compared to the other two mutagens. The frequency values for the individual mutant types were varied and randomly distributed at different mutagenic treatments. The highest percentage of color mutants arose after treatments with 0.25% of EMS and the lowest at 20 kR of gamma rays. The mutants were quite distinct, as compared to the control and often had more attractive ornamental features compared to the starting material. The major commercial benefit of the application of this technology has so far been obtaining of novel flower mutants that can be used as an initial material for further breeding of new cultivars.

  2. Usefulness of portable near infrared spectroscopy in olive breeding programs

    Energy Technology Data Exchange (ETDEWEB)

    Leon-Moreno, L.

    2012-11-01

    The usefulness of portable near infrared (NIR) spectroscopy as a simple and efficient method to determine some of the main selection traits in olive breeding is evaluated in this work. Calibration models were developed and evaluated using partial least squares (PLS) regression from samples collected in different selection steps of the breeding work and under different experimental conditions. The results showed that accurate enough models (values of correlation between actual and predicted constituent higher than 0.9) were obtained for oil and moisture content in both cross validation and prediction results. Portable NIR spectroscopy could be used for selection of genotypes on the basis of these characters, providing similar ranking of genotypes than reference methods both in different selection steps of the breeding process (progenies and selection plots) and different experimental conditions (on-tree or under laboratory conditions). The advantages of this technique to improve the efficiency of the evaluation process in olive breeding programs are discussed. (Author) 21 refs.

  3. Plant breeding by using radiation mutation - Development of radiation indicator plants by molecular breeding

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jang Ryol; Kwak, Sang Soo; Kwon, Seok Yoon [Korea Research Institute of Bioscience and Biotechnology, Taejon (Korea)

    2000-04-01

    - tSOD1, cytosolic CuZnSOD cDNA was cloned from tobacco cDNA library by PCR. To develop the under-producing the transgenic plants, the vectors were constructed using by antisense and co-supressing technology. The transgenic tobacco plants were confirmed that over 60% of kanamycin-resistant plants were introduced the foreign gene by PCR and transformed one copy through Southern blot analysis. - In an attempt to identify marker genes for gamma irradiation of plants, expression patterns of diverse genes upon gamma irradiation of young tobacco plants were investigated. With the knowledge of distinctive expression patterns of diverse genes, irradiation-indicating marker plants could be developed by engineering and monitoring multiple radiation-responsive genes. Additionally, a gamma irradiation-responsive NtTMK1 receptor-like kinase gene was molecular biologically characterized. -Uranium reductase gene (Cytochrome C3) and radiation resistance gene (recA) have been cloned from Desulfovibrio and Deinococcus radiodurans. -Two plant transformation vectors (pCYC3 and pDrecA) have been constructed. - Tobacco transgenic plants of have been obtained. 52 refs., 5 figs. (Author)

  4. Mitochondrial D-loop sequence variation among Italian horse breeds

    Directory of Open Access Journals (Sweden)

    Zanotti Marta

    2004-11-01

    Full Text Available Abstract The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences.

  5. Detection of low-abundance KRAS mutations in colorectal cancer using microfluidic capillary electrophoresis-based restriction fragment length polymorphism method with optimized assay conditions.

    Directory of Open Access Journals (Sweden)

    Huidan Zhang

    Full Text Available Constitutively active KRAS mutations have been found to be involved in various processes of cancer development, and render tumor cells resistant to EGFR-targeted therapies. Mutation detection methods with higher sensitivity will increase the possibility of choosing the correct individual therapy. Here, we established a highly sensitive and efficient microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP platform for low-abundance KRAS genotyping with the combination of µCE and RFLP techniques. By using our self-built sensitive laser induced fluorescence (LIF detector and a new DNA intercalating dye YOYO-1, the separation conditions of µCE for ΦX174 HaeIII DNA marker were first optimized. Then, a Mav I digested 107-bp KRAS gene fragment was directly introduced into the microfluidic device and analyzed by µCE, in which field amplified sample stacking (FASS technique was employed to obtain the enrichment of the RFLP digestion products and extremely improved the sensitivity. The accurate analysis of KRAS statuses in HT29, LS174T, CCL187, SW480, Clone A, and CX-1 colorectal cancer (CRC cell lines by µCE-based RFLP were achieved in 5 min with picoliter-scale sample consumption, and as low as 0.01% of mutant KRAS could be identified from a large excess of wild-type genomic DNA (gDNA. In 98 paraffin-embedded CRC tissues, KRAS codon 12 mutations were discovered in 28 (28.6%, significantly higher than that obtained by direct sequencing (13, 13.3%. Clone sequencing confirmed these results and showed this system could detect at least 0.4% of the mutant KRAS in CRC tissue slides. Compared with direct sequencing, the new finding of the µCE-based RFLP platform was that KRAS mutations in codon 12 were correlated with the patient's age. In conclusion, we established a sensitive, fast, and cost-effective screening method for KRAS mutations, and successfully detected low-abundance KRAS mutations in clinical

  6. Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle.

    Science.gov (United States)

    Judge, M M; Kelleher, M M; Kearney, J F; Sleator, R D; Berry, D P

    2017-06-01

    Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using

  7. Paternity Testing, a Poor Man’s Marker Assisted Breeding Strategy to Increase Selection Gains in Outbred Forage Species

    Science.gov (United States)

    Many methods to incorporate molecular markers into breeding programs have been proposed. Most existing marker assisted selection strategies use selection based on molecular marker linkage to achieve selection gains. Such strategies are often prohibitively expensive in forage breeding (Riday, 2007)...

  8. The association of two single nucleotide polymorphisms (SNPs) in growth hormone (GH) gene with litter size and superovulation response in goat-breeds

    Science.gov (United States)

    Zhang, Chunyan; Liu, Yun; Huang, Kunkun; Zeng, Wenbing; Xu, Deqing; Wen, Qunying; Yang, Liguo

    2011-01-01

    Two active mutations (A 781 G and A 1575 G) in growth hormone (GH) gene, and their associations with litter size (LS), were investigated in both a high prolificacy (Matou, n = 182) and a low prolificacy breed (Boer, n = 352) by using the PCR-RFLP method. Superovulation experiments were designed in 57 dams, in order to evaluate the effect of different genotypes of the GH gene on superovulation response. Two genotypes (AA and AB, CC and CD) in each mutation were detected in these two goat breeds. Neither BB nor DD homozygous genotypes were observed. The genotypic frequencies of AB and CC were significantly higher than those of AA and CD. In the third parity, Matou dams with AB or CC genotypes had significantly larger litter sizes than those with AA and CD (p superovulation treatments, a significantly higher number of corpora lutea and ova, with a lower incidence of ovarian cysts, were harvested in the AB and CC genotypes than in AA and CD. These results show that the two loci of GH gene are highly associated with abundant prolificacy and superovulation response in goat breeds. PMID:21637543

  9. Localization of canine brachycephaly using an across breed mapping approach.

    Directory of Open Access Journals (Sweden)

    Danika Bannasch

    Full Text Available The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10-30 and control (20-60 samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.

  10. Achievements in NS rapeseed hybrids breeding

    Directory of Open Access Journals (Sweden)

    Marjanović-Jeromela Ana

    2016-01-01

    Full Text Available The increased production of oilseed rape (Brassica napus L. is evident on a global scale, but also in Serbia in the last decade. Rapeseed is used primarily for vegetable oil and processing industry, but also as a source of protein for animal feed and green manure. Following the cultivation of varieties, breeding and cultivation of hybrid rapeseed started in the 1990's, to take advantage of heterosis in F1 generation, while protecting the breeder's rights during seed commercialization. The breeding of hybrid oilseed rape requires high quality starting material (lines with good combining abilities for introduction of male sterility. Ogura sterility system is primarily used at the Institute of Field and Vegetable Crops, Novi Sad, Serbia. To use this system, separate lines are modified with genes for cytoplasmic male sterility (cms female line - mother line and restoration of fertility (Rf male lines - father line. In order to maintain the sterility of the mother line it is necessary to produce a maintainer line of cytoplasmic male sterility. Creation of these lines and hybrids at the Institute of Field and Vegetable Crops was successfully monitored with intense use of cytogenetic laboratory methods. The structure and vitality of pollen, including different phases during meiosis were checked so that cms stability was confirmed during the introduction of these genes into different lines. Rapeseed breeding program in Serbia resulted in numerous varieties through collaboration of researchers engaged in breeding and genetics of this plant species. So far, in addition to 12 varieties of winter rapeseed and two varieties of spring rapeseed, a new hybrid of winter rapeseed NS Ras was registered in Serbia. NS Ras is an early-maturing hybrid characterized by high seed yield and oil content. Average yield of NS Ras for two seasons and three sites was 4256 kg ha-1 of seed and 1704 kg ha-1 of oil. Three promising winter rapeseed hybrids are in the process of

  11. Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds.

    Science.gov (United States)

    Ramayo-Caldas, Yuliaxis; Renand, Gilles; Ballester, Maria; Saintilan, Romain; Rocha, Dominique

    2016-04-23

    Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds. Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Our results suggest that systems biology approaches that explore

  12. Impacts of Water Levels on Breeding Canada Geese and Methods for Mitigation and Management in the Southern Flathead Valley, Montana, 1983-1987 Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Mackey, Dennis L.; Gregory, Shari K.; Matthews, William C. Jr.; Claar, James J.; Ball, I. Joseph

    1987-11-01

    Kerr Hydroelectric Dam is located at the south end of Flathead Lake, controls water levels on the lake and the Flathead River below the dam, and is currently operated as a load control facility. Current operation of Kerr Dam creates the greatest yearly water level fluctuations on both the lake and river during the Canada goose (Branta canadensis moffitti) brood and nesting period. Data collected from 1980-1982 indicated that goose nest numbers on the river were lower than during the 1950's, and that brood habitat on the lake may be limiting the goose population there. Our study was conducted from 1983-1987 to determine the effects of Kerr Dam operation on Canada goose populations and habitat on the south half of Flathead Lake and the Flathead River, and to formulate management and mitigation recommendations. Nesting geese on the river appeared to be negatively affected by a lack of nest sites free from predators, and responded to available artificial nest structures with an increase in nest numbers and nesting success. Under current dam operation, river channel depths and widths do not discourage access to nesting islands by mammalian predators during some years and high predation on ground nests occurs. Intensively used brood areas on the lake and river were identified and described. Brood habitat on the lake was lower in quality and quantity than on the river due to dam operations. Gosling mortality on the lake was high, almost 2 times higher than on the river. Lake broods expended more energy obtaining food than river broods. Losses of brood habitat in the form of wet meadow marshes were documented and mitigation options developed. Management/mitigation alternatives and monitoring methods for nesting and brooding geese were identified.

  13. Future perspectives of in vitro culture and plant breeding

    DEFF Research Database (Denmark)

    Kuligowska, Katarzyna; Lütken, Henrik Vlk; Hegelund, Josefine Nymark

    2015-01-01

    Conventional breeding and plant improvement increasingly become inadequate to keep up with progression and high quality demands. Thus biotechnological techniques are more and more adopted. Initially, biotechnological tools have supported conventional breeding by in vitro culture techniques......, comprising micropropagation, speeding up multiplication and improving uniformity. Also, crossing barriers of incompatible plants have been overcome using in vitro methods and embryo rescue techniques in wide hybridization approaches. Marker-assisted breeding is employed for targeted selection of DNA...... fragments from parental plants in respect to identification of desired characteristics in offspring or among hybrid plants. Phylogeny-assisted breeding and knowledge about genetic relationships support the ability to develop new hybrids. Finally, chemical and radiation induced mutagenesis are established...

  14. Does genomic selection have a future in plant breeding?

    Science.gov (United States)

    Jonas, Elisabeth; de Koning, Dirk-Jan

    2013-09-01

    Plant breeding largely depends on phenotypic selection in plots and only for some, often disease-resistance-related traits, uses genetic markers. The more recently developed concept of genomic selection, using a black box approach with no need of prior knowledge about the effect or function of individual markers, has also been proposed as a great opportunity for plant breeding. Several empirical and theoretical studies have focused on the possibility to implement this as a novel molecular method across various species. Although we do not question the potential of genomic selection in general, in this Opinion, we emphasize that genomic selection approaches from dairy cattle breeding cannot be easily applied to complex plant breeding.

  15. Mapping Mutations on Phylogenies

    DEFF Research Database (Denmark)

    Nielsen, Rasmus

    2005-01-01

    This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety...... of different applications, for example, in the detection of correlated evolution and to identify selection acting on DNA sequences. However, many uses of parsimony mappings have been criticized because they focus on only one of many possible mappings and/or because they do not incorporate statistical...... uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping....

  16. DHPLC/SURVEYOR nuclease: a sensitive, rapid and affordable method to analyze BRCA1 and BRCA2 mutations in breast cancer families.

    Science.gov (United States)

    Pilato, Brunella; De Summa, Simona; Danza, Katia; Papadimitriou, Stavros; Zaccagna, Paolo; Paradiso, Angelo; Tommasi, Stefania

    2012-09-01

    Hereditary breast cancer accounts for about 10% of all breast cancers and BRCA1 and BRCA2 genes have been identified as validated susceptibility genes for this pathology. Testing for BRCA gene mutations is usually based on a pre-screening approach, such as the partial denaturation DHPLC method, and capillary direct sequencing. However, this approach is time consuming due to the large size of BRCA1 and BRCA2 genes. Recently, a new low cost and time saving DHPLC protocol has been developed to analyze gene mutations by using SURVEYOR(®) Nuclease digestion and DHPLC analysis. A subset of 90 patients, enrolled in the Genetic Counseling Program of the National Cancer Centre of Bari (Italy), was performed to validate this approach. Previous retrospective analysis showed that 9/90 patients (10%) were mutated in BRCA1 and BRCA2 genes and these data were confirmed by the present approach. DNA samples underwent touchdown PCR and, subsequently, SURVEYOR(®) nuclease digestion. BRCA1 and BRCA2 amplicons were divided into groups depending on amplicon size to allow multiamplicon digestion. The product of this reaction were analyzed on Transgenomic WAVE Nucleic Acid High Sensitivity Fragment Analysis System. The operator who performed the DHPLC surveyor approach did not know the sequencing results at that time. The SURVEYOR(®) Nuclease DHPLC approach was able to detect all alterations with a sensitivity of 95%. Furthermore, in order to save time and reagents, a multiamplicon setting preparation was validated.

  17. Breeding performance in the Italian chicken breed Mericanel della Brianza

    Directory of Open Access Journals (Sweden)

    Silvia Cerolini

    Full Text Available In Italy, 90 local avian breeds were described; the majority (61% were classified as extinct and only 8.9% as still widely spread. Therefore, efforts for conservation of Italian avian breeds are urgently required. The aim of this study was to record the breeding performance of the Italian breed Mericanel della Brianza to multiply a small population, in order to develop a conservation programme. Fourteen females and eight males were available at the beginning of the reproductive season in 2009 and organised into eight families (1 male/1-2 females kept in floor pens. Birds received a photoperiod of 14L:10D and were fed ad libitum. Breeding performance was recorded from March to June. Egg production and egg weight were recorded daily; eggs were set every two weeks and fertility, embryo mortality and hatchability were recorded. Mean egg production was 37% and mean egg weight was 34±3.49 g. High fertility values from 94% to 87% were recorded in the first three settings and the overall mean fertility value was 81.6%. Overall hatchability was only 49.6% owing to a high proportion of dead embryos. Embryo mortality occurred mainly between days 2 and 7 of incubation and during hatching. The highest hatchability values were recorded in settings 1 and 2, 69% and 60% respectively, and a large decrease was found in the subsequent settings. Marked variations in egg production, fertility, hatchability and embryo mortality were found among families. The present results represent the basic know ledge of reproductive parameters necessary to improve the reproductive efficiency of the breed within a conservation plan.

  18. Breeding performance in the Italian chicken breed Mericanel della Brianza

    Directory of Open Access Journals (Sweden)

    Stefano P. Marelli

    2010-11-01

    Full Text Available In Italy, 90 local avian breeds were described, the majority (61% were classified extinct and only 8.9 % still diffused. Therefore, efforts for conservation of Italian avian breeds are urgently required. The aim of this study was to record the breeding performance of the Italian breed Mericanel della Brianza and multiply a small population, in order to develop a conservation program. Fourteen females and 8 males were available at the beginning of the reproductive season in 2009 and organized in 8 families (1 male/1-2 females kept in floor pens. Birds received a photoperiod of 14L:10D and fed ad libitum. Breeding performance was recorded from March to June. Egg production and egg weight were recorded daily; eggs were set every 2 weeks and fertility, embryo mortality and hatchability were recorded. Mean egg production was 37% and mean egg weight was 34±3.49 g. High fertility values were recorded in the first three settings, from 94 to 87%, and the overall mean fertility value was 81.6%. Overall hatchability was only 49.6% due to a high proportion of dead embryos. Embryo mortality occurred mainly between day 2 and 7 of incubation and during hatch. Highest hatchability values were recorded in setting 1 and 2, 69 and 60% respectively, and a great decrease was found in the following settings. Great variations in egg production, fertility, hatchability and embryo mortality were found among families. The present results are the basic knowledge on reproductive parameters necessary to improve the reproductive efficiency of the breed within a conservation plan.

  19. Evolution, plant breeding and biodiversity

    Directory of Open Access Journals (Sweden)

    Salvatore Ceccarelli

    2011-11-01

    Full Text Available This paper deals with changes in biodiversity during the course of evolution, plant domestication and plant breeding. It shows than man has had a strong influence on the progressive decrease of biodiversity, unconscious at first and deliberate in modern times. The decrease in biodiversity in the agricultures of the North causes a severe threat to food security and is in contrasts with the conservation of biodiversity which is part of the culture of several populations in the South. The concluding section of the paper shows that man could have guided evolution in a different way and shows an example of participatory plant breeding, a type of breeding which is done in collaboration with farmers and is based on selection for specific adaptation. Even though participatory plant breeding has been practiced for only about 20 years and by relatively few groups, the effects on both biodiversity and crop production are impressive. Eventually the paper shows how participatory plant breeding can be developed into ‘evolutionary plant breeding’ to cope in a dynamic way with climate changes.

  20. CASSAVA BREEDING I: THE VALUE OF BREEDING VALUE

    Directory of Open Access Journals (Sweden)

    Hernán Ceballos

    2016-08-01

    Full Text Available Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials - UYT. This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g. high number of their progenies reaching the UYT, suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05. Breeding value (e.g. average SIN at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g. S1 or S2 genotypes would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0 parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele

  1. Cassava Breeding I: The Value of Breeding Value

    Science.gov (United States)

    Ceballos, Hernán; Pérez, Juan C.; Joaqui Barandica, Orlando; Lenis, Jorge I.; Morante, Nelson; Calle, Fernando; Pino, Lizbeth; Hershey, Clair H.

    2016-01-01

    Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials—UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and

  2. Behaviour characteristics estimation tool of genetic distance between sheep breeds

    Directory of Open Access Journals (Sweden)

    Eko Handiwirawan

    2014-12-01

    Full Text Available Information on the estimation of genetic distances and differentiation among sheep breeds are needed in crossing and conservation programs. This research aims to study of utilizing behaviour characteristic variables to differentiate and estimate genetic distance between the sheep breeds. The study was conducted at Cilebut and Bogor Animal House of Indonesian Research Institute for Animal Production. Five sheep breeds used were Barbados Black Belly Cross (BC, Garut Composite (KG, Garut Local (LG, Sumatera Composite (KS and St. Croix Cross (SC, with total sample of 50 heads. A total of 10 variables of behavior traits were observed in this study. Analysis of variances and significance tests were applied to compare between sheep breeds and performed for all of behavior traits using PROC GLM of SAS Program ver. 9.0. PROC CANDISC was used for canonical discriminant analyses, the hierarchical clustering was performed using the PROC CLUSTER by Average Linkage method (Unweighted Pair-Group Method Using Arithmetic Averages, UPGMA, and the dendogram for the five sheep breeds was described using PROC TREE. The differentiator variables for the behavior traits were standing and feeding duration. The canonical plotting based on behavioral characteristics could differentiate BC, KS and LG (with KG and SC sheeps. Estimation of genetic distance based on the behavior traits is less accurate for grouping of sheep breeds.

  3. ITER breeding blanket module design and analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kuroda, Toshimasa; Enoeda, Mikio; Kikuchi, Shigeto [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment] [and others

    1998-11-01

    The ITER breeding blanket employs a ceramic breeder and Be neutron multiplier both in small spherical pebble form. Radial-poloidal cooling panels are arranged in the blanket box to remove the nuclear heating in these materials and to reinforce the blanket structure. At the first wall, Be armor is bonded onto the stainless steel (SS) structure to provide a low Z plasma-compatible surface and to protect the first wall/blanket structure from the direct contact with the plasma during off-normal events. Thermo-mechanical analyses and investigation of fabrication procedure have been performed for this breeding blanket. To evaluate thermo-mechanical behavior of the pebble beds including the dependency of the effective thermal conductivity on stress, analysis methods have been preliminary established by the use of special calculation option of ABAQUS code, which are briefly summarized in this report. The structural response of the breeding blanket module under internal pressure of 4 MPa (in case of in-blanket LOCA) resulted in rather high stress in the blanket side (toroidal end) wall, thus addition of a stiffening rib or increase of the wall thickness will be needed. Two-dimensional elasto-plastic analyses have been performed for the Be/SS bonded interface at the first wall taking a fabrication process based on HIP bonding and thermal cycle due to pulsed plasma operation into account. The stress-strain hysteresis during these process and operation was clarified, and a procedure to assess and/or confirm the bonding integrity was also proposed. Fabrication sequence of the breeding blanket module was preliminarily developed based on the procedure to fabricate part by part and to assemble them one by one. (author)

  4. Results and current trends of nuclear methods used in agriculture

    Energy Technology Data Exchange (ETDEWEB)

    Horacek, P. (Ceskoslovenska Komise pro Atomovou Energii, Prague)

    1983-11-01

    The significance is evaluated of nuclear methods for agricultural research. The number of breeds induced by radiation mutations is increasing. The main importance of radiation mutation breeding consists in obtaining sources of the desired genetic properties for further hybridization. Radiostimulation is conducted with the aim of increasing yields. The irradiation of foods has not substantially increased worldwide. Very important is the irradiation of excrements and sludges which after such inactivation of pathogenic microorganisms may be used as humus-forming manure or as feed additives. In some countries the method is successfully being used of sexual sterilization for eradication of insect pests. The application of labelled compounds in the nutrition, physiology and protection of plants, farm animals and in food hygiene makes it possible to acquire new and accurate knowledge very quickly. Radioimmunoassay is a highly promising method in this respect. Labelling compounds with the stable /sup 15/N isotope is used for the research of nitrogen metabolism.

  5. Optimizing the molecular diagnosis of GALNS: novel methods to define and characterize Morquio-A syndrome-associated mutations.

    Science.gov (United States)

    Caciotti, Anna; Tonin, Rodolfo; Rigoldi, Miriam; Ferri, Lorenzo; Catarzi, Serena; Cavicchi, Catia; Procopio, Elena; Donati, Maria Alice; Ficcadenti, Anna; Fiumara, Agata; Barone, Rita; Garavelli, Livia; Rocco, Maja Di; Filocamo, Mirella; Antuzzi, Daniela; Scarpa, Maurizio; Mooney, Sean D; Li, Biao; Skouma, Anastasia; Bianca, Sebastiano; Concolino, Daniela; Casalone, Rosario; Monti, Elena; Pantaleo, Marilena; Giglio, Sabrina; Guerrini, Renzo; Parini, Rossella; Morrone, Amelia

    2015-03-01

    Morquio A syndrome (MPS IVA) is a systemic lysosomal storage disorder caused by the deficiency of N-acetylgalactosamine-6-sulfatase (GALNS), encoded by the GALNS gene. We studied 37 MPS IV A patients and defined genotype-phenotype correlations based on clinical data, biochemical assays, molecular analyses, and in silico structural analyses of associated mutations. We found that standard sequencing procedures, albeit identifying 14 novel small GALNS genetic lesions, failed to characterize the second disease-causing mutation in the 16% of the patients' cohort. To address this drawback and uncover potential gross GALNS rearrangements, we developed molecular procedures (CNV [copy-number variation] assays, QF-PCRs [quantitative fluorescent-PCRs]), endorsed by CGH-arrays. Using this approach, we characterized two new large deletions and their corresponding breakpoints. Both deletions were heterozygous and included the first exon of the PIEZO1 gene, which is associated with dehydrated hereditary stomatocitosis, an autosomal-dominant syndrome. In addition, we characterized the new GALNS intronic lesion c.245-11C>G causing m-RNA defects, although identified outside the GT/AG splice pair. We estimated the occurrence of the disease in the Italian population to be approximately 1:300,000 live births and defined a molecular testing algorithm designed to help diagnosing MPS IVA and foreseeing disease progression.

  6. Diet of canvasbacks during breeding

    Science.gov (United States)

    Austin, J.E.; Serie, J.R.; Noyes, J.H.

    1990-01-01

    We examined diets of canvasbacks (Aythya valisineria) breeding in southwestern Manitoba during 1977-81. Percent volume of animal foods consumed did not differ between males and females nor among prenesting, rapid follicle growth, laying, incubation, and renesting periods in females (mean = 50.1%). Tubers and shoots of fennelleaf pondweed (Potamogeton pectinatus) and midge larvae (Chironomidae) were the predominant foods, comprising on average 45% and 23% of the diet volume, respectively. Continued importance of plant foods to canvasbacks throughout reproduction contrasts with the mostly invertebrate diets of other prairie-breeding ducks, and does not fit current theories of nutritional ecology of breeding anatids (i.e., females meet the protein requirements of reproduction by consuming a high proportion of animal foods).

  7. Emperor penguins breeding on iceshelves.

    Science.gov (United States)

    Fretwell, Peter T; Trathan, Phil N; Wienecke, Barbara; Kooyman, Gerald L

    2014-01-01

    We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land). Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

  8. Rearch advancement of the strain breeding which can produce chymosin in China%我国凝乳酶产生菌育种的研究进展

    Institute of Scientific and Technical Information of China (English)

    张超垒; 王成忠; 张志国; 张玲梅

    2011-01-01

    In terms of natural screening,mutation breeding and the breeding of gene engineering, this paper reviewed the rearch advancement of the strain breeding which can produce chymosin in China.%综述了目前我国在凝乳酶产生菌在自然选育、诱变育种和基因工程育种这3方面的研究进展情况.

  9. Sport horses : breeding specialist from a single breeding programme?

    NARCIS (Netherlands)

    Rovere, G.A.

    2016-01-01

    Summary The general goal of this thesis was to provide information useful for the breeding programme of the Royal Dutch Warmblood Studbook (KWPN) in relation with the ongoing specialisation of the population. Data provided by KWPN consisted of records from studbook-first inspection,

  10. Development of breeding objectives for beef cattle breeding ...

    African Journals Online (AJOL)

    Mnr J F Kluyts

    The purpose of this article is to review the development of breeding objectives in beef cattle ... selection criteria, and estimation of phenotypic and genetic parameters. ... Unfortunately, the evolution from a performance .... The beef cattle industry has a history of chasing and promoting maximum values (e.g. maximum weight).

  11. Breed base representation in dairy animals of 5 breeds

    Science.gov (United States)

    Inheritance of DNA from different dairy breeds can be determined by genotyping, just as individual ancestors such as parents, grandparents, or even great grandparents can be identified correctly in a high percentage of the cases by genotyping even if not reported or reported incorrectly in pedigrees...

  12. 尸食性蚤蝇幼虫活体测量的新方法%A New Method of Measuring Living Body Length During Growth of Carrion-breeding Phorid Flies Larvae

    Institute of Scientific and Technical Information of China (English)

    冯典兴; 刘广纯

    2012-01-01

    蝇蛆体长是判断死后间隔时间最常应用的指标.为了准确测量幼虫的体长,本文提出利用Olympus三维重构图像处理系统进行活体测量的新方法,在20℃和28℃两个恒温下,对蛆症异蚤蝇Megaselia scalaris(Loew)幼虫体长变化进行了观察、测量.结果表明:该方法简便、易行,适于尸食性蚤蝇幼虫体长的测量.对两个恒温下体长随时间的变化情况进行了模拟,模拟效果较好.%The body length of maggots is a indicator often used for the post-mortem interval estimation. In order to accurately measure the larvae body length, a new method of living measurement is proposed using Olympus 3D reconstruction and image processing system. Under two constant temperature conditions of 20 ~C and 28 ~C, the length changes of Megaselia scalaris (Loew) larvae were observed and measured. The results show that the method is simple, and easy to operate, and suitable for the measurement of carrion-breeding phorid flies larvae length. The dependence of the larval change in length on two temperature conditions can be well simulated with linear regression.

  13. Towards social acceptance of plant breeding by genome editing.

    Science.gov (United States)

    Araki, Motoko; Ishii, Tetsuya

    2015-03-01

    Although genome-editing technologies facilitate efficient plant breeding without introducing a transgene, it is creating indistinct boundaries in the regulation of genetically modified organisms (GMOs). Rapid advances in plant breeding by genome-editing require the establishment of a new global policy for the new biotechnology, while filling the gap between process-based and product-based GMO regulations. In this Opinion article we review recent developments in producing major crops using genome-editing, and we propose a regulatory model that takes into account the various methodologies to achieve genetic modifications as well as the resulting types of mutation. Moreover, we discuss the future integration of genome-editing crops into society, specifically a possible response to the 'Right to Know' movement which demands labeling of food that contains genetically engineered ingredients.

  14. Flesh color association with polymorphism of the tyrosinase gene in different Chinese chicken breeds.

    Science.gov (United States)

    Zhang, J Q; Chen, H; Sun, Z J; Liu, X L; Qiang-Ba, Y Z; Gu, Y L

    2010-01-01

    In order to study genetic variation of tyrosinase gene in four different flesh color chicken breeds selected from special districts including Guyuan, Wenchang, Tibetan and Hisex chicken, five loci of the TYR gene exon-1 and one locus of 5' flanking region were analyzed in PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus located in exon-1, there were three genotypes (TT, CC, TC), respectively, in three Chinese chicken breeds, and Genotype CC had not been detected in Hisex chicken. At TYR3 locus located in 5' flanking region, there were three genotypes (GG, AA and GA) in Chinese local chicken breeds and genotype AA had not been detected in Hisex chicken breed. It was concluded that there were many variations of TYR gene in Chinese local chicken breeds. DNA sequencing of PCR products for different genotypes showed that there were two mutation sites, respectively, C to T at TYR1 locus and G to A at TYR3 locus. Mutation at TYR1 locus did not cause any amino acid variation. The chi-square analysis revealed that there were significant statistical differences generally between flesh color and the two loci among four chicken populations (P chicken breeds. This study provided original information for elucidating the possible roles of exon-1 of TYR gene and 5' flanking region in chickens with different flesh color chicken.

  15. Comparison of molecular breeding values based on within- and across-breed training in beef cattle.

    Science.gov (United States)

    Kachman, Stephen D; Spangler, Matthew L; Bennett, Gary L; Hanford, Kathryn J; Kuehn, Larry A; Snelling, Warren M; Thallman, R Mark; Saatchi, Mahdi; Garrick, Dorian J; Schnabel, Robert D; Taylor, Jeremy F; Pollak, E John

    2013-08-16

    Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported. Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype. With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero. Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained

  16. Genetic variation within the Icelandic cattle breed: assessment using microsatellites and analysis of single nucleotide polymorphisms in the Leptin and DGAT1 genes

    OpenAIRE

    Margrét Guðrún Ásbjarnardóttir 1981

    2008-01-01

    Sufficient genetic variation within domestic breeds is a crucial factor in all breeding work. It is a prerequisite for future breeding progress and is used in research and development of breeding methods at the molecular level. The present study estimates genetic variation within the Icelandic cattle breed using two approaches. The data consisted of genomic DNA samples from 100 heifers in first pregnancy collected at 45 dairy farms located in the four major dairy regions in Iceland. Fir...

  17. Genetic Diversity of Old Chicken Breeds Kept in Poland

    Directory of Open Access Journals (Sweden)

    Fabio Maretto

    2013-09-01

    Full Text Available The aim of this study was to compare the genetic variation of five local chicken breeds reared in Poland. Twenty-seven microsatellite markers were investigated in 138 birds belonging to five breeds: Miniature Cochin (MCO, Gold Italian (GI, Green Legged Partridge (GLP, Silver Italian (SI and White Leghorn (WL. One hundred eighty five alleles were detected in the overall population, with a mean number of 6.85 ± 3.32 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.287 to a maximum of 0.458 and from 0.397 to 0.499 for the GI and SI breeds, respectively. The overall population heterozygote deficiency was 0.430, the average Wright’s inbreeding coefficient (FIS was 0.061 and the heterozygote deficiency due to breed subdivision was 0.393. Wright’s fixation index was slightly positive for all breeds excluding MCO (FIS = -0.476 and the estimated molecular inbreeding (fij within breed ranged from 0.296 (GLP and SI to 0.361 (WL evidencing limited coancestry. Mean allelic richness, obtained with rarefaction method based on sixteen observations, was 2.12 being the WL the less variable (1.79. Tomiuk and Loeschcke’s DTL genetic distance values were used to draw a neighbornet network which separated the cluster made of MCO and GLP from the cluster of GI, WL and SI. The results arising from our microsatellites analysis represent a starting point for the valorization of these local Polish chicken breeds for monitoring and preserving their genetic variability.

  18. Root phenotyping: from component trait in the lab to breeding.

    Science.gov (United States)

    Kuijken, René C P; van Eeuwijk, Fred A; Marcelis, Leo F M; Bouwmeester, Harro J

    2015-09-01

    In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Mutations in GABRB3

    DEFF Research Database (Denmark)

    Møller, Rikke S; Wuttke, Thomas V; Helbig, Ingo

    2017-01-01

    OBJECTIVE: To examine the role of mutations in GABRB3 encoding the β3 subunit of the GABAA receptor in individual patients with epilepsy with regard to causality, the spectrum of genetic variants, their pathophysiology, and associated phenotypes. METHODS: We performed massive parallel sequencing...... of GABRB3 in 416 patients with a range of epileptic encephalopathies and childhood-onset epilepsies and recruited additional patients with epilepsy with GABRB3 mutations from other research and diagnostic programs. RESULTS: We identified 22 patients with heterozygous mutations in GABRB3, including 3...... probands from multiplex families. The phenotypic spectrum of the mutation carriers ranged from simple febrile seizures, genetic epilepsies with febrile seizures plus, and epilepsy with myoclonic-atonic seizures to West syndrome and other types of severe, early-onset epileptic encephalopathies...

  20. Impact of Molecular Technologies on Faba Bean (Vicia faba L. Breeding Strategies

    Directory of Open Access Journals (Sweden)

    Tao Yang

    2012-07-01

    Full Text Available Faba bean (Vicia faba L. is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly suitable for faba bean. However, traditional breeding methods such as recurrent mass selection have been established in faba bean and used successfully in breeding for resistance to diseases. Molecular breeding strategies that integrate the latest innovations in genetics and genomics with traditional breeding strategies have many potential applications for future faba bean cultivar development. Hence, considerable efforts have been undertaken in identifying molecular markers, enriching genetic and genomic resources using high-throughput sequencing technologies and improving genetic transformation techniques in faba bean. However, the impact of research on practical faba bean breeding and cultivar release to farmers has been limited due to disconnects between research and breeding objectives and the high costs of research and implementation. The situation with faba bean is similar to other small crops and highlights the need for coordinated, collaborative research programs that interact closely with commercially focused breeding programs to ensure that technologies are implemented effectively.

  1. Integrating genomic selection into dairy cattle breeding programmes: a review.

    Science.gov (United States)

    Bouquet, A; Juga, J

    2013-05-01

    Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However

  2. Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle.

    Science.gov (United States)

    Barendse, W; Harrison, B E; Hawken, R J; Ferguson, D M; Thompson, J M; Thomas, M B; Bunch, R J

    2007-08-01

    The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 sigma(p) (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 sigma(p) (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive x dominance components of epistasis than additive x additive and dominance x dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.

  3. MT BB: Tomato cultivar for practical classes of plant genetics and breeding

    Directory of Open Access Journals (Sweden)

    Fernando Angelo Piotto

    2013-01-01

    Full Text Available MT BB cultivar originated from a backcross program which aimed at adding two recessive mutations that alter leaf architecture(potato leaf – c and flower color (white flower – wf to Micro-Tom cultivar, which is a tomato miniature. MT BB was developedfor use in practical classes of genetics and breeding in both undergraduate and graduate courses.

  4. Effective use of physical/chemical mutagens in crop hybrid breeding in China

    Energy Technology Data Exchange (ETDEWEB)

    Liu Luxiang; Wang Jing [Chinese Academy of Agricultural Sciences, Institute for Application of Atomic Energy, Beijing (China)

    2001-03-01

    Crop heterosis utilization was one of the greatest achievements in the agriculture production in the 20th century. It is proved that every breakthrough in crop hybrid breeding was predicated on the discovery or successful development of new heterosis germplasm. In recent years, in order to open up the scope and ways of using crop heterosis, it has been paid much close attention to apply mutation techniques to hybrid breeding. Useful tool materials like male sterile mutant lines, fertile restoration mutants in many crops have been obtained by effective use of physical/chemical mutagens. Brief introduction is made in this paper on the newest research improvement concerning the effective use of the techniques of mutation induction in China to create special useful genes, enrich the diversity of germplasm and promote the rapid development of crop hybrid breeding. (author)

  5. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  6. The evolution of potato breeding

    Science.gov (United States)

    Potato cultivars in most regions of the world are tetraploid and clonally propagated. For over a century, the breeding strategy has been phenotypic recurrent selection. However, the polyploid nature of the crop prevents breeders from eliminating deleterious alleles and assembling positive alleles fo...

  7. Rose breeding: past, present, prospects

    NARCIS (Netherlands)

    Vries, de D.P.; Dubois, L.A.M.

    1996-01-01

    In this review the PAST, PRESENT and PROSPECT will be considered as three separate periods in the history of the breeding and development of rose cultivars. The recurring theme is the genetic variation. This theme was chosen because there is justified doubt as to sufficient genetic variation

  8. Rose breeding: past, present, prospects

    NARCIS (Netherlands)

    Vries, de D.P.; Dubois, L.A.M.

    1996-01-01

    In this review the PAST, PRESENT and PROSPECT will be considered as three separate periods in the history of the breeding and development of rose cultivars. The recurring theme is the genetic variation. This theme was chosen because there is justified doubt as to sufficient genetic variation availab

  9. Development of an allele-specific, loop-mediated, isothermal amplification method (AS-LAMP to detect the L1014F kdr-w mutation in Anopheles gambiae s. l.

    Directory of Open Access Journals (Sweden)

    Badolo Athanase

    2012-07-01

    Full Text Available Abstract Background Malaria control relies heavily on treated bed nets and indoor residual spraying with pyrethroid insecticides. Unfortunately, the resistance to pyrethroid insecticides, mainly due to the kdr mutation, is spreading in the main malaria vector Anopheles gambiae s.l., decreasing the insecticides’ efficacy. To manage the insecticide resistance rapidly and flexibly, simple and effective tools for the early detection of resistant mosquitoes are needed. This study aimed to develop an allele-specific, loop-mediated, isothermal amplification (AS-LAMP method to detect the West African-type kdr mutation (kdr-w; L1014F in field-collected mosquitoes. Methods DNA fragments of the wild-type and the mutated kdr gene were used to select the primers and develop the method. The primers were designed with the mutation at the 5’ end of the backward inner primer (BIP. The AS-LAMP method was compared to the AS-PCR method using the genomic DNA of 120 field-collected mosquitoes. Results The AS-LAMP method could discriminate between the wild-type homozygote, the heterozygote, and the kdr-w homozygote within 75 min. The AS-LAMP method has the advantage of being faster and at least as sensitive and specific as the AS-PCR method. Conclusions The AS-LAMP method can be used to detect the kdr mutation for quick decision-making, even in less well-equipped laboratories.

  10. Accuracies of genomically estimated breeding values from pure-breed and across-breed predictions in Australian beef cattle.

    Science.gov (United States)

    Boerner, Vinzent; Johnston, David J; Tier, Bruce

    2014-10-24

    The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australian Beef Cooperative Research Center (Beef CRC) investigated these issues by deriving genomic prediction equations (PE) from a training set of animals that covers a range of breeds and crosses including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Belmont Red, Santa Gertrudis and Tropical Composite. This paper presents accuracies of genomically estimated breeding values (GEBV) that were calculated from these PE in the commercial pure-breed beef cattle seed stock sector. PE derived by the Beef CRC from multi-breed and pure-breed training populations were applied to genotyped Angus, Limousin and Brahman sires and young animals, but with no pure-breed Limousin in the training population. The accuracy of the resulting GEBV was assessed by their genetic correlation to their phenotypic target trait in a bi-variate REML approach that models GEBV as trait observations. Accuracies of most GEBV for Angus and Brahman were between 0.1 and 0.4, with accuracies for abattoir carcass traits generally greater than for live animal body composition traits and reproduction traits. Estimated accuracies greater than 0.5 were only observed for Brahman abattoir carcass traits and for Angus carcass rib fat. Averaged across traits within breeds, accuracies of GEBV were highest when PE from the pooled across-breed training population were used. However, for the Angus and Brahman breeds the difference in accuracy from using pure-breed PE was small. For the Limousin breed no reasonable results could be achieved for any trait. Although accuracies were generally low compared to published accuracies estimated within breeds, they are in line with those derived in other multi-breed populations. Thus PE developed by the Beef CRC can contribute to the implementation of genomic selection in

  11. Seleção para aumento de produtividade e qualidade de frutos em abobrinha 'Piramoita' comparando dois métodos de melhoramento Selection for fruit yield and quality in 'Piramoita' summer squash comparing two breeding methods

    Directory of Open Access Journals (Sweden)

    Antonio Ismael Inácio Cardoso

    2007-01-01

    Full Text Available Este trabalho teve por objetivo comparar dois métodos de melhoramento quanto à seleção visando ao aumento de produtividade e qualidade de frutos na cv. Piramoita. Foram realizados três ciclos de seleção recorrente, com seleção de progênies autofecundadas (S1 e recombinação das melhores progênies para obtenção das populações melhoradas no primeiro (SR-1, segundo (SR-2 e terceiro (SR-3 ciclos. No método do "Single Seed Descent" (SSD as plantas foram autofecundadas por cinco gerações até a obtenção e avaliação de progênies S5. As nove melhores progênies foram selecionadas obtendo-se progênies endogâmicas selecionadas (SSD-1 a SSD-9 e essas progênies também foram intercruzadas para se obter a população P-SSD. Todas as populações obtidas (SR-1, SR-2, SR-3, P-SSD, SSD-1 a SSD-9, juntamente com a população original (cv. Piramoita, totalizando 14 tratamentos, foram avaliadas em um experimento em blocos ao acaso, com seis repetições e cinco plantas por parcela. As características avaliadas foram: produção de frutos (número e massa total e comercial, massa média de fruto comercial e taxa de frutos comerciais. Foram obtidos aumentos crescentes de produção de frutos comerciais com os ciclos de seleção recorrente, sendo a população SR-3 superior à 'Piramoita' para número de frutos por planta. Foi obtida uma progênie por SSD melhor que a população inicial e tão produtiva quanto à população SR-3. Deste modo, o método SSD pode vir a ser ótima alternativa no melhoramento genético de abobrinha, sem a necessidade de avaliação e seleção de progênies a cada safra, apenas quando essas já estiverem praticamente homozigotas.The objective of this work was to compare two breeding methods to improve fruit yield and quality in 'Piramoita' summer squash. Three cycles of recurrent selection were made, with evaluation and selection of S1 progenies and recombination of plants from selected progenies to obtain

  12. 奶牛乳房炎检测方法与分子抗病育种研究进展%Advances of Bovine Mastitis Detection Methods and Molecular Disease-Resistance Breeding Studies

    Institute of Scientific and Technical Information of China (English)

    韦艺媛; 俞英

    2011-01-01

    奶牛乳房炎即奶牛乳腺发生炎症反应,是一种常见的奶牛疾病,对乳业造成的经济损失极大.本文通过分析其致病原因,对奶牛乳房炎的检测方法做出总结,在分析传统检测方法的基础上,介绍最新的检测方法,说明乳房炎检测逐渐向低成本高效率的趋势发展.另外还以乳房炎抗性候选基因和表观遗传标记为出发点,对乳房炎发生发展的预测方法做了介绍,并就乳房炎研究方向针对奶牛本身的分子抗病育种方向发展的趋势进行了展望.%Bovine mastitis is a common disease of dairy cows and characterized by inflammation of mammary glands, which can decrease milk productions and canse significant economic losses of dairy industry. This review not only gives a summary of conventional detection methods but also presents the lastest detection ways for bovine mastitis. It is concluded that the techniques for detecting mastitis are becoming more economical and efficient. Furthermore, the paper gives a comprehensive description for the candidate genes and epigenetic marks associated with bovine mastitis resistance. Finally, the developments and applications for molecular breeding on Dairy mastitis-resistance are prospected.

  13. Breeding management method of long-term artificial cultivation of tree shrew in beijing area%北京地区实验树鼩的饲养管理方法

    Institute of Scientific and Technical Information of China (English)

    赵琰; 吴婷婷; 李翼飞; 孙晔; 孙慧; 胡丽娜; 屈会化; 王庆国

    2013-01-01

    树鼩作为低等灵长类动物,在生物学研究中的价值日益引起研究者重视,将其作为实验动物的实验需求越来越多.作为南方亚热带动物,树鼩如何适应北方地区的生活是北方地区将其用作实验动物的前提.本实验室探索出适宜树鼩居住的饲养笼具,确定了饲养环境温度、湿度、光照时间、噪声及通风等条件,制定了规范化的卫生管理标准,建立了北京地区长期人工培育树鼩的饲养管理方法,为今后利用树鼩进行中医药病证结合动物模型的研究奠定了基础.%Tree shrew, a species of lower primates, its value in biomedical research has draw attention of researchers, and have been more and more demanded as a laboratory animal. However, tree shrew as a southern subtropical animal, how to adapt it to live in northern China becomes the premise that tree shrew can be used as a laboratory animal in northern China. Our laboratory has explored feeding cage, which is suitable for tree shrew living, determined feeding environmental conditions, such as temperature, humidity, illumination time, noise, ventilation, etc. , formulated the health management standard and established breeding management method of long-term artificial cultivation of tree shrew in Beijing area. Therefore, we have laid the foundation for the application of tree shrew in research on traditional Chinese medicine syndrome combined with establishment of disease animal models in the future.

  14. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    Directory of Open Access Journals (Sweden)

    Windig Jack J

    2008-07-01

    Full Text Available Abstract Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers and current merits (economic, ecological and cultural merits. Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04 as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83. We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan.

  15. Reliabilities of genomic estimated breeding values in Danish Jersey

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind; Guldbrandtsen, Bernt; Su, Guosheng;

    2012-01-01

    In order to optimize the use of genomic selection in breeding plans, it is essential to have reliable estimates of the genomic breeding values. This study investigated reliabilities of direct genomic values (DGVs) in the Jersey population estimated by three different methods. The validation methods...... of DGV. The data set consisted of 1003 Danish Jersey bulls with conventional estimated breeding values (EBVs) for 14 different traits included in the Nordic selection index. The bulls were genotyped for Single-nucleotide polymorphism (SNP) markers using the Illumina 54 K chip. A Bayesian method was used...... index pre-selection only. Averaged across traits, the estimates of reliability of DGVs ranged from 0.20 for validation on the most recent 3 years of bulls and up to 0.42 for expected reliabilities. Reliabilities from the cross-validation were on average 0.24. For the individual traits, the reliability...

  16. Native Pig and Chicken Breed Database: NPCDB.

    Science.gov (United States)

    Jeong, Hyeon-Soo; Kim, Dae-Won; Chun, Se-Yoon; Sung, Samsun; Kim, Hyeon-Jeong; Cho, Seoae; Kim, Heebal; Oh, Sung-Jong

    2014-10-01

    Indigenous (native) breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB) which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/) provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed's characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  17. Impact of Molecular Technologies on Faba Bean (Vicia faba L.) Breeding Strategies

    OpenAIRE

    Tao Yang; Xuxiao Zong; Haobing Li; Tony Leonforte; Sukhjiwan Kaur; Ana Torres; Jeff Paull; Annathurai Gnanasambandam; Michael Materne

    2012-01-01

    Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly...

  18. Study for identification FecXI and FecXH mutations in Tunisian Barbarine sheep

    Directory of Open Access Journals (Sweden)

    Jemmali Borni,

    2011-02-01

    Full Text Available A total of 334 ewes recorded with twining births from the Tunisian fat tail Barbarine sheep were genotyped in the objective to identify the FecXI and FecXH mutations. The genotyping was carried out by forced restriction fragment length polymorphism PCR (RFLP-PCR. None of mutations was detected in Barbarine sheep. Results showed that all analyzed ewes were homozygous non carriers. These results suggest that fecundity of this breed is not linked to the same mutations. Therefore, it is necessary to seek for other mutations or fecundity genes in order to develop marker assistance selection techniques and study the prolific mechanism of the Barbarine breed.

  19. Feasibility of new breeding techniques for organic farming

    DEFF Research Database (Denmark)

    Andersen, Martin Marchman; Landes, Xavier; Xiang, Wen

    2015-01-01

    of new breeding techniques (NBTs) for rewilding, a process involving the reintroduction of properties from the wild relatives of crops, as a method to close the productivity gap. The most efficient methods of rewilding are based on modern biotechnology techniques, which have yet to be embraced...

  20. PRRT2 gene mutations

    Science.gov (United States)

    Gardiner, Alice R.; Bhatia, Kailash P.; Stamelou, Maria; Dale, Russell C.; Kurian, Manju A.; Schneider, Susanne A.; Wali, G.M.; Counihan, Tim; Schapira, Anthony H.; Spacey, Sian D.; Valente, Enza-Maria; Silveira-Moriyama, Laura; Teive, Hélio A.G.; Raskin, Salmo; Sander, Josemir W.; Lees, Andrew; Warner, Tom; Kullmann, Dimitri M.; Wood, Nicholas W.; Hanna, Michael

    2012-01-01

    ABSTRACT Objective: The proline-rich transmembrane protein (PRRT2) gene was recently identified using exome sequencing as the cause of autosomal dominant paroxysmal kinesigenic dyskinesia (PKD) with or without infantile convulsions (IC) (PKD/IC syndrome). Episodic neurologic disorders, such as epilepsy, migraine, and paroxysmal movement disorders, often coexist and are thought to have a shared channel-related etiology. To investigate further the frequency, spectrum, and phenotype of PRRT2 mutations, we analyzed this gene in 3 large series of episodic neurologic disorders with PKD/IC, episodic ataxia (EA), and hemiplegic migraine (HM). Methods: The PRRT2 gene was sequenced in 58 family probands/sporadic individuals with PKD/IC, 182 with EA, 128 with HM, and 475 UK and 96 Asian controls. Results: PRRT2 genetic mutations were identified in 28 out of 58 individuals with PKD/IC (48%), 1/182 individuals with EA, and 1/128 individuals with HM. A number of loss-of-function and coding missense mutations were identified; the most common mutation found was the p.R217Pfs*8 insertion. Males were more frequently affected than females (ratio 52:32). There was a high proportion of PRRT2 mutations found in families and sporadic cases with PKD associated with migraine or HM (10 out of 28). One family had EA with HM and another large family had typical HM alone. Conclusions: This work expands the phenotype of mutations in the PRRT2 gene to include the frequent occurrence of migraine and HM with PKD/IC, and the association of mutations with EA and HM and with familial HM alone. We have also extended the PRRT2 mutation type and frequency in PKD and other episodic neurologic disorders. PMID:23077024

  1. Selective breeding in organic dairy production

    NARCIS (Netherlands)

    Nauta, W.J.

    2009-01-01

    Organic dairy farming started to take off in the early 1990s, when the European Union laid down organic standards for animal production. Until now, however, only incidental steps have been taken towards organic breeding and organic farmers mainly use breeding stock from conventional breeding program

  2. Vision of breeding for organic agriculture

    NARCIS (Netherlands)

    Nauta, W.J.; Groen, A.; Roep, D.; Veerkamp, R.F.; Baars, T.

    2003-01-01

    Taking the current breeding situation as the starting point, a number of scenarios are described for each animal sector which could gradually lead to a system of breeding which is more organic both in its aims and in the chain-based approach. The naturalness of the breeding techniques is an

  3. Selective breeding in organic dairy production

    NARCIS (Netherlands)

    Nauta, W.J.

    2009-01-01

    Organic dairy farming started to take off in the early 1990s, when the European Union laid down organic standards for animal production. Until now, however, only incidental steps have been taken towards organic breeding and organic farmers mainly use breeding stock from conventional breeding program

  4. Selective breeding in organic dairy production

    NARCIS (Netherlands)

    Nauta, W.J.

    2009-01-01

    Organic dairy farming started to take off in the early 1990s, when the European Union laid down organic standards for animal production. Until now, however, only incidental steps have been taken towards organic breeding and organic farmers mainly use breeding stock from conventional breeding

  5. Assessment of tritium breeding requirements for fusion power reactors

    Energy Technology Data Exchange (ETDEWEB)

    Jung, J.

    1983-12-01

    This report presents an assessment of tritium-breeding requirements for fusion power reactors. The analysis is based on an evaluation of time-dependent tritium inventories in the reactor system. The method presented can be applied to any fusion systems in operation on a steady-state mode as well as on a pulsed mode. As an example, the UWMAK-I design was analyzed and it has been found that the startup inventory requirement calculated by the present method significantly differs from those previously calculated. The effect of reactor-parameter changes on the required tritium breeding ratio is also analyzed for a variety of reactor operation scenarios.

  6. Grooming relationships between breeding females and adult group members in cooperatively breeding moustached tamarins (Saguinus mystax).

    Science.gov (United States)

    Löttker, Petra; Huck, Maren; Zinner, Dietmar P; Heymann, Eckhard W

    2007-10-01

    Grooming is the most common form of affiliative behavior in primates that apart from hygienic and hedonistic benefits offers important social benefits for the performing individuals. This study examined grooming behavior in a cooperatively breeding primate species, characterized by single female breeding per group, polyandrous matings, dizygotic twinning, delayed offspring dispersal, and intensive helping behavior. In this system, breeding females profit from the presence of helpers but also helpers profit from staying in a group and assisting in infant care due to the accumulation of direct and indirect fitness benefits. We examined grooming relationships of breeding females with three classes of partners (breeding males, potentially breeding males, (sub)adult non-breeding offspring) during three reproductive phases (post-partum ovarian inactivity, ovarian activity, pregnancy) in two groups of wild moustached tamarins (Saguinus mystax). We investigated whether grooming can be used to regulate group size by either "pay-for-help" or "pay-to-stay" mechanisms. Grooming of breeding females with breeding males and non-breeding offspring was more intense and more balanced than with potentially breeding males, and most grooming occurred during the breeding females' pregnancies. Grooming was skewed toward more investment by the breeding females with breeding males during the phases of ovarian activity, and with potentially breeding males during pregnancies. Our results suggest that grooming might be a mechanism used by female moustached tamarins to induce mate association with the breeding male, and to induce certain individuals to stay in the group and help with infant care.

  7. A simple language to script and simulate breeding schemes: the breeding scheme language

    Science.gov (United States)

    It is difficult for plant breeders to determine an optimal breeding strategy given that the problem involves many factors, such as target trait genetic architecture and breeding resource availability. There are many possible breeding schemes for each breeding program. Although simulation study may b...

  8. Conditional mutations in Drosophila melanogaster: On the occasion of the 150th anniversary of G. Mendel's report in Brünn.

    Science.gov (United States)

    Chadov, Boris F; Fedorova, Nina B; Chadova, Eugenia V

    2015-01-01

    The basis for modern genetics was laid by Gregor Mendel. He proposed that traits belonging to the intraspecific variability class be studied. However, individuals of one species possess traits of another class. They are related to intraspecific similarity. Individuals never differ from each other in these traits. By analogy with traits varying within a species and determined by genes, it is conjectured that intraspecific similarity is determined by genes, too. If so, mutations in these genes can be obtained. This paper provides a review of works published in 2000-2014 that: (1) propose breeding methods for detection of mutations in Drosophila melanogaster genes that lead intraspecific similarity; these mutations were called conditional; (2) describe collections of conditional mutations in chromosomes X, 2, and 3 of Drosophila; (3) show unusual features of epigenetic nature in the mutants; and (4) analyze these features of the mutants. Based on the peculiarities of manifestation it is supposed that the recognized conditional mutations occur in genes responsible for intraspecific similarity. The genes presumably belong to the so-called regulatory network of the Drosophila genome. This approach expands the scope of breeding analysis introduced by G. Mendel for heredity studies 150 years ago. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Emperor penguins breeding on iceshelves.

    Directory of Open Access Journals (Sweden)

    Peter T Fretwell

    Full Text Available We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land. Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

  10. Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method.

    Science.gov (United States)

    Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan

    2015-10-01

    The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV.

  11. Opportunities for Products of New Plant Breeding Techniques.

    Science.gov (United States)

    Schaart, Jan G; van de Wiel, Clemens C M; Lotz, Lambertus A P; Smulders, Marinus J M

    2016-05-01

    Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.

  12. Assortative mating and fragmentation within dog breeds

    Directory of Open Access Journals (Sweden)

    Hailer Frank

    2008-01-01

    Full Text Available Abstract Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic

  13. Assortative mating and fragmentation within dog breeds.

    Science.gov (United States)

    Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

    2008-01-28

    There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have

  14. Breeding quinoa (Chenopodium quinoa Willd.)

    DEFF Research Database (Denmark)

    Zurita-Silva, Andrés; Fuentes, Francisco; Zamora, Pablo

    2014-01-01

    Quinoa (Chenopodium quinoa Willd.) originated in the Andean region of South America; this species is associated with exceptional grain nutritional quality and is highly valued for its ability to tolerate abiotic stresses. However, its introduction outside the Andes has yet to take off on a large...... scale. In the Andes, quinoa has until recently been marginally grown by small-scale Andean farmers, leading to minor interest in the crop from urban consumers and the industry. Quinoa breeding programs were not initiated until the 1960s in the Andes, and elsewhere from the 1970s onwards. New molecular...... tools available for the existing quinoa breeding programs, which are critically examined in this review, will enable us to tackle the limitations of allotetraploidy and genetic specificities. The recent progress, together with the declaration of "The International Year of the Quinoa" by the Food...

  15. Tracing cattle breeds with principal components analysis ancestry informative SNPs.

    Directory of Open Access Journals (Sweden)

    Jamey Lewis

    Full Text Available The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs for 19 breeds (13 taurine, three zebu, and three hybrid breeds, seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products.

  16. Analysis of copy number variations among diverse cattle breeds

    Science.gov (United States)

    Liu, George E.; Hou, Yali; Zhu, Bin; Cardone, Maria Francesca; Jiang, Lu; Cellamare, Angelo; Mitra, Apratim; Alexander, Leeson J.; Coutinho, Luiz L.; Dell'Aquila, Maria Elena; Gasbarre, Lou C.; Lacalandra, Gianni; Li, Robert W.; Matukumalli, Lakshmi K.; Nonneman, Dan; de A. Regitano, Luciana C.; Smith, Tim P.L.; Song, Jiuzhou; Sonstegard, Tad S.; Van Tassell, Curt P.; Ventura, Mario; Eichler, Evan E.; McDaneld, Tara G.; Keele, John W.

    2010-01-01

    Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or ∼1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. PMID:20212021

  17. Genomic tools in cowpea breeding programs: status and perspectives

    Directory of Open Access Journals (Sweden)

    Ousmane eBoukar

    2016-06-01

    Full Text Available Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA. It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS, promises an increase in the number of

  18. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

    Science.gov (United States)

    Boukar, Ousmane; Fatokun, Christian A; Huynh, Bao-Lam; Roberts, Philip A; Close, Timothy J

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  19. Bioleaching of Arsenic-Rich Gold Concentrates by Bacterial Flora before and after Mutation

    Directory of Open Access Journals (Sweden)

    Xuehui Xie

    2013-01-01

    Full Text Available In order to improve the bioleaching efficiency of arsenic-rich gold concentrates, a mixed bacterial flora had been developed, and the mutation breeding method was adopted to conduct the research. The original mixed bacterial flora had been enrichedin acid mine drainage of Dexing copper mine, Jiangxi Province, China. It was induced by UV (ultraviolet, ultrasonic, and microwave, and their combination mutation. The most efficient bacterial flora after mutation was collected for further bioleaching of arsenic-rich gold concentrates. Results indicated that the bacterial flora after mutation by UV 60 s combined with ultrasonic 10 min had the best oxidation rate of ferrous, the biggest density of cells, and the most activity of total protein. During bioleaching of arsenic-rich gold concentrates, the density of the mutant bacterial cells reached to 1.13×108 cells/mL at 15 days, more than 10 times compared with that of the original culture. The extraction of iron reached to 95.7% after 15 days, increased by 9.9% compared with that of the original culture. The extraction of arsenic reached to 92.6% after 12 days, which was increased by 46.1%. These results suggested that optimum combined mutation could improve leaching ability of the bacterial flora more significantly.

  20. Bioleaching of arsenic-rich gold concentrates by bacterial flora before and after mutation.

    Science.gov (United States)

    Xie, Xuehui; Yuan, Xuewu; Liu, Na; Chen, Xiaoguang; Abdelgadir, Awad; Liu, Jianshe

    2013-01-01

    In order to improve the bioleaching efficiency of arsenic-rich gold concentrates, a mixed bacterial flora had been developed, and the mutation breeding method was adopted to conduct the research. The original mixed bacterial flora had been enrichedin acid mine drainage of Dexing copper mine, Jiangxi Province, China. It was induced by UV (ultraviolet), ultrasonic, and microwave, and their combination mutation. The most efficient bacterial flora after mutation was collected for further bioleaching of arsenic-rich gold concentrates. Results indicated that the bacterial flora after mutation by UV 60 s combined with ultrasonic 10 min had the best oxidation rate of ferrous, the biggest density of cells, and the most activity of total protein. During bioleaching of arsenic-rich gold concentrates, the density of the mutant bacterial cells reached to 1.13 × 10⁸ cells/mL at 15 days, more than 10 times compared with that of the original culture. The extraction of iron reached to 95.7% after 15 days, increased by 9.9% compared with that of the original culture. The extraction of arsenic reached to 92.6% after 12 days, which was increased by 46.1%. These results suggested that optimum combined mutation could improve leaching ability of the bacterial flora more significantly.

  1. SOYBEAN - MOLECULAR ASPECTS OF BREEDING

    Directory of Open Access Journals (Sweden)

    Aleksandra Sudarić

    2012-12-01

    Full Text Available The book Soybean: Molecular Aspects of Breeding focuses recent progress in our understanding of the genetics and molecular biology of soybean. This book is divided into four parts and contains 22 chapters. Part I, Molecular Biology and Biotechnology focuses advances in molecular biology and laboratory procedures that have been developed recently to manipulate DNA. Part II, Breeding for abiotic stress covers proteomics approaches form as a powerful tool for investigating the molecular mechanisms of the plant responses to various types of abiotic stresses. Part III, Breeding for biotic stress addresses issues related to application of molecular based strategies in order to increase soybean resistance to various biotic factors. Part IV, Recent Technology reviews recent technologies into the realm of soybean monitoring, processing and product use. While the information accumulated in this book is of primary interest for plant breeders, valuable insights are also offered to agronomists, molecular biologists, physiologists, plant pathologists, food scientists and students. The book is a result of efforts made by many experts from different countries (USA, Japan, Croatia, Serbia, China, Canada, Malawi, Iran, Hong Kong, Brasil, Mexico.

  2. Genetic polymorphism of β-lactoglobulin and κ-casein of cattle breeds in Croatia

    Directory of Open Access Journals (Sweden)

    Ante Ivanković

    2011-12-01

    Full Text Available Profitable milk production respects the interests of producers, processing industries, consumer requirements and welfare of animals. Development of new methods of direct gene analysis responsible for milk proteins polymorphism provide new tools to raise the profitability of milk production and dairy products through implementation of breed genetic profile in breeding program. Because of necessity to determinate genetic profiles of cattle breeds in Croatia using new analytical methods, the ratio of dominant allelic polymorphic variants of beta-lactoglobulin (β-Lg and kappa-casein (κ-CN is defined. The share of beta-lactoglobulin B variant is dominant in all investigated cattle breeds (>52.9 %. Kappa- casein allelic variant A is dominant in selected cattle breeds (60.7-76.4 %, while the share of B variant is significantly more presented in autochthonous cattle breeds (48.2-84.1 %. Knowledge about genetic profile of breeds due to studied polymorphic variants of milk proteins is useful in further breeding development and economic reaffirmation of cattle breeds, especially autochthonous ones.

  3. Androgen receptor-beta mRNA levels in different tissues in breeding and post-breeding male and female sticklebacks, Gasterosteus aculeatus

    Directory of Open Access Journals (Sweden)

    Hoffmann Erik

    2012-03-01

    Full Text Available Abstract Background Androgens induce male characters by activating androgen receptors (AR. Previous quantitative studies on AR in fishes have been limited to few tissues and/or a single season/reproductive state. The aim of this investigation was to study the possible role of AR-beta expression levels in the control of male traits in the three-spined stickleback. To that end, AR-beta expression levels in major tissues in breeding and post-breeding male and female sticklebacks were examined. Methods AR-beta mRNA levels were quantified in ten tissues; eye, liver, axial muscle, heart, brain, intestine, ovary, testis, kidney and pectoral muscle in six breeding and post-breeding males and females using reverse transcription quantitative PCR. Results Breeding in contrast to post-breeding males built nests and showed secondary sexual characters (e.g. kidney hypertrophy and elevated androgen levels. Post-breeding females had lower ovarian weights and testosterone levels than breeding females. AR-beta was expressed in all studied tissues in both sexes and reproductive states with the highest expression in the gonads and in the kidneys. The kidney is an androgen target organ in sticklebacks, from which breeding males produce the protein spiggin, which is used in nest-building. There was also high AR-beta expression in the intestine, an organ that appears to take over hyperosmo-regulation in fresh water when the kidney hypertrophies in mature males and largely loses this function. The only tissue that showed effects of sex or reproductive state on AR-beta mRNA levels was the kidneys, where post-breeding males displayed higher AR-beta mRNA levels than breeding males. Conclusion The results indicate that changes in AR-beta mRNA levels play no or little role in changes in androgen dependent traits in the male stickleback.

  4. Method for Optimal Sensor Deployment on 3D Terrains Utilizing a Steady State Genetic Algorithm with a Guided Walk Mutation Operator Based on the Wavelet Transform

    Science.gov (United States)

    Unaldi, Numan; Temel, Samil; Asari, Vijayan K.

    2012-01-01

    One of the most critical issues of Wireless Sensor Networks (WSNs) is the deployment of a limited number of sensors in order to achieve maximum coverage on a terrain. The optimal sensor deployment which enables one to minimize the consumed energy, communication time and manpower for the maintenance of the network has attracted interest with the increased number of studies conducted on the subject in the last decade. Most of the studies in the literature today are proposed for two dimensional (2D) surfaces; however, real world sensor deployments often arise on three dimensional (3D) environments. In this paper, a guided wavelet transform (WT) based deployment strategy (WTDS) for 3D terrains, in which the sensor movements are carried out within the mutation phase of the genetic algorithms (GAs) is proposed. The proposed algorithm aims to maximize the Quality of Coverage (QoC) of a WSN via deploying a limited number of sensors on a 3D surface by utilizing a probabilistic sensing model and the Bresenham's line of sight (LOS) algorithm. In addition, the method followed in this paper is novel to the literature and the performance of the proposed algorithm is compared with the Delaunay Triangulation (DT) method as well as a standard genetic algorithm based method and the results reveal that the proposed method is a more powerful and more successful method for sensor deployment on 3D terrains. PMID:22666078

  5. Obtaining induced mutations of drought tolerance in sorghum

    Energy Technology Data Exchange (ETDEWEB)

    Hoeman, S.; Razzak, M.T. [National Atomic Energy Agency, Batan (Indonesia). Center for Application of Isotopes and Radiation; Nakanishi, Tomoko M. [Tokyo Univ. (Japan). Graduate School of Agricultural and Life Sciences

    2003-01-01

    Since sorghum plant (Sorghum bicolor L.) has a big potential to be cultivated in Indonesia especially in drought-prone areas, improvement of sorghum had been carried out through mutation breeding methods. The seeds of the sorghum plant was irradiated by gamma rays emitted from cobalt-60 source. The total dose was 0.4 kGy. Through selection process in the M2 generation, a number of promising mutant lines of sorghum have been obtained and registered in the M3 generation. In the M4, a number of 100 mutant lines were tested against drought in Gunung Kidul District during the dry season in 2000. Results of the test showed that mutant line DU/20/Psj/1, DU/20/Psj/4, DU/20/Psj/24, JA/30/Cty/21, ET/40/Psj/4 and DU/20/Psj/10 had relatively high grain yield compared to the control variety. (author)

  6. Genetic diversity of eleven European pig breeds

    Directory of Open Access Journals (Sweden)

    Foulley Jean-Louis

    2000-03-01

    Full Text Available Abstract A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall FST = 0.27, and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

  7. Direct benefits and the evolution of female-biased cooperative breeding in Seychelles warblers

    NARCIS (Netherlands)

    Richardson, David S.; Burke, Terry; Komdeur, Jan; Dunn, P.

    2002-01-01

    Inclusive fitness benefits have been suggested to be a major selective force behind the evolution of cooperative breeding. We investigated the fitness benefits selecting for cooperative breeding in the Seychelles warbler, Acroccphalus sechellensis. A microsatellite-based genotyping method was used t

  8. A general review of competition genetic effects with an emphasis on swine breeding.

    Science.gov (United States)

    Chen, C Y; Johnson, R K; Newman, S; Van Vleck, L D

    2007-09-30

    A review of previous studies is presented on estimates of genetic parameters and responses to selection with traditional breeding approaches, on correlations between agonistic behavior and growth performance, and on theoretical frameworks for selection incorporating interactions among individuals and on practical methods for incorporating competition effects in breeding programs.

  9. Effect of Bacillus subtilis microecological probiotics on livestock breeding

    Directory of Open Access Journals (Sweden)

    Xiaohui ZHOU

    2016-10-01

    Full Text Available As a kind of green and healthy microecologics, Bacillus subtilis could balance the intestinal flora, promote the nutrient absorption and enhance immunity. Microecologics is one of the ideal antibiotics alternative, which are effective in preventing and treating animal disease and promoting the growth and development of the animal. Because of its advantages, such as no toxin side effect and no residual or drug-resistant, microecologics has been used in livestock breeding widely. Here, we concluded the characteristics and mechanism of Bacillus subtilis,elaborated application of microecologics on livestock breeding, discussed its problems and suggested its solved methods. In the end, the future of microecologics was expected in order to provide a reference for subsequent livestock breeding.

  10. Seasonal organic pig production with a local breed

    DEFF Research Database (Denmark)

    Kongsted, Anne Grete; Claudi-Magnussen, C.; Horsted, Klaus

    2009-01-01

    It is important that organic pork differs markedly from conventional pork regarding taste, appearance and production methods in order to overcome the heavy price competition. That is the hypothesis behind thecurrent project. A seasonal outdoor rearing system based on a traditional and local breed...... is believed to bea feasible strategy for producing organic pork with high credibility and superior eating quality. The studyincluded a comparison between a modern genotype and the Danish Black-Spotted pig which does almostnot exist in the modern pig production of today. 17 gilts farrowed outdoors in April...... to the modern genotype and thefat of the Black-Spotted pig was characterised as having a special nutty taste. In conclusion, preliminaryresults indicate that the local breed differs markedly with respect to several meat quality aspects comparedto the modern breed but also shows clear disadvantages regarding...

  11. Influence of Duroc breed inclusion into Polish Landrace maternal line on pork meat quality traits.

    Science.gov (United States)

    Guzek, Dominika; Głąbska, Dominika; Głąbski, Krzysztof; Wierzbicka, Agnieszka

    2016-05-31

    Crossbreeding with Duroc breed allows to improve meat quality, but no data is available regarding specific influence of Duroc breed on characteristics of meat in the case of crossbreeding with various breeds. The aim of the present research was to evaluate the effect of crossbreeding Polish Landrace dames with Duroc sires on quality features of meat in reference to Polish Landrace breed. The objects of the study were Longissimus dorsi lumborum pork muscles obtained from Polish Landrace breed and Polish Landrace x Duroc crossbreed animals. Sarcomere length measurements were conducted using microscopic method and basic chemical composition measurement was analyzed using spectrophotometric scanning. Texture analysis of meat samples, performed after thermal treatment was expressed by Warner-Bratzler shear force and color analysis was obtained using CIE L*a*b* color system. No differences in sarcomere length, shear force as well as components of color values between pork meat originated from Polish Landrace breed and Polish Landrace x Duroc crossbreed were observed. Analysis of basic chemical composition revealed higher fat and lower ash contents in the case of meat of Polish Landrace breed animals. It was concluded that the actual impact of breed on meat characteristics is possibly altered by other factors. It may be suggested that influence of basic chemical composition on color of meat is breed-related.

  12. The relevance of milk protein polymorphisms for dairy cattle breeding.

    NARCIS (Netherlands)

    Bovenhuis, H.

    1992-01-01

    An isoelectric focusing method is described that is suitable for phenotyping a large number of milk samples due to its short separation time and its high capacity. To estimate milk protein gene frequencies for breeds represented in the crossbred population and to estimate the fraction of animals mis

  13. Induction of Parthenogenesis in Plants and Application in Breeding

    Institute of Scientific and Technical Information of China (English)

    MOU Chun-hong; LI Wen-li; WU Xian-jun; WANG Bin; XIE Zhao-hui; HU Yan-yu; WANG Xu-dong

    2003-01-01

    Parthenogenesis is a kind of reproductive mode by which the egg develops into embryo without fertilization and grows into plant finally. This article summarizes the advances of inducing parthenogenesis in plants in relation to induction methods, affecting factors and the studies in embryology. In addition, the application of parthenogenesis in breeding is also discussed.

  14. Public perceptions of reproductive biotechnologies: the case of farm animal breeding and reproduction in France and the United Kingdom.

    Science.gov (United States)

    Ouédraogo, Arouna P

    2004-01-01

    Results of previous qualitative and quantitative stages of the research project demonstrated that, although consumers had poor knowledge about breeding and reproduction procedures, they were concerned about the impact of breeding practices on their food items. They acknowledged breeding and reproduction to be at the very core of animal-based food chain process. Since however modern breeding programmers beg so much for genetics, their practices increasingly raised consumer concerns. This paper presents results of a research addressing this issue and based on interviews of livestock breeders and specialized scientists. This research was undertaken within the frame of an EU funded project (Sustainable Farm Animal Breeding and Reproduction Project, 2000-2003). Interviews were performed according to the methodology of focus groups and results were used to prepare a discussion guide, including definitions of breeding techniques such as artificial insemination, embryo transfer, in vitro fertilization, and molecular genetics. Farm animal breeding and reproduction methods raised high level of concerns in conventional terms like safety, healthiness and quality of food, factory farming and related consequences on environment, international issues, and cost. Several propositions were presented that deal with modern farm animal breeding and reproduction, EU regulation of breeding procedures, education of consumers on breeding methods, and labelling of products on breeding and reproduction grounds.

  15. Discussion on research methods of bacterial resistant mutation mechanisms under selective culture--uncertainty analysis of data from the Luria-Delbrück fluctuation experiment.

    Science.gov (United States)

    Jin, Jianling; Wei, Gang; Yang, Weiqiang; Zhang, Huaiqiang; Gao, Peiji

    2012-11-01

    Whether bacterial drug-resistance is drug-induced or results from rapid propagation of random spontaneous mutations in the flora prior to exposure, remains a long-term key issue concerned and debated in both genetics and medicinal fields. In a pioneering study, Luria and Delbrück exposed E. coli to T1 phage, to investigate whether the number of resistant colonies followed the Poisson distribution. They deduced that the development of resistant colonies is independent of phage presence. Similar results have since been obtained on solid medium containing antibacterial agents. Luria and Delbrück's conclusions were long considered a gold standard for analyzing drug resistance mutations. More recently, the concept of adaptive mutation has triggered controversy over this approach. Microbiological observation shows that, following exposure to drugs of various concentrations, drug-resistant cells emerge and multiply depending on the time course, and show a process function, inconsistent with the definition of Poisson distribution (which assumes not only that resistance is independent of drug quantity but follows no specific time course). At the same time, since cells tend to aggregate after division rather than separating, colonies growing on drug plates arise from the multiplication of resistant bacteria cells of various initial population sizes. Thus, statistical analysis based on equivalence of initial populations will yield erroneous results. In this paper, 310 data from the Luria-Delbrück fluctuation experiment were reanalyzed from this perspective. In most cases, a high-end abnormal value, resulting from the non-synchronous variation of the two above-mentioned time variables, was observed. Therefore, the mean value cannot be regarded as an unbiased expectation estimate. The ratio between mean value and variance was similarly incomparable, because two different sampling methods were used. In fact, the Luria-Delbrück data appear to follow an aggregated, rather than

  16. Estimating the annual number of breeding attempts from breeding dates using mixture models.

    Science.gov (United States)

    Cornulier, Thomas; Elston, David A; Arcese, Peter; Benton, Tim G; Douglas, David J T; Lambin, Xavier; Reid, Jane; Robinson, Robert A; Sutherland, William J

    2009-11-01

    Well-established statistical methods exist to estimate variation in a number of key demographic rates from field data, including life-history transition probabilities and reproductive success per attempt. However, our understanding of the processes underlying population change remains incomplete without knowing the number of reproductive attempts individuals make annually; this is a key demographic rate for which we have no satisfactory method of estimating. Using census data to estimate this parameter from requires disaggregating the overlying temporal distributions of first and subsequent breeding attempts. We describe a Bayesian mixture method to estimate the annual number of reproductive attempts from field data to provide a new tool for demographic inference. We validate our method using comprehensive data on individually-marked song sparrows Melospiza melodia, and then apply it to more typical nest record data collected over 45 years on yellowhammers Emberiza citrinella. We illustrate the utility of our method by testing, and rejecting, the hypothesis that declines in UK yellowhammer populations have occurred concurrently with declines in annual breeding frequency.

  17. Computational Modelling of Pisum Sativum L. Superoxide Dismutase and Prediction of Mutational Variations through in silico Methods

    Directory of Open Access Journals (Sweden)

    Nathan Vinod Kumar

    2014-06-01

    Full Text Available Superoxide dismutase (SOD is one of the major enzymes expressed in the oxidative stress pathway in plants. Its expression is also evident in other taxonomic group in oxidative reactions. Pisum sativum a common plant is being studied in the present work where SOD is characterized using computational tools. SOD sequence of P. sativum [CAA42737.1] Ala and Leu rich protein with alkaline pI value was used as query sequence and used to obtain nine similar sequences through BLASTp. Phylogenetic tree was constructed using MEGA 5.0 based on neighbour joining method. Physiochemical parameters and amino acid composition was studied and compared with query sequences and other similar sequences. Secondary structures were predicted to understand the dominant components. Homology modeling of P. sativum SOD was done using SWISS MODEL and quality was evaluated using standard methods. 27 active sites were detected in SOD predicted model which were Lys rich.

  18. Breeding schemes in reindeer husbandry

    Directory of Open Access Journals (Sweden)

    Lars Rönnegård

    2003-04-01

    Full Text Available The objective of the paper was to investigate annual genetic gain from selection (G, and the influence of selection on the inbreeding effective population size (Ne, for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection.

  19. A new high-throughput method for simultaneous detection of drug resistance associated mutations in Plasmodium vivax dhfr, dhps and mdr1 genes

    Directory of Open Access Journals (Sweden)

    Siba Peter

    2011-09-01

    Full Text Available Abstract Background Reports of severe cases and increasing levels of drug resistance highlight the importance of improved Plasmodium vivax case management. Whereas monitoring P. vivax resistance to anti-malarial drug by in vivo and in vitro tests remain challenging, molecular markers of resistance represent a valuable tool for high-scale analysis and surveillance studies. A new high-throughput assay for detecting the most relevant markers related to P. vivax drug resistance was developed and assessed on Papua New Guinea (PNG patient isolates. Methods Pvdhfr, pvdhps and pvmdr1 fragments were amplified by multiplex nested PCR. Then, PCR products were processed through an LDR-FMA (ligase detection reaction - fluorescent microsphere assay. 23 SNPs, including pvdhfr 57-58-61 and 173, pvdhps 382-383, 553, 647 and pvmdr1 976, were simultaneously screened in 366 PNG P. vivax samples. Results Genotyping was successful in 95.4% of the samples for at least one gene. The coexistence of multiple distinct haplotypes in the parasite population necessitated the introduction of a computer-assisted approach to data analysis. Whereas 73.1% of patients were infected with at least one wild-type genotype at codons 57, 58 and 61 of pvdhfr, a triple mutant genotype was detected in 65.6% of the patients, often associated with the 117T mutation. Only one patient carried the 173L mutation. The mutant 647P pvdhps genotype allele was approaching genetic fixation (99.3%, whereas 35.1% of patients were infected with parasites carrying the pvmdr1 976F mutant allele. Conclusions The LDR-FMA described here allows a discriminant genotyping of resistance alleles in the pvdhfr, pvdhps, and pvmdr1 genes and can be used in large-scale surveillance studies.

  20. Domestic dogs and cancer research: a breed-based genomics approach.

    Science.gov (United States)

    Davis, Brian W; Ostrander, Elaine A

    2014-01-01

    Domestic dogs are unique from other animal models of cancer in that they generally experience spontaneous disease. In addition, most types of cancer observed in humans are found in dogs, suggesting that canines may be an informative system for the study of cancer genetics. Domestic dogs are divided into over 175 breeds, with members of each breed sharing significant phenotypes. The breed barrier enhances the utility of the model, especially for genetic studies where small numbers of genes are hypothesized to account for the breed cancer susceptibility. These facts, combined with recent advances in high-throughput sequencing technologies allows for an unrivaled ability to use pet dog populations to find often subtle mutations that promote cancer susceptibility and progression in dogs as a whole. The meticulous record keeping associated with dog breeding makes the model still more powerful, as it facilitates both association analysis and family-based linkage studies. Key to the success of these studies is their cooperative nature, with owners, scientists, veterinarians and breed clubs working together to avoid the cost and unpopularity of developing captive populations. In this article we explore these principals and advocate for colony-free, genetic studies that will enhance our ability to diagnose and treat cancer in dogs and humans alike.

  1. Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds.

    Science.gov (United States)

    Allais, S; Levéziel, H; Hocquette, J F; Rousset, S; Denoyelle, C; Journaux, L; Renand, G

    2014-10-01

    Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are

  2. Reducing dimensionality for prediction of genome-wide breeding values

    Directory of Open Access Journals (Sweden)

    Woolliams John A

    2009-03-01

    Full Text Available Abstract Partial least square regression (PLSR and principal component regression (PCR are methods designed for situations where the number of predictors is larger than the number of records. The aim was to compare the accuracy of genome-wide breeding values (EBV produced using PLSR and PCR with a Bayesian method, 'BayesB'. Marker densities of 1, 2, 4 and 8 Ne markers/Morgan were evaluated when the effective population size (Ne was 100. The correlation between true breeding value and estimated breeding value increased with density from 0.611 to 0.681 and 0.604 to 0.658 using PLSR and PCR respectively, with an overall advantage to PLSR of 0.016 (s.e = 0.008. Both methods gave a lower accuracy compared to the 'BayesB', for which accuracy increased from 0.690 to 0.860. PLSR and PCR appeared less responsive to increased marker density with the advantage of 'BayesB' increasing by 17% from a marker density of 1 to 8Ne/M. PCR and PLSR showed greater bias than 'BayesB' in predicting breeding values at all densities. Although, the PLSR and PCR were computationally faster and simpler, these advantages do not outweigh the reduction in accuracy, and there is a benefit in obtaining relevant prior information from the distribution of gene effects.

  3. Breeding for behavioural change in farm animails

    DEFF Research Database (Denmark)

    Sandøe, Peter; D'eath, RB; Lawrence, AB

    2009-01-01

    examples, such as breeding for good maternal behaviour, could enhance welfare, production and naturalness, although dilemmas emerge where improved welfare could result from breeding away from natural behaviour. Selection against certain behaviours may carry a risk of creating animals which are generally......In farm animal breeding, behavioural traits are rarely included in selection programmes despite their potential to improve animal production and welfare. Breeding goals have been broadened beyond production traits in most farm animal species to include health and functional traits......, and opportunities exist to increase the inclusion of behaviour in breeding indices. On a technical level, breeding for behaviour presents a number of particular challenges compared to physical traits. It is much more difficult and time-consuming to directly measure behaviour in a consistent and reliable manner...

  4. Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra

    Science.gov (United States)

    Shewaramani, Sonal; Finn, Thomas J.; Kassen, Rees; Rainey, Paul B.

    2017-01-01

    Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes. PMID:28103245

  5. Biological evolution model with conditional mutation rates

    Science.gov (United States)

    Saakian, David B.; Ghazaryan, Makar; Bratus, Alexander; Hu, Chin-Kun

    2017-05-01

    We consider an evolution model, in which the mutation rates depend on the structure of population: the mutation rates from lower populated sequences to higher populated sequences are reduced. We have applied the Hamilton-Jacobi equation method to solve the model and calculate the mean fitness. We have found that the modulated mutation rates, directed to increase the mean fitness.

  6. Benzimidazole -Resistance in Haemonchus Contortus: New PCR-RFLP Method for the Detection of Point Mutation at Codon 167 of Isotype 1 Β-Tubulin Gene

    Directory of Open Access Journals (Sweden)

    A Eslami

    2012-12-01

    Full Text Available Background: Due to the lack of a suitable and economic test for the analysis of the polymorphism at codon 167, we developed a new PCR-RFLP technique, based on a modified forward primer (UT-HC167 MF-primer, to identify simultaneously the SNPs at codons 167 and 200 of isotype 1 β-tubu­lin gene of Haemonchus contortus.Methods: There already are several safe and easy methods for identification of point mutations at codons 198 and 200. Due to the lack of a reliable and easy method for the detection of the single nucleo­tide polymorphism (SNP at codon 167, we developed an innovative PCR-RFLP technique based on a modified forward primer (UT-HC167 MF-primer, in which the nucleotide T at the posi­tion 443 was substituted through a nucleotide A creating a restriction site for restriction endonuc­lease SnaB I in the nucleotide sequences including codon 167. A total of 138 adult male H. contortus were collected from three different geo-climatic areas of Iran. The isolated genomic DNA of each single worm was amplified by PCR using primers flanking codon 167. The PCR product (527 bp was then amplified by semi-nested PCR using the UT-HC167 MF-primer and the reverse primer achiev­ing a PCR product of 451 bp in length. This PCR product was subsequently digested with the restriction endonucleases SnaB I and TaaI for analysis of the mutations at codons 167 and 200, respec­tively.Results: All worms had two alleles encoding for phenylalanine (BZss homozygote for both codons.Conclusion: Using the UT-HC167 MF-primer and a suitable reverse primer designed upstream from codon 200, it is possible to amplify a PCR product which can be used for analysis of the SNPs at all three mentioned codons using RFLP.

  7. The Breeding Bird Survey, 1966

    Science.gov (United States)

    Robbins, C.S.; Van Velzen, W.T.

    1967-01-01

    A Breeding Bird Survey of a large section on North America was conducted during June 1966. Cooperators ran a total of 585 Survey routes in 26 eastern States and 4 Canadian Provinces. Future coverage of established routes will enable changes in the abundance of North American breeding birds to be measured. Routes are selected at random on the basis of one-degree blocks of latitude and longitude. Each 241/2-mile route, with 3-minute stops spaced one-half mile apart, is driven by automobile. All birds heard or seen at the stops are recorded on special forms and the data are then transferred to machine punch cards. The average number of birds per route is tabulated by State, along with the total number of each species and the percent of routes and stops upon which they were recorded. Maps are presented showing the range and abundance of selected species. Also, a year-to-year comparison is made of populations of selected species on Maryland routes in 1965 and 1966.

  8. Molecular tools for breeding basidiomycetes.

    Science.gov (United States)

    Ramírez, L; Larraya, L M; Pisabarro, A G

    2000-09-01

    The industrial production of edible basidiomycetes is increasing every year as a response to the increasing public demand of them because of their nutritional properties. About a dozen of fungal species can be currently produced for food with sound industrial and economic bases. Notwithstanding, this production is threatened by biotic and abiotic factors that make it necessary to improve the fungal strains currently used in industry. Breeding of edible basidiomycetes, however, has been mainly empirical and slow since the genetic tools useful in the selection of the new genetic material to be introduced in the commercial strains have not been developed for these fungi as it was for other organisms. In this review we will discuss the main genetic factors that should be considered to develop breeding approaches and tools for higher basidiomycetes. These factors are (i) the genetic system controlling fungal mating; (ii) the genomic structure and organisation of these fungi; and (iii) the identification of genes involved in the control of quantitative traits. We will discuss the weight of these factors using the oyster mushroom Pleurotus ostreatus as a model organism for most of the edible fungi cultivated industrially.

  9. Plastome Mutations and Recombination Events in Barley Chloroplast Mutator Seedlings.

    Science.gov (United States)

    Landau, Alejandra; Lencina, Franco; Pacheco, María G; Prina, Alberto R

    2016-05-01

    The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome Targeting Induced Local Lesions in Genomes (TILLING) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of 5 different one nucleotide polymorphisms. Besides, 4 large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelle DNA.

  10. Chemical classification of cattle. 1. Breed groups.

    Science.gov (United States)

    Baker, C M; Manwell, C

    1980-01-01

    From approximately 1000 papers with data on protein polymorphism in some 216 breeds of cattle, 10 polymorphic proteins were compared in means and variances of gene frequencies (arcsin p 1/2) for ten well-recognized breed groups for 196 of the breeds. The polymorphic proteins were alpha-lactalbumin, beta-lactoglobulin, caseins (alpha s1, beta and chi), serum albumin, transferrin, haemoglobin, amylase I and carbonic anhydrase II. The breed groups were North European, Pied Lowland, European Red brachyceros, Channel Island brachyceros, Upland brachyceros, primigenius-brachyceros mixed, primigenius, Indian Zebu, African Humped (with Zebu admixture), and African Humped (Sanga). The coherence within groups and the differences between groups are often impressive. Only carbonic anhydrase II fails to differentiate at least some of the major breed groups. In some cases paradoxical distributions of rare genetic variants can be explained by a more detailed inspection of breed history. The chemical data support the morphological and geographical divisions of cattle into major breed groups. There are three distinct but related brachyceros groups; for some polymorphisms the two Channel Island breeds, the Jersey and the Guernsey, are quite divergent. Although some authorities have considered the Pied Lowland as primigenius, it is a very distinct breed group.

  11. The productivity of various pure breed and cross breed of imported pigs during lactation period

    Directory of Open Access Journals (Sweden)

    Djamuara Aritonang

    2001-03-01

    Full Text Available A study has been conducted to evaluate the productivity of pure breeds and cross breeds of imported pigs. Sixteen strains of pigs with five best sows were selected based on litter size and birth weight on the second parity. The results of the study showed that the pure breed performance was better than the cross breeds, as shown by the litter size, birth and weaned weight, less mortality, better mothering ability and better feed efficiency. Between pure breed, the Landrace and Yorkshire were better than other sows and between the cross breed, the LH and YL performed better than other crossbreeds. It is recommended that the pure breed especially Landrace and Yorkshire and LH and YL of cross breed are better than others

  12. Study on the Method of Creation of Cabbage Breeding New Materials Using Biological Technology%利用生物技术创造甘蓝育种新材料的方法研究

    Institute of Scientific and Technical Information of China (English)

    王文涛; 苏浴源; 栗淑芳; 申领艳; 康少辉

    2012-01-01

    以5个甘蓝品种为试材,从基因型以及培养基中的有机成分、蔗糖浓度和激素浓度4个方面,对利用生物技术创造甘蓝育种新材料的方法进行了研究。结果表明:不同品种之间的遗传差异影响了参试甘蓝花药胚状体的诱导频率;培养基中的有机成分、蔗糖浓度和激素浓度均对胚状体诱导频率有较大影响。并建立了1套通过甘蓝花粉培养诱导产生单倍体植株的技术:取未授粉甘蓝花药和花粉,接种在蔗糖浓度为10%、附加NAA0.2mg/L+6-BA2mg/L的MS培养基中,诱导胚状体产生及萌发;将胚状体接种在附加NAA0.2mg/L的MS培养基中进行生根诱导,30d后生根率达89%,且根数较多,平均根长1.0~2.0cm,芽苗生长健壮。利用该技术获得单倍体再生植株所需要的时间一般为80d左右。%Using 5 cabbage varieties as materials, the method of creation of cabbage breeding new materials by biological technology was studied from four aspects of genotype and organic component, sucrose concentration and hormone concentration in the culture medium. The results showed that induction frequency of anther embryoids of tested cabbage was affected by genetic differences of different varieties. Organic component, sucrose concentration and hormone concentration in the culture medium had great influences on embryoid induction frequency. A set of technology of induced haploid plants by cabbage pollen culture was established, the unpollinated anthers and pollen of cabbage were nurtured in MS medium with 10% of sucrose concentration and adding NAA 0.2 mg/L + 6-BA 2 mg/L to induce embryoids generation and germination, then the embryoids were inoculated on the MS medium with NAA 0. 2 mg/L for 30 days to root induction, and the rate of rooting reached to 89% , the number of roots was large, the average root length was 1.0 - 2.0 cm, bud seedling growed healthy. The time required to obtain haploid

  13. Efforts to accelerate domestication of winged bean (Psophocarpus tetragonolobus (L.) DC.) by means of induced mutations and tissue culture.

    NARCIS (Netherlands)

    Klu, G.Y.P.

    1996-01-01

    This thesis describes mutation breeding and tissue culture techniques developed for accelerated domestication of winged bean ( Psophocarpustetragonolobus (L.) DC.). The tissue culture techniques, which are the first steps towards genetic transformation of the crop, include: (1) direct adventitious s

  14. Analysis of beta-casein gene (CSN2 polymorphism in different breeds of cattle

    Directory of Open Access Journals (Sweden)

    Martina Miluchová

    2014-11-01

    Full Text Available Normal 0 21 false false false SK X-NONE X-NONE MicrosoftInternetExplorer4 The goal of work was identification of b - casein gene polymorphism in different breeds of cow. The beta - casein constitutes up to 45 % of the casein of bovine milk. The most common forms of beta-casein in dairy cattle breeds are A1 and A2, while B is less common. The b-casein A1 variant was associated with the incidence of diabetes mellitus 1st type, coronary heart disease and autism. The A2 variant reduces serum cholesterol. The material involved 287 cows (Simmental breed – 111 cows, Pinzgau breed – 89 cows, Holstein breed – 87 cows. Bovine genomic DNA was extracted from whole blood by using commercial kit and used in order to estimate b - casein genotypes by means of PCR-RFLP method. In the populations included in the study were detected all three genotypes – homozygote genotype A1A1, heterozygote genotype A1A2 and homozygote genotype A2A2 with frequencies 0.1261, 0.3333 and 0.5405 in Simmental breed; 0.1379, 0.4598 and 0.4023 in Holstein breed, 0.3034, 0.5168 and 0.1798 in Pinzgau breed. In population of Simmental breed and Holstein breed was higher frequency of allele A2 (0.7072 and 0.6322. In opposite, in population of Pinzgau breed was present higher frequency of the allele A1 (0.5618.

  15. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...

  16. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    NARCIS (Netherlands)

    Gizaw, S.; Komen, J.; Windig, J.J.; Hanotte, O.; Arendonk, van J.A.M.

    2008-01-01

    Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livel

  17. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...

  18. Artificiat insemination vercus natural breeding in a multi.breed beef ...

    African Journals Online (AJOL)

    calving-to-breeding period the following breeding season and a reduced ..... the first four weeks of the calving season, while only 49 9o of the calves born as a result ... breeding season rather than leaving the job to the bulls later in the season.

  19. Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes

    NARCIS (Netherlands)

    Gizaw, S.; Arendonk, van J.A.M.; Valle-Zarate, A.; Haile, A.; Rischkowsky, B.; Dessie, T.; Mwai, A.O.

    2014-01-01

    A simulation study was conducted to optimize a cooperative village-based sheep breeding scheme for Menz sheep of Ethiopia. Genetic gains and profits were estimated under nine levels of farmers' participation and three scenarios of controlled breeding achieved in the breeding programme, as well as un

  20. Incidence of the mask phenotype M264V mutation in Labrador Retrievers.

    Science.gov (United States)

    Conant, E K; Juras, R; Cothran, E G

    2011-12-01

    The introduction of SNP (Single Nucleotide Polymorphism) chips allows for the rapid typing of multiple markers for many individuals at one time. Our lab routinely types dogs using a custom designed combined panel of SNPs for parentage verification and a number of genes for diagnostic tests using an OpenArray platform manufactured by BioTrove (Woburn, MA, USA). By utilizing the same SNP panel across a wide array of canine breeds it is possible to detect trait-associated SNPs in breeds not thought to carry those traits. We genotyped 245 Labrador Retrievers on the canine SNP chip and found 13 animals heterozygous for the M264V mutation associated with autosomal dominant mask trait, and one animal homozygous for this trait. The color genotypes for these animals were further examined. In standard colored Labradors (black, chocolate, and yellow), the mask phenotype would never be distinguishable. As illustrated by this example, we feel this SNP panel is a valuable method for discovering traits not known to exist in a breed.

  1. The association of SNPs in Hsp90β gene 5' flanking region with thermo tolerance traits and tissue mRNA expression in two chicken breeds.

    Science.gov (United States)

    Chen, Zhuo-Yu; Gan, Jian-Kang; Xiao, Xiong; Jiang, Li-Yan; Zhang, Xi-Quan; Luo, Qing-Bin

    2013-09-01

    Thermo stress induces heat shock proteins (HSPs) expression and HSP90 family is one of them that has been reported to involve in cellular protection against heat stress. But whether there is any association of genetic variation in the Hsp90β gene in chicken with thermo tolerance is still unknown. Direct sequencing was used to detect possible SNPs in Hsp90β gene 5' flanking region in 3 chicken breeds (n = 663). Six mutations, among which 2 SNPs were chosen and genotypes were analyzed with PCR-RFLP method, were found in Hsp90β gene in these 3 chicken breeds. Association analysis indicated that SNP of C.-141G>A in the 5' flanking region of the Hsp90β gene in chicken had some effect on thermo tolerance traits, which may be a potential molecular marker of thermo tolerance, and the genotype GG was the thermo tolerance genotype. Hsp90β gene mRNA expression in different tissues detected by quantitative real-time PCR assay were demonstrated to be tissue dependent, implying that different tissues have distinct sensibilities to thermo stress. Besides, it was shown time specific and varieties differences. The expression of Hsp90β mRNA in Lingshan chickens in some tissues including heart, liver, brain and spleen were significantly higher or lower than that of White Recessive Rock (WRR). In this study, we presume that these mutations could be used in marker assisted selection for anti-heat stress chickens in our breeding program, and WRR were vulnerable to tropical thermo stress whereas Lingshan chickens were well adapted.

  2. Breeding for Grass Seed Yield

    DEFF Research Database (Denmark)

    Boelt, Birte; Studer, Bruno

    2010-01-01

    Seed yield is a trait of major interest for many fodder and amenity grass species and has received increasing attention since seed multiplication is economically relevant for novel grass cultivars to compete in the commercial market. Although seed yield is a complex trait and affected...... by agricultural practices as well as environmental factors, traits related to seed production reveal considerable genetic variation, prerequisite for improvement by direct or indirect selection. This chapter first reports on the biological and physiological basics of the grass reproduction system, then highlights...... important aspects and components affecting the seed yield potential and the agronomic and environmental aspects affecting the utilization and realization of the seed yield potential. Finally, it discusses the potential of plant breeding to sustainably improve total seed yield in fodder and amenity grasses....

  3. Establishment of pyrosequencing method to detect isocitrate dehydrogenase 1 mutations%异柠檬酸脱氢酶1基因突变焦磷酸测序检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    王丹慧; 蔡彦宁; 张燕莉; 高杰; 杨彩侠

    2014-01-01

    Objective The present study aimed to establish a pyrosequencing method for IDH1 mutation examination, and quantify the sensitivity of this method. Furthermore, we tried to compare the differences between the direct sequencing and pyrosequencing for IDH1 mutation examination. Methods Plasmids carrying either wide-type or mutant IDH1 gene were constructed, and used to optimize the pyrosequencing method. The exact amount of mutant plasmids mixed with wide-type plasmids were served as templates for the pyrosequencing reaction to quantify the sensitivity of pyrosequencing based mutation examination. Both direct sequencing and pyroquencing methods were used to detect IDH1 mutations in 96 gliomas. Results Pyrosequencing detected as low as 2 % IDH1 mutation mixed in wide-type gene. Among the 96 glioma samples examined, 32. 3% of the samples were identified as carrying IDH1 mutations based on direct sequencing, while 74. 0% based on pyrosequencing method. Conclusion Pyrosequencing is a reliable and sensitive method in detecting IDH1 mutation, which is suitable for molecular diagnosis.%目的建立异柠檬酸脱氢酶1(isocitrate dehydrogenase 1,IDH1)基因突变的焦磷酸测序检测方法,确定该方法的检测灵敏度。分析焦磷酸测序法与直接测序法对于鉴定IDH1突变的差异。方法构建携带野生型和突变型IDH1基因的质粒,使用质粒优化焦磷酸测序方法。使用已知比例的野生型和突变型质粒作为模版,确定突变的检测灵敏度。针对96例胶质瘤患者手术切除标本的基因组DNA,分别使用直接测序法和焦磷酸测序法,鉴定IDH1基因突变类型,并比较。结果使用焦磷酸测序能够检测到低至2%的IDH1突变。直接测序检出突变阳性率为32.3%、焦磷酸测序检出突变阳性率为74.0%。结论焦磷酸测序法检测IDH1基因突变灵敏可靠,适合临床分子诊断。

  4. Rice improvement through radiation-induced mutation for cultivation in South Vietnam

    Energy Technology Data Exchange (ETDEWEB)

    Do Khac Thinh; Hung Phi Oanh; Nguyen Thi Cuc; Nguyen Ngoc Quynh [Institute of Agricultural Science of South Vietnam, Ho Chi Minh (Viet Nam)

    2001-03-01

    For past years, rice varieties cultivated in South Vietnam originated from domestic hybridisation or from IRRI. Rice mutation breeding has been initiated for recent years. To meet the requirement of rice production diversification in different agro-ecological areas and rice genetic resources, from 1993 Institute of Agricultural Science of South Vietnam has carried out rice improvement by induced mutation of radiation. The mutagen was gamma rays of {sup 60}Co. The goal is to create inherited variations, which cannot be obtained from other breeding methods, specially important characters of rice varieties (high tolerance to acid sulfate soil, lodging resistance combined with early maturity), which were difficult to gain by hybridisation. With {sup 60}Co gamma rays, doses of 10-20 krad, dose rate of 280 krad/h, dry and germinated seeds of introduced and local rice varieties (IR 64, IR 9729, IR 50404, IR 59606, Jasmine 85, Nang Huong, Tam Xoan) were irradiated. The irradiated seeds were immediately sown within 24 and 94 hrs for wet seeds and dry seeds after treatment, respectively. Population of 10,000-15,000 plants were established and evaluated by IRRI evaluation standard from M2-M7 generations. 365 lines, varieties were selected with better behaviours than original varieties as lodging resistance, earliness, potential yield, leaf characters, tolerant ability to adverse conditions etc. Some good varieties (VND95-19, VND95-20) have been approved as leading national varieties and released for large-scale production in South Vietnam. (author)

  5. 100-year history of the development of bread winter wheat breeding programs

    Directory of Open Access Journals (Sweden)

    М. А. Литвиненко

    2016-05-01

    Full Text Available Purpose. Review of the main achievements of the Wheat Breeding and Seed ProductionDepartment in the Plant Breeding and Genetic Institute – National Centre of Seed and Cultivar Investigation in the developing theoretical principles of breeding and creation of winter wheat varieties of different types during 100-year (1916–2016 period of breeding programs realization. Results. The main theoretical, methodical developments and breeding achievements of Wheat Breeding and Seed Production Department during 100-year (1916–2016 history have been considered. In the course of the Department activity, the research and metho­dology grounds of bread winter wheat breeding and seed production have been laid, 9 stages of breeding programs development have been accomplished. As a result, more than 130 varieties of different types have been created, 87 of them have been released in some periods or registered in the State registers of plants varieties of Ukraine and other countries and grown in the total sowing area about 220 million hectares.

  6. Foreign meat identification by DNA breed assignment for the Chinese market.

    Science.gov (United States)

    Rogberg-Muñoz, A; Wei, S; Ripoli, M V; Guo, B L; Carino, M H; Castillo, N; Villegas Castagnaso, E E; Lirón, J P; Morales Durand, H F; Melucci, L; Villarreal, E; Peral-García, P; Wei, Y M; Giovambattista, G

    2014-12-01

    Methods for individual identification are usually employed for traceability, whereas breed identification is useful to detect commercial frauds. In this study, Chinese Yellow Cattle (CYC) samples plus data from six Bos taurus breeds, two Bos indicus breeds, and one composite breed were used to develop an allocation test based on 22 microsatellites. The test allowed discriminating all foreign breeds from the CYC, although some CYC individuals were wrongly allocated as Limousin or Holstein, probably due to the recent introduction of these breeds into China. In addition, CYC evidenced a previously reported Zebu cline (south-north) and a possible structure within the B. taurus component that should be confirmed. An independent test performed with meat samples of unknown breed origin from Argentina allocated 92% of them to either Angus, Hereford, or their crossbreed, but none was identified as CYC. We conclude that the test is a suitable tool to certify meat of foreign breed origin and to detect adulterations of CYC beef labeled as imported meat.

  7. Some critical considerations on rice high-yielding breeding in China

    Institute of Scientific and Technical Information of China (English)

    ZHU Lihong

    2007-01-01

    Views and comments concerning rice highyielding breeding in China had been touched upon:(1) historical development of rice breeding in China and its prominent contributions recounted;current challenges evolved from rapid population increase,erosion of key natural resources and socioeconomic changes envisaged;(2) concept of extra or super high-yielding rice breeding and related ideas embraced nowadays in the main rice-producing countries assessed;the conception of so-called superrice in China could have been misled and misunderstood,and no substantial genetical differences could be affirmed yet between superrice and modern high-yielding rice;(3) two strategical approaches of rice production and breeding in China would have been persistent in the construction of most favorable-to-growth rice fields to plant rice varieties with high-yielding potentiality as well as renovation and rejuvenation of less favorable rice fields to plant most adaptableto-ecoenvironment varieties with promising productivity;in addition,breeding for rice varieties compatible with the specific rice regions ridden by adverse ecoenvironments;(4) overview of the relationship between the development of genetical researches and the perspective of rice breeding;integration of the classical genetical principles and breeding methods and techniques wherefrom with molecular biotechniques underscored.Finally,appeal to the breeders to adhere to due attentions to the development of genetics and promote pragmatism and traditional ethic solemnly so as to live up to implementing the national rice breeding mandates.

  8. 鱼类育种研究进展%The research process of fish genetic breeding

    Institute of Scientific and Technical Information of China (English)

    江丽华; 金媛; 毛勇

    2012-01-01

    本文概括了鱼类的选择育种、驯化及杂交育种等传统鱼类育种方法,叙述了现代生物技术在鱼类育种中的应用,主要有多倍体育种、雌、雄核发育、核移植、转基因育种、分子标记辅助育种、基因组育种;并提出了当今鱼类育种出现的问题。同时,做出了鱼类育种必将走向基因组育种之路的展望,为鱼类育种的发展提供参考。%The paper reported the outlook of fish breeding,the first part was about traditional breeding methods of selective breeding,domestication and cross-breeding,secondly,modern biotechnology in fish breeding was also described,it included polyploidy breeding,androgenesis,nuclear transfer,transgenic,molecular marker assisted breeding and genome breeding.And the challenge and tendency were posed finally.

  9. Analysis of the Genetic Diversity and Origin of Some Chinese Domestic Duck Breeds

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; CHEN Guo-hong; CHEN Yang; ZHEN Ting; HUANG Zheng-yang; CHEN Chang-yi; LI Xin-yu; DUAN Xiu-jun; DONG Biao; XU Qi

    2014-01-01

    Twelve lfuorescence-labeled microsatellite markers were used to analyze the genetic diversity of 12 domestic duck breeds and 2 wild duck breeds to determine the relationship and origin of Chinese domestic duck breeds. Gene frequency, effective number of alleles (Ne), expected heterozygosity (He), polymorphism information contents (PIC), inbreeding coefficient in population (Fis), standard genetic distance (DS), and genetic distance (DA) were calculated by FSTAT and distance and phylogenetic analysis after the dates which were output from the Microsatellite-Toolkit software. Genetic distances between 12 domestic duck breeds and 2 wild duck breeds were analyzed by variance analysis. Unweighted pair group method with arithmetic mean (UPGMA) and phylogenetic trees used for cluster analysis were structured. The results indicated that 11 loci had medium-or high-level genetic diversity among the 12 loci, which could be efifciently used in the detection of the genetic parameters of each population. The values of He were 0.5414 to 0.7343, those of PIC proved similar, and those of Fis were 0.1101 to 0.3381 among all populations. All breeds were clustered into three groups by UPGMA phylogenetic trees. Banzui duck was clustered into a separate group. Differences of the DA were analysed by t-test. The results showed that difference in DA between the 12 domestic duck breeds and Lvtou duck and the Banzui duck were very signiifcant (P<0.01), indicating that these 12 domestic duck breeds originated from Lvtou wild duck, but not Banzui duck.

  10. Mutation scanning of peach floral genes

    Directory of Open Access Journals (Sweden)

    Wilde H Dayton

    2011-05-01

    Full Text Available Abstract Background Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. Results HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. Conclusions Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.

  11. Cattle breeding goals and production circumstances

    NARCIS (Netherlands)

    Groen, A.F.

    1989-01-01

    This thesis gives the results of a study on the relationship between cattle breeding goals and production circumstances. The relationship between breeding goals and production circumstances mostly arises from the influences of production circumstances on the economic values of genetic

  12. Breed predisposition to canine gastric carcinoma

    DEFF Research Database (Denmark)

    Seim-Wikse, Tonje; Jörundsson, Einar; Nødtvedt, Ane

    2013-01-01

    Previous research has indicated a breed predisposition to gastric carcinoma in dogs. However, results to date are inconsistent since several studies have failed to prove such a predisposition. Better knowledge of breeds at risk could facilitate early detection of gastric carcinoma in dogs. The ai...

  13. Breed predisposition to canine gastric carcinoma

    DEFF Research Database (Denmark)

    Seim-Wikse, Tonje; Jörundsson, Einar; Nødtvedt, Ane;

    2013-01-01

    Previous research has indicated a breed predisposition to gastric carcinoma in dogs. However, results to date are inconsistent since several studies have failed to prove such a predisposition. Better knowledge of breeds at risk could facilitate early detection of gastric carcinoma in dogs. The ai...

  14. Genetic diversity of 11 European pig breeds

    NARCIS (Netherlands)

    Lavall, G.; Iannuccelli, N.; Legault, C.; Milan, D.; Groenen, M.A.M.; Andersson, L.; Fredholm, M.; Geldermann, H.; Foulley, J.L.; Chevalet, C.; Ollivier, L.

    2000-01-01

    A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosi

  15. Cattle breeding goals and production circumstances.

    NARCIS (Netherlands)

    Groen, A.F.

    1989-01-01

    This thesis gives the results of a study on the relationship between cattle breeding goals and production circumstances. The relationship between breeding goals and production circumstances mostly arises from the influences of production circumstances on the economic values of geneticim

  16. Lily breeding research in the Netherlands

    NARCIS (Netherlands)

    Tuyl, van J.M.; Holsteijn, van H.M.C.

    1996-01-01

    At the Centre for Plant Breeding and Reproduction Research (CPRO-DLO) in Wageningen lily breeding research in the Netherlands is concentrated. To this end sources of germplasm (genetic material) are maintained in a lily species and cultivar collection. Research is done on long term storage of this c

  17. Plant Breeding: Surprisingly, Less Sex Is Better.

    Science.gov (United States)

    van Dijk, Peter J; Rigola, Diana; Schauer, Stephen E

    2016-02-01

    Introduction of apomixis, asexual reproduction through seeds, into crop species has the potential to dramatically transform plant breeding. A new study demonstrates that traits can be stably transferred between generations in newly produced apomictic lines, and heralds a breeding revolution needed to increase food production for the growing planet.

  18. Breeding for behavioural change in farm animals

    DEFF Research Database (Denmark)

    D'Eath, R.B.; Conington, J.; Lawrence, A.B.

    2010-01-01

    In farm animal breeding, behavioural traits are rarely included in selection programmes despite their potential to improve animal production and welfare. Breeding goals have been broadened beyond production traits in most farm animal species to include health and functional traits, and opportunit...

  19. Breeding for behavioural change in farm animails

    DEFF Research Database (Denmark)

    Sandøe, Peter; D'eath, RB; Lawrence, AB

    2009-01-01

    examples, such as breeding for good maternal behaviour, could enhance welfare, production and naturalness, although dilemmas emerge where improved welfare could result from breeding away from natural behaviour. Selection against certain behaviours may carry a risk of creating animals which are generally...

  20. Impact of selective breeding on European aquaculture

    NARCIS (Netherlands)

    Janssen, K.; Chavanne, H.; Berentsen, P.; Komen, H.

    2016-01-01

    Objectives of this study were to determine the combined market share of breeding companies in aquaculture production in Europe, to describe the main characteristics of breeding companies and their programs, and to provide per species estimates on cumulative genetic gain in growth performance. Sur

  1. DGAT1 and ABCG2 polymorphism in Indian cattle (Bos indicus and buffalo (Bubalus bubalis breeds

    Directory of Open Access Journals (Sweden)

    Mishra Bina

    2006-11-01

    Full Text Available Abstract Background Indian cattle (Bos indicus and riverine buffalo (Bubalus bubalis give a poor yield of milk but it has a high fat and protein percentage compared to taurine cattle. The identification of QTLs (Quantitative Trait Loci on BTA14 and BTA6 and its subsequent fine mapping has led to identification of two non conservative mutations affecting milk production and composition. Our objective was to estimate the frequency of K232A (DGAT1 – diacylglycerol – acyltransferase 1 and Y581S (ABCG2 – ATP binding cassette sub family G member 2 polymorphisms in diverse cattle and buffalo breeds of India having large variation in terms of milk production. Results We screened the reported missense mutations in six cattle and five buffalo breeds. The DGAT1K and ABCG2Y alleles were found to be fixed in Indian cattle and buffalo breeds studied. Conclusion This study provides an indirect evidence that all the Indian cattle and buffalo breeds have fixed alleles with respect to DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent.

  2. Breeding for behavioural change in farm animals

    DEFF Research Database (Denmark)

    D'Eath, R.B.; Conington, J.; Lawrence, A.B.

    2010-01-01

    In farm animal breeding, behavioural traits are rarely included in selection programmes despite their potential to improve animal production and welfare. Breeding goals have been broadened beyond production traits in most farm animal species to include health and functional traits...... in order to evaluate the large numbers of animals necessary for a breeding programme. For this reason, the development and validation of proxy measures of key behavioural traits is often required. Despite these difficulties, behavioural traits have been introduced by certain breeders. For example, ease...... of handling is now included in some beef cattle breeding programmes. While breeding for behaviour is potentially beneficial, ethical concerns have been raised. Since animals are adapted to the environment rather than the other way around, there may be a loss of 'naturalness' and/or animal integrity. Some...

  3. Selection criteria in organic cattle breeding

    Directory of Open Access Journals (Sweden)

    Savić Mila

    2014-01-01

    Full Text Available The central issue in process of organizing organic cattle breeding is the knowledge about specificities of this kind of production, good knowledge of breed characteristics (body composition, immune tolerance, expressed predisposition towards some diseases, production properties. Research centres, in collaboration with producers, have defined the essential features on which the selection programmes in organic cattle breeding are based on. Of the greatest importance for veterinary service is the fact that selection programmes in organic cattle breeding are in the first place based on giving priority to healthy animals, with strong immune system, good reproductive characteristics, which can be in production system for a long period. Additional important selective criteria is specific body resistance and adaptability of autochtonous breeds to environmental conditions. [Projekat Ministarstva nauke Republike Srbije, br. TP 31085

  4. Minisequencing mitochondrial DNA pathogenic mutations

    Directory of Open Access Journals (Sweden)

    Carracedo Ángel

    2008-04-01

    Full Text Available Abstract Background There are a number of well-known mutations responsible of common mitochondrial DNA (mtDNA diseases. In order to overcome technical problems related to the analysis of complete mtDNA genomes, a variety of different techniques have been proposed that allow the screening of coding region pathogenic mutations. Methods We here propose a minisequencing assay for the analysis of mtDNA mutations. In a single reaction, we interrogate a total of 25 pathogenic mutations distributed all around the whole mtDNA genome in a sample of patients suspected for mtDNA disease. Results We have detected 11 causal homoplasmic mutations in patients suspected for Leber disease, which were further confirmed by standard automatic sequencing. Mutations m.11778G>A and m.14484T>C occur at higher frequency than expected by change in the Galician (northwest Spain patients carrying haplogroup J lineages (Fisher's Exact test, P-value Conclusion We here developed a minisequencing genotyping method for the screening of the most common pathogenic mtDNA mutations which is simple, fast, and low-cost. The technique is robust and reproducible and can easily be implemented in standard clinical laboratories.

  5. Breeding the oil palm (Elaeis guineensis Jacq. for climate change

    Directory of Open Access Journals (Sweden)

    Rival Alain

    2017-01-01

    Full Text Available Breeding the oil palm (Elaeis guineensis Jacq. for climate change requires multidisciplinary and collaborative research by nature: indeed – besides genetics and structural and functional genomics – almost all disciplines related to life sciences are involved. Research work also relies on the identification of genetic variation in the strategies of response to stress developed by the plant: this implies the exploration of resources provided by natural variation, germplasm collections, selected genitors from breeding programs together with material of interest collected from smallholders. The phenotyping of selected plant material under biotic/abiotic stress will involve new methods for high-throughput phenotyping and genomic approaches will be followed for the identification of genes underlying the variation of traits which will be used as selection targets. Also, improvements in understanding how climate change may influence chemical and physical processes in soils, how this may affect nutrient availability, and how the plant responds to changed availability of nutrients will also influence oil palm breeding programs. Molecular approaches and tools have great potential to optimize patterns of plant breeding, especially for perennial species. In recent years, there has been an exponential increase in molecular resources and methods aimed at identifying polymorphisms which control the traits of interest and exploring the mechanisms linking these polymorphisms to phenotypes. With genomic resources becoming increasingly available for the oil palm (sequencing, resequencing and chips development the exploration of the genetic basis of complex traits such as oil yield or resistance to disease is now possible. Consequently the availability and sharing of such a large amount of data is currently reshaping most of oil palm breeding strategies.

  6. Milk oligosaccharides over time of lactation from different dog breeds.

    Directory of Open Access Journals (Sweden)

    Shirin Macias Rostami

    Full Text Available The partnership of humans and dogs goes back to over 10'000 years, yet relatively little is known about a dog's first extra-uterine nutrition particularly when it comes to milk oligosaccharides. We set out to identify and quantify milk oligosaccharides over the course of lactation from different dog breeds (Labrador retriever, Schnauzer and 3 Alaskan husky crossbreeds. To this end, 2 different chromatographic methods with fluorescence and mass spectrometry detection were developed and one was validated for quantification. Besides lactose and lactose-sulphate, we identified 2 different trisaccharides composed of 3 hexose units, 3'sialyllactose (3'SL, 6'sialyllactose (6'SL, 2'fucosyllactose (2'FL, and a tetrasaccharide composed of 2 hexoses, an N-acetylhexosamine and a deoxyhexose. 3'SL was present at the highest levels in milk of all dog breeds starting at around 7.5 g/L and dropping to about 1.5 g/L in the first 10 days of lactation. 6'SL was about 10 times less abundant and 2'FL and the tetrasaccharide had rather varying levels in the milk of the different breeds with the tetrasaccharide only detectable in the Alaskan husky crossbreeds. The longitudinal and quantitative data of milk oligosaccharides from different dog breeds are an important basis to further our understanding on their specific biological roles and also on the specific nutritional requirements of lactating puppies.

  7. Progress and Strategies in Cross Breeding of Poplars in China

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The advance in intrasection and intersection cross breeding of poplars in China over the past 50 years is reviewed. Great progress has been made in Sections Leuce and Aigeiros, and satisfactory results of intersection hybridization have been achieved in the crossing between Sections Tacamahaca and Aigeiros. The modes of hybridization include single cross, double cross, triple cross, backcross, etc. It is known that using hybrids as parents to cross with other species or hybrids is an effective and easy way to obtain heterosis. Fast growth, cold and drought tolerance, pest and disease resistance, narrow crowns and rootage, etc. are breeding goals. The conventional artificial crossing is still a major breeding method, and a combination of the conventional artificial crossing with physical radiation and chemical induction can create new triploid individuals that possess higher yield potential. The super clones cultivated have already displayed enormous socioeconomic and ecological benefits in practice. Finally, the problems that investigators have to face at present are discussed as well as some strategies in poplar cross breeding in China.

  8. Genetic diversity in Tunisian horse breeds

    Directory of Open Access Journals (Sweden)

    B. Jemmali

    2017-06-01

    Full Text Available This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49, 7.35 (0.54, 6.3 (0.44, and 6 (0.38 for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03 in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02 in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05 and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

  9. Breeding and feeding ecology of pigeon guillemots (Cepphus columba) at Naked Island, Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report covers the breeding and feeding ecology of the pigeon guillemot at Naked Island, Alaska, as well as surveys of the Naked Island complex. Methods...

  10. Patterns of molecular genetic variation among cat breeds.

    Science.gov (United States)

    Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

    2008-01-01

    Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

  11. Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values.

    Science.gov (United States)

    Přibyl, J; Bauer, J; Čermák, V; Pešek, P; Přibylová, J; Šplíchal, J; Vostrá-Vydrová, H; Vostrý, L; Zavadilová, L

    2015-10-01

    Estimated breeding values (EBVs) and genomic enhanced breeding values (GEBVs) for milk production of young genotyped Holstein bulls were predicted using a conventional BLUP - Animal Model, a method fitting regression coefficients for loci (RRBLUP), a method utilizing the realized genomic relationship matrix (GBLUP), by a single-step procedure (ssGBLUP) and by a one-step blending procedure. Information sources for prediction were the nation-wide database of domestic Czech production records in the first lactation combined with deregressed proofs (DRP) from Interbull files (August 2013) and domestic test-day (TD) records for the first three lactations. Data from 2627 genotyped bulls were used, of which 2189 were already proven under domestic conditions. Analyses were run that used Interbull values for genotyped bulls only or that used Interbull values for all available sires. Resultant predictions were compared with GEBV of 96 young foreign bulls evaluated abroad and whose proofs were from Interbull method GMACE (August 2013) on the Czech scale. Correlations of predictions with GMACE values of foreign bulls ranged from 0.33 to 0.75. Combining domestic data with Interbull EBVs improved prediction of both EBV and GEBV. Predictions by Animal Model (traditional EBV) using only domestic first lactation records and GMACE values were correlated by only 0.33. Combining the nation-wide domestic database with all available DRP for genotyped and un-genotyped sires from Interbull resulted in an EBV correlation of 0.60, compared with 0.47 when only Interbull data were used. In all cases, GEBVs had higher correlations than traditional EBVs, and the highest correlations were for predictions from the ssGBLUP procedure using combined data (0.75), or with all available DRP from Interbull records only (one-step blending approach, 0.69). The ssGBLUP predictions using the first three domestic lactation records in the TD model were correlated with GMACE predictions by 0.69, 0.64 and 0

  12. CROSSING OF HOLSTEIN HORSE BREED WITH SOME OTHER BREEDS

    Directory of Open Access Journals (Sweden)

    Josip Ljubešić

    2000-06-01

    Full Text Available An experiment of crossing a heavier-weight semi-breed horse (Holstein with mares of Croatian Posavian type draft horse resulted in possibility of such further crossing. Attained product meets today’s market requirements: firstly as an export-meat category that meets Italian market requirements, since other markets are not well known, secondly, it can be used as a sport-tourist-recreation horse. It must be pointed out that all produced hybrids did not meet the needs of these two basic criteria. In spite of being potential slaughtery head with good utilization, each produced head can be, according to its exterial properties, used as a sporttourist animal that showed certain usable values and results proven by the experiment. The hybrids showed some hereditory draft horse properties shown on enclosed photos. In addition, exterier measures show that former knowledge on hybrids can respond the question of a horse raising on non-utilized pastures which they got used to very well. Thus these horses are able to be estimated by their body development just as our native draft Posavian type horse including possibility of using them as a sport-tourist-recreation horse.

  13. Livestock breeding for sustainability to mitigate global warming, with ...

    African Journals Online (AJOL)

    Livestock breeding for sustainability to mitigate global warming, with the emphasis ... is essential in implementing efficient breeding systems to cope with climate change. Sophisticated statistical models continue to support animal breeding and ...

  14. CF Mutation Panel

    Science.gov (United States)

    ... Testing; Cystic Fibrosis Transmembrane Conductance Regulator Mutation Analysis; CFTR Mutation Analysis Formal name: Cystic Fibrosis Gene Mutation ... an elevated immunoreactive trypsinogen (IRT) or positive sweat chloride test , to confirm the diagnosis of cystic fibrosis. ...

  15. Comparison of the Analytical Performance Between cobas EGFR Assay and PCR-Clamp Method in the Detection of EGFR Mutations in Japanese Non-Small Cell Lung Cancer Patients.

    Science.gov (United States)

    Ai, Tomohiko; Yuri, Maiko; Tabe, Yoko; Kakimoto, Atsushi; Morishita, Soji; Tsuchiya, Koji; Takamochi, Kazuya; Kodama, Yuzo; Takahashi, Fumiyuki; Shigeki, Misawa; Horii, Takashi; Suzuki, Kenji; Takahashi, Kazuhisa; Miida, Takashi; Ohsaka, Akimichi

    2017-05-01

    EGFR, a tyrosine-kinase, plays an important role in the progression of lung cancer. Since genetic abnormality of EGFR alters the effects of tyrosine-kinase inhibitors targeting EGFR, molecular analyses of EGFR have recently gained more attention in the treatment of lung cancer. However, several different techniques are available and which method is superior has not been determined. In this study, we compared two recently developed PCR-based techniques, PCR-clamp method and cobas EGFR assay. Ninety-four surgical samples and 58 biopsy samples from patients suffering from non-small cell lung cancers (NSCLCs) were included in the study. Samples with positive and negative genetic abnormalities, 66 and 28 respectively, were chosen for PCR-Clamp methods. Those same samples were reanalyzed with cobas EGFR assay. The concordance between PCR-Clamp and cobas EGFR methods was 95.7%. PCR-Clamp failed to detect four mutations that were detected with cobas EGFR assay. These two methods were further tested by analyzing 58 random biopsy samples. The concordance for the biopsy samples was 93.1%, and PCR-Clamp, again, failed to detect three mutations that were detected with cobas EGFR assay. Our results showed both methods detected most of the known EGFR mutations and the concordance was similar to those previously reported in different ethnicities. However, in our study, PCR-Clamp method failed to detect a total of seven mutations that were detected with cobas EGFR assay. Thus, we concluded that cobas EGFR assay is an easier and more accurate screening assay than PCR-Clamp method in detecting EGFR genetic abnormalities.

  16. Future Prospects for Ascochyta Blight Resistance Breeding in Cool Season Food Legumes

    OpenAIRE

    Rubiales, D.; Fondevilla, S.

    2012-01-01

    Legume cultivation is strongly hampered by the occurrence of ascochyta blights. Strategies of control have been developed but only marginal successes achieved. Breeding for disease resistance is regarded the most cost efficient method of control. Significant genetic variation for disease resistance exists in most legume crops with numerous germplasm lines maintained, providing an excellent resource for plant breeders. Fast and reliable screening methods have been adjusted to fulfill breeding ...

  17. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.

    Science.gov (United States)

    Wallner, Barbara; Vogl, Claus; Shukla, Priyank; Burgstaller, Joerg P; Druml, Thomas; Brem, Gottfried

    2013-01-01

    The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion "Eclipse" or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.

  18. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.

    Directory of Open Access Journals (Sweden)

    Barbara Wallner

    Full Text Available The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT, all clearly distinct from the Przewalski horse (E. przewalskii. The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3 are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion "Eclipse" or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.

  19. Detection of knockdown resistance (kdr mutations in Anopheles gambiae: a comparison of two new high-throughput assays with existing methods

    Directory of Open Access Journals (Sweden)

    Ball Amanda

    2007-08-01

    Full Text Available Abstract Background Knockdown resistance (kdr is a well-characterized mechanism of resistance to pyrethroid insecticides in many insect species and is caused by point mutations of the pyrethroid target site the para-type sodium channel. The presence of kdr mutations in Anopheles gambiae, the most important malaria vector in Africa, has been monitored using a variety of molecular techniques. However, there are few reports comparing the performance of these different assays. In this study, two new high-throughput assays were developed and compared with four established techniques. Methods Fluorescence-based assays based on 1 TaqMan probes and 2 high resolution melt (HRM analysis were developed to detect kdr alleles in An. gambiae. Four previously reported techniques for kdr detection, Allele Specific Polymerase Chain Reaction (AS-PCR, Heated Oligonucleotide Ligation Assay (HOLA, Sequence Specific Oligonucleotide Probe – Enzyme-Linked ImmunoSorbent Assay (SSOP-ELISA and PCR-Dot Blot were also optimized. The sensitivity and specificity of all six assays was then compared in a blind genotyping trial of 96 single insect samples that included a variety of kdr genotypes and African Anopheline species. The relative merits of each assay was assessed based on the performance in the genotyping trial, the length/difficulty of each protocol, cost (both capital outlay and consumable cost, and safety (requirement for hazardous chemicals. Results The real-time TaqMan assay was both the most sensitive (with the lowest number of failed reactions and the most specific (with the lowest number of incorrect scores. Adapting the TaqMan assay to use a PCR machine and endpoint measurement with a fluorimeter showed a slight reduction in sensitivity and specificity. HRM initially gave promising results but was more sensitive to both DNA quality and quantity and consequently showed a higher rate of failure and incorrect scores. The sensitivity and specificity of AS

  20. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

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    Rangel-Figueiredo Teresa

    2010-06-01

    Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

  1. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Science.gov (United States)

    2010-01-01

    Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the

  2. Identification of Y chromosome genetic variations in Chinese indigenous horse breeds.

    Science.gov (United States)

    Ling, Yinghui; Ma, Yuehui; Guan, Weijun; Cheng, Yuejiao; Wang, Yanping; Han, Jianlin; Jin, Dapeng; Mang, Lai; Mahmut, Halik

    2010-01-01

    Y chromosome acts as a single nonrecombining unit that is male specific and in effect haploid, thus ensuring the preservation of mutational events as a single haplotype via male lines. In this study, 6 Y chromosome-specific microsatellites (SSR) were tested for the patrilineal genetic variations of 573 male samples from Chinese domestic horse (30 breeds), Przewalski's horse, and donkey. All the 6 loci appeared as a haplotype block in Przewalski's horse and the domestic donkey. There were notable differences, however, at Y chromosome markers between horse and donkey. There were 2 haplotypes of Eca.YA16 in the domestic horse breeds, Haplotype A (Allele A: 156 bp) and Haplotype B (Allele B: 152 bp). Allele A was the common allele among 30 horse breeds, and Allele B was found in 11 horse breeds. This is the first description of a Y chromosome variant for horses. The 2 haplotypes of Y chromosome discovered in the domestic horse breeds in China could be helpful in unveiling their intricate genetic genealogy.

  3. Pituitary dwarfism in Saarloos and Czechoslovakian wolfdogs is associated with a mutation in LHX3.

    Science.gov (United States)

    Voorbij, A M W Y; Leegwater, P A; Kooistra, H S

    2014-01-01

    Pituitary dwarfism in German Shepherd Dogs is associated with autosomal recessive inheritance and a mutation in LHX3, resulting in combined pituitary hormone deficiency. Congenital dwarfism also is encountered in breeds related to German Shepherd Dogs, such as Saarloos and Czechoslovakian wolfdogs. To investigate whether Saarloos and Czechoslovakian wolfdog dwarfs have the same LHX3 mutation as do Germans Shepherd Dog dwarfs. A specific aim was to determine the carrier frequency among Saarloos and Czechoslovakian wolfdogs used for breeding. Two client-owned Saarloos wolfdogs and 4 client-owned Czechoslovakian wolfdogs with pituitary dwarfism, 239 clinically healthy client-owned Saarloos wolfdogs, and 200 client-owned clinically healthy Czechoslovakian wolfdogs. Genomic DNA was amplified using polymerase chain reaction (PCR). In the Saarloos and Czechoslovakian wolfdog dwarfs, PCR products were analyzed by sequencing. DNA fragment length analysis was performed on the samples from the clinically healthy dogs. Saarloos and Czechoslovakian wolfdog dwarfs have the same 7 bp deletion in intron 5 of LHX3 as do German Shepherd Dog dwarfs. The frequency of carriers of this mutation among clinically healthy Saarloos and Czechoslovakian wolfdogs used for breeding was 31% and 21%, respectively. An LHX3 mutation is associated with pituitary dwarfism in Saarloos and Czechoslovakian wolfdogs. The rather high frequency of carriers of the mutated gene in the 2 breeds emphasizes the need for screening before breeding. If all breeding animals were genetically tested for the presence of the LHX3 mutation and a correct breeding policy would be implemented, this disease could be eradicated completely. Copyright © 2014 by the American College of Veterinary Internal Medicine.

  4. Breeding objectives for Targhee sheep.

    Science.gov (United States)

    Borg, R C; Notter, D R; Kuehn, L A; Kott, R W

    2007-11-01

    Breeding objectives were developed for Targhee sheep under rangeland production conditions. Traits considered were those for which EPD were available from the US National Sheep Improvement Program and included direct and maternal effects on 120-d weaning weight (WW and MM, respectively); yearling weight (YW); yearling fleece weight, fiber diameter, and staple length; and percent lamb crop (PLC), measured as the number of lambs born per 100 ewes lambing. A bioeconomic model was used to predict the effects of a change of 1 additive SD in EPD for each trait, holding all other traits constant at their mean, on animal performance, feed requirements, feed costs, and economic returns. Resulting economic weightings were then used to derive selection indexes. Indexes were derived separately for 3 prolificacy levels (1.41, 1.55, and 1.70 lambs/ewe lambing), 2 triplet survival levels (50 and 67%), 2 lamb pricing policies (with or without discounting of prices for heavy feeder lambs), and 3 forage cost scenarios (renting pasture, purchasing hay, or reducing flock size to accommodate increased nutrient requirements for production). Increasing PLC generally had the largest impact on profitability, although an increase in WW was equally important, with low feed costs and no discounting of prices for heavy feeder lambs. Increases in PLC were recommended at all 3 prolificacy levels, but with low triplet survival the value of increasing PLC eventually declined as the mean litter size increased to approximately 2.15 lambs/ewe lambing and above. Increasing YW (independent of WW) increased ewe maintenance costs and reduced profitability. Predicted changes in breeding values for WW and YW under index selection varied with lamb pricing policy and feed costs. With low feed costs or no discounts for heavy lambs, YW increased at a modest rate in association with increasing WW, but with high feed costs or discounting of heavy lambs, genetic trends in WW were reduced by approximately 50% to

  5. Conservation and Improvement Strategy for Fogera Cattle: A Lesson for Ethiopia Ingenious Cattle Breed Resource

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    Assemu Tesfa

    2017-01-01

    Full Text Available The paper is initiated to design appropriate conservation strategies and breeding scheme for Fogera cattle breed that will be used as a guide for other Ethiopian indigenous cattle breed. Two types of data, on-farm and on-station, were used; the on-farm data was collected from three districts, namely, Fogera, Dera, and Bahir Dar Zuria; those are expected as the home of the breed. A total of 150 farmers, which are knowledgeable and having at least one cattle of Fogera phenotype in their herd, were purposively selected and interviewed. Additionally, farmer’s focus group discussion (FGD was conducted to capture the historical background, population, and distribution of the breed. SPSS (version 16 and index method was used to analyze the quantitative and scoring data’s, respectively. A meeting at national and regional level was also conducted to evaluate the existing conservation strategy and to identify the major stakeholders for the strategy. The main reasons to conserve Fogera breed are due to presence of interrelated constraints, presence of unique traits of the breed, better attitude of farmers, and decreasing population trend of the breed. Community-based in situ conservation strategy, to ensure the participation of the community, was designed for the breed. With the conservation strategy, related activities like feed development, animal health interventions, market linkage, and development of cooperatives will be implemented to improve the working environment. The stakeholders that are identified as an actor in the strategy should realize their honest participation for the sustainability of conservation and improvement of the breed.

  6. A genetic dissection of breed composition and performance enhancement in the Alaskan sled dog

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    Runstadler Jonathan

    2010-07-01

    Full Text Available Abstract Background The Alaskan sled dog offers a rare opportunity to investigate the development of a dog breed based solely on performance, rather than appearance, thus setting the breed apart from most others. Several established breeds, many of which are recognized by the American Kennel Club (AKC, have been introduced into the sled dog population to enhance racing performance. We have used molecular methods to ascertain the constitutive breeds used to develop successful sled dog lines, and in doing so, determined the breed origins of specific performance-related behaviors. One hundred and ninety-nine Alaskan sled dogs were genotyped using 96 microsatellite markers that span the canine genome. These data were compared to that from 141 similarly genotyped purebred dog breeds. Sled dogs were evaluated for breed composition based on a variety of performance phenotypes including speed, endurance and work ethic, and the data stratified based on population structure. Results We observe that the Alaskan sled dog has a unique molecular signature and that the genetic profile is sufficient for identifying dogs bred for sprint versus distance. When evaluating contributions of existing breeds we find that the Alaskan Malamute and Siberian Husky contributions are associated with enhanced endurance; Pointer and Saluki are associated with enhanced speed and the Anatolian Shepherd demonstrates a positive influence on work ethic. Conclusion We have established a genetic breed profile for the Alaskan sled dog, identified profile variance between sprint and distance dogs, and established breeds associated with enhanced performance attributes. These data set the stage for mapping studies aimed at finding genes that are associated with athletic attributes integral to the high performing Alaskan sled dog.

  7. MORE ON THE APPROVAL OF ANTONINSKO-ZOZULENETSKIY CARPS OF UKRAINIAN BREEDS

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    O. Oleksiyenko

    2015-12-01

    Full Text Available Purpose. To perform an analysis the fish breeding, biological, productive, exterior indicators of Antoninsko-Zozulenetskiy carps of Ukrainian scaly and Ukrainian framed breeds, their genetic characteristics as well as to provide the methods of the creation of these carps as a selective achievement. Methodology. The works were carried out in accordance with conventional techniques in fish farming and breeding. Carp breeding was conducted by the method of mass continuously improving selection of fish the aim of which is that a complex of fish breeding and management activities create conditions contributing to the development of productive qualities in the selected carp, while selection and breeding activities form and reproduce the leading pedigree group of the stock. Findings. In the conditions of the development of fisheries industry, especially important are the problems of selection and breeding works aimed at improving the biological and economic features of fish farming objects by improving the existing and developing new breeds, inbreeding, zonal types, lines, etc., creating a progressive heterotic structure of breeds and forming highly productive pedigree stocks of fish breeding objects. The main object of commercial fish farming in Ukraine, as in many countries, is carp, so his selection is given much attention. The starting material for producing the Antoninsko-Zozulenetskiy Ukrainian scaly and Ukrainian framed breeds was carp population of Antoninskiy State fish hatchery (Khmelnytsky region, which was a cross between native carp with mirror Galician carp. The principal method of carp breeding was a massive, continuously improving selection with high intensity among younger age groups. An importance during the selection was given to the growth rate of the fish, their exterior and constitutional "strength." For the brood, individuals with the highest body weight, scaly cover of which corresponded to accepted standards, beautiful high

  8. Breeding, genetic and genomic of citrus for disease resistance

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    Marcos A. Machado

    2011-10-01

    Full Text Available Although the citriculture is one of the most important economic activities in Brazil, it is based on a small number of varieties. This fact has contributed for the vulnerability of the culture regarding the phytosanitary problems. A higher number of varieties/genotypes with potential for commercial growing, either for the industry or fresh market, has been one of the main objectives of citrus breeding programs. The genetic breeding of citrus has improved, in the last decades, due to the possibility of an association between biotechnological tools and classical methods of breeding. The use of molecular markers for early selection of zygotic seedlings from controlled crosses resulted in the possibility of selection of a high number of new combination and, as a consequence, the establishment of a great number of hybrids in field experiments. The faster new tools are incorporated in the program, the faster is possibility to reach new genotypes that can be tested as a new variety. Good traits should be kept or incorporate, whereas bad traits have to be excluded or minimized in the new genotype. Scion and rootstock can not be considered separately, and graft compatibility, fruit quality and productivity are essential traits to be evaluated in the last stages of the program. The mapping of QTLs has favored breeding programs of several perennial species and in citrus it was possible to map several characteristics with qualitative and quantitative inheritance. The existence of linkage maps and QTLs already mapped, the development of EST and BAC library and the sequencing of the Citrus complete genome altogether make very demanding and urgent the exploration of such data to launch a wider genetic study of citrus. The rising of information on genome of several organisms has opened new approaches looking for integration between breeding, genetic and genome. Genome assisted selection (GAS involves more than gene or complete genome sequencing and is becoming

  9. Native Pig and Chicken Breed Database: NPCDB

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    Hyeon-Soo Jeong

    2014-10-01

    Full Text Available Indigenous (native breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/ provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed’s characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  10. LINE CONSTRUCTION OF NONIUS BREED IN SLOVAKIA

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    Eva Mlyneková

    2013-12-01

    Full Text Available Nowadays breeding has become the problem often solved in European states and it has been paid much attention by breeding organizations. In terms of hippology as well as some urgent requirements from the side of nonius breeders we have focussed on this particular breed especially from the reason of its further survival and development in Slovakia. The aim of this paper was to evaluate the growth indicators as well as the achievement level of the stallions since 1927 to the present. Based on our research of the nonius body lines we can state that at present there are 3 stallions that are followers of the N VIII horse line founder. In general, there are 12 stallions that are active within this breed in Slovakia. It was statistically confirmed that this particular breed grew much stronger through the goal-directed breeding work, improved nutrition as well as the immediate breeding site. It was quite complicated to evaluate the performance tests because the individual indicators were significantly influenced by the subjective views of the commitee members performing the evaluation. The next factor which prevents the objective evaluation is the fact that in the period up to 1979, the performance tests were valued by the 100 point system and from the year 1980 by the 10 point system. That is why we take the performance test results into account only as supplemental ones, which can provide a kind of amendment to the observed biological parameters.

  11. Advances in Japanese pear breeding in Japan.

    Science.gov (United States)

    Saito, Toshihiro

    2016-01-01

    The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan's history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars 'Chojuro' and 'Nijisseiki' around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars 'Niitaka' and 'Shinko' were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including 'Kosui', 'Hosui', and 'Akizuki', which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, 'Gold Nijisseiki' has become a leading cultivar. Moreover, 'Nansui' from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress.

  12. Overlapping DSPP mutations cause dentin dysplasia and dentinogenesis imperfecta.

    Science.gov (United States)

    McKnight, D A; Simmer, J P; Hart, P S; Hart, T C; Fisher, L W

    2008-12-01

    Dentinogenesis imperfecta (DGI) and dentin dysplasia (DD) are allelic disorders due to mutations in DSPP. Typically, the phenotype breeds true within a family. Recently, two reports showed that 3 different net -1 bp frameshift mutations early in DSPP's repeat domain caused DD, whereas 6 more 3' frameshift mutations were associated with DGI. Here we identify a DD kindred with a novel -1 bp frameshift (c.3141delC) that falls within the portion of the DSPP repeat domain previously associated solely with the DGI phenotype. This new frameshift mutation shows that overlapping DSPP mutations can give rise to either DGI or DD phenotypes. Furthermore, the consistent kindred presentation of the DD or DGI phenotype appears to be dependent on an as-yet-undescribed genetic modifier closely linked to DSPP.

  13. Modeling Virtual Organization Architecture with the Virtual Organization Breeding Methodology

    Science.gov (United States)

    Paszkiewicz, Zbigniew; Picard, Willy

    While Enterprise Architecture Modeling (EAM) methodologies become more and more popular, an EAM methodology tailored to the needs of virtual organizations (VO) is still to be developed. Among the most popular EAM methodologies, TOGAF has been chosen as the basis for a new EAM methodology taking into account characteristics of VOs presented in this paper. In this new methodology, referred as Virtual Organization Breeding Methodology (VOBM), concepts developed within the ECOLEAD project, e.g. the concept of Virtual Breeding Environment (VBE) or the VO creation schema, serve as fundamental elements for development of VOBM. VOBM is a generic methodology that should be adapted to a given VBE. VOBM defines the structure of VBE and VO architectures in a service-oriented environment, as well as an architecture development method for virtual organizations (ADM4VO). Finally, a preliminary set of tools and methods for VOBM is given in this paper.

  14. Modeling Virtual Organization Architecture with the Virtual Organization Breeding Methodology

    CERN Document Server

    Paszkiewicz, Zbigniew

    2011-01-01

    While Enterprise Architecture Modeling (EAM) methodologies become more and more popular, an EAM methodology tailored to the needs of virtual organizations (VO) is still to be developed. Among the most popular EAM methodologies, TOGAF has been chosen as the basis for a new EAM methodology taking into account characteristics of VOs presented in this paper. In this new methodology, referred as Virtual Organization Breeding Methodology (VOBM), concepts developed within the ECOLEAD project, e.g. the concept of Virtual Breeding Environment (VBE) or the VO creation schema, serve as fundamental elements for development of VOBM. VOBM is a generic methodology that should be adapted to a given VBE. VOBM defines the structure of VBE and VO architectures in a service-oriented environment, as well as an architecture development method for virtual organizations (ADM4VO). Finally, a preliminary set of tools and methods for VOBM is given in this paper.

  15. Breeding Practices in Sheep Farming

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    M.A. Shejal

    2009-02-01

    Full Text Available The sheep is an important economic livestock species, contributing greatly to the Indian economy, especially in arid, semi arid and mountain areas. The current population in world is 1110.78 millions, around 44.85 millions (1987 sheeps in India (ICAR., 2002. Sheeps are mostly reared for meat and wool. The average annual wool production per sheep is between 3.5 to 5.5 kg of fine quality wool in Australia, New Zealand and U.S.S.R., where as in India except Magra sheep which annually yield more than 2 kg wool having staple length 5.8 cm, the average of rest of the wool produced is less than 1.0 kg per sheep of inferior quality (Banerjee G.C., 1998. Therefore many farmers in southern India adapted sheep rearing for meat production than for wool production. For yielding more production from sheep farming one should have sound knowledge of general information related to the reproduction and different breeding practices. [Vet. World 2009; 2(1.000: 43-44

  16. Efeitos da oferta de forragem, do método de pastejo, dos dias de avaliação e da raça no comportamento e temperamento de ovinos Effect of forage supply, methods of grazing, evaluation days and breed on the behavior and the temperament of sheep

    Directory of Open Access Journals (Sweden)

    José Manuel Díaz Gómez

    2010-08-01

    Full Text Available Objetivou-se estudar comportamento e o temperamento de ovinos de três raças (Suffolk, Texel, Ile de France submetidas a dois métodos de pastejo (contínuo e rotacionado, com duas ofertas de forragem (10 e 20 kg de MS de pastagem de azevém/100 kg de peso vivo/dia durante quatro avaliações, entre agosto e novembro de 2006. Utilizou-se o delineamento completamente casualizado em parcelas subsubdivididas, de modo que os métodos de pastejo e as ofertas de forragem constituíram as parcelas, as raças as subparcelas e os dias de avaliação as subsubparcelas. Foram utilizadas 48 fêmeas ovinas com peso médio inicial de 27,59 kg e idade entre 15 e 25 meses. Na avaliação do temperamento, efetuaram-se medidas comportamentais pelo teste de arena, tipo de marcha e tempo de fuga e atributos fisiológicos, como temperatura corporal e frequências cardiorrespiratórias. No método contínuo com baixa oferta de forragem, observou-se maior número de micções. Conforme as avaliações ocorreram, houve aumento da movimentação, das tentativas de fuga, mas menor número de vocalizações durante o isolamento. A raça Ile de France apresentou maior número de tentativas de fuga e de dejeções durante o isolamento. No pastejo rotacionado com alta oferta de forragem, o ganho de peso foi menor. A movimentação no isolamento e na presença do observador foi negativamente relacionada ao ganho de peso. As variáveis descritoras do temperamento apresentaram baixa repetibilidade. O temperamento dos ovinos foi modificado principalmente pelo dia de avaliação e pela raça, ao contrário do sistema de pastejo e da oferta de pasto, embora esses fatores tenham apresentado interação com os dias de avaliação e a raça do animal.This work aimed to study the temperament and the behavior of three sheep breeds (Suffolk, Texel, Ile de France submitted to two grazing methods (continuous and rotational with two forage supplies (10 and 20 kg of Italian ryegrass DM/100

  17. Management and Breeding Soundness of Mature Bulls.

    Science.gov (United States)

    Palmer, Colin W

    2016-07-01

    Mature bulls must be fed a balanced ration, vaccinated appropriately, and undergo a breeding soundness evaluation to ensure they meet what is required of a short, but intense breeding season. To be classified as a satisfactory potential breeder, minimum standards for physical soundness, scrotal circumference, sperm motility, and sperm morphology must be achieved using an accepted bull-breeding soundness evaluation format. Sperm production requires approximately 70 days. Heat and stress are the most common insults to spermatogenesis, causing an increase in morphologic abnormalities with obesity-associated scrotal fat accumulation being the most frequent cause of elevated testicular temperature in mature bulls.

  18. Effectiveness of a 95 SNP panel for the screening of breed label fraud in the Chinese meat market.

    Science.gov (United States)

    Rogberg-Muñoz, A; Wei, S; Ripoli, M V; Guo, B L; Carino, M H; Lirón, J P; Prando, A J; Vaca, R J A; Peral-García, P; Wei, Y M; Giovambattista, G

    2016-01-01

    Breed assignment has proved to be useful to control meat trade and protect the value of special productions. Meat-related frauds have been detected in China; therefore, 95 SNPs selected from the ISAG core panel were evaluated to develop an automated and technologically updated tool to screen breed label fraud in the Chinese meat market. A total of 271 animals from four Chinese yellow cattle (CYC) populations, six Bos taurus breeds, two Bos indicus and one composite were used. The allocation test distinguished European, Japanese and Zebu breeds, and two Chinese genetic components. It correctly allocated Japanese Black, Zebu and British breeds in 100, 90 and 89% of samples, respectively. CYC evidenced the Zebu, Holstein and Limousin introgression. The test did not detect CYC components in any of the 25 samples from Argentinean butchers. The method could be useful to certify Angus, Hereford and Japanese Black meat, but a modification in the panel would be needed to differentiate other breeds.

  19. 产γ聚谷氨酸菌株的诱变选育及其种子液工艺优化%Breeding high γ-polyglutamic acid-producing strain by composite mutation and the optimization of its seeds culture

    Institute of Scientific and Technical Information of China (English)

    张瑞; 周俊; 王舒雅; 沈立真; 陈怡露; 郑涛; 雍晓雨

    2015-01-01

    Bacillus amyloliquefaciens C1,isolated by our laboratory as aγ⁃polyglutamic acid producer,was treated with composite mutation method of ultraviolet and nitrosoguanidine. The liquid seed medium was also optimized by single⁃factor and orthogonal experiments. The resulted mutant strain C1⁃6 was screened with a γ⁃polyglutamic acid productivity of 24�2 g/L, increased by 31�5% compared with the original strain C1. C1⁃6 had a good genetic stability after 8 generations by transfer of culture experiment. Corn flour and soybean cake were selected as the carbon and nitrogen source respectively for C1⁃6 through single⁃factor experiments. Finally,the results of orthogonal experiments showed that the optimized liquid seed medium component was K2 HPO4 1�0 g/L,MgSO4 0�5 g/L,soybean cake 15�0 g/L and corn flour 5�0 g/L. In 150 mL shake flask,the optimal temperature,original pH and medium volume were 37 ℃, pH 6�5 and 30 mL,respectively,the larger biomass is obtained,the OD600 is 6�31.%以已筛选的1株产γ多聚谷氨酸解淀粉芽胞杆菌C1为出发菌株,对其进行紫外线亚硝基胍( NTG)复合诱变,并运用单因素试验和正交试验设计对诱变菌株的种子培养工艺进行优化。通过复合诱变选育得到1株能够稳定遗传的正突变菌株C16,其摇瓶发酵生产γ PGA的产量由18�4 g/L提高到24�2 g/L,增加了31�5%,且传代8次后仍能保持稳定。通过单因子试验筛选到玉米粉和黄豆粉作为C16生长的C源和N源。正交试验后, C16在成分为K2HPO41�0 g/L、MgSO40�5 g/L、黄豆粉15�0 g/L、玉米粉5�0 g/L,pH 6�5的培养基中,37℃、装液量1/5(150 mL三角瓶装液30 mL)的培养条件下可获得较大的生物量,OD600达到6�31。

  20. HNPCC: Six new pathogenic mutations

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    Epplen Joerg T

    2004-06-01

    Full Text Available Abstract Background Hereditary non-polyposis colorectal cancer (HNPCC is an autosomal dominant disease with a high risk for colorectal and endometrial cancer caused by germline mutations in DNA mismatch-repair genes (MMR. HNPCC accounts for approximately 2 to 5% of all colorectal cancers. Here we present 6 novel mutations in the DNA mismatch-repair genes MLH1, MSH2 and MSH6. Methods Patients with clinical diagnosis of HNPCC were counselled. Tumor specimen were analysed for microsatellite instability and immunohistochemistry for MLH1, MSH2 and MSH6 protein was performed. If one of these proteins was not detectable in the tumor mutation analysis of the corresponding gene was carried out. Results We identified 6 frameshift mutations (2 in MLH1, 3 in MSH2, 1 in MSH6 resulting in a premature stop: two mutations in MLH1 (c.2198_2199insAACA [p.N733fsX745], c.2076_2077delTG [p.G693fsX702], three mutations in MSH2 (c.810_811delGT [p.C271fsX282], c.763_766delAGTGinsTT [p.F255fsX282], c.873_876delGACT [p.L292fsX298] and one mutation in MSH6 (c.1421_1422dupTG [p.C475fsX480]. All six tumors tested for microsatellite instability showed high levels of microsatellite instability (MSI-H. Conclusions HNPCC in families with MSH6 germline mutations may show an age of onset that is comparable to this of patients with MLH1 and MSH2 mutations.

  1. Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Robert King

    Full Text Available Targeted Induced Local Lesions in Genomes (TILLING is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the TaGA20ox1 homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in TaGA20ox1, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues.

  2. The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations.

    Science.gov (United States)

    Lipinski, Monika J; Froenicke, Lutz; Baysac, Kathleen C; Billings, Nicholas C; Leutenegger, Christian M; Levy, Alon M; Longeri, Maria; Niini, Tirri; Ozpinar, Haydar; Slater, Margaret R; Pedersen, Niels C; Lyons, Leslie A

    2008-01-01

    The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds. The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age.

  3. Waterfowl Breeding Population and Habitat Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Waterfowl Breeding Population and Habitat Survey was initiated experimentally in 1947 and became operational in 1955. It is conducted cooperatively by the U.S....

  4. Western Ontario: Waterfowl breeding population survey: 1986

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1986. The primary purpose of the survey is to provide...

  5. California Least Tern Breeding Survey 1995 Season

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sterna antillarum browni) nested at 37 sites along the coast of California. This 7% decrease in breeding population size from 1994 brings to an end the trend since...

  6. Final Performance Report : Snowy Plover Breeding Distribution

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Surveys of breeding populations and nesting habitat of the snowy plover were conducted from January to August, 1989 along the Gulf Coast of Florida and Alabama....

  7. Waterfowl breeding population survey: Southern Saskatchewan: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Saskatchewan during 2000. The primary purpose of the survey is to provide...

  8. Waterfowl breeding pair survey: Southern Alberta: 1981

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Alberta during 1981. The primary purpose of the survey is to provide...

  9. Waterfowl breeding population survey: Southern Manitoba: 1983

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Manitoba during 1983. The primary purpose of the survey is to provide...

  10. Waterfowl breeding population survey for Montana: 1993

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Montana during 1993. The primary purpose of the survey is to provide information on...

  11. Waterfowl breeding population survey for Montana: 1998

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Montana during 1998. The primary purpose of the survey is to provide information on...

  12. Waterfowl breeding population survey: Southern Saskatchewan: 1983

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Saskatchewan during 1983. The primary purpose of the survey is to provide...

  13. Central Quebec: Waterfowl breeding population survey: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Central Quebec during 2000. The primary purpose of the survey is to provide...

  14. Western Ontario: Waterfowl breeding population survey: 1989

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1989. The primary purpose of the survey is to provide...

  15. Western Ontario: Waterfowl breeding population survey: 1995

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1995. The primary purpose of the survey is to provide...

  16. Western Ontario: Waterfowl breeding population survey: 1993

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1993. The primary purpose of the survey is to provide...

  17. Western Ontario: Waterfowl breeding population survey: 1994

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1994. The primary purpose of the survey is to provide...

  18. Western Ontario: Waterfowl breeding population survey: 1996

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1996. The primary purpose of the survey is to provide...

  19. Western Ontario: Waterfowl breeding population survey: 1987

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1987. The primary purpose of the survey is to provide...

  20. Western Ontario: Waterfowl breeding population survey: 1992

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1992. The primary purpose of the survey is to provide...

  1. Western Ontario: Waterfowl breeding population survey: 1990

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1990. The primary purpose of the survey is to provide...

  2. Western Ontario: Waterfowl breeding population survey: 1997

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1997. The primary purpose of the survey is to provide...

  3. Western Ontario: Waterfowl breeding population survey: 1988

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1988. The primary purpose of the survey is to provide...

  4. Blood group and protein polymorphism gene frequencies for the andalusian horse breed: a comparison with four american horse breeds

    OpenAIRE

    Aguilar Sánchez, P.; Rodríguez-Gallardo, P.P.; Andrés Cara, D.F. de; J.L Vega-Pla

    1992-01-01

    Gene frecuencies at seventeen blood group and protein polymorphism loci for the andalusian horse breed are given. Standard methods of starch and polyacrylamide gel electrophoresis were used to identify inherited variants at the following enzyme and other protein loci: albumin (Al), transferrin (Tf), carboxylesterase (Es), A1B glycoprotein (Xk), vitamin D binding protein (Gc), protease inhibitor (Pi), 6-phosphogluconate dehydrogenase (PGD), phosphoglucomutase (PGM) and glucosephosphate isomera...

  5. Evaluation of CFTR gene mutations in Adana

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    Ozlem Goruroglu Ozturk

    2013-04-01

    Full Text Available ABSTRACT Objective: Cystic fibrosis is the most common autosomal recessive inherited disorder seen in the white populations. It develops in result of mutations of cystic fibrosis transmembrane regulator (CFTR gene. Rate of these mutations vary in different geographical regions. In this study, we aimed to determine the frequency of CFTR gene mutations in Adana. Methods: DNA samples of 63 subjects (21 women, 42 men who were diagnosed as cystic fibrosis at Balcali Hospital of Cukurova University, were studied for 19 different CFTR mutations by the strip assay method which is based on reverse hybridization. Results: In cystic fibrosis diagnosed patients, 19 mutations were observed of which 9 were homozygous and 10 were heterozygous. ∆F508 frequency was found as 11.9%, and rate of homozygous was found as 66.7%. Mutation frequencies of W1282X and N1303K were found as 2.40% and 4.80% respectively and rate of homozygous mutations were 50% for both. I148T mutation frequency was found as 3.20% and all were heterozygous. For the whole 19 mutations, frequency of mutation in 63 subjects was 22.3%. Conclusion: Detection of CFTR gene mutations by the strip assay method by reverse hybridization is an easy, fast and informative method. However, due to improvability of the common mutations in probable cystic fibrosis patients because of heterogenity in this region, it is still a major problem and does not exclude cystic fibrosis diagnosis. But this problematic issue can be overcome by evaluating the whole exons of CFTR mutations by advanced molecular tecniques. Key words: CFTR, cystic fibrosis, molecular diagnosis, reverse hibridisation [Cukurova Med J 2013; 38(2.000: 202-208

  6. Potential benefits of genomic selection on genetic gain of small ruminant breeding programs.

    Science.gov (United States)

    Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Elsen, J M

    2013-08-01

    In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the

  7. Genetic diversity in native and commercial breeds of pigs in Portugal assessed by microsatellites.

    Science.gov (United States)

    Vicente, A A; Carolino, M I; Sousa, M C O; Ginja, C; Silva, F S; Martinez, A M; Vega-Pla, J L; Carolino, N; Gama, L T

    2008-10-01

    Population structure and genetic diversity in the Portuguese native breeds of pigs Alentejano (AL), Bísaro (BI), and Malhado de Alcobaça (MA) and the exotic breeds Duroc (DU), Landrace (LR), Large White (LW), and Pietrain were analyzed by typing 22 microsatellite markers in 249 individuals. In general, the markers used were greatly polymorphic, with mean total and effective number of alleles per locus of 10.68 and 4.33, respectively, and an expected heterozygosity of 0.667 across loci. The effective number of alleles per locus and expected heterozygosity were greatest in BI, LR, and AL, and least in DU. Private alleles were found in 9 of the 22 markers analyzed, mostly in AL, but also in the other breeds, with the exception of LW. The proportion of loci not in Hardy-Weinberg equilibrium in each breed analyzed ranged between 0.23 (AL) and 0.41 (BI, LW, and Pietrain), mostly because of a less than expected number of heterozygotes in those loci. With the exception of MA, all breeds showed a significant deficit in heterozygosity (F(IS); P < 0.05), which was more pronounced in BI (F(IS) = 0.175) and AL (F(IS) = 0.139), suggesting that inbreeding is a major concern, especially in these breeds that have gone through a genetic bottleneck in the recent past. The analysis of relationships among breeds, assessed by different methods, indicates that DU and AL are the more distanced breeds relative to the others, with the closest relationship being observed between LR and MA. The degree of differentiation between subpopulations (F(ST)) indicates that 0.184 of the total genetic variability can be attributed to differences among breeds. The analysis of individual distances based on allele sharing indicates that animals of the same breed generally cluster together, but subdivision is observed in the BI and LR breeds. Furthermore, the analysis of population structure indicates there is very little admixture among breeds, with each one being identified with a single ancestral

  8. Prunus transcription factors: Breeding perspectives

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    Valmor João Bianchi

    2015-06-01

    Full Text Available Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs. In peach, 1,533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq and RNA sequencing (RNA-Seq. New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.

  9. Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies.

    Directory of Open Access Journals (Sweden)

    Pascale Quignon

    Full Text Available BACKGROUND: In canine genetics, the impact of population structure on whole genome association studies is typically addressed by sampling approximately equal numbers of cases and controls from dogs of a single breed, usually from the same country or geographic area. However one way to increase the power of genetic studies is to sample individuals of the same breed but from different geographic areas, with the expectation that independent meiotic events will have shortened the presumed ancestral haplotype around the mutation differently. Little is known, however, about genetic variation among dogs of the same breed collected from different geographic regions. METHODOLOGY/PRINCIPAL FINDINGS: In this report, we address the magnitude and impact of genetic diversity among common breeds sampled in the U.S. and Europe. The breeds selected, including the Rottweiler, Bernese mountain dog, flat-coated retriever, and golden retriever, share susceptibility to a class of soft tissue cancers typified by malignant histiocytosis in the Bernese mountain dog. We genotyped 722 SNPs at four unlinked loci (between 95 and 271 per locus on canine chromosome 1 (CFA1. We showed that each population is characterized by distinct genetic diversity that can be correlated with breed history. When the breed studied has a reduced intra-breed diversity, the combination of dogs from international locations does not increase the rate of false positives and potentially increases the power of association studies. However, over-sampling cases from one geographic location is more likely to lead to false positive results in breeds with significant genetic diversity. CONCLUSIONS: These data provide new guidelines for association studies using purebred dogs that take into account population structure.

  10. [Pain caused by breeding: definition, judgment, pathogenesis].

    Science.gov (United States)

    Herzog, A

    1997-02-01

    Special terms of the "German Animal Protection Law (section 11b)"and the "European Agreement for Protection of Domestic Animals" particularly "torture-breeding, genetic characteristics, well-being, soundness, pains, injuries and specific use" are commented. Examples of torture-breedings are discussed: Dog (Merle-faktor, brachycephalie, atrichosis), cat (Mans-factor, W-gene, folded-ears), birds (tuffs, ear-drops, tailesness, hypertrophy of bill-warts, abnormal position of tarsal-joints, hypertrophy of imposing behavior).

  11. Determination Testing of Seed Hardness of Staple Breeding Wheat Seed in Gansu Province of China

    Directory of Open Access Journals (Sweden)

    Fei Dai

    2015-02-01

    Full Text Available Seed hardness is one of the important indexes of grain classification. It has close relationship with grain powder, flour quality, seed storage and processing, resist insect pest and so on. In this study, which applied based on the grain hardness indentation loading curve method and chose 3 kind of staple breeding wheat seed to determine the seed hardness in Gansu province. The experimental results showed that the average hardness value of staple breeding wheat seed was 22.42 MPa~57.85 MPa and the dispersion of the hardness value was small, which also between 3~12%. The seed hardness of breeding wheat of Western drought-resistant No.1 was maximum (52.36~61.36MPa and the seed hardness of breeding wheat of Western drought-resistant No.3 between two parties of the other breeding wheat, which was 42.12~50.20MPa. The seed hardness of breeding wheat of Western drought-resistant No.2 was minimum, which were 58.10~62.91% and 47.91~54.66% lower than the rest of the two breeding wheat seed hardness respectively. The findings will provide theoretical basis for seed production and processing and the stimulation analysis by EDEM.

  12. The distributions of Chinese yak breeds in response to climate change over the past 50 years.

    Science.gov (United States)

    Wu, Jianguo

    2016-07-01

    The effects of prior climate change on yak breed distributions are uncertain. Here, we measured changes in the distributions of 12 yak breeds over the past 50 years in China and examined whether the changes could be attributed to climate change. Long-term records of yak breed distribution, grey relational analysis, fuzzy sets classification techniques and attribution methods were used. Over the past 50 years, the distributions of several yak breeds have changed in multiple directions, mainly shifting northward or westward, and most of these changes are related to the thermal index. Driven by climate change over the past years, the suitable range and the distribution centers of certain yak breeds have changed with fluctuation and have mainly shifted northward, eastward or southward. The consistency of observed versus predicted changes in distribution boundaries or distribution centers is higher for certain yak breeds. Changes in the eastern distribution boundary of two yak breeds over the past 50 years can be attributed to climate change.

  13. Polymorphism analysis of the hsp70 stress gene in Broiler chickens (Gallus gallus of different breeds

    Directory of Open Access Journals (Sweden)

    Carmen Maria Mazzi

    2003-01-01

    Full Text Available The promoter region and the beginning of the coding region of the hsp70 stress gene were analysed in broiler chickens of a commercial breed (Hubbard-Pettersen, a breed selected for weight gain (PP1 and a non-selected breed (naked-neck Label Rouge. The naked neck gene (Naked neck, Na, which reduces feathering in birds and is thus related to heat resistance, was present in both PP1 and Label Rouge breeds. Genomic DNA was restricted with PstI and Southern blotting analysis of the samples revealed the absence of polymorphic sites for that enzyme in the promoter region and beginning of the coding region of the hsp70 gene of studied birds. PCR-SSCP analysis of these regions, however, indicated the presence of polymorphisms in the beginning of the coding region and the sequencing of the PCR products confirmed and identified two polymorphic sites in this region: a transition A ® G in position +258 and a transversion C ® G in position +276. Both mutations were considered to be silent, since they did not modify the aminoacid sequence of the protein Hsp70. The promoter region of the hsp70 gene was identical in all studied birds, indicating that the regulation pattern of this gene must be the same in all birds at the promoter region. Three different alleles (hsp70-1, hsp70-2 and hsp70-3 were identified for the hsp70 gene from the observed mutations. The allele hsp70-3 was detected in only two breeds, Hubbard-Pettersen and PP1, but at a low frequency (0,016 and 0,006, respectively.

  14. Testicular Histomorphometric Evaluation of Zebu Bull Breeds

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    Paulo Antônio Terrabuio Andreussi

    2014-12-01

    Full Text Available The objective of this study was to evaluate the quantitative histology and testicular biometrics in zebu bulls of different breeds. Testicular fragments of Nelore (n=10, Polled Nelore (n=6, Gir (n=5, Guzerat (n=5 and Tabapuã bulls (n=5 were used. The fragments were perfusion-fixed in Karnovsky solution, embedded in glycol methacrylate and stained with toluidine blue-1% sodium borate. The Nelore animals had a higher tubular volumetric proportion (85.2% and greater height of the seminiferous epithelium (73.2 µm than the Gir, Guzerat and Tabapuã breeds. The Nelore animals also had a higher volumetric proportion of Leydig cells (5.2% than the Guzerat and Tabapuã breeds. There was no significant difference for any of these parameters between the Nelore and Polled Nelore breeds. The gonadosomatic index, seminiferous tubule diameter, cross-sectional area of the seminiferous tubule and tubule length (total length and length per gram of testicular parenchyma did not vary among the breeds studied. The morphometric parameters evaluated suggested that the genetic selection applied to the Nelore and Polled Nelore breeds improved the efficiency of spermatogenesis in these breeders.

  15. Neutronic Comparison of Tritium-Breeding Performance of Candidate Tritium-Breeding Materials

    Institute of Scientific and Technical Information of China (English)

    郑善良; 吴宜灿

    2003-01-01

    Tritium self-sustainment, which will meet the fuel requirement of fusion reactor, isone of the key issues of fusion power development. The tritium breeding performances of varioustritium-breedin