Schnable, Patrick S; Ware, Doreen; Fulton, Robert S; Stein, Joshua C; Wei, Fusheng; Pasternak, Shiran; Liang, Chengzhi; Zhang, Jianwei; Fulton, Lucinda; Graves, Tina A; Minx, Patrick; Reily, Amy Denise; Courtney, Laura; Kruchowski, Scott S; Tomlinson, Chad; Strong, Cindy; Delehaunty, Kim; Fronick, Catrina; Courtney, Bill; Rock, Susan M; Belter, Eddie; Du, Feiyu; Kim, Kyung; Abbott, Rachel M; Cotton, Marc; Levy, Andy; Marchetto, Pamela; Ochoa, Kerri; Jackson, Stephanie M; Gillam, Barbara; Chen, Weizu; Yan, Le; Higginbotham, Jamey; Cardenas, Marco; Waligorski, Jason; Applebaum, Elizabeth; Phelps, Lindsey; Falcone, Jason; Kanchi, Krishna; Thane, Thynn; Scimone, Adam; Thane, Nay; Henke, Jessica; Wang, Tom; Ruppert, Jessica; Shah, Neha; Rotter, Kelsi; Hodges, Jennifer; Ingenthron, Elizabeth; Cordes, Matt; Kohlberg, Sara; Sgro, Jennifer; Delgado, Brandon; Mead, Kelly; Chinwalla, Asif; Leonard, Shawn; Crouse, Kevin; Collura, Kristi; Kudrna, Dave; Currie, Jennifer; He, Ruifeng; Angelova, Angelina; Rajasekar, Shanmugam; Mueller, Teri; Lomeli, Rene; Scara, Gabriel; Ko, Ara; Delaney, Krista; Wissotski, Marina; Lopez, Georgina; Campos, David; Braidotti, Michele; Ashley, Elizabeth; Golser, Wolfgang; Kim, HyeRan; Lee, Seunghee; Lin, Jinke; Dujmic, Zeljko; Kim, Woojin; Talag, Jayson; Zuccolo, Andrea; Fan, Chuanzhu; Sebastian, Aswathy; Kramer, Melissa; Spiegel, Lori; Nascimento, Lidia; Zutavern, Theresa; Miller, Beth; Ambroise, Claude; Muller, Stephanie; Spooner, Will; Narechania, Apurva; Ren, Liya; Wei, Sharon; Kumari, Sunita; Faga, Ben; Levy, Michael J; McMahan, Linda; Van Buren, Peter; Vaughn, Matthew W; Ying, Kai; Yeh, Cheng-Ting; Emrich, Scott J; Jia, Yi; Kalyanaraman, Ananth; Hsia, An-Ping; Barbazuk, W Brad; Baucom, Regina S; Brutnell, Thomas P; Carpita, Nicholas C; Chaparro, Cristian; Chia, Jer-Ming; Deragon, Jean-Marc; Estill, James C; Fu, Yan; Jeddeloh, Jeffrey A; Han, Yujun; Lee, Hyeran; Li, Pinghua; Lisch, Damon R; Liu, Sanzhen; Liu, Zhijie; Nagel, Dawn Holligan; McCann, Maureen C; SanMiguel, Phillip; Myers, Alan M; Nettleton, Dan; Nguyen, John; Penning, Bryan W; Ponnala, Lalit; Schneider, Kevin L; Schwartz, David C; Sharma, Anupma; Soderlund, Carol; Springer, Nathan M; Sun, Qi; Wang, Hao; Waterman, Michael; Westerman, Richard; Wolfgruber, Thomas K; Yang, Lixing; Yu, Yeisoo; Zhang, Lifang; Zhou, Shiguo; Zhu, Qihui; Bennetzen, Jeffrey L; Dawe, R Kelly; Jiang, Jiming; Jiang, Ning; Presting, Gernot G; Wessler, Susan R; Aluru, Srinivas; Martienssen, Robert A; Clifton, Sandra W; McCombie, W Richard; Wing, Rod A; Wilson, Richard K
We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
Advances in sequencing technology have made it possible to sequence the 2500 MB B73 maize genome, both cheaply and in a relatively short time. Nearly simultaneously, other sequencing-based data are on the leading edge of a data tsunami: sequenced differences (currently >300,000 SNP for >1000 inbre...
Regina S Baucom
Full Text Available Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75% of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR retrotransposon class of retroelements, with >400 families (>350 newly discovered contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families and LINEs (at least 30 families, were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to
Baucom, Regina S; Estill, James C; Chaparro, Cristian; Upshaw, Naadira; Jogi, Ansuya; Deragon, Jean-Marc; Westerman, Richard P; Sanmiguel, Phillip J; Bennetzen, Jeffrey L
Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially
González-Muñoz, Eliécer; Avendaño-Vázquez, Aida-Odette; Montes, Ricardo A Chávez; de Folter, Stefan; Andrés-Hernández, Liliana; Abreu-Goodger, Cei; Sawers, Ruairidh J H
Purple acid phosphatases (PAPs) play an important role in plant phosphorus nutrition, both by liberating phosphorus from organic sources in the soil and by modulating distribution within the plant throughout growth and development. Furthermore, members of the PAP protein family have been implicated in a broader role in plant mineral homeostasis, stress responses and development. We have identified 33 candidate PAP encoding gene models in the maize (Zea mays ssp. mays var. B73) reference genome. The maize Pap family includes a clear single-copy ortholog of the Arabidopsis gene AtPAP26, shown previously to encode both major intracellular and secreted acid phosphatase activities. Certain groups of PAPs present in Arabidopsis, however, are absent in maize, while the maize family contains a number of expansions, including a distinct radiation not present in Arabidopsis. Analysis of RNA-sequencing based transcriptome data revealed accumulation of maize Pap transcripts in multiple plant tissues at multiple stages of development, and increased accumulation of specific transcripts under low phosphorus availability. These data suggest the maize PAP family as a whole to have broad significance throughout the plant life cycle, while highlighting potential functional specialization of individual family members.
Eliécer eGonzález Muñoz
Full Text Available Purple acid phosphatases (PAPs play an important role in plant phosphorus nutrition, both by liberating phosphorus from organic sources in the soil and by modulating distribution within the plant throughout growth and development. Furthermore, members of the PAP protein family have been implicated in a broader role in plant mineral homeostasis, stress responses and development. We have identified 33 candidate PAP encoding gene models in the maize (Zea mays ssp. mays var. B73 reference genome. The maize Pap family includes a clear single-copy ortholog of the Arabidopsis gene AtPAP26, shown previously to encode both major intracellular and secreted acid phosphatase activities. Certain groups of PAPs present in Arabidopsis, however, are absent in maize, while the maize family contains a number of expansions, including a distinct radiation not present in Arabidopsis. Analysis of RNA-sequencing based transcriptome data revealed accumulation of maize Pap transcripts in multiple plant tissues at multiple stages of development, and increased accumulation of specific transcripts under low phosphorus availability. These data suggest the maize PAP family as a whole to have broad significance throughout the plant life cycle, while highlighting potential functional specialization of individual family members.
Martin W Ganal
Full Text Available SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS, and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations - IBM (B73×Mo17 and LHRF (F2×F252 - were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding.
Lee, Michael; Sharopova, Natalya; Beavis, William D; Grant, David; Katt, Maria; Blair, Deborah; Hallauer, Arnel
The effects of intermating on recombination and the development of linkage maps were assessed in maize. Progeny derived from a common population (B73 x Mo17) before and after five generations of intermating were genotyped at the same set of 190 RFLP loci. Intermating resulted in nearly a four-fold increase in the genetic map distance and increased the potential for improved genetic resolution in 91% of the intervals evaluated. This mapping population and related information should connect research involving dense genetic maps, physical mapping, gene isolation, comparative genomics, analysis of quantitative trait loci and investigations of heterosis.
Today, rising tropospheric ozone concentrations are estimated to reduce maize yields by 10% in the US. Exposure to ozone decreases plant productivity by reducing photosynthesis. As ozone enters the plant, it reacts to form reactive oxygen species that overwhelm the detoxification potential of the le...
The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-...
Venkatesh, Tyamagondlu V; Harrigan, George G; Perez, Tim; Flint-Garcia, Sherry
The present study provides an assessment of the compositional diversity in maize B73 hybrids derived both from the Nested Association Mapping (NAM) founder lines and from a diverse collection of landrace accessions from North and South America. The NAM founders represent a key population of publicly available lines that are used extensively in the maize community to investigate the genetic basis of complex traits. Landraces are also of interest to the maize community as they offer the potential to discover new alleles that could be incorporated into modern maize lines. The compositional analysis of B73 hybrids from the 25 NAM founders and 24 inbred lines derived from landraces included measurements of proximates (protein, fat, ash, and starch), fibers, minerals, amino acids, fatty acids, tocopherols (α-, γ-, and δ-), β-carotene, phytic acid, and raffinose. Grain was harvested from a replicated trial in New York, USA. For each data set (NAM and landrace) canonical discriminant analysis allowed separation of distinct breeding groups (tropical, temperate, flint, mixed/intermediate) within each data set. Overall, results highlighted extensive variation in all composition components assessed for both sets of hybrids. The variation observed for some components within the landraces may therefore be of value for increasing their levels in modern maize lines. The study described here provided significant information on contributions of conventional breeding to crop compositional variation, as well as valuable information on key genetic resources for the maize community in the development of new improved lines.
Ordas, Bernardo; Malvar, Rosa A; Santiago, Rogelio; Sandoya, German; Romay, Maria C; Butron, Ana
The Mediterranean corn borer or pink stem borer (MCB, Sesamia nonagrioides Lefebvre) causes important yield losses as a consequence of stalk tunneling and direct kernel damage. B73 and Mo17 are the source of the most commercial valuable maize inbred lines in temperate zones, while the intermated B73 x Mo17 (IBM) population is an invaluable source for QTL identification. However, no or few experiments have been carried out to detect QTL for corn borer resistance in the B73 x Mo17 population. The objective of this work was to locate QTL for resistance to stem tunneling and kernel damage by MCB in the IBM population. We detected a QTL for kernel damage at bin 8.05, although the effect was small and two QTL for stalk tunneling at bins 1.06 and 9.04 in which the additive effects were 4 cm, approximately. The two QTL detected for MCB resistance were close to other QTL consistently found for European corn borer (ECB, Ostrinia nubilalis Hübner) resistance, indicating mechanisms of resistance common to both pests or gene clusters controlling resistance to different plagues. The precise mapping achieved with the IBM population will facilitate the QTL pyramiding and the positional cloning of the detected QTL.
Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard
Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.
Sen, Taner Z; Harper, Lisa C; Schaeffer, Mary L; Andorf, Carson M; Seigfried, Trent E; Campbell, Darwin A; Lawrence, Carolyn J
As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers' needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers' needs. Here, we document the survey's outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/
Palmer, Lance E; Rabinowicz, Pablo D; O'Shaughnessy, Andrew L; Balija, Vivekanand S; Nascimento, Lidia U; Dike, Sujit; de la Bastide, Melissa; Martienssen, Robert A; McCombie, W Richard
Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.
The Maize Genetics and Genomics Database (MaizeGDB) is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data. In addition, MaizeGDB provides contact information for over 2400 maize cooperative researchers, facilitating interactions between members of the rapidly expanding maize community. MaizeGDB represents the synthesis of all data available previously from ZmDB and from MaizeDB—databases that have been superseded by Maiz...
Harper, Lisa; Gardiner, Jack; Andorf, Carson; Lawrence, Carolyn J
MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project's website ( http://www.maizegdb.org ) are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. In addition, pre-compiled reports are made available for particular types of data and bulletin boards are provided to facilitate communication and coordination among members of the community of maize geneticists.
Jamann, Tiffany M.; Sood, Shilpa; Wisser, Randall J.; Holland, James B.
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials. PMID:28045987
Using the genomic DNAs of maize and rice as probes respectively,the homology of maize and rice genomes was assessed by genomic in situ hybridization. When rice genomic DNAs were hybridized to maize, all chromosomes displayed many multiple discrete regions, while each rice chromosome delineated a single consecutive chromosomal region after they were hybridized with maize genomic DNAs. The results indicate that the genomes of maize and rice share high homology, and confirm the proposal that maize and rice are diverged from a common ancestor.
Full Text Available Abstract Background Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs. Hsf genes are represented by a large multigene family in plants and investigation of the Hsf gene family will serve to elucidate the mechanisms by which plants respond to stress. In recent years, reports of genome-wide structural and evolutionary analysis of the entire Hsf gene family have been generated in two model plant systems, Arabidopsis and rice. Maize, an important cereal crop, has represented a model plant for genetics and evolutionary research. Although some Hsf genes have been characterized in maize, analysis of the entire Hsf gene family were not completed following Maize (B73 Genome Sequencing Project. Results A genome-wide analysis was carried out in the present study to identify all Hsfs maize genes. Due to the availability of complete maize genome sequences, 25 nonredundant Hsf genes, named ZmHsfs were identified. Chromosomal location, protein domain and motif organization of ZmHsfs were analyzed in maize genome. The phylogenetic relationships, gene duplications and expression profiles of ZmHsf genes were also presented in this study. Twenty-five ZmHsfs were classified into three major classes (class A, B, and C according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 10 subclasses. Moreover, phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice were distributed in all three classes, it also revealed diverse Hsf gene family expression patterns in classes and subclasses. Chromosomal/segmental duplications played a key role in Hsf gene family expansion in maize by investigation of gene duplication events. Furthermore, the transcripts of 25 ZmHsf genes were detected in the leaves by heat shock using quantitative real-time PCR. The result demonstrated that ZmHsf genes exhibit different
Candice N Hansey
Full Text Available Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%. However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis.
About 85% of the maize genome consists of highly repetitive Sequences that are interspersed by low copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the Construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient ...
Wang, Qinghua; Dooner, Hugo K
Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic bz regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight bz haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.
We are developing a pachytene cytogenetic FISH (Fluorescence in situ Hybridization) map of the maize (Zea mays L.) genome using maize marker-selected sorghum BACs (Bacterial Artificial Chromosome) as described by Koumbaris and Bass (2003, Plant J. 35:647). The two main projects are the production of...
Yi Jiang; Biao Zeng; Hainan Zhao; Mei Zhang; Shaojun Xie; Jinsheng Lai
Transcription factors (TFs) are important regulators of gene expression.To better understand TFencoding genes in maize (Zea mays L.),a genome-wide TF prediction was performed using the updated B73 reference genome.A total of 2 298 TF genes were identified,which can be classified into 56 families.The largest family,known as the MYB superfamily,comprises 322 MYB and MYB-related TF genes.The expression patterns of 2014 (87.64％) TF genes were examined using RNA-seq data,which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues (including root,shoot,leaf,ear,tassel and kernel).Similarly,98 kernel-specific TF genes were further analyzed,and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage,while 69 of the genes were expressed in the late kernel developmental stage.Identification of these TFs,particularly the tissue-specific ones,provides important information for the understanding of development and transcriptional regulation of maize.
The present study expands metabolomic assessments of maize beyond commercial elite lines to include two sets of publicly available lines used extensively in the scientific community to investigate the genetic basis of complex plant traits or that may serve as a source of new alleles for improving mo...
Hufford, Matthew B; Xu, Xun; van Heerwaarden, Joost; Pyhäjärvi, Tanja; Chia, Jer-Ming; Cartwright, Reed A; Elshire, Robert J; Glaubitz, Jeffrey C; Guill, Kate E; Kaeppler, Shawn M; Lai, Jinsheng; Morrell, Peter L; Shannon, Laura M; Song, Chi; Springer, Nathan M; Swanson-Wagner, Ruth A; Tiffin, Peter; Wang, Jun; Zhang, Gengyun; Doebley, John; McMullen, Michael D; Ware, Doreen; Buckler, Edward S; Yang, Shuang; Ross-Ibarra, Jeffrey
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Full Text Available Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17 and their F1 hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex, five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity, and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization. Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an
Jiao, Yinping; Zhao, Hainan; Ren, Longhui; Song, Weibin; Zeng, Biao; Guo, Jinjie; Wang, Baobao; Liu, Zhipeng; Chen, Jing; Li, Wei; Zhang, Mei; Xie, Shaojun; Lai, Jinsheng
The success of modern maize breeding has been demonstrated by remarkable increases in productivity over the last four decades. However, the underlying genetic changes correlated with these gains remain largely unknown. We report here the sequencing of 278 temperate maize inbred lines from different stages of breeding history, including deep resequencing of 4 lines with known pedigree information. The results show that modern breeding has introduced highly dynamic genetic changes into the maize genome. Artificial selection has affected thousands of targets, including genes and non-genic regions, leading to a reduction in nucleotide diversity and an increase in the proportion of rare alleles. Genetic changes during breeding happen rapidly, with extensive variation (SNPs, indels and copy-number variants (CNVs)) occurring, even within identity-by-descent regions. Our genome-wide assessment of genetic changes during modern maize breeding provides new strategies as well as practical targets for future crop breeding and biotechnology.
Jian-Hong Xu; Joachim Messing
Comparative analyses of the sequence of entire genomes have shown that gene duplications,chromosomal segmental duplications.or even whole genome duplications(WGD)have played prominent roles in the evolution of many eukaryotic species.Here,we used the ancient duplication of a well known transcription factor in maize,encoded by the Opaque-2(02)IOCUS,to examine the generaI features of divergences of chromosomaI segmentaI duplications in a lineagespecific manner.We took advantage of contiguous chromosomal sequence information in rice(Oryza sativa,Nipponbare).sorghum(Sorghum bicoloc Btx623),and maize(Zea mays,B73)that were aligned by conserved gene order(synteny).This analysis showed that the maize O2 locus is contained within a 1.25 million base-pair(Mb)segment on chromosome 7.which was duplicated≈56 million years ago(mya)before the split of rice and maize 50 mya.The duplicated region on chromosome 1 is only half the size and contains the maize OHP gene.which does not restore the o2 mutation although it encodes a protein with the same DNA and protein binding properties in endosperm.The segmental duplication iS not only found in rice,but also in sorghum,which split from maize 11.9 mya.A detailed analysis of the duplicated regions provided examples for complex rearrangements including deletions.duplications,conversions,inversions,and translocations.Furthermore,the rice and sorghum genomes appeared to be more stable than the maize genome,probably because maize underwent allotetraploidization and then diploidization.
To better understand maize endosperm filling and maturation, we developed a novel functional genomics platform that combined Bulked Segregant RNA and Exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. Using gamma-irradiation of B73 maize to...
Du, Chunguang; Buckler, Edward; Muse, Spencer
PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on 'Maize Evolutionary Genomics'. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web.
Barbazuk, W Brad; Bedell, Joseph A; Rabinowicz, Pablo D
Plant, and particularly cereal genomes, are challenging to sequence due to their large size and high repetitive DNA content. Gene-enrichment strategies are alternative or complementary approaches to complete genome sequencing that yield, rapidly and inexpensively, useful sequence data from large and complex genomes. The maize genome is large (2.7 Gbp) and contains large amounts of conserved repetitive elements. Furthermore, the high allelic diversity found between maize inbred lines may necessitate sequencing several inbred lines in order to recover the maize "gene pool". Two gene-enrichment approaches, methylation filtration (MF) and high C(o)t (HC) sequencing have been tested in maize and their ability to sample the gene space has been examined. Combined with other genomic sequencing strategies, gene-enriched genomic sequencing is a practical way to examine the maize gene pool, to order and orient the genic sequences on the genome, and to enable investigation of gene content of other complex plant genomes.
Stirnberg, Alexandra; Djamei, Armin
The biotrophic fungus Ustilago maydis, the causal agent of corn smut disease, uses numerous small secreted effector proteins to suppress plant defence responses and reshape the host metabolism. However, the role of specific effectors remains poorly understood. Here, we describe the identification of ApB73 (Apathogenic in B73), an as yet uncharacterized protein essential for the successful colonization of maize by U. maydis. We show that apB73 is transcriptionally induced during the biotrophic stages of the fungal life cycle. The deletion of the apB73 gene results in cultivar-specific loss of gall formation in the host. The ApB73 protein is conserved among closely related smut fungi. However, using virulence assays, we show that only the orthologue of the maize-infecting head smut Sporisorium reilianum can complement the mutant phenotype of U. maydis. Although microscopy shows that ApB73 is secreted into the biotrophic interface, it seems to remain associated with fungal cell wall components or the fungal plasma membrane. Taken together, the results show that ApB73 is a conserved and important virulence factor of U. maydis that localizes to the interface between the pathogen and its host Zea mays.
Berger Dave K
Full Text Available Abstract Background Microarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a reporter - gene model match, (b number of reporters per gene model, (c potential for cross hybridization, (d sense/antisense orientation of reporters, (e position of reporter on B73 genome sequence (for eQTL studies, and (f functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database. Description Genomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i "annotation by sense gene model" (23,668 reporters, (ii "annotation by antisense gene model" (4,330; (iii "annotation by gDNA" without a WGS transcript hit (1,549; (iv "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390; (v "ambiguous annotation" (2,608; and (vi "inconclusive annotation" (6,489. Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank. The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to
Liu, Renyi; Vitte, Clémentine; Ma, Jianxin; Mahama, A Assibi; Dhliwayo, Thanda; Lee, Michael; Bennetzen, Jeffrey L
Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains approximately 37,000 candidate genes with homologues in other plant species. An additional approximately 5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with approximately 30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.
Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits which have been validated with fine-mapping and functional analysis. Many sequence variants associated with complex traits in maize have small effects and low repeatability, howev...
Liu, Sanzhen; Zheng, Jun; Migeon, Pierre; Ren, Jie; Hu, Ying; He, Cheng; Liu, Hongjun; Fu, Junjie; White, Frank F.; Toomajian, Christopher; Wang, Guoying
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement. PMID:28186206
Barrière, Yves; Courtial, Audrey; Chateigner-Boutin, Anne-Laure; Denoue, Dominique; Grima-Pettenati, Jacqueline
The knowledge of the gene families mostly impacting cell wall digestibility variations would significantly increase the efficiency of marker-assisted selection when breeding maize and grass varieties with improved silage feeding value and/or with better straw fermentability into alcohol or methane. The maize genome sequence of the B73 inbred line was released at the end of 2009, opening up new avenues to identify the genetic determinants of quantitative traits. Colocalizations between a large set of candidate genes putatively involved in secondary cell wall assembly and QTLs for cell wall digestibility (IVNDFD) were then investigated, considering physical positions of both genes and QTLs. Based on available data from six RIL progenies, 59 QTLs corresponding to 38 non-overlapping positions were matched up with a list of 442 genes distributed all over the genome. Altogether, 176 genes colocalized with IVNDFD QTLs and most often, several candidate genes colocalized at each QTL position. Frequent QTL colocalizations were found firstly with genes encoding ZmMYB and ZmNAC transcription factors, and secondly with genes encoding zinc finger, bHLH, and xylogen regulation factors. In contrast, close colocalizations were less frequent with genes involved in monolignol biosynthesis, and found only with the C4H2, CCoAOMT5, and CCR1 genes. Close colocalizations were also infrequent with genes involved in cell wall feruloylation and cross-linkages. Altogether, investigated colocalizations between candidate genes and cell wall digestibility QTLs suggested a prevalent role of regulation factors over constitutive cell wall genes on digestibility variations.
Arteaga, María Clara; Moreno-Letelier, Alejandra; Mastretta-Yanes, Alicia; Vázquez-Lobo, Alejandra; Breña-Ochoa, Alejandra; Moreno-Estrada, Andrés; Eguiarte, Luis E.; Piñero, Daniel
The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law. PMID:26981357
María Clara Arteaga
Full Text Available The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311, while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively. The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.
Arteaga, María Clara; Moreno-Letelier, Alejandra; Mastretta-Yanes, Alicia; Vázquez-Lobo, Alejandra; Breña-Ochoa, Alejandra; Moreno-Estrada, Andrés; Eguiarte, Luis E; Piñero, Daniel
The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (H E = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (H E = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.
Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes.Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other plant species.In this study,a total of 1003 maize lipid-related genes were cloned and annotated,including 42 genes with experimental validation,732 genes with full-length cDNA and protein sequences in public databases and 229 newly cloned genes.Ninety-seven maize lipid-related genes with tissue-preferential expression were discovered by in silico gene expression profiling based on 1984483 maize Expressed Sequence Tags collected from 182 cDNA libraries.Meanwhile,70 QTL clusters for maize kernel oil were identified,covering 34.5% of the maize genome.Fifty-nine (84%) QTL clusters co-located with at least one lipid-related gene,and the total number of these genes amounted to 147.Interestingly,thirteen genes with kernel-preferential expression profiles fell within QTL clusters for maize kernel oil content.All the maize lipid-related genes identified here may provide good targets for maize kernel oil QTL cloning and thus help us to better understand the molecular mechanism of maize kernel oil accumulation.
Kong, Xiangpei; Lv, Wei; Zhang, Dan; Jiang, Shanshan; Zhang, Shizhong; Li, Dequan
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signal transduction model in animals, yeast and plants. Plant MAPK cascades have been implicated in development and stress responses. Although MAPKKKs have been investigated in several plant species including Arabidopsis and rice, no systematic analysis has been conducted in maize. In this study, we performed a bioinformatics analysis of the entire maize genome and identified 74 MAPKKK genes. Phylogenetic analyses of MAPKKKs from maize, rice and Arabidopsis have classified them into three subgroups, which included Raf, ZIK and MEKK. Evolutionary relationships within subfamilies were also supported by exon-intron organizations and the conserved protein motifs. Further expression analysis of the MAPKKKs in microarray databases revealed that MAPKKKs were involved in important signaling pathways in maize different organs and developmental stages. Our genomics analysis of maize MAPKKK genes provides important information for evolutionary and functional characterization of this family in maize.
Full Text Available Mitogen-activated protein kinase (MAPK cascades are highly conserved signal transduction model in animals, yeast and plants. Plant MAPK cascades have been implicated in development and stress responses. Although MAPKKKs have been investigated in several plant species including Arabidopsis and rice, no systematic analysis has been conducted in maize. In this study, we performed a bioinformatics analysis of the entire maize genome and identified 74 MAPKKK genes. Phylogenetic analyses of MAPKKKs from maize, rice and Arabidopsis have classified them into three subgroups, which included Raf, ZIK and MEKK. Evolutionary relationships within subfamilies were also supported by exon-intron organizations and the conserved protein motifs. Further expression analysis of the MAPKKKs in microarray databases revealed that MAPKKKs were involved in important signaling pathways in maize different organs and developmental stages. Our genomics analysis of maize MAPKKK genes provides important information for evolutionary and functional characterization of this family in maize.
Early Transcriptomic Adaptation to Na2CO3 Stress Altered the Expression of a Quarter of the Total Genes in the Maize Genome and Exhibited Shared and Distinctive Profiles with NaCl and High pH Stresses
LiMin Zhang; XiangGuo Liu; XinNing Qu; Ying Yu; SiPing Han; Yao Dou; YaoYao Xu; HaiChun Jing; DongYun Hao
Sodium carbonate (Na2CO3) presents a huge challenge to plants by the combined damaging effects of Naþ, high pH, and CO32-. Little is known about the cellular responses to Na2CO3 stress. In this study, the transcriptome of maize (Zea mays L. cv. B73) roots exposed to Na2CO3 stress for 5 h was compared with those of NaCl and NaOH stresses. The expression of 8,319 genes, representing over a quarter of the total number of genes in the maize genome, was altered by Na2CO3 stress, and the downregulated genes (5,232) outnumbered the upregulated genes (3,087). The effects of Na2CO3 differed from those of NaCl and NaOH, primarily by downregulating different categories of genes. Pathways commonly altered by Na2CO3, NaCl, and NaOH were enriched in phenylpropanoid biosynthesis, oxidation of unsaturated fatty acids, ATP-binding cassette (ABC) transporters, as well as the metabolism of secondary metabolites. Genes for brassinosteroid biosynthesis were specifically upregulated by Na2CO3, while genes involved in ascorbate and aldarate metabolism, protein processing in the endoplasmic reticulum and by N-glycosylation, fatty acid biosynthesis, and the circadian rhythm were downregulated. This work provides the first holistic picture of early transcriptomic adaptation to Na2CO3 stress, and highlights potential molecular pathways that could be manipulated to improve tolerance in maize.
Owens, Brenda F; Lipka, Alexander E; Magallanes-Lundback, Maria; Tiede, Tyler; Diepenbrock, Christine H; Kandianis, Catherine B; Kim, Eunha; Cepela, Jason; Mateos-Hernandez, Maria; Buell, C Robin; Buckler, Edward S; DellaPenna, Dean; Gore, Michael A; Rocheford, Torbert
Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A.
Andorf, Carson M; Kopylov, Mykhailo; Dobbs, Drena; Koch, Karen E; Stroupe, M Elizabeth; Lawrence, Carolyn J; Bass, Hank W
The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This G4 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationally identified 149,988 non-telomeric G4 motifs in maize (Zea mays L., B73 AGPv2), 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5' UTR and the other at the 5' end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia (group VII ERFs), oxidative stress (DJ-1/GATase1), and energy status (AMPK/SnRK) pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.
Svitashev, Sergei; Schwartz, Christine; Lenderts, Brian; Young, Joshua K.; Mark Cigan, A.
Targeted DNA double-strand breaks have been shown to significantly increase the frequency and precision of genome editing. In the past two decades, several double-strand break technologies have been developed. CRISPR–Cas9 has quickly become the technology of choice for genome editing due to its simplicity, efficiency and versatility. Currently, genome editing in plants primarily relies on delivering double-strand break reagents in the form of DNA vectors. Here we report biolistic delivery of pre-assembled Cas9–gRNA ribonucleoproteins into maize embryo cells and regeneration of plants with both mutated and edited alleles. Using this method of delivery, we also demonstrate DNA- and selectable marker-free gene mutagenesis in maize and recovery of plants with mutated alleles at high frequencies. These results open new opportunities to accelerate breeding practices in a wide variety of crop species. PMID:27848933
Saha, Rajib; Suthers, Patrick F; Maranas, Costas D
The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.
Full Text Available The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize. Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular. GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3. The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.
Thatcher, Shawn R; Danilevskaya, Olga N; Meng, Xin; Beatty, Mary; Zastrow-Hayes, Gina; Harris, Charlotte; Van Allen, Brandon; Habben, Jeffrey; Li, Bailin
Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.
Thatcher, Shawn R.; Meng, Xin; Beatty, Mary; Zastrow-Hayes, Gina; Harris, Charlotte; Habben, Jeffrey; Li, Bailin
Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition. PMID:26582726
Wang, Fei; Li, Zhaoying; Fan, Jun; Li, Pengfei; Hu, Wei; Wang, Gang; Xu, Zhengkai; Song, Rentao
Transposon tagging is an important tool for gene isolation and functional studies. In maize, several transposon-tagging systems have been developed, mostly using Activator/Dissociation (Ac/Ds) and Mutator systems. Here, we establish another Ac-based transposon system with the donor Ac tightly linked with sugary1 (su1) on maize chromosome 4S. Newly transposed Ac (tr-Acs) were detected based on a negative dosage effect, and long-distance-transposed Ac events were identified and isolated from the donor Ac by a simple backcross scheme. In this study, we identified 208 independent long-distance-transposed Ac lines. Thirty-one flanking sequences of these tr-Acs were isolated and localized in the maize genome. As found in previous studies, the tr-Acs preferentially inserted into genic sequences. The distribution of tr-Acs is not random. In our study, the tr-Acs preferentially transposed into chromosomes 1, 2, 9 and 10. We discuss the preferential distribution of tr-Acs from Ac systems. Our system is complementary to two other Ac-based regional-mutagenesis systems in maize, and the combined use of these systems will achieve an even and high-density distribution of Ac elements throughout the maize genome for functional-genomics studies.
Ramos Madrigal, Jazmin; Smith, Bruce D.; Moreno Mayar, José Victor
The complex evolutionary history of maize (Zea mays L. ssp. mays) has been clarified with genomic-level data from modern landraces and wild teosinte grasses [1, 2], augmenting archaeological findings that suggest domestication occurred between 10,000 and 6,250 years ago in southern Mexico [3, 4......]. Maize rapidly evolved under human selection, leading to conspicuous phenotypic transformations, as well as adaptations to varied environments . Still, many questions about the domestication process remain unanswered because modern specimens do not represent the full range of past diversity due...... to abandonment of unproductive lineages, genetic drift, on-going natural selection, and recent breeding activity. To more fully understand the history and spread of maize, we characterized the draft genome of a 5,310-year-old archaeological cob excavated in the Tehuacan Valley of Mexico. We compare this ancient...
Alvarez-Quinto, Robert A; Espinoza-Lozano, Rodrigo F; Mora-Pinargote, Carlos A; Quito-Avila, Diego F
The complete genomic sequence of a variant of the recently reported maize-associated totivirus (MATV) from China was obtained from commercial maize in Ecuador. The genome of MATV-Ec (Ecuador) (4,998 bp) is considerably longer than that of MATV-Ch (China) (3,956 bp), the main difference due to a ≈ 1-kb-long capsid-protein-encoding fragment that is completely absent from the Chinese genome. Sequence alignments between MATV-Ec and MATV-Ch showed an overall identity of 82% at the nucleotide level, whereas at the amino acid level, the viruses exhibited 95% and 94% identity for the putative capsid protein and the RNA-dependent RNA polymerase (RdRp), respectively. Phylogenetic analysis of the viral RdRp domain indicated that MATV-Ec and MATV-Ch share a common ancestor with other plant-associated totiviruses, with Panax notoginseng virus A as the closest relative. MATV-Ec was detected in 46% (n = 80) of maize plants tested in this study, but not in endophytic fungi isolated from plants positive for the virus.
Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.
Full Text Available MicroRNAs (miRNAs are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
Han, Yahui; Ding, Ting; Su, Bo; Jiang, Haiyang
Members of the chalcone synthase (CHS) family participate in the synthesis of a series of secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in protecting land plants against various environmental stresses during the evolutionary process. Our research was conducted on comprehensive investigation of CHS genes in maize (Zea mays L.), including their phylogenetic relationships, gene structures, chromosomal locations and expression analysis. Fourteen CHS genes (ZmCHS01-14) were identified in the genome of maize, representing one of the largest numbers of CHS family members identified in one organism to date. The gene family was classified into four major classes (classes I-IV) based on their phylogenetic relationships. Most of them contained two exons and one intron. The 14 genes were unevenly located on six chromosomes. Two segmental duplication events were identified, which might contribute to the expansion of the maize CHS gene family to some extent. In addition, quantitative real-time PCR and microarray data analyses suggested that ZmCHS genes exhibited various expression patterns, indicating functional diversification of the ZmCHS genes. Our results will contribute to future studies of the complexity of the CHS gene family in maize and provide valuable information for the systematic analysis of the functions of the CHS gene family.
Full Text Available There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.
Prasanna, B M
Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. 'Seeds of Discovery' (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is
B M Prasanna
Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. ‘Seeds of Discovery’ (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this
Ramos-Madrigal, Jazmín; Smith, Bruce D; Moreno-Mayar, J Víctor; Gopalakrishnan, Shyam; Ross-Ibarra, Jeffrey; Gilbert, M Thomas P; Wales, Nathan
The complex evolutionary history of maize (Zea mays L. ssp. mays) has been clarified with genomic-level data from modern landraces and wild teosinte grasses [1, 2], augmenting archaeological findings that suggest domestication occurred between 10,000 and 6,250 years ago in southern Mexico [3, 4]. Maize rapidly evolved under human selection, leading to conspicuous phenotypic transformations, as well as adaptations to varied environments . Still, many questions about the domestication process remain unanswered because modern specimens do not represent the full range of past diversity due to abandonment of unproductive lineages, genetic drift, on-going natural selection, and recent breeding activity. To more fully understand the history and spread of maize, we characterized the draft genome of a 5,310-year-old archaeological cob excavated in the Tehuacan Valley of Mexico. We compare this ancient sample against a reference panel of modern landraces and teosinte grasses using D statistics, model-based clustering algorithms, and multidimensional scaling analyses, demonstrating the specimen derives from the same source population that gave rise to modern maize. We find that 5,310 years ago, maize in the Tehuacan Valley was on the whole genetically closer to modern maize than to its wild counterpart. However, many genes associated with key domestication traits existed in the ancestral state, sharply contrasting with the ubiquity of derived alleles in living landraces. These findings suggest much of the evolution during domestication may have been gradual and encourage further paleogenomic research to address provocative questions about the world's most produced cereal.
Karn, Avinash; Gillman, Jason D; Flint-Garcia, Sherry A
Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared to maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (teosinte NILs) was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing ten geographically diverse parviglumis accessions into the B73 (reference genome inbred) background. The NILs were grown in two replications in 2009 and 2010 in Columbia, Missouri and Aurora, New York, respectively, and Near Infrared Reflectance (NIR) spectroscopy and Nuclear Magnetic Resonance (NMR) calibrations were developed and used to rapidly predict total kernel starch, protein and oil content on a dry matter basis in bulk whole grains of teosinte NILs. Our joint-linkage quantitative trait locus (QTL) mapping analysis identified two starch, three protein and six oil QTLs, which collectively explained 18%, 23% and 45% of the total variation, respectively. A range of strong additive allelic effects for kernel starch, protein and oil content were identified relative to the B73 allele. Our results support our hypothesis that teosinte harbors stronger alleles for kernel composition traits than maize, and that teosinte can be exploited for the improvement of kernel composition traits in modern maize germplasm.
Maud I. Tenaillon
Full Text Available Little is known about the factors driving within species Genome Size (GS variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27. However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.
Song, Jian; Guo, Baojian; Song, Fangwei; Peng, Huiru; Yao, Yingyin; Zhang, Yirong; Sun, Qixin; Ni, Zhongfu
Gibberellin (GA) is an essential phytohormone that controls many aspects of plant development. To enhance our understanding of GA metabolism in maize, we intensively screened and identified 27 candidate genes encoding the seven GA metabolic enzymes including ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox), using all available public maize databases. The results indicate that maize genome contains three CPS, four KS, two KO and one KAO genes, and most of them are arranged separately on the maize genome, which differs from that in rice. In addition, the enzymes catalyzing the later steps (ZmGA20ox, ZmGA3ox and ZmGA2ox) are also encoded by gene families in maize, but GA3ox enzyme is likely to be encoded by single gene. Expression profiling analysis exhibited that transcripts of 15 GA metabolic genes could be detected during maize seed germination, which provides further evidence for the notion that increased synthesis of active GA in the embryo is required for triggering germination events. Moreover, a variety of temporal genes expression patterns of GA metabolic genes were detected, which revealed the complexity of underlying mechanism for GA regulated seed germination.
Lorenz, Aaron J; Beissinger, Timothy M; Silva, Renato Rodrigues; de Leon, Natalia
Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in the WQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17,719 high-quality, informative single nucleotide polymorphisms. Likewise, no strong genomic signatures were left by selection on silage yield and quality in the WQS despite genetic gain for these traits. These results could be due to the genetic complexity underlying these traits, or the role of selection on standing genetic variation. Variation in loss of diversity through drift was observed across the genome. Some large regions experienced much greater loss in diversity than what is expected, suggesting limited recombination combined with small populations in recurrent selection programs could easily lead to fixation of large swaths of the genome.
Lorenz, Aaron J.; Beissinger, Timothy M.; Silva, Renato Rodrigues; de Leon, Natalia
Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in the WQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17,719 high-quality, informative single nucleotide polymorphisms. Likewise, no strong genomic signatures were left by selection on silage yield and quality in the WQS despite genetic gain for these traits. These results could be due to the genetic complexity underlying these traits, or the role of selection on standing genetic variation. Variation in loss of diversity through drift was observed across the genome. Some large regions experienced much greater loss in diversity than what is expected, suggesting limited recombination combined with small populations in recurrent selection programs could easily lead to fixation of large swaths of the genome. PMID:25645532
Bioenergy crops currently provide the only source of alternative energy with the potential to reduce the use of fossil transportation fuels in a way that is compatible with existing engine technology, including in developing countries. Even though bioenergy research is currently receiving considerable attention, many of the concepts are not new,but rather build on intense research efforts from 30 years ago. A major difference with that era is the availability of genomics tools that have the potential to accelerate crop improvement significantly. This review is focused on maize, sorghum and sugarcane as representatives of bioenergy grasses that produce sugar and/or lignocellulosic biomass.Examples of how genetic mapping, forward and reverse genetics, high-throughput expression profiling and comparative genomics can be used to unravel and improve bioenergy traits will be presented.
Gerke, Justin P; Edwards, Jode W; Guill, Katherine E; Ross-Ibarra, Jeffrey; McMullen, Michael D
Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture's reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome.
Li, Qing; Gent, Jonathan I; Zynda, Greg; Song, Jawon; Makarevitch, Irina; Hirsch, Cory D; Hirsch, Candice N; Dawe, R Kelly; Madzima, Thelma F; McGinnis, Karen M; Lisch, Damon; Schmitz, Robert J; Vaughn, Matthew W; Springer, Nathan M
The maize genome is relatively large (∼ 2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼ 100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.
Realini, María Florencia; Poggio, Lidia; Cámara-Hernández, Julián; González, Graciela Esther
Genome size variation accompanies the diversification and evolution of many plant species. Relationships between DNA amount and phenotypic and cytological characteristics form the basis of most hypotheses that ascribe a biological role to genome size. The goal of the present research was to investigate the intra-specific variation in the DNA content in maize populations from Northeastern Argentina and further explore the relationship between genome size and the phenotypic traits seed weight and length of the vegetative cycle. Moreover, cytological parameters such as the percentage of heterochromatin as well as the number, position and sequence composition of knobs were analysed and their relationships with 2C DNA values were explored. The populations analysed presented significant differences in 2C DNA amount, from 4.62 to 6.29 pg, representing 36.15 % of the inter-populational variation. Moreover, intra-populational genome size variation was found, varying from 1.08 to 1.63-fold. The variation in the percentage of knob heterochromatin as well as in the number, chromosome position and sequence composition of the knobs was detected among and within the populations. Although a positive relationship between genome size and the percentage of heterochromatin was observed, a significant correlation was not found. This confirms that other non-coding repetitive DNA sequences are contributing to the genome size variation. A positive relationship between DNA amount and the seed weight has been reported in a large number of species, this relationship was not found in the populations studied here. The length of the vegetative cycle showed a positive correlation with the percentage of heterochromatin. This result allowed attributing an adaptive effect to heterochromatin since the length of this cycle would be optimized via selection for an appropriate percentage of heterochromatin. PMID:26644343
In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...
Wang, Guifeng; Zhong, Mingyu; Wang, Jiajia; Zhang, Jushan; Tang, Yuanping; Wang, Gang; Song, Rentao
The actin-based myosin system is essential for the organization and dynamics of the endomembrane system and transport network in plant cells. Plants harbour two unique myosin groups, class VIII and class XI, and the latter is structurally and functionally analogous to the animal and fungal class V myosin. Little is known about myosins in grass, even though grass includes several agronomically important cereal crops. Here, we identified 14 myosin genes from the genome of maize (Zea mays). The relatively larger sizes of maize myosin genes are due to their much longer introns, which are abundant in transposable elements. Phylogenetic analysis indicated that maize myosin genes could be classified into class VIII and class XI, with three and 11 members, respectively. Apart from subgroup XI-F, the remaining subgroups were duplicated at least in one analysed lineage, and the duplication events occurred more extensively in Arabidopsis than in maize. Only two pairs of maize myosins were generated from segmental duplication. Expression analysis revealed that most maize myosin genes were expressed universally, whereas a few members (XI-1, -6, and -11) showed an anther-specific pattern, and many underwent extensive alternative splicing. We also found a short transcript at the O1 locus, which conceptually encoded a headless myosin that most likely functions at the transcriptional level rather than via a dominant-negative mechanism at the translational level. Together, these data provide significant insights into the evolutionary and functional characterization of maize myosin genes that could transfer to the identification and application of homologous myosins of other grasses.
Farfan, Ivan D Barrero; De La Fuente, Gerald N; Murray, Seth C; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L; Kolomiets, Mike
The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.
Ivan D Barrero Farfan
Full Text Available The primary maize (Zea mays L. production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.
Xin Zhang; Jie Zong; Jianhua Liu; Jinyuan Yin; Dabing Zhang
WUSCHEL-related homeobox(WOX)genes form a large gene family specifically expressed in plants.They are known to play important roles in regulating the development of plant tissues and organs by determining cell fate.Recent available whole genome sequences allow us to do more comprehensive phylogenetic analysis of the WOX genes in plants.In the present study,we identified 11 and 21 WOXs from sorghum(Sorghum bicolor)and maize(Zea mays),respectively.The 72 WOX genes from rice(Oryza sativa),sorghum,maize,Arabidopsis(Arabidopsis thaliana)and poplar(Populus trichocarpa)were grouped into three well supported clades with nine subgroups according to the amino acid sequences of their homodomains.Their phylogenetic relationship was also supported by the observation of the motifs outside the homodomain.We observed the variation of duplication events among the nine sub-groups between monocots and eudicots,for instance,more gene duplication events of WOXs within subgroup A for monocots,while,less for dicots in this subgroup.Furthermore,we observed the conserved intron/exon structural patterns of WOX genes in rice,sorghum and Arabidopsis.In addition,WUS(Wuschel)-box and EAR(the ERF-associated amphiphilic repression)-like motif were observed to be conserved among several WOX subgroups in these five plants.Comparative analysis of expression patterns of WOX genes in rice and Arabidopsis suggest that the WOX genes play conserved and various roles in plants.This work provides insights into the evolution of the WOX gene family and is useful for future research.
Xu, Jie; Liu, Ling; Xu, Yunbi; Chen, Churun; Rong, Tingzhao; Ali, Farhan; Zhou, Shufeng; Wu, Fengkai; Liu, Yaxi; Wang, Jing; Cao, Moju; Lu, Yanli
Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study. PMID:23804557
Da Silva, Helena Sofia Pereira
Maize ("Zea mays L.") is a model species well suited for the dissection of complex traits which are often of commercial value. The purpose of this research was to gain a deeper understanding of the genetic control of maize kernel composition traits starch, protein, and oil concentration, and also kernel weight and grain yield. Germplasm with…
Rowena Y Kelley
Full Text Available BACKGROUND: Aspergillus flavus infection and aflatoxin contamination of maize pose negative impacts in agriculture and health. Commercial maize hybrids are generally susceptible to this fungus. Significant levels of host plant resistance have been observed in certain maize inbred lines. This study was conducted to identify maize genes associated with host plant resistance or susceptibility to A. flavus infection and aflatoxin accumulation. RESULTS: Genome wide gene expression levels with or without A. flavus inoculation were compared in two resistant maize inbred lines (Mp313E and Mp04:86 in contrast to two susceptible maize inbred lines (Va35 and B73 by microarray analysis. Principal component analysis (PCA was used to find genes contributing to the larger variances associated with the resistant or susceptible maize inbred lines. The significance levels of gene expression were determined by using SAS and LIMMA programs. Fifty candidate genes were selected and further investigated by quantitative RT-PCR (qRT-PCR in a time-course study on Mp313E and Va35. Sixteen of the candidate genes were found to be highly expressed in Mp313E and fifteen in Va35. Out of the 31 highly expressed genes, eight were mapped to seven previously identified quantitative trait locus (QTL regions. A gene encoding glycine-rich RNA binding protein 2 was found to be associated with the host hypersensitivity and susceptibility in Va35. A nuclear pore complex protein YUP85-like gene was found to be involved in the host resistance in Mp313E. CONCLUSION: Maize genes associated with host plant resistance or susceptibility were identified by a combination of microarray analysis, qRT-PCR analysis, and QTL mapping methods. Our findings suggest that multiple mechanisms are involved in maize host plant defense systems in response to Aspergillus flavus infection and aflatoxin accumulation. These findings will be important in identification of DNA markers for breeding maize lines
Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in China. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize genome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotransposons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to confirm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.
Fu, H; Park, W; Yan, X; Zheng, Z; Shen, B; Dooner, H K
The bronze (bz) locus exhibits the highest rate of recombination of any gene in higher plants. To investigate the possible basis of this high rate of recombination, we have analyzed the physical organization of the region around the bz locus. Two adjacent bacterial artificial chromosome clones, comprising a 240-kb contig centered around the Bz-McC allele, were isolated, and 60 kb of contiguous DNA spanning the two bacterial artificial chromosome clones was sequenced. We find that the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes, at least eight of which are shown to be transcribed, are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. We have isolated nearly full length cDNAs corresponding to the five proximal genes in the cluster. The average intertranscript distance between them is just 1 kb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. At least 11 small insertions, including several previously described miniature inverted repeat transposable elements, were detected in the introns and 3' untranslated regions of genes and between genes. The gene-rich region is flanked at the proximal and distal ends by retrotransposon blocks. Thus, the maize genome appears to have scattered regions of high gene density similar to those found in other plants. The unusually high rate of intragenic recombination seen in bz may be related to the very high gene density of the region.
Mei, Xiupeng; Liu, Chaoxian; Yu, Tingting; Liu, Xiaoli; Xu, De; Wang, Jiuguang; Wang, Guoqiang; Cai, Yilin
Gene imprinting describes an epigenetic phenomenon, whereby genetically identical alleles are differentially expressed dependent on parent-of-origin. Some imprinted genes belonged to NUCLEAR FACTOR Y (NF-Y) transcription factors, which were involved in many important metabolic processes in plant. The characterizations of imprinted genes are of great importance for their function exploration. In this paper, 15 non-redundant NF-YC genes were identified in the maize genome and the paternally expressed gene NF-YC8 was further analyzed. NF-YC8 primarily expressed in maize immature ear and tassel and phylogenetic analysis showed that NF-YC8 was highly homologous with Arabidopsis thaliana NF-YC2 genes which function in regulation of the flowering processes, ER stress response. Furthermore, NF-YC8 was a differential, gene-specific imprinted gene at 14 DAP and persistently imprinted throughout later endosperm development in the B73/Mo17 genetic background. Bisulfite sequencing for NF-YC8 in maize endosperm showed that the paternal alleles were higher methylated (CG, CHG and CHH contexts) than maternal alleles in the 5' upstream region, and the coding region was highly methylated in CG context. Additionally, TE (CG, CHG and CHH contexts) and repetitive region (CG and CHG contexts) were all highly methylated. These results are the first description of evolution and molecular characterization of maize NF-YC8 and will provide new references for maize NF-YC genetic analysis.
Juan Huang; Jianhua Zhang; Wenzhen Li; Wei Hu; Lichao Duan; Yang Feng; Fazhan Qiu
Maize seedlings are very sensitive to chilling,especially during the transition phase from heterotrophic to autotrophic growth.Genetic dissection of the genetic basis of chilling tolerance would provide useful information for genetic improvement of maize inbreds.In this study,genome-wide association analysis was conducted to explore the genetic architecture of maize chilling tolerance at the seed germination and seedling stages with an association panel of 125 inbreds.Ten tolerance indices (ratios of the performance of 10 germination rates and seedling growth-related traits under chilling stress and control conditions)were investigated to assess the ability of chilling tolerance of the inbreds,and a total of 43 single nucleotide polymorphisms associated with chilling tolerance were detected,with none of them being related to chilling tolerance at both the germination and seedling stages simultaneously.Correlation analysis also revealed that the genetic basis of chilling tolerance at the seed germination stage is generally different from that at the seedling stage.In addition,a total of 40 candidate genes involving 31 of the 43 single nucleotide polymorphisms were predicted,and were grouped into five categories according to their functions.The possible roles of these candidate genes in chilling tolerance were also discussed.
Small, I D; Isaac, P G; Leaver, C J
Four genomic arrangements of the maize mitochondrial atpA gene (encoding the alpha subunit of the F(1) ATPase), have been characterized. Most N (fertile) and S (male-sterile) cytoplasms contain two atpA arrangements of equal abundance. Prolonged exposure of blots of maize mitochondrial DNA probed with atpA-specific sequences show that cytoplasms previously reported to lack one of the atpA arrangements do contain the second arrangement but at low levels. Similarly, restriction fragments containing the atpA gene previously thought unique to male-sterile S and T cytoplasms are present in low abundance in fertile cytoplasms. These observations suggest that fertile and male-sterile cytoplasms of maize may be more closely related than previously thought, and suggest possible mechanisms to explain the observed mitochondrial genome diversity.
Mercy G Lung'aho
Full Text Available BACKGROUND: Maize is a major cereal crop widely consumed in developing countries, which have a high prevalence of iron (Fe deficiency anemia. The major cause of Fe deficiency in these countries is inadequate intake of bioavailable Fe, where poverty is a major factor. Therefore, biofortification of maize by increasing Fe concentration and or bioavailability has great potential to alleviate this deficiency. Maize is also a model system for genomic research and thus allows the opportunity for gene discovery. Here we describe an integrated genetic and physiological analysis of Fe nutrition in maize kernels, to identify loci that influence grain Fe concentration and bioavailability. METHODOLOGY: Quantitative trait locus (QTL analysis was used to dissect grain Fe concentration (FeGC and Fe bioavailability (FeGB from the Intermated B73 × Mo17 (IBM recombinant inbred (RI population. FeGC was determined by ion coupled argon plasma emission spectroscopy (ICP. FeGB was determined by an in vitro digestion/Caco-2 cell line bioassay. CONCLUSIONS: Three modest QTL for FeGC were detected, in spite of high heritability. This suggests that FeGC is controlled by many small QTL, which may make it a challenging trait to improve by marker assisted breeding. Ten QTL for FeGB were identified and explained 54% of the variance observed in samples from a single year/location. Three of the largest FeGB QTL were isolated in sister derived lines and their effect was observed in three subsequent seasons in New York. Single season evaluations were also made at six other sites around North America, suggesting the enhancement of FeGB was not specific to our farm site. FeGB was not correlated with FeGC or phytic acid, suggesting that novel regulators of Fe nutrition are responsible for the differences observed. Our results indicate that iron biofortification of maize grain is achievable using specialized phenotyping tools and conventional plant breeding techniques.
Feng, Shangguo; Yue, Runqing; Tao, Sun; Yang, Yanjun; Zhang, Lei; Xu, Mingfeng; Wang, Huizhong; Shen, Chenjia
Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The responsiveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.
Shangguo Feng; Runqing Yue; Sun Tao Yanjun Yang; Lei Zhang; Mingfeng Xu; Huizhong Wang; Chenjia Shen
Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The respon-siveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.
Martin-Ortigosa, Susana; Peterson, David J; Valenstein, Justin S; Lin, Victor S-Y; Trewyn, Brian G; Lyznik, L Alexander; Wang, Kan
The delivery of proteins instead of DNA into plant cells allows for a transient presence of the protein or enzyme that can be useful for biochemical analysis or genome modifications. This may be of particular interest for genome editing, because it can avoid DNA (transgene) integration into the genome and generate precisely modified "nontransgenic" plants. In this work, we explore direct protein delivery to plant cells using mesoporous silica nanoparticles (MSNs) as carriers to deliver Cre recombinase protein into maize (Zea mays) cells. Cre protein was loaded inside the pores of gold-plated MSNs, and these particles were delivered by the biolistic method to plant cells harboring loxP sites flanking a selection gene and a reporter gene. Cre protein was released inside the cell, leading to recombination of the loxP sites and elimination of both genes. Visual selection was used to select recombination events from which fertile plants were regenerated. Up to 20% of bombarded embryos produced calli with the recombined loxP sites under our experimental conditions. This direct and reproducible technology offers an alternative for DNA-free genome-editing technologies in which MSNs can be tailored to accommodate the desired enzyme and to reach the desired tissue through the biolistic method.
Moses M Muraya
Full Text Available A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS, assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents. Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs, of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful
Domagojimi; Hrvoje Lepedu; Vlatka Jurkovi; Jasenka Antunovi; Vera Cesar
Chlorophyl fluorescence transient from initial to maximum fluorescence (“P”step) throughout two intermedi-ate steps (“J”and“I”) (JIP-test) is considered a reliable early quantitative indicator of stress in plants. The JIP-test is particularly useful for crop plants when applied in variable field environments. The aim of the present study was to conduct a quantitative trait loci (QTL) analysis for nine JIP-test parameters in maize during flowering in four field environ-ments differing in weather conditions. QTL analysis and identification of putative candidate genes might help to explain the genetic relationship between photosynthesis and different field scenarios in maize plants. The JIP-test param-eters were analyzed in the intermated B73 ? Mo17 (IBM) maize population of 205 recombinant inbred lines. A set of 2,178 molecular markers across the whole maize genome was used for QTL analysis revealing 10 significant QTLs for seven JIP-test parameters, of which five were co-localized when combined over the four environments indicating polygenic inheritance and pleiotropy. Our results demonstrate that QTL analysis of chlorophyl fluorescence parameters was capable of detecting one pleiotropic locus on chromosome 7, coinciding with the gene gst23 that may be associated with efficient photosynthe-sis under different field scenarios.
Carpita, Nicholas; McCann, Maureen
Our objectives were to apply bioinformatics and high throughput sequencing technologies to identify and classify the genes involved in cell wall formation in maize and switchgrass. Targets for genetic modification were to be identified and cell wall materials isolated and assayed for enhanced performance in bioprocessing. We annotated and assembled over 750 maize genes into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice, and Arabidopsis sequences revealed differences in gene family structure. In addition, differences in expression between gene family members of Arabidopsis, maize and rice underscored the need for a grass-specific genetic model for functional analyses. A forward screen of mature leaves of field-grown maize lines by near-infrared spectroscopy yielded several dozen lines with heritable spectroscopic phenotypes, several of which near-infrared (nir) mutants had altered carbohydrate-lignin compositions. Our contributions to the maize genome sequencing effort built on knowledge of copy number variation showing that uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. For example, although about 25% of all duplicated genes remain genome-wide, all of the cellulose synthase (CesA) homologs were retained. We showed that guaiacyl and syringyl lignin in lignocellulosic cell-wall materials from stems demonstrate a two-fold natural variation in content across a population of maize Intermated B73 x Mo7 (IBM) recombinant inbred lines, a maize Association Panel of 282 inbreds and landraces, and three populations of the maize Nested Association Mapping (NAM) recombinant inbred lines grown in three years. We then defined quantitative trait loci (QTL) for stem lignin content measured using pyrolysis molecular-beam mass spectrometry, and glucose and xylose yield measured using an enzymatic hydrolysis assay. Among five multi-year QTL for lignin
Gonzalez García, Eric; Ressmann, Anna K; Gaertner, Peter; Zirbs, Ronald; Mach, Robert L; Krska, Rudolf; Bica, Katharina; Brunner, Kurt
To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.
Full Text Available NAC proteins are plant-specific transcription factors (TFs. Although they play a pivotal role in regulating distinct biological processes, TFs in maize are yet to be investigated comprehensively. Within the maize genome, we identified 152 putative NAC domain-encoding genes (ZmNACs, including eight membrane-bound members, by systematic sequence analysis and physically mapped them onto ten chromosomes of maize. In silico analysis of the ZmNACs and comparison with similar genes in other plants such as Arabidopsis, rice, and soybean, revealed a similar NAC sequence architecture. Phylogenetically, the ZmNACs were arranged into six distinct subgroups (I–VI possessing conserved motifs. Phylogenetic analysis using stress-related NAC TFs from Arabidopsis, rice, and soybean as seeding sequences identified 24 of the 152 ZmNACs (all from Group II as putative stress-responsive genes, including one dehydration-responsive ZmSNAC1 gene reported earlier. One drought-tolerant genotype (HKI577 and one susceptible genotype (PC13T-3 were used for studying the expression pattern of the NAC genes during drought stress. qRT-PCR based expression profiles of 11 genes predicted to be related to stress confirmed strong differential gene expression during drought stress. Phylogenetic analyses revealed that ZmNAC18, ZmNAC51, ZmNAC145, and ZmNAC72, which were up-regulated in the tolerant genotype and down-regulated in the susceptible genotype, belonged to the same group to which also belong other drought-responsive genes, namely SNAC1, OsNAC6, ANAC019, and ANAC055, which act as a transcriptional activator and are strongly induced under stress from various abiotic sources. Differentially expressed ZmNAC genes, alone or in combination with each other or with other type(s of TFs, may control the general cellular machinery and regulate stress-responsive downstream genes. Alternatively, they may serve as a platform to regulate a broad set of genes, which are subsequently fine
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequenci...
Zerjal, Tatiana; Joets, Johann; Alix, Karine; Grandbastien, Marie-Angèle; Tenaillon, Maud I
Miniature inverted-repeat transposable elements (MITEs) are short, non autonomous DNA elements that are widespread and abundant in plant genomes. The high sequence and size conservation observed in many MITE families suggest that they have spread recently throughout their respective host genomes. Here we present a maize genome wide analysis of three Tourist-like MITE families, mPIF, and two previously uncharacterized families, ZmV1 and Zead8. We undertook a bioinformatic analysis of MITE insertion sites, developed methyl-sensitive transposon display (M-STD) assays to estimate the associated level of CpG methylation at MITE flanking regions, and conducted a population genetics approach to investigate MITE patterns of expansion. Our results reveal that the three MITE families insert into genomic regions that present specific molecular features: they are preferentially AT rich, present low level of cytosine methylation as compared to the LTR retrotransposon Grande, and target site duplications are flanked by large and conserved palindromic sequences. Moreover, the analysis of MITE distances from predicted genes shows that 73% of 263 copies are inserted at less than 5 kb from the nearest predicted gene, and copies from Zead8 family are significantly more abundant upstream of genes. By employing a population genetic approach we identified contrasting patterns of expansion among the three MITE families. All elements seem to have inserted roughly 1 million years ago but ZmV1 and Zead8 families present evidences for activity of several master copies within the last 0.4 Mya.
TANG Wanhu; ZHANG Zuxin; ZOU Xiling; ZHENG Yonglian
In this study, SSH (Suppression Subtractive Hybridization) and cDNA microarray were used to identify genes associated with waterlogging response of maize roots. Mo17 and Hz32 are two maize inbred lines with differential tolerance to hypoxia. Seedlings of the inbred lines with two leaves were submerged in hypoxia buffer. SSH libraries were constructed with cDNA samples from roots. Both forward and reverse subtractions were performed for each inbred line, and 105 positive clones induced by hypoxia were selected by differential screening. The treated and control message RNA were hybridized with the cDNA microarray of Mo17, sequentially, 57 of 3-fold differentially expressed clones were obtained. A total of 162 positive clones were all sequenced. Bioinformatics analysis showed these positive clones represent 85 TUGs, including genes involved in several biochemistry pathways, such as glycolysis, protection, signal transduction, cell construction and energy metabolism and 41 EST with unknown function. Comparison between Mo17 and Hz32 indicates that genes related to hypoxia tolerance have different expression patterns in submerged roots. Several positive clones' expression patterns were revealed by Northern or RT-PCR, and a new gene (Sicyp51), which may contribute to hypoxia tolerance, was identified.
Chateigner-Boutin, Anne-Laure; Ordaz-Ortiz, José J.; Alvarado, Camille; Bouchet, Brigitte; Durand, Sylvie; Verhertbruggen, Yves; Barrière, Yves; Saulnier, Luc
Cell walls are comprised of networks of entangled polymers that differ considerably between species, tissues and developmental stages. The cell walls of grasses, a family that encompasses major crops, contain specific polysaccharide structures such as xylans substituted with feruloylated arabinose residues. Ferulic acid is involved in the grass cell wall assembly by mediating linkages between xylan chains and between xylans and lignins. Ferulic acid contributes to the physical properties of cell walls, it is a hindrance to cell wall degradability (thus biomass conversion and silage digestibility) and may contribute to pest resistance. Many steps leading to the formation of grass xylans and their cross-linkages remain elusive. One explanation might originate from the fact that many studies were performed on lignified stem tissues. Pathways leading to lignins and feruloylated xylans share several steps, and lignin may impede the release and thus the quantification of ferulic acid. To overcome these difficulties, we used the pericarp of the maize B73 line as a model to study feruloylated xylan synthesis and crosslinking. Using Fourier-transform infra-red spectroscopy and biochemical analyses, we show that this tissue has a low lignin content and is composed of approximately 50% heteroxylans and approximately 5% ferulic acid. Our study shows that, to date, maize pericarp contains the highest level of ferulic acid reported in plant tissue. The detection of feruloylated xylans with a polyclonal antibody shows that the occurrence of these polysaccharides is developmentally regulated in maize grain. We used the genomic tools publicly available for the B73 line to study the expression of genes within families involved or suggested to be involved in the phenylpropanoid pathway, xylan formation, feruloylation and their oxidative crosslinking. Our analysis supports the hypothesis that the feruloylated moiety of xylans originated from feruloylCoA and is transferred by a member
Shuaidong Hu; Thomas Lübberstedt; Guangwu Zhao; Michael Lee
Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-rela...
PAN Yu; ZHANG Li-quan; CHEN Xu-qing; XIE Hua; DENG Lei; LI Xiang-long; ZHANG Xiao-dong; HAN Li-xin; YANG Feng-ping; XUE Jing
Thebsd-pg (bundle sheath defective pale green) mutant is a novel maize mutation, controled by a single recessive gene, which was isolated from offspring of maize plantlets regenerated from tissue calus of the maize inbred line 501. The char-acterization was that the biogenesis and development of the chloroplasts was mainly interfered in bundle sheath cels rather than in mesophyl cels. For mapping thebsd-pg, an F2 population was derived from a cross between the mutant bsd-pg and an inbred line Xianzao 17. Using speciifc locus ampliifed fragment sequencing (SLAF-Seq) technology, a total of 5783 polymorphic SLAFs were analysed with 1771 homozygous aleles between maternal and paternal parents. There were 49 SLAFs, which had a ratio of paternal to maternal aleles of 2:1 in bulked normal lines, and three trait-related candidate regions were obtained on chromosome 1 with a size of 3.945 Mb. For the ifne mapping, new simple sequence repeats (SSRs) markers were designed by utilizing information of the B73 genome and the candidate regions were localized a size of 850934 bp on chromosome 1 between umc1603 and umc1395, including 35 candidate genes. These results provide a foundation for the cloning ofbsd-pg by map-based strategy, which is essential for revealing the functional differentiation and coordination of the two cel types, and helps to elucidate a comprehensive understanding of the C4 photosynthesis pathway and related processes in maize leaves.
Zoschke, Reimo; Barkan, Alice
Chloroplast genomes encode ∼ 37 proteins that integrate into the thylakoid membrane. The mechanisms that target these proteins to the membrane are largely unexplored. We used ribosome profiling to provide a comprehensive, high-resolution map of ribosome positions on chloroplast mRNAs in separated membrane and soluble fractions in maize seedlings. The results show that translation invariably initiates off the thylakoid membrane and that ribosomes synthesizing a subset of membrane proteins subsequently become attached to the membrane in a nuclease-resistant fashion. The transition from soluble to membrane-attached ribosomes occurs shortly after the first transmembrane segment in the nascent peptide has emerged from the ribosome. Membrane proteins whose translation terminates before emergence of a transmembrane segment are translated in the stroma and targeted to the membrane posttranslationally. These results indicate that the first transmembrane segment generally comprises the signal that links ribosomes to thylakoid membranes for cotranslational integration. The sole exception is cytochrome f, whose cleavable N-terminal cpSecA-dependent signal sequence engages the thylakoid membrane cotranslationally. The distinct behavior of ribosomes synthesizing the inner envelope protein CemA indicates that sorting signals for the thylakoid and envelope membranes are distinguished cotranslationally. In addition, the fractionation behavior of ribosomes in polycistronic transcription units encoding both membrane and soluble proteins adds to the evidence that the removal of upstream ORFs by RNA processing is not typically required for the translation of internal genes in polycistronic chloroplast mRNAs.
MaizeGDB is the open-access global repository for maize genetic and genomic information – from single genes that determine nutritional quality to whole genome-scale data for complex traits including yield and drought tolerance. The data and tools at MaizeGDB enable researchers from Ethiopia to Ghan...
Yuqiu; Guo; Xiaohong; Yang; Subhash; Chander; Jianbing; Yan; Jun; Zhang; Tongming; Song; Jiansheng; Li
Oil, protein and starch are key chemical components of maize kernels. A population of 245 recombinant inbred lines(RILs) derived from a cross between a high-oil inbred line, By804, and a regular inbred line, B73, was used to dissect the genetic interrelationships among oil, starch and protein content at the individual QTL level by unconditional and conditional QTL mapping. Combined phenotypic data over two years with a genetic linkage map constructed using 236 markers, nine, five and eight unconditional QTL were detected for oil, protein and starch content, respectively. Some QTL for oil, protein and starch content were clustered in the same genomic regions and the direction of their effects was consistent with the sign of their correlation. In conditional QTL mapping, 37(29/8) unconditional QTL were not detected or showed reduced effects, four QTL demonstrated similar effects under unconditional and conditional QTL mapping, and 17 additional QTL were identified by conditional QTL mapping. These results imply that there is a strong genetic relationship among oil, protein and starch content in maize kernels. The information generated in the present investigation could be helpful in marker-assisted breeding for maize varieties with desirable kernel quality traits.
Mejía-Guerra, María Katherine; Li, Wei; Galeano, Narmer F; Vidal, Mabel; Gray, John; Doseff, Andrea I; Grotewold, Erich
Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop.
Liu, Hanmei; Wang, Xuewen; Wei, Bin; Wang, Yongbin; Liu, Yinghong; Zhang, Junjie; Hu, Yufeng; Yu, Guowu; Li, Jian; Xu, Zhanbin; Huang, Yubi
In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1-5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement.
In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome’, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome’s complexity hinde...
Laurie, John D; Ali, Shawkat; Linning, Rob; Mannhaupt, Gertrud; Wong, Philip; Güldener, Ulrich; Münsterkötter, Martin; Moore, Richard; Kahmann, Regine; Bakkeren, Guus; Schirawski, Jan
Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.
Laurie, John D.; Ali, Shawkat; Linning, Rob; Mannhaupt, Gertrud; Wong, Philip; Güldener, Ulrich; Münsterkötter, Martin; Moore, Richard; Kahmann, Regine; Bakkeren, Guus; Schirawski, Jan
Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts. PMID:22623492
Song, Kitae; Kim, Hyo Chul; Shin, Seungho; Kim, Kyung-Hee; Moon, Jun-Cheol; Kim, Jae Yoon; Lee, Byung-Moo
Flowering time is an important factor determining yield and seed quality in maize. A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools. Our results identified a total of 619 genes and 126 transcripts whose expression was altered by drought stress in the maize B73 leaves under short-day condition. Among drought responsive genes, we also identified 20 genes involved in flowering times. Gene Ontology (GO) enrichment analysis was used to predict the functions of the drought-responsive genes and transcripts. GO categories related to flowering time included reproduction, flower development, pollen–pistil interaction, and post-embryonic development. Transcript levels of several genes that have previously been shown to affect flowering time, such as PRR37, transcription factor HY5, and CONSTANS, were significantly altered by drought conditions. Furthermore, we also identified several drought-responsive transcripts containing C2H2 zinc finger, CCCH, and NAC domains, which are frequently involved in transcriptional regulation and may thus have potential to alter gene expression programs to change maize flowering time. Overall, our results provide a genome-wide analysis of differentially expressed genes (DEGs), novel transcripts, and isoform variants expressed during the reproductive stage of maize plants subjected to drought stress and short-day condition. Further characterization of the drought-responsive transcripts identified in this study has the potential to advance our understanding of the mechanisms that regulate flowering time under drought stress.
Beatty Mary; Luck Stanley; Holloway Beth; Rafalski J-Antoni; Li Bailin
Abstract Background Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid pop...
Holloway, Beth; Luck, Stanley; Beatty, Mary; Rafalski, J-Antoni; Li, Bailin
Background Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population i...
Smith, Alan M; Hansey, Candice N; Kaeppler, Shawn M
Transposable elements (TEs) are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced TEs that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP), which is transcribed at high levels in long-term maize black Mexican sweet (BMS) tissue culture and is transcribed in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected novel TCUP insertions in two long-term tissue-cultured cell lines of the genotype Hi-II A × B and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.
Full Text Available Full-length cDNA (FLcDNA sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs, only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org.
Full Text Available Transposable elements are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced transposable elements that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP, which is transcribed at high levels in long-term maize Black Mexican Sweet (BMS tissue culture and up-regulated in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected movement of TCUP in two long-term tissue cultured cell lines of the genotype Hi-II AxB and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.
Andrade, Luciano Rogério Braatz de; Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant'Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms.
Bousios, Alexandros; Kourmpetis, Yiannis A I; Pavlidis, Pavlos; Minga, Evangelia; Tsaftaris, Athanasios; Darzentas, Nikos
Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the difficulty in correctly assigning retrotransposon families into genera, Sireviruses have hardly featured in recent research. As a result, analysis at this key level of classification and details of their colonization and impact on plant genomes are currently lacking. Recently, however, it became possible to accurately assign elements from diverse families to this genus in one step, based on highly conserved sequence motifs. Hence, Sirevirus dynamics in the relatively obese maize genome can now be comprehensively studied. Overall, we identified >10 600 intact and approximately 28 000 degenerate Sirevirus elements from a plethora of families, some brought into the genus for the first time. Sireviruses make up approximately 90% of the Copia population and it is the only genus that has successfully infiltrated the genome, possibly by experiencing intense amplification during the last 600 000 years, while being constantly recycled by host mechanisms. They accumulate in chromosome-distal gene-rich areas, where they insert in between gene islands, mainly in preferred zones within their own genomes. Sirevirus LTRs are heavily methylated, while there is evidence for a palindromic consensus target sequence. This work brings Sireviruses in the spotlight, elucidating their lifestyle and history, and suggesting their crucial role in the current genomic make-up of maize, and possibly other plant hosts.
Sheibani-Tezerji, Raheleh; Naveed, Muhammad; Jehl, Marc-André; Sessitsch, Angela; Rattei, Thomas; Mitter, Birgit
The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7, and S8), which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7), commensal (S8), to a beneficial, growth-promoting effect (S6) in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.
Full Text Available The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7 and S8, which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7, commensal (S8, to a beneficial, growth-promoting effect (S6 in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.
Junyi Xu; Jijuan Cao; Dongmei Cao; Tongtong Zhao; Xin Huang; Piqiao Zhang; Fengxia Luan
In order to establish a specific identification method for genetically modified (GM) wheat,exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies.Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA,herbicide-resistant bar,ubiquitin promoter,and high-molecular-weight gluten subunit.The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank:AY494981.1).A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence.This specific PCR method was validated by GM wheat,GM corn,GM soybean,GM rice,and non-GM wheat.The specifically amplified target band was observed only in GM wheat B73-6-1.This method is of high specificity,high reproducibility,rapid identification,and excellent accuracy for the identification of GM wheat B73-6-1.
Hazen, Samuel P; Hawley, Robin M; Davis, Georgia L; Henrissat, Bernard; Walton, Jonathan D
Quantitative trait loci (QTLs) affecting sugar composition of the cell walls of maize (Zea mays) pericarp were mapped as an approach to the identification of genes involved in cereal wall biosynthesis. Mapping was performed using the IBM (B73 x Mo17) recombinant inbred line population. There were statistically significant differences between B73 and Mo17 in content of xylose (Xyl), arabinose (Ara), galactose (Gal), and glucose. Thirteen QTLs were found, affecting the content of Xyl (two QTLs), Ara (two QTLs), Gal (five QTLs), Glc (two QTLs), Ara + Gal (one QTL), and Xyl + Glc (one QTL). The chromosomal regions corresponding to two of these, affecting Ara + Gal and Ara on maize chromosome 3, could be aligned with a syntenic region on rice (Oryza sativa) chromosome 1, which has been completely sequenced and annotated. The contiguous P1-derived artificial chromosome rice clones covering the QTLs were predicted to encode 117 and 125 proteins, respectively. Two of these genes encode putative glycosyltransferases, displaying similarity to carbohydrate-active enzyme database family GT4 (galactosyltransferases) or to family GT64 (C-terminal domain of animal heparan synthases). The results illustrate the potential of using natural variation, emerging genomic resources, and homeology within the Poaceae to identify candidate genes involved in the essential process of cell wall biosynthesis.
Full Text Available Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL on leaf angle detected by inclusive composite interval mapping (ICIM. ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs. Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.
Chuanxiao; Xie; Jianfeng; Weng; Wenguo; Liu; Cheng; Zou; Zhuanfang; Hao; Wenxue; Li; Minshun; Li; Xiaosen; Guo; Gengyun; Zhang; Yunbi; Xu; Xinhai; Li; Shihuang; Zhang
Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study(GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a-log10 P value for surrounding SNPs higher than the Bonferroni threshold(α/n, α < 0.001) when a mixed linear model(MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium(LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of π and Tajima’s D were significantly(P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing(180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
Full Text Available The assignment of functions to genes in the carotenoid biosynthesis pathway is necessary to understand how the pathway is regulated and to obtain the basic information required for metabolic engineering. Few carotenoid ε-hydroxylases have been functionally characterized in plants although this would provide insight into the hydroxylation steps in the pathway. We therefore isolated mRNA from the endosperm of maize (Zea mays L., inbred line B73 and cloned a full-length cDNA encoding CYP97C19, a putative heme-containing carotenoid ε hydroxylase and member of the cytochrome P450 family. The corresponding CYP97C19 genomic locus on chromosome 1 was found to comprise a single-copy gene with nine introns. We expressed CYP97C19 cDNA under the control of the constitutive CaMV 35S promoter in the Arabidopsis thaliana lut1 knockout mutant, which lacks a functional CYP97C1 (LUT1 gene. The analysis of carotenoid levels and composition showed that lutein accumulated to high levels in the rosette leaves of the transgenic lines but not in the untransformed lut1 mutants. These results allowed the unambiguous functional annotation of maize CYP97C19 as an enzyme with strong zeinoxanthin ε-ring hydroxylation activity.
Full Text Available Abstract Background Horizontal transfers (HTs refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum, as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae. Results We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers. Conclusion This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.
胡雪微; 杨克军; 李佐同; 张海燕; 刘鑫; 赵莹; 聂江山; 韩雨; 赵长江
油菜素内酯信号激酶(BSKs)是一类参与油菜素内酯(BR)信号转导的植物特异受体类胞质激酶。本研究采用生物信息学的方法在玉米基因组水平鉴定玉米BSKs基因家族,对基因结构、启动子元件、蛋白质结构和性质、基因表达模式及候选互作蛋白等进行分析。鉴定的14个玉米BSKs基因分别定位在玉米的1、2、4、5和9号染色体上,1号染色体上多达6个；编码蛋白包含典型的PKc和TPR结构域, N端由延长链和螺旋结构组成,定位于叶绿体,多为亲水性、酸性蛋白,可能与热激蛋白、含CS结构域蛋白及受体BRI1互作。玉米BSKs基因在从种子萌发到成熟的整个生长发育期,以及不同组织和器官呈现不同的表达模式；基因启动子上含有大量激素和非生物逆境诱导的顺式作用元件,其中激素SA及NaCl诱导相关元件数量最多,表明玉米BSKs基因可能在不同生育期受多种激素调控,并参与玉米对多种逆境的应答调控。该研究有助于解析单子叶C4作物玉米BSKs基因在生长发育及逆境胁迫响应中的功能。%Brassinosteroid signaling kinases (BSKs) are novel plant speciifc receptor-like cytoplasmic kinases in-volved in the brassinosteroid (BR) signal transduction pathway. In this study, a family of maize (Zea mays) BSKs genes was identiifed from maize genome using bioinformatic methods, and their structures, promoter elements, protein structure and properties, gene expression pattern and candidate interacting proteins were analyzed. The results revealed that 14 maize BSKs genes located on chromosome 1, 2, 4, 5 and 9, respectively, with up to 6 of them on chromosome 1. The encoded proteins had typical PKc and TPR motifs and a complicated N-terminal made up of extending chains and helixes;they localized in chloroplast and most of them were hydrophilic and acidic, interacting probably with heat shock proteins, proteins with CS domain and BRI1. Differential
Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The t...
Yang, Ning; Lu, Yanli; Yang, Xiaohong; Huang, Juan; Zhou, Yang; Ali, Farhan; Wen, Weiwei; Liu, Jie; Li, Jiansheng; Yan, Jianbing
Association mapping is a powerful approach for dissecting the genetic architecture of complex quantitative traits using high-density SNP markers in maize. Here, we expanded our association panel size from 368 to 513 inbred lines with 0.5 million high quality SNPs using a two-step data-imputation method which combines identity by descent (IBD) based projection and k-nearest neighbor (KNN) algorithm. Genome-wide association studies (GWAS) were carried out for 17 agronomic traits with a panel of 513 inbred lines applying both mixed linear model (MLM) and a new method, the Anderson-Darling (A-D) test. Ten loci for five traits were identified using the MLM method at the Bonferroni-corrected threshold -log10 (P) >5.74 (α=1). Many loci ranging from one to 34 loci (107 loci for plant height) were identified for 17 traits using the A-D test at the Bonferroni-corrected threshold -log10 (P) >7.05 (α=0.05) using 556809 SNPs. Many known loci and new candidate loci were only observed by the A-D test, a few of which were also detected in independent linkage analysis. This study indicates that combining IBD based projection and KNN algorithm is an efficient imputation method for inferring large missing genotype segments. In addition, we showed that the A-D test is a useful complement for GWAS analysis of complex quantitative traits. Especially for traits with abnormal phenotype distribution, controlled by moderate effect loci or rare variations, the A-D test balances false positives and statistical power. The candidate SNPs and associated genes also provide a rich resource for maize genetics and breeding.
Full Text Available Association mapping is a powerful approach for dissecting the genetic architecture of complex quantitative traits using high-density SNP markers in maize. Here, we expanded our association panel size from 368 to 513 inbred lines with 0.5 million high quality SNPs using a two-step data-imputation method which combines identity by descent (IBD based projection and k-nearest neighbor (KNN algorithm. Genome-wide association studies (GWAS were carried out for 17 agronomic traits with a panel of 513 inbred lines applying both mixed linear model (MLM and a new method, the Anderson-Darling (A-D test. Ten loci for five traits were identified using the MLM method at the Bonferroni-corrected threshold -log10 (P >5.74 (α=1. Many loci ranging from one to 34 loci (107 loci for plant height were identified for 17 traits using the A-D test at the Bonferroni-corrected threshold -log10 (P >7.05 (α=0.05 using 556809 SNPs. Many known loci and new candidate loci were only observed by the A-D test, a few of which were also detected in independent linkage analysis. This study indicates that combining IBD based projection and KNN algorithm is an efficient imputation method for inferring large missing genotype segments. In addition, we showed that the A-D test is a useful complement for GWAS analysis of complex quantitative traits. Especially for traits with abnormal phenotype distribution, controlled by moderate effect loci or rare variations, the A-D test balances false positives and statistical power. The candidate SNPs and associated genes also provide a rich resource for maize genetics and breeding.
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.
Hahnke, Sarah; Wibberg, Daniel; Tomazetto, Geizecler; Pühler, Alfred; Klocke, Michael; Schlüter, Andreas
The bacterium Clostridium bornimense M2/40 is a mesophilic, anaerobic bacterium isolated from a two-phase biogas reactor continuously fed with maize silage and 5% wheat straw. Grown on glucose, it produced H2, CO2, formiate, lactate and propionate as the main fermentation products, of which some compounds serve as substrates for methanogenic Archaea to form methane. Here, the whole genome sequence of the bacterium consisting of two circular replicons is reported. This genome information provides the basis for further studies addressing metabolic features of the isolate and its role in anaerobic biomass degradation.
Sanguineti Maria C
Full Text Available Abstract Background Collections of nearly isogenic lines where each line carries a delimited portion of a donor source genome into a common recipient genetic background are known as introgression libraries and have already shown to be instrumental for the dissection of quantitative traits. By means of marker-assisted backcrossing, we have produced an introgression library using the extremely early-flowering maize (Zea mays L. variety Gaspé Flint and the elite line B73 as donor and recipient genotypes, respectively, and utilized this collection to investigate the genetic basis of flowering time and related traits of adaptive and agronomic importance in maize. Results The collection includes 75 lines with an average Gaspé Flint introgression length of 43.1 cM. The collection was evaluated for flowering time, internode length, number of ears, number of nodes (phytomeres, number of nodes above the ear, number and proportion of nodes below the ear and plant height. Five QTLs for flowering time were mapped, all corresponding to major QTLs for number of nodes. Three additional QTLs for number of nodes were mapped. Besides flowering time, the QTLs for number of nodes drove phenotypic variation for plant height and number of nodes below and above the top ear, but not for internode length. A number of apparently Mendelian-inherited phenotypes were also observed. Conclusions While the inheritance of flowering time was dominated by the well-known QTL Vgt1, a number of other important flowering time QTLs were identified and, thanks to the type of plant material here utilized, immediately isogenized and made available for fine mapping. At each flowering time QTL, early flowering correlated with fewer vegetative phytomeres, indicating the latter as a key developmental strategy to adapt the maize crop from the original tropical environment to the northern border of the temperate zone (southern Canada, where Gaspé Flint was originally cultivated. Because of
Thomas Kai Wolfgruber
Full Text Available The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR have presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 x 10-6 and 5 x 10-5 for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb of the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length centromeric retrotransposons from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. This repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to facilitate the repair of frequent DSBs in centromeres.
Full Text Available Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM Syn4 recombinant inbred line (RIL population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h and optimum temperature (28°C/24 h between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM were umc1303 (265.1 cM on chromosome 4, umc1 (246.4 cM on chromosome 5, umc62 (459.1 cM on chromosome 6, bnl14.28a (477.4 cM on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org. Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.
Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael
Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.
Yang, Hua; Liu, Xinye; Xin, Mingming; Du, Jinkun; Hu, Zhaorong; Peng, HuiRu; Sun, Qixin; Ni, Zhongfu; Yao, Yingyin
Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes. PMID:26908760
A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limite...
Full Text Available The auxin influx carriers auxin resistant 1/like aux 1 (AUX/LAX, efflux carriers pin-formed (PIN (together with PIN-like proteins and efflux/conditional P-glycoprotein (ABCB are major protein families involved in auxin polar transport. However, how they function in responses to exogenous auxin and abiotic stresses in maize is largely unknown. In this work, the latest updated maize (Zea mays L. reference genome sequence was used to characterize and analyze the ZmLAX, ZmPIN, ZmPILS and ZmABCB family genes from maize. The results showed that five ZmLAXs, fifteen ZmPINs, nine ZmPILSs and thirty-five ZmABCBs were mapped on all ten maize chromosomes. Highly diversified gene structures, nonconservative transmembrane helices and tissue-specific expression patterns suggested the possibility of function diversification for these genes. Quantitative real-time polymerase chain reaction (qRT-PCR was used to analyze the expression patterns of ZmLAX, ZmPIN, ZmPILS and ZmABCB genes under exogenous auxin and different environmental stresses. The expression levels of most ZmPIN, ZmPILS, ZmLAX and ZmABCB genes were induced in shoots and were reduced in roots by various abiotic stresses (drought, salt and cold stresses. The opposite expression response patterns indicated the dynamic auxin transport between shoots and roots under abiotic stresses. Analysis of the expression patterns of ZmPIN, ZmPILS, ZmLAX and ZmABCB genes under drought, salt and cold treatment may help us to understand the possible roles of maize auxin transporter genes in responses and tolerance to environmental stresses.
Yang, Liming; Jiang, Tingbo; Fountain, Jake C; Scully, Brian T; Lee, Robert D; Kemerait, Robert C; Chen, Sixue; Guo, Baozhu
Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964) with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP), and protein profiles were investigated in developing kernels (35 DAP) using iTRAQ (isobaric tags for relative and absolute quantitation). Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.
Full Text Available Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964 with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP, and protein profiles were investigated in developing kernels (35 DAP using iTRAQ (isobaric tags for relative and absolute quantitation. Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.
Full Text Available In angiosperms, the endosperm nurtures embryo and provides nutrients for seed germination. We have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP and endosperms at 7, 10, and 15 DAP by using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicates these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and qRT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize which might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which leads to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10 and 15 DAP according to the reads abundance with SNPs and CAPS experiment.
Li, Jiao; Guo, Yuqi; Cui, Weiling; Xu, Aihua; Tian, Zengyuan
Alternative splicing (AS) in eukaryotic organisms is closely related to the gene regulation in plant abiotic stress responses, in which serine/arginine-rich proteins (SR proteins) act as key regulators. The genome sequence of maize inbred line B73 was analyzed, showing that the promoter regions of SR genes possess about three to eight kinds of cis-acting regulatory elements. Twenty-seven SR genes encode alkaline proteins, and 23 of which are divided into five subgroups in terms of the first RNA recognition motif (RRM) at the amino terminal. The expression of SR genes showed tissue-specific and genotype-dependent features under drought stress in the hybrid Zhengdan-958 and its parents, Zheng-58 and Chang-7-2 via bidirectional hierarchical clustering. SR genes were down-regulated in roots while they were up-regulated in shoots under drought stress. However, SR genes were down-regulated in both roots and shoots in three different rehydration stages after severe drought stress. Additionally, a widespread alternative splicing exists in all SR genes although SR genes showed differential expression tendency under drought stress and/or during rehydration stages. Results above will deepen our understanding of the molecular mechanisms of plant response to abiotic stress from the perspective of AS-network.
Full Text Available ZAG2 has been identified as a maternally expressed imprinted gene in maize endosperm. Our study revealed that paternally inherited ZAG2 alleles were imprinted in maize endosperm and embryo at 14 days after pollination (DAP, and consistently imprinted in endosperm at 10, 12, 16, 18, 20, 22, 24, 26, and 28 DAP in reciprocal crosses between B73 and Mo17. ZAG2 alleles were also imprinted in reciprocal crosses between Zheng 58 and Chang 7-2 and between Huang C and 178. ZAG2 alleles exhibited differential imprinting in hybrids of 178 × Huang C and B73 × Mo17, while in other hybrids ZAG2 alleles exhibited binary imprinting. The tissue-specific expression pattern of ZAG2 showed that ZAG2 was expressed at a high level in immature ears, suggesting that ZAG2 plays important roles in not only kernel but ear development.
The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data, and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on beh...
Sauer, Johannes; Balint, Borbala
This research aims at shedding empirical light on the relative efficiency of small-scale maize producers in Romania. Farmers in transition countries still face heavily distorted price systems resulting from imperfect market conditions and socioeconomic and institutional constraints. To capture...
Full Text Available Genetic markers, from morphological to molecular, in function with early Heterosis is a prerequisite for the successful commercial maize production. It does not appear in any cross of two inbred lines, and therefore, the determination of combining abilities of parental lines is essential. The most commonly used method for determining combining abilities is diallel analysis. Besides conventional methods for diallel analysis, a new biplot approach has been sugested. In this paper, we studied the combining ability for grain yield in a set of genotypes obtained by diallel crossing system of six inbred lines. Both, the Griffing’s conventional method and the biplot approach have been used for diallel analysis. Comparing the GCA values from biplot analysis and Griffing’s method, similar results can be observed, with the exception of NS L 1051 and NS L 1000 whose ranks are interchanged. Biplot analysis enables the SCA estimation of parent inbred, and the highest SCA has inbred B73D. Biplot analysis also allows the estimation of the best crosses. Inbred B73D shows the best results when crossed with testers Mo17Ht, NS L 1051 and N152, inbred N152 combines best with testers NS L 1001 and NS L 1000, whereas the cross of inbred NS L 1051 with tester B73D results with the highest grain yield per plant in comparison with other testers.
Over 10,000 new mutants have been added to the UniformMu reverse genetics resource in release 7, bringing the total to over 67,000 germinal transposon insertions. These are available in 11,140 independent seed stocks. Close to half of the maize filtered gene set (42%) is represented by at least one ...
Salazar-Vidal, M. Nancy; Acosta-Segovia, Edith; Sánchez-León, Nidia; Ahern, Kevin R.; Brutnell, Thomas P.; Sawers, Ruairidh J. H.
Phosphorus is an essential nutrient for all plants, but also one of the least mobile, and consequently least available, in the soil. Plants have evolved a series of molecular, metabolic and developmental adaptations to increase the acquisition of phosphorus and to maximize the efficiency of use within the plant. In Arabidopsis (Arabidopsis thaliana), the AtPHO1 protein regulates and facilitates the distribution of phosphorus. To investigate the role of PHO1 proteins in maize (Zea mays), the B73 reference genome was searched for homologous sequences, and four genes identified that were designated ZmPho1;1, ZmPho1;2a, ZmPho1;2b and ZmPho1;3. ZmPho1;2a and ZmPho1;2b are the most similar to AtPHO1, and represent candidate co-orthologs that we hypothesize to have been retained following whole genome duplication. Evidence was obtained for the production of natural anti-sense transcripts associated with both ZmPho1;2a and ZmPho1;2b, suggesting the possibility of regulatory crosstalk between paralogs. To characterize functional divergence between ZmPho1;2a and ZmPho1;2b, a program of transposon mutagenesis was initiated using the Ac/Ds system, and, here, we report the generation of novel alleles of ZmPho1;2a and ZmPho1;2b. PMID:27648940
Impact of genetic structures on haploid genome-based quantification of genetically modified DNA: theoretical considerations, experimental data in MON 810 maize kernels (Zea mays L.) and some practical applications.
Zhang, David; Corlet, Aurélie; Fouilloux, Stephane
Real-time Polymerase Chain Reaction (PCR) based assays are widely used to estimate the content of genetically modified (GM) materials in food, feed and seed. It has been known that the genetic structures of the analyte can significantly influence the GM content expressed by the haploid genome (HG) % estimated using real-time PCR assays; this kind of influence is also understood as the impact of biological factors. The influence was first simulated at theoretical level using maize as a model. We then experimentally assessed the impact of biological factors on quantitative results, analysing by quantitative real-time PCR six maize MON 810 hybrid kernels with different genetic structures: (1) hemizygous from transgenic male parent, (2) hemizygous from transgenic female parent and (3) homozygous at the transgenic locus. The results obtained in the present study showed clear influences of biological factors on GM DNA quantification: 1% of GM materials by weight (wt) for the three genetic structures contained 0.39, 0.55 and 1.0% of GM DNA by HG respectively, from quantitative real-time PCR analyses. The relationships between GM wt% and GM HG% can be empirically established as: (1) in the case of the presence of a single GM trait: GM HG% = GM wt% x (0.5 +/- 0.167Y), where Y is the endosperm DNA content (%) in the total DNA of a maize kernel, (2) in the case of the presence of multiple GM traits: GM HG% = N x GM wt% x (0.5 +/- 0.167Y), where N is the number of GM traits (stacked or not) present in an unknown sample. This finding can be used by stakeholders related to GMO for empirical prediction from one unit of expression to another in the monitoring of seed and grain production chains. Practical equations have also been suggested for haploid copy number calculations, using hemizygous GM materials for calibration curves.
Swanson-Wagner, Ruth; Briskine, Roman; Schaefer, Robert; Hufford, Matthew B; Ross-Ibarra, Jeffrey; Myers, Chad L; Tiffin, Peter; Springer, Nathan M
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation.
Tomazetto, Geizecler; Hahnke, Sarah; Maus, Irena; Wibberg, Daniel; Pühler, Alfred; Schlüter, Andreas; Klocke, Michael
The bacterium Peptoniphilus sp. strain ING2-D1G (DSM 28672), a mesophilic and obligate anaerobic bacterium belonging to the order Clostridiales was isolated from a biogas-producing lab-scale completely stirred tank reactor (CSTR) optimized for anaerobic digestion of maize silage in co-fermentation with pig and cattle manure. In this study, the whole genome sequence of Peptoniphilus sp. strain ING2-D1G, a new isolate potentially involved in protein breakdown and acidogenesis during biomass degradation, is reported. The chromosome of this strain is 1.6Mb in size and encodes genes predicted to be involved in the production of acetate, lactate and butyrate specifying the acidogenic metabolism of the isolate.
方永丰; 李永生; 白江平; 慕平; 孟亚雄; 张金林; 王汉宁; 尚勋武
Leaf senescence is a character of plant development. Delayed leaf senescence or stay green character has received considerable attention because of its negative impact on photosynthesis and its role in nutrient redistribution within the plant. In the past few decades, a wealth of QTLs (quantitative trait locus) mapping data for stay green and its related traits in maize has been produced using molecular marker approaches. In order to unlock the full potential of the information contained in these independent experiments, 173 stay-green and related QTLs in maize were collected from maize genomic database (maize GDB), and were compiled to construct the integration QTL map for stay-green in maize (Zea mays). The high-scale genetic linkage map of maize IBM2 2008 Neighbors was used as reference and the map were constructed with BioMercator 2. 1 software based on the method of meta analysis. Five consensus QTL for maize stay green were identified on maize chromosomes 1,4,5 and 9, respectively. After project the consensus QTL region on maize physical map of B73 Ref-Gen_v2, a total of 1 445 candidate genes in the consensus QTL region were discovered and downloaded from Plant GDB(http://www. plantgdb. org/). Meanwhile, according to the results of gene ontology analysis, most candidate genes might take part in the cell development, catalytic process, enzymatic activity and other biological progresses. The sequences of eight stay-green candidate genes were identified by comparatively analyzing the sequences of stay-green gene sequence from other crops. Using a syntonic conservation approach, which is used to comparatively analyze the rice genetic map and maize physical map, one rice gene (sgr) that is coding for the senescence-inducible chloroplast stay-green protein was projected onto the physical map of maize B73RefGen_v2. Therefore, the results suggested that this approach provided an useful tool for identifying QTL conferring stay-green and other candidate genes in maize
Naumann, Todd A; Wicklow, Donald T
Stenocarpella maydis causes both dry-ear rot and stalk rot of maize. Maize inbred lines have varying levels of resistance to ear rot caused by S. maydis. The genetic basis of resistance appears to rely on multiple genetic factors, none of which are known. The commonly used stiff-stalk inbred line B73 has been shown to be strongly susceptible to ear rot caused by S. maydis. Here, we report that the ChitA protein alloform from B73, ChitA-F, encoded by a known allele of the chiA gene, is susceptible to modification by a protein (Stm-cmp) secreted by S. maydis. We also identify a new allele of chiA (from inbred line LH82) which encodes ChitA-S, an alloform of ChitA that is resistant to Stm-cmp modification. Chitinase zymogram analysis of seed from a commercial field showed the presence of both ChitA alloforms in healthy ears, and showed that ChitA-F but not ChitA-S was modified in ears rotted by S. maydis. The ChitA-F protein was purified from inbred line B73 and ChitA-S from LH82. ChitA-F was modified more efficiently than ChitA-S by S. maydis protein extracts in vitro. The chiA gene from LH82 was cloned and sequenced. It is a novel allele that encodes six polymorphisms relative to the known allele from B73. This is the first demonstration that the susceptibility to modification of a fungal targeted plant chitinase differs among inbred lines. These findings suggest that the LH82 chiA allele may be a specific genetic determinant that contributes to resistance to ear rot caused by S. maydis whereas the B73 allele may contribute to susceptibility.
Rius, Sebastián P; Emiliani, Julia; Casati, Paula
P1 is a R2R3-MYB transcription factor that regulates the accumulation of a specific group of flavonoids in maize floral tissues, such as flavones and phlobaphenes. P1 is also highly expressed in leaves of maize landraces adapted to high altitudes and higher levels of UV-B radiation. In this work, we analyzed the epigenetic regulation of the P1 gene by UV-B in leaves of different maize landraces. Our results demonstrate that DNA methylation in the P1 proximal promoter, intron1 and intron2 is decreased by UV-B in all lines analyzed; however, the basal DNA methylation levels are lower in the landraces than in B73, a low altitude inbred line. DNA demethylation by UV-B is accompanied by a decrease in H3 methylation at Lys 9 and 27, and by an increase in H3 acetylation. smRNAs complementary to specific regions of the proximal promoter and of intron 2 3' end are also decreased by UV-B; interestingly, P1 smRNA levels are lower in the landraces than in B73 both under control conditions and after UV-B exposure, suggesting that smRNAs regulate P1 expression by UV-B in maize leaves. Finally, we investigated if different P1 targets in flower tissues are also regulated by this transcription factor in response to UV-B. Some targets analyzed show an induction in maize landraces in response to UV-B, with higher basal expression levels in the landraces than in B73; however, not all the transcripts analyzed were found to be regulated by UV-B in leaves.
Sebastian Pablo Rius
Full Text Available P1 is a R2R3-MYB transcription factor that regulates the accumulation of a specific group of flavonoids in maize floral tissues, such as flavones and phlobaphenes. P1 is also highly expressed in leaves of maize landraces adapted to high altitudes and higher levels of UV-B radiation. In this work, we analyzed the epigenetic regulation of the P1 gene by UV-B in leaves of different maize landraces. Our results demonstrate that DNA methylation in the P1 proximal promoter, intron1 and intron2 is decreased by UV-B in all lines analyzed; however, the basal DNA methylation levels are lower in the landraces than in B73, a low altitude inbred line. DNA demethylation by UV-B is accompanied by a decrease in H3 methylation at Lys 9 and 27, and by an increase in H3 acetylation. smRNAs complementary to specific regions of the proximal promoter and of intron 2 3' end are also decreased by UV-B; interestingly, P1 smRNA levels are lower in the landraces than in B73 both under control conditions and after UV-B exposure, suggesting that smRNAs regulate P1 expression by UV-B in maize leaves. Finally, we investigated if different P1 targets in flower tissues are also regulated by this transcription factor in response to UV-B. Some targets analyzed show an induction in maize landraces in response to UV-B, with higher basal expression levels in the landraces than in B73; however, not all the transcripts analyzed were found to be regulated by UV-B in leaves.
Xue, Shang; Bradbury, Peter J; Casstevens, Terry; Holland, James B
Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domestication-related traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.
Full Text Available Abstract Background Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc, mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR phenotype, but the molecular mechanism(s underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. Conclusions In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.
Gallavotti, Andrea; Whipple, Clinton J.
• Premise of the study: Positional (or map-based) cloning is a common approach to identify the molecular lesions causing mutant phenotypes. Despite its large and complex genome, positional cloning has been recently shown to be feasible in maize, opening up a diverse collection of mutants to molecular characterization. • Methods and Results: Here we outline a general protocol for positional cloning in maize. While the general strategy is similar to that used in other plant species, we focus on the unique resources and approaches that should be considered when applied to maize mutants. • Conclusions: Positional cloning approaches are appropriate for maize mutants and quantitative traits, opening up to molecular characterization the large array of genetic diversity in this agronomically important species. The cloning approach described should be broadly applicable to other species as more plant genomes become available. PMID:25606355
Bousios, A.; Kourmpetis, Y.I.A.; Pavlidis, P.; Minga, E.; Tsaftaris, A.; Darzentas, N.
Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the di
The 50th Annual Maize Genetics Conference was held February 27 - March 2, 2008 at the Marriott Wardman Park Hotel in Washington, D.C. As the golden anniversary of the Conference and coinciding with the release of a draft of the maize genome sequence, this was a special meeting. To publicize this unique occasion, meeting organizers hosted a press conference, which was attended by members of the press representing science and non-science publications, and an evening reception at the Smithsonian National Museum of Natural History, where the draft sequence was announced and awards were presented to Dr. Mary Clutter and Senator Kit Bond to thank them for their outstanding contributions to maize genetics and genomics research. As usual, the Conference provided an invigorating forum for exchange of recent research results in many areas of maize genetics, e.g., cytogenetics, development, molecular genetics, transposable element biology, biochemical genetics, and genomics. Results were shared via both oral and poster presentations. Invited talks were given by four distinguished geneticists: Vicki Chandler, University of Arizona; John Doebley, University of Wisconsin; Susan Wessler, University of Georgia; and Richard Wilson, Washington University. There were 46 short talks and 241 poster presentations. The Conference was attended by over 500 participants. This included a large number of first-time participants in the meeting and an increasingly visible presence by individuals from underrepresented groups. Although we do not have concrete counts, there seem to be more African American, African and Hispanic/Latino attendees coming to the meeting than in years past. In addition, this meeting attracted many participants from outside the U.S. Student participation continues to be hallmark of the spirit of free exchange and cooperation characteristic of the maize genetics community. With the generous support provided by DOE, USDA NSF, and corporate/private donors, organizers were
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
This chapter describes the resources held at the Maize Genetics Cooperation • Stock Center in detail and also provides some information about the North Central Regional Plant Introduction Station (NCRPIS) in Ames, IA, Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT) in Mexico, and the N...
Full Text Available The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT germplasm bank collection, 94 CIMMYT maize lines (CMLs and 54 U.S. Germplasm Enhancement of Maize (GEM lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants. Clustering analyses (CA based on Modified Rogers Distance (MRD clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.
Tai, Huanhuan; Lu, Xin; Opitz, Nina; Marcon, Caroline; Paschold, Anja; Lithio, Andrew; Nettleton, Dan; Hochholdinger, Frank
Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
Nitrate (NOequation image) and ammonium (NHequation image) are the predominant forms of nitrogen (N) available to plants in agricultural soils. Nitrate concentrations are generally ten times higher than those of NHequation image and this ratio is consistent across a wide range of soil types. The possible contribution of these small concentrations of NHequation image to the overall N budget of crop plants is often overlooked. In this study the importance of this for the growth and nitrogen budget of maize (Zea mays L.) was investigated, using agriculturally relevant concentrations of NHequation image. Maize inbred line B73 was grown hydroponically for 30 d at low (0.5 mM) and sufficient (2.5 mM) levels of NOequation image. Ammonium was added at 0.05 mM and 0.25 mM to both levels of NOequation image. At low NOequation image levels, addition of NHequation image was found to improve the growth of maize plants. This increased plant growth was accompanied by an increase in total N uptake, as well as total phosphorus, sulphur and other micronutrients in the shoot. Ammonium influx was higher than NOequation image influx for all the plants and decreased as the total N in the nutrient medium increased. This study shows that agriculturally relevant proportions of NHequation image supplied in addition to NOequation image can increase growth of maize.
David M Wills
Full Text Available A reduction in number and an increase in size of inflorescences is a common aspect of plant domestication. When maize was domesticated from teosinte, the number and arrangement of ears changed dramatically. Teosinte has long lateral branches that bear multiple small ears at their nodes and tassels at their tips. Maize has much shorter lateral branches that are tipped by a single large ear with no additional ears at the branch nodes. To investigate the genetic basis of this difference in prolificacy (the number of ears on a plant, we performed a genome-wide QTL scan. A large effect QTL for prolificacy (prol1.1 was detected on the short arm of chromosome 1 in a location that has previously been shown to influence multiple domestication traits. We fine-mapped prol1.1 to a 2.7 kb "causative region" upstream of the grassy tillers1 (gt1 gene, which encodes a homeodomain leucine zipper transcription factor. Tissue in situ hybridizations reveal that the maize allele of prol1.1 is associated with up-regulation of gt1 expression in the nodal plexus. Given that maize does not initiate secondary ear buds, the expression of gt1 in the nodal plexus in maize may suppress their initiation. Population genetic analyses indicate positive selection on the maize allele of prol1.1, causing a partial sweep that fixed the maize allele throughout most of domesticated maize. This work shows how a subtle cis-regulatory change in tissue specific gene expression altered plant architecture in a way that improved the harvestability of maize.
YAN Jianbing; TANG Hua; HUANG Yiqin; ZHENG Yonglian; SUBHASH Chander; LI Jiansheng
By adding thirty-one markers in the previous linkage map, a new genetic linkage map containing 205 markers was constructed, spanning a total of 2305.4 cM with an average interval of 11.2 cM. The genotypic errors in the whole genome were detected by the statistical method and removed manually. The precision of the linkage map was improved significantly. Main and epistatic QTL were detected by R/qtl, and main QTL were confirmed and refined by multiple interval mapping (MIM). Finally, MIM detected seven QTL for rows number, and five QTL for each grain yield, kernels per row and 100-kernel weight. The contribution to genetic variations of QTL varied from 35.3% for grain yield to 61.5% for rows number. Only kernels per row exhibited significant epistatic interactions between QTL. Twenty-four epistatic QTL were detected which distributed on almost all the ten chromosomes. About two-third epistatic QTL were observed between main QTL and another locus, which had no significant effects. These results indicate rather clearly that there are a number of QTL affecting trait expressions, not directly but indirectly through interactions with other loci. Thus, epistatic QTL effects may play a crucial role, if not more important than main QTL effects, in the genetic variation for the measured traits in present study.
Zhu, Jinjie; Song, Ning; Sun, Silong; Yang, Weilong; Zhao, Haiming; Song, Weibin; Lai, Jinsheng
CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) is an adaptive immune system in bacteria and archaea to defend against invasion from foreign DNA fragments. Recently, it has been developed as a powerful targeted genome editing tool for a wide variety of species. However, its application in maize has only been tested with transiently expressed somatic cells or with a limited number of stable transgenic T0 plants. The exact efficiency and specificity of the CRISPR/Cas system in the highly complex maize genome has not been documented yet. Here we report an extensive study of the well-studied type II CRISPR-Cas9 system for targeted genome editing in maize, with the codon-optimized Cas9 protein and the short non-coding guide RNA generated through a functional maize U6 snRNA promoter. Targeted gene mutagenesis was detected for 90 loci by maize protoplast assay, with an average cleavage efficiency of 10.67%. Stable knockout transformants for maize phytoene synthase gene (PSY1) were obtained. Mutations occurred in germ cells can be stably inherited to the next generation. Moreover, no off-target effect was detected at the computationally predicted putative off-target loci. No significant difference between the transcriptomes of the Cas9 expressed and non-expressed lines was detected. Our results confirmed that the CRISPR-Cas9 could be successfully applied as a robust targeted genome editing system in maize.
The origin and evolution of B chromosomes could be explained by the specific DNA sequence on them.But the specific sequences known were quite limited. To investigate maize B chromosome sqicific DNA sequeces, maize genomes with and without B chromosomes were analyzed by AFLP. Only 5 markers were found specific to genomes with B chromosomes among about 2000 AFLP markers. Southern hybridization and sequence analysis revealed that only the sequence of M8-2D was a B chromosome specific sequence.This sequence contained the telomeric repeat unit AGGGTTT conserved in plant chromosome telomeres.In addition, the sequence of M8-2D shared low homology to clones from maize chromosome 4 centromere as well. M8-2D were localized to B chromosome centromeric and telomeric regions.
Yan, Jian; Lipka, Alexander E; Schmelz, Eric A; Buckler, Edward S; Jander, Georg
Plants produce a wide variety of defensive metabolites to protect themselves against herbivores and pathogens. Non-protein amino acids, which are present in many plant species, can have a defensive function through their mis-incorporation during protein synthesis and/or inhibition of biosynthetic pathways in primary metabolism. 5-Hydroxynorvaline was identified in a targeted search for previously unknown non-protein amino acids in the leaves of maize (Zea mays) inbred line B73. Accumulation of this compound increases during herbivory by aphids (Rhopalosiphum maidis, corn leaf aphid) and caterpillars (Spodoptera exigua, beet armyworm), as well as in response to treatment with the plant signalling molecules methyl jasmonate, salicylic acid and abscisic acid. In contrast, ethylene signalling reduced 5-hydroxynorvaline abundance. Drought stress induced 5-hydroxynorvaline accumulation to a higher level than insect feeding or treatment with defence signalling molecules. In field-grown plants, the 5-hydroxynorvaline concentration was highest in above-ground vegetative tissue, but it was also detectable in roots and dry seeds. When 5-hydroxynorvaline was added to aphid artificial diet at concentrations similar to those found in maize leaves and stems, R. maidis reproduction was reduced, indicating that this maize metabolite may have a defensive function. Among 27 tested maize inbred lines there was a greater than 10-fold range in the accumulation of foliar 5-hydroxynorvaline. Genetic mapping populations derived from a subset of these inbred lines were used to map quantitative trait loci for 5-hydroxynorvaline accumulation to maize chromosomes 5 and 7.
HUANG Yi-qin; LI Jian-sheng
The classification of heterotic groups is essential to maize breeding because knowledge of heterotic groups could be interest to both the combination of outstanding hybrids and the improvement of elite inbred lines. RFLP has provided a powerful tool to assign maize inbred lines into heterotic groups. In this investigation, 45 inbred lines, used widely in south and southwest China, were chosen for RFLP analysis,among which 4 lines came from American, representing different heterotic groups in U.S. corn belt. 54 RFLP core markers covering 10 chromosomes of maize were used. A total DNA of each sample was digested with EcoR I, BamH Ⅰ and Hind Ⅲ . The procedure of RFLP was employed as described by a manual from maize RFLP lab at University of Missouri, Columbia. A total of 860 bands were detected among 45 inbred lines based on RFLP analysis, which were involved in 212 loci. Alleles at each locus ranged from 2 to 9 with an average of 4.06. In total, The 45 inbred lines were classified into 6 heterotic groups according to RFLP data with Ward's method. 3 heterotic groups, including Mo17, B73 and Oh43 respectively, seemed to be the same to U. S. heterotic groups. 21 inbred lines, most of which derived from Chinese local germplasm, were classified together into two heterotic groups, indicating domistic germplasm was different from U. S.germplasm at the molecular level and played an important role in maize hybrid production in China. Two inbred lines from tropic germplasm were assigned in the same group. These results provided useful information for our understanding maize heterotic groups and heterotic patterns in China.
Wu, Xun; Li, Yongxiang; Fu, Junjie; Li, Xin; Li, Chunhui; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu
Maize foundation parents (FPs) play no-alternative roles in hybrid breeding because they were widely used in the development of new lines and hybrids. The combination of different identity-by-descent (IBD) segments and genes could account for the formation patterns of different FPs, and knowledge of these IBD regions would provide an extensive foundation for the development of new candidate FP lines in future maize breeding. In this paper, a panel of 304 elite lines derived from FPs, i.e., B73, 207, Mo17, and Huangzaosi (HZS), was collected and analyzed using 43,252 single nucleotide polymorphism (SNP) markers. Most IBD segments specific to particular FP groups were identified, including 116 IBD segments in B73, 105 in Mo17, 111 in 207, and 190 in HZS. In these regions, 423 quantitative trait nucleotides (QTNs) associated with 15 agronomic traits and 804 candidate genes were identified. Some known adaptation-related genes, e.g., dwarf8 and vgt1 in HZS, zcn8 and epc in Mo17, and ZmCCT in 207, were validated as being tightly linked to particular IBD segments. In addition, numerous new candidate genes were also identified. For example, GRMZM2G154278 in HZS, which belongs to the cell cycle control family, was closely linked to a QTN of the ear height/plant height (EH/PH) trait; GRMZM2G051943 in 207, which encodes an endochitinase precursor (EP) chitinase, was closely linked to a QTN for kernel density; and GRMZM2G170586 in Mo17 was closely linked to a QTN for ear diameter. Complex correlations among these genes were also found. Many IBD segments and genes were included in the formation of FP lines, and complex regulatory networks exist among them. These results provide new insights on the genetic basis of complex traits and provide new candidate IBD regions or genes for the improvement of special traits in maize production. PMID:27997600
Yang, Liming; Fountain, Jake C; Wang, Hui; Ni, Xinzhi; Ji, Pingsheng; Lee, Robert D; Kemerait, Robert C; Scully, Brian T; Guo, Baozhu
Drought stress decreases crop growth, yield, and can further exacerbate pre-harvest aflatoxin contamination. Tolerance and adaptation to drought stress is an important trait of agricultural crops like maize. However, maize genotypes with contrasting drought tolerances have been shown to possess both common and genotype-specific adaptations to cope with drought stress. In this research, the physiological and metabolic response patterns in the leaves of maize seedlings subjected to drought stress were investigated using six maize genotypes including: A638, B73, Grace-E5, Lo964, Lo1016, and Va35. During drought treatments, drought-sensitive maize seedlings displayed more severe symptoms such as chlorosis and wilting, exhibited significant decreases in photosynthetic parameters, and accumulated significantly more reactive oxygen species (ROS) and reactive nitrogen species (RNS) than tolerant genotypes. Sensitive genotypes also showed rapid increases in enzyme activities involved in ROS and RNS metabolism. However, the measured antioxidant enzyme activities were higher in the tolerant genotypes than in the sensitive genotypes in which increased rapidly following drought stress. The results suggest that drought stress causes differential responses to oxidative and nitrosative stress in maize genotypes with tolerant genotypes with slower reaction and less ROS and RNS production than sensitive ones. These differential patterns may be utilized as potential biological markers for use in marker assisted breeding.
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...
Lemmon, Zachary H.; Bukowski, Robert; Sun, Qi; Doebley, John F.
Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues. PMID:25375861
Zachary H Lemmon
Full Text Available Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem. Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.
Lemmon, Zachary H; Bukowski, Robert; Sun, Qi; Doebley, John F
Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.
Full Text Available Quality protein maize (QPM contains the opaque-2 gene along with numerous modifiers for kernel hardness. Therefore, QPM is maize with high nutritive value of endosperm protein, with substantially higher content of two essential amino acids - lysine and tryptophan, and with good agronomical performances. Although QPM was developed primarily for utilization in the regions where, because of poverty, maize is the main staple food, it has many advantages for production and consumption in other parts of the world, too. QPM can be used for production of conventional and new animal feed, as well as for human nurture. As the rate of animal weight gain is doubled with QPM and portion viability is better, a part of normal maize production could be available for other purposes, such as, for example, ethanol production. Thus, breeding QPM is set as a challenge to produce high quality protein maize with high yield and other important agronomical traits, especially with today's food and feed demands and significance of energy crisis.
Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a...
Iqbal, Muhammad Shahzad; Jabbar, Basit; Sharif, Muhammad Nauman; Ali, Qurban; Husnain, Tayyab; Nasir, Idrees A.
Maize Chlorotic Mottle Virus (MCMV) is a deleterious pathogen which causes Maize Lethal Necrosis Disease (MLND) that results in substantial yield loss of Maize crop worldwide. The positive-sense RNA genome of MCMV (4.4 kb) encodes six proteins: P32 (32 kDa protein), RNA dependent RNA polymerases (P50 and P111), P31 (31 kDa protein), P7 (7 kDa protein), coat protein (25 kDa). P31, P7 and coat protein are encoded from sgRNA1, located at the 3′end of the genome and sgRNA2 is located at the extremity of the 3′genome end. The objective of this study is to locate the possible attachment sites of Zea mays derived miRNAs in the genome of MCMV using four diverse miRNA target prediction algorithms. In total, 321 mature miRNAs were retrieved from miRBase (miRNA database) and were tested for hybridization of MCMV genome. These algorithms considered the parameters of seed pairing, minimum free energy, target site accessibility, multiple target sites, pattern recognition and folding energy for attachment. Out of 321 miRNAs only 10 maize miRNAs are predicted for silencing of MCMV genome. The results of this study can hence act as the first step towards the development of MCMV resistant transgenic Maize plants through expression of the selected miRNAs.
Full Text Available Grain yield is the primary trait of interest in maize breeding programs. Worldwide, drought is the most pervasive limitation to the achievement of yield potential in maize. Drought tolerance of maize has been considerably improved through conventional breeding. Traditional breeding methods have numerous limitations, so development of new molecular genetics techniques could help in elucidation of genetic basis of drought tolerance .In order to map QTLs underlying yield and yield components under drought 116 F3 families of DTP79xB73 cross were evaluated in the field trials. Phenotypic correlations calculated using Pearson’s coefficients were high and significant. QTL detection was performed using composite interval mapping option in WinQTL Cartographer v 2.5. Over all nine traits 45 QTLs were detected: five for grain yield per plant and 40 for eight yield components. These QTLs were distributed on all chromosomes except on chromosome 9. Percent of phenotypic variability determined for the identified QTLs for all the traits was in the range from 27.46 to 95.85%. Different types of gene action were found for the QTLs identified for analyzed traits. [Projekat Ministarstva nauke Republike Srbije, br. TR31068
Baltazar, Baltazar M; de Jesús Sánchez-Gonzalez, José; de la Cruz-Larios, Lino; Schoper, John B
teosinte to introgress the maize genes into the teosinte genome. This approach would slow introgression and may help explain why teosinte continues to co-exist as a separate entity even though it normally grows in the vicinity of much larger populations of maize.
Debbie M. Figueroa
Full Text Available The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.
Figueroa, Debbie M; Davis, James D; Strobel, Cornelia; Conejo, Maria S; Beckham, Katherine D; Ring, Brian C; Bass, Hank W
The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.
Waters, Amanda J; Makarevitch, Irina; Noshay, Jaclyn; Burghardt, Liana T; Hirsch, Candice N; Hirsch, Cory D; Springer, Nathan M
Plants respond to abiotic stress through a variety of physiological, biochemical, and transcriptional mechanisms. Many genes exhibit altered levels of expression in response to abiotic stress, which requires concerted action of both cis- and trans-regulatory features. In order to study the variability in transcriptome response to abiotic stress, RNA sequencing was performed using 14-day-old maize seedlings of inbreds B73, Mo17, Oh43, PH207 and B37 under control, cold and heat conditions. Large numbers of genes that responded differentially to stress between parental inbred lines were identified. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and each of the three other inbred lines. By evaluating allele-specific transcript abundance in the F1 hybrids, we were able to measure the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Although examples of trans-regulatory variation were observed, cis-regulatory variation was more common for both steady-state and stress-responsive expression differences. The genes with cis-allelic variation for response to cold or heat stress provided an opportunity to study the basis for regulatory diversity.
FU Jie; TANG Qi-lin; YANG Xiu-yan; CHENG Ming-jun; LÜ Gui-hua; WANG Pei; WU Yuan-qi; ZHENG Ming-min; ZHOU Shu-feng; RONG Ting-zhao
Hybridization, which al ows for gene lfow between crops, is dififcult between maize and Zea perennis. In this study, we aim to initiate and study gene lfow between maize and Z. perennis via a special aneuploid plant (MDT) derived from an interspeciifc hybrid of the two species. The chromosome constitution and morphological characters of MDT as wel as certain backcross progenies were examined. Results from genomic in situ hybridization (GISH) indicate that aneuploid MDT consisted of nine maize chromosomes and 30 Z. perennis chromosomes. The backcross progenies of MDT×maize displayed signiifcant diversity of vegetative and ear morphology;several unusual plants with speciifc chromosome constitution were founded in its progenies. Some special perennial progeny with several maize chromosomes were obtained by backcrossing MDT with Z. perennis, and the ifrst whole chromosome introgression from maize to Z. perennis was detected in this study. With this novel material and method, a number of maize-tetraploid teosinte addition or substitution lines can be generated for further study, which has great signiifcance to maize and Z. perennis genetic research, especial y for promoting introgression and transferring desirable traits.
Xiaojian Peng; Yang Zhao; Xiaoming Li; Min Wu; Wenbo Chai; Lei Sheng; Yu Wang; Qing Dong; Haiyang Jiang; Beijiu Cheng
NAC transcription factors comprise a large plant-specific gene family. Increasing evidence suggests that members of this family have diverse functions in plant growth and development. In this study, we performed a genomewide survey of NAC type genes in maize (Zea mays L.). A complete set of 148 nonredundant NAC genes (ZmNAC1–ZmNAC148) were identified in the maize genome using Blast search tools, and divided into 12 groups (a–l) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental and tandem duplication contributed largely to the expansion of the maize NAC gene family. The a/s ratio suggested that the duplicated genes of maize NAC family mainly experienced purifying selection, with limited functional divergence after duplication events. Microarray analysis indicated most of the maize NAC genes were expressed across different developmental stages. Moreover, 19 maize NAC genes grouped with published stress-responsive genes from other plants were found to contain putative stress-responsive cis-elements in their promoter regions. All these stress-responsive genes belonged to the group d (stress-related). Further, these genes showed differential expression patterns over time in response to drought treatments by quantitative real-time PCR analysis. Our results reveal a comprehensive overview of the maize NAC, and form the foundation for future functional research to uncover their roles in maize growth and development.
Full Text Available Maize is an important food and feed crop in many countries. It is also one of the most important target crops for the application of biotechnology. Currently, there are more biotech traits available on the market in maize than in any other crop. Generation of transgenic events is a crucial step in the development of biotech traits. For commercial applications, a high throughput transformation system producing a large number of high quality events in an elite genetic background is highly desirable. There has been tremendous progress in Agrobacterium-mediated maize transformation since the publication of the Ishida et al. (1996 paper and the technology has been widely adopted for transgenic event production by many labs around the world. We will review general efforts in establishing efficient maize transformation technologies useful for transgenic event production in trait research and development. The review will also discuss transformation systems used for generating commercial maize trait events currently on the market. As the number of traits is increasing steadily and two or more modes of action are used to control key pests, new tools are needed to efficiently transform vectors containing multiple trait genes. We will review general guidelines for assembling binary vectors for commercial transformation. Approaches to increase transformation efficiency and gene expression of large gene stack vectors will be discussed. Finally, recent studies of targeted genome modification and transgene insertion using different site-directed nuclease technologies will be reviewed.
Gupta, Smriti; Gallavotti, Andrea; Stryker, Gabrielle A; Schmidt, Robert J; Lal, Shailesh K
We recently described a maize mutant caused by an insertion of a Helitron type transposable element (Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, E. and Hannah, L.C., 2003, Plant Cell, 15: 381-391). Here we describe another Helitron insertion in the barren stalk1 gene of maize. The termini of a 6525 bp insertion in the proximal promoter region of the mutant reference allele of maize barren stalk1 gene (ba1-ref) shares striking similarity to the Helitron insertion we reported in the Shrunken-2 gene. This insertion is embedded with pseudogenes that differ from the pseudogenes discovered in the mutant Shrunken-2 insertion. Using the common terminal ends of the mutant insertions as a query, we discovered other Helitron insertions in maize BAC clones. Based on the comparison of the insertion site and PCR amplified genomic sequences, these elements inserted between AT dinucleotides. These putative non-autonomous Helitron insertions completely lacked sequences similar to RPA (replication protein A) and DNA Helicases reported in other species. A blastn analysis indicated that both the 5' and 3' termini of Helitrons are repeated in the maize genome. These data provide strong evidence that Helitron type transposable elements are active and may have played an essential role in the evolution and expansion of the maize genome.
Char, Si Nian; Unger-Wallace, Erica; Frame, Bronwyn; Briggs, Sarah A; Main, Marcy; Spalding, Martin H; Vollbrecht, Erik; Wang, Kan; Yang, Bing
Transcription activator-like effector nuclease (TALEN) technology has been utilized widely for targeted gene mutagenesis, especially for gene inactivation, in many organisms, including agriculturally important plants such as rice, wheat, tomato and barley. This report describes application of this technology to generate heritable genome modifications in maize. TALENs were employed to generate stable, heritable mutations at the maize glossy2 (gl2) locus. Transgenic lines containing mono- or di-allelic mutations were obtained from the maize genotype Hi-II at a frequency of about 10% (nine mutated events in 91 transgenic events). In addition, three of the novel alleles were tested for function in progeny seedlings, where they were able to confer the glossy phenotype. In a majority of the events, the integrated TALEN T-DNA segregated independently from the new loss of function alleles, producing mutated null-segregant progeny in T1 generation. Our results demonstrate that TALENs are an effective tool for genome mutagenesis in maize, empowering the discovery of gene function and the development of trait improvement.
Henry, Clémence; Bledsoe, Samuel W; Griffiths, Cara A; Kollman, Alec; Paul, Matthew J; Sakr, Soulaiman; Lagrimini, L Mark
Little is known about how salt impacts primary metabolic pathways of C4 plants, particularly related to kernel development and seed set. Osmotic stress was applied to maize (Zea mays) B73 by irrigation with increasing concentrations of NaCl from the initiation of floral organs until 3 d after pollination. At silking, photosynthesis was reduced to only 2% of control plants. Salt treatment was found to reduce spikelet growth, silk growth, and kernel set. Osmotic stress resulted in higher concentrations of sucrose (Suc) and hexose sugars in leaf, cob, and kernels at silking, pollination, and 3 d after pollination. Citric acid cycle intermediates were lower in salt-treated tissues, indicating that these sugars were unavailable for use in respiration. The sugar-signaling metabolite trehalose-6-phosphate was elevated in leaf, cob, and kernels at silking as a consequence of salt treatment but decreased thereafter even as Suc levels continued to rise. Interestingly, the transcripts of trehalose pathway genes were most affected by salt treatment in leaf tissue. On the other hand, transcripts of the SUCROSE NONFERMENTING-RELATED KINASE1 (SnRK1) marker genes were most affected in reproductive tissue. Overall, both source and sink strength are reduced by salt, and the data indicate that trehalose-6-phosphate and SnRK1 may have different roles in source and sink tissues. Kernel abortion resulting from osmotic stress is not from a lack of carbohydrate reserves but from the inability to utilize these energy reserves.
Pauly, Markus; Hake, Sarah; Kraemer, Florian J
The disclosure relates to a maize plant, seed, variety, and hybrid. More specifically, the disclosure relates to a maize plant containing a Cal-1 allele, whose expression results in increased cell wall-derived glucan content in the maize plant. The disclosure also relates to crossing inbreds, varieties, and hybrids containing the Cal-1 allele to produce novel types and varieties of maize plants.
Luciana Lasry Benchimol
Full Text Available A microsatellite marker (SSR was chosen to simulate a target allele and three criteria (02, 04 and 06 markers per chromosome were tested to evaluate the most efficient parameters for performing marker-assisted backcross (MAB selection. We used 53 polymorphic SSRs to genotype 186 BC1 maize (Zea mays L. plants produced by crossing the inbred maize lines L-08-05 (donor parent and L-14-4B (recurrent parent. The second backcross (BC2 generation was produced with 180 plants and screened with markers which were not recovered from the first backcross (BC1 generation. A total of 480 plants were evaluated in the third backcross (BC3 generation from which 48 plants were selected for parental genotype recovery. Recurrent genotype recovery averages in three backcross generations were compatible with those expected in BC4 or BC5, indicating genetic gain due to the marker-assisted backcrossing. The target marker (polymorphic microsatellite PHI037 was efficiently transferred. Six markers per chromosome showed a high level of precision for parental estimates at different levels of maize genome saturation and donor alleles were not present in the selected recovered pure lines. Phenotypically, the plants chosen based on this criterion (06 markers per chromosome were closer to the recurrent parent than any other selected by other criteria (02 or 04 markers per chromosome. This approach allowed the understanding that six microsatellites per chromosome is a more efficient parameter than 02 and 04 markers per chromosome for deriving a marker-assisted backcross (MAB experiment in three backcross generations.
Krakowsky, M D; Lee, M; Coors, J G
While maize silage is a significant feed component in animal production operations, little information is available on the genetic bases of fiber and lignin concentrations in maize, which are negatively correlated with digestibility. Fiber is composed largely of cellulose, hemicellulose and lignin, which are the primary components of plant cell walls. Variability for these traits in maize germplasm has been reported, but the sources of the variation and the relationships between these traits in different tissues are not well understood. In this study, 191 recombinant inbred lines of B73 (low-intermediate levels of cell wall components, CWCs) x De811 (high levels of CWCs) were analyzed for quantitative trait loci (QTL) associated with CWCs in the leaf sheath. Samples were harvested from plots at two locations in 1998 and one in 1999 and assayed for neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL). QTL were detected on all ten chromosomes, most in tissue specific clusters in concordance with the high genotypic correlations for CWCs within the same tissue. Adjustment of NDF for its subfraction, ADF, revealed that most of the genetic variation in NDF was probably due to variation in ADF. The low to moderate genotypic correlations for the same CWC across leaf sheath and stalk tissues indicate that some genes for CWCs may only be expressed in certain tissues. Many of the QTL herein were detected in other populations, and some are linked to candidate genes for cell wall carbohydrate biosynthesis.
Meng Luo; Jia Liu; R. Dewey Lee; Brian T. Scully; Baozhu Guo
Preharvest aflatoxin contamination of grain grown on the US southeastern Coast Plain is provoked and aggravated by abiotic stress. The primary abiotic stress is drought along with high temperatures. The objectives of the present study were to monitor gene expression in developing kernels in response to drought stress and to identify drought-responsive genes for possible use in germplasm assessment. The maize breeding line Tex6 was used, and gene expression profiles were analyzed in developing kernels under drought stress verses well-watered conditions at the stages of 25, 30, 35, 40, 45 d after pollination (DAP) using the 70 mer maize oligo-arrays. A total of 9 573 positive array spots were detected with unique gene IDs, and 7 988 were common in both stressed and well-watered samples. Expression patterns of some genes in several stress response-associated pathways, including abscisic acid, jasmonic acid and phenylalanine ammonia-lyase, were examined, and these specific genes were responsive to drought stress positively. Real-time quantitative polymerase chain reaction validated microarray expression data.The comparison between Tex6 and B73 revealed that there were significant differences in specific gene expression, patterns and levels. Several defense-related genes had been downregulated, even though some defense-related or drought responsive genes were upregulated at the later stages.
Hansen, Elly Møller; Eriksen, Jørgen
During the last 20 years the area with maize in Denmark has increased dramatically and reached 163,000 ha in 2008. Silage maize is easy to grow, is a suitable fodder for cows and goes well with grass-clover in the diet. This means that silage maize is often found in crop rotations with grass-clover on sandy soils in western Denmark. The ploughing in of grass-clover fields poses a serious risk of increased nitrate leaching on a coarse sandy soil, even when carried out in spring. With increased...
Full Text Available Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a certain trait, the following specific procedures in evaluation of the trait are necessary: the estimation of a popping volume and flake quality in popping maize; the determination of sugars and harvest maturity in sweet maize; the determination of oil in selected samples of high-oil maize types, and so forth. Breeding programmes for speciality maize, except high-amylose maize, have been implemented at the Maize Research Institute, Zemun Polje, Belgrade, for the last 45 years. A great number of high-yielding sweet maize hybrids, popping maize, high-oil and high-lysine, flint and white-seeded maize hybrids were developed during this 45-year period. Auspicious selection and breeding for these traits is facilitated by the abundant genetic variability and technical and technological possibilities necessary for successful selection.
Chaoxian Liu; Xiaoli Liu; Lei Lei; Haiying Guan; Yilin Cai
The maize mutant gene Vestigial glume 1 (Vg1) has been fine-mapped to a narrow region by map-based cloning and the candidate gene for Vg1 spanned 19.5 kb. Here we report Vg1 genomic fosmid library construction and screening. The fosmid library of Vg1 consisted of 574,000 clones with an average insert size of 36.4 kb, representing 7.9-fold coverage of the maize genome. Fosmid stability assays indicated that clones were stable during propagation in the fosmid system. Using Vg1 candidate gene-specific primers, a positive clone was successfully identified. This discovery will pave the way for identifying the function of Vg1 in maize development.
Chaoxian Liu; Xiaoli Liu; Lei Lei; Haiying Guan; Yilin Cai
The maize mutant gene Vestigial glume 1(Vg1) has been fine-mapped to a narrow region by map-based cloning and the candidate gene for Vg1 spanned 19.5 kb. Here we report Vg1 genomic fosmid library construction and screening. The fosmid library of Vg1 consisted of574,000 clones with an average insert size of 36.4 kb, representing 7.9-fold coverage of the maize genome. Fosmid stability assays indicated that clones were stable during propagation in the fosmid system. Using Vg1 candidate gene-specific primers, a positive clone was successfully identified. This discovery will pave the way for identifying the function of Vg1 in maize development.
Yongsheng TAO; Zuxin ZHANG; Yonglin CHEN; Lijia LI; Yonglian ZHENG
The rice BAC-DNA was used as probes and fluorescence in situ hybridization (FISH) was applied to the interphase and metaphase mitotic chromosomes of maize. To optimize the BAC-FISH technique, we respect-ively assayed the effect of several factors, including maize or rice genomic Cot DNA used as blocking reagent of DNA, washing temperatures and FAD concentration in the washing buffer and in the hybrid solution. The results show that Cot DNA of maize genome blocked the repet-itive sequence of the rice BAC-DNA when the Cot value was below 50. Meanwhile, it was necessary to adjust the Cot value according to the different probes and their ratios. Decreasing the concentration of FAD in the hybridization mixtures, adjusting the washing rate after hybridization, and most especially, blocking the rice-specific repetitive sequences of BAC-DNA could improve the positive signals of BAC-FISH.
Full Text Available The maize mutant gene Vestigial glume 1 (Vg1 has been fine-mapped to a narrow region by map-based cloning and the candidate gene for Vg1 spanned 19.5 kb. Here we report Vg1 genomic fosmid library construction and screening. The fosmid library of Vg1 consisted of 574,000 clones with an average insert size of 36.4 kb, representing 7.9-fold coverage of the maize genome. Fosmid stability assays indicated that clones were stable during propagation in the fosmid system. Using Vg1 candidate gene-specific primers, a positive clone was successfully identified. This discovery will pave the way for identifying the function of Vg1 in maize development.
DNA methylation plays an important role in gene expression regulation during biological development and tissue differentiation in plants. This study adopted methylation-sensitive Amplified fragment length polymorphism (AFLP) to compare the levels of DNA cytosine methylation at CCGG sites in tassel, bracteal leaf, and ear leaf from maize inbred lines, 18 White and 18 Red, respectively, and also examined specific methylation patterns of the three tissues. Significant differences in cytosine methylation level among the three tissues and the same changing tendency in two inbred lines were detected. Both MSAP (methylation sensitive amplification polymorphism) ratio and full methylation level were the highest in bracteal leaf, and the lowest in tassel. Meanwhile, different methylation levels were observed in the same tissue from the inbred lines, 18 White and 18 Red. Full methylation of internal cytosine was the dominant type in the maize genome. The differential methylation patterns in the three tissues were observed. In addition, sequencing of nine differentially methylated fragments and the subsequent blast search revealed that the cytosine methylated 5′-CCGG-3′ sequences were distributed in repeating sequences, in the coding and noncoding regions. Southern hybridization was used to verify the methylation polymorphism. These results clearly demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and the complexity of DNA methylation change during plant growth and development. The different methylation levels may be related to specific gene expression in various tissues.
Yijun WANG; Mingliang XU; Dexiang DENG; Yunlong BIAN
Transposable elements are widely distributed in eukaryotes. Due to its high copy numbers, high forward mutation rate and preferential insertion into low-copy DNA sequences, among others, the Mutator system has been widely used as a mutagen in genomic research. The discovery, classification, transposition specificity and epige-netic regulation of Mutator transposons were described. The application of Mutator tagging in plant genomic research was also presented. The role of Mu-like elements in genome evolution was briefly depicted. Moreover, the direction of Mutator transposon research in the future was discussed.
In order to isolate mitochondrial genes easily, we have developed a new method to construct S-type CMS maize mitochondrial gene library by means of embedding mitochondria and enzymatic digesting mitochondria in situ, preparing mtDNA by electrophoresis, digesting LMP agarose with β-agarase, using BAC vector and electroporation. About 2 500 white clones of Mo17 CMS-J mitochondrial gene library were obtained with the average size of 18.24 kb, ranging from 5 to 40 kb, 63.6% inserts came from mitochondrial genome and represented 48 ′ mitochondrial genome equivalents. All the probes had detected the positive clones in the gene library. It is helpful to elucidating the maize mitochondrial genome structure and mechanism of S-type CMS, and may give some valuable reference to the construction of other plant mitochondrial genome library.
Rabinowicz, Pablo D; McCombie, W Richard; Martienssen, Robert A
The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.
Allison M Krill
Full Text Available BACKGROUND: Aluminum (Al toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. METHODOLOGY: An association panel of 282 diverse maize inbred lines and three F2 linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. CONCLUSIONS: Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays AltSB like (ZmASL, Zea mays aluminum-activated malate transporter2 (ALMT2, S-adenosyl-L-homocysteinase (SAHH, and Malic Enzyme (ME. These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.
Andersen, Jeppe Reitan; Zein, Imad; Wenzel, Gerhard;
genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD...
Fescemyer, Howard W; Sandoya, Germán V; Gill, Torrence A; Ozkan, Seval; Marden, James H; Luthe, Dawn S
Understanding the molecular mechanisms underlying insect compensatory responses to plant defenses could lead to improved plant resistance to herbivores. The Mp708 inbred line of maize produces the maize insect resistant 1-cysteine protease (Mir1-CP) toxin. Reduced feeding and growth of fall armyworm larvae fed on Mp708 was previously linked to impairment of nutrient utilization and degradation of the midgut (MG) peritrophic matrix (PM) by Mir1-CP. Here we examine the biochemical and transcriptional responses of fall armyworm larvae to Mir1-CP. Insect Intestinal Mucin (IIM) was severely depleted from pure PMs treated in vitro with recombinant Mir1-CP. Larvae fed on Mp708 midwhorls excrete frass largely depleted of IIM. Cracks, fissures and increased porosity previously observed in the PM of larvae fed on Mp708 midwhorls could ensue when Mir1-CP degrades the IIM that cross-links chitin fibrils in the PM. Both targeted and global transcriptome analyses were performed to determine how complete dissolution of the structure and function of the PM is prevented, enabling larvae to continue growing in the presence of Mir1-CP. The MGs from fall armyworm fed on Mp708 upregulate expression of genes encoding proteins involved in PM production as an apparent compensation to replace the disrupted PM structure and restore appropriate counter-current MG gradients. Also, several families of digestive enzymes (endopeptidases, aminopeptidases, lipases, amylase) were more highly expressed in MGs from larvae fed on Mp708 than MGs from larvae fed on diets lacking Mir1-CP (artificial diet, midwhorls from Tx601 or B73 maize). Impaired growth of larvae fed on Mp708 probably results from metabolic costs associated with higher production of PM constituents and digestive enzymes in a compensatory attempt to maintain MG function.
Avramova, Viktoriya; AbdElgawad, Hamada; Vasileva, Ivanina; Petrova, Alexandra S.; Holek, Anna; Mariën, Joachim; Asard, Han; Beemster, Gerrit T. S.
We studied the impact of drought on growth regulation in leaves of 13 maize varieties with different drought sensitivity and geographic origins (Western Europe, Egypt, South Africa) and the inbred line B73. Combining kinematic analysis of the maize leaf growth zone with biochemical measurements at a high spatial resolution allowed us to examine the correlation between the regulation of the cellular processes cell division and elongation, and the molecular redox-regulation in response to drought. Moreover, we demonstrated differences in the response of the maize lines to mild and severe levels of water deficit. Kinematic analysis indicated that drought tolerant lines experienced less impact on leaf elongation rate due to a smaller reduction of cell production, which, in turn, was due to a smaller decrease of meristem size and number of cells in the leaf meristem. Clear differences in growth responses between the groups of lines with different geographic origin were observed in response to drought. The difference in drought tolerance between the Egyptian hybrids was significantly larger than between the European and South-African hybrids. Through biochemical analyses, we investigated whether antioxidant activity in the growth zone, contributes to the drought sensitivity differences. We used a hierarchical clustering to visualize the patterns of lipid peroxidation, H2O2 and antioxidant concentrations, and enzyme activities throughout the growth zone, in response to stress. The results showed that the lines with different geographic region used different molecular strategies to cope with the stress, with the Egyptian hybrids responding more at the metabolite level and African and the European hybrids at the enzyme level. However, drought tolerance correlated with both, higher antioxidant levels throughout the growth zone and higher activities of the redox-regulating enzymes CAT, POX, APX, and GR specifically in leaf meristems. These findings provide evidence for a link
Lazarow, Katina; Doll, My-Linh; Kunze, Reinhard
Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.
Maluleke, Mary H; Addo-Bediako, Abraham; Ayisi, Kingsley K
Lepidopterous stem borers seriously affect production of maize, Zea mays L., in sub-Saharan Africa. Intercropping maize with legumes such as lablab, Lablab purpurens (L.), is one of the effective systems to control stem borers. Sole culture maize and maize/lablab intercrop system of different lablab densities were planted at two locations to investigate the effects of intercrop system on incidence and severity of stem borers with particular reference to Chilo partellus (Swinhoe) (Lepidoptera: Pyralidae). Stem borer infestation was found to be more severe in sole culture maize than maize in maize/lablab intercrop. There was a significantly negative relationship between lablab densities and maize grain yields, suggesting a possible competition for resources between the two crops. It was concluded that density of lablab and date of planting of lablab in maize/lablab intercropping have significant affects on stem borer populations and maize grain yields.
Zhao, Yang; Tong, Haiqing; Cai, Ronghao; Peng, Xiaojian; Li, Xiaoyu; Gan, Defang; Zhu, Suwen
Rare-cold-inducible (RCI2) genes are structurally conserved members that encode small, highly hydrophobic proteins involved in response to various abiotic stresses. Phylogenetic and functional analyses of these genes have been conducted in Arabidopsis, but an extensive investigation of the RCI2 gene family has not yet been carried out in maize. In the present study, 10 RCI2 genes were identified in a fully sequenced maize genome. Structural characterization and expression pattern analysis of 10 ZmRCI2s (Zea mays RCI2 genes) were subsequently determined. Sequence and phylogenetic analyses indicated that ZmRCI2s are highly conserved, and most of them could be grouped with their orthologues from other organisms. Chromosomal location analysis indicated that ZmRCI2s were distributed unevenly on seven chromosomes with two segmental duplication events, suggesting that maize RCI2 gene family is an evolutionarily conserved family. Putative stress-responsive cis-elements were detected in the 2-kb promoter regions of the 10 ZmRCI2s. In addition, the 10 ZmRCI2s showed different expression patterns in maize development based on transcriptome analysis. Further, microarray and quantitative real-time PCR (qRT-PCR) analysis showed that each maize RCI2 genes were responsive to drought stress, suggesting their important roles in drought stress response. The results of this work provide a basis for future cloning and application studies of maize RCI2 genes.
Yang Zhao; Haiqing Tong; Ronghao Cai; Xiaojian Peng; Xiaoyu Li; Defang Gan; Suwen Zhu
Rare-cold-inducible (RCI2) genes are structurally conserved members that encode small, highly hydrophobic proteins involved in response to various abiotic stresses. Phylogenetic and functional analyses of these genes have been conducted in Arabidopsis, but an extensive investigation of the RCI2 gene family has not yet been carried out in maize. In the present study, 10 RCI2 genes were identified in a fully sequenced maize genome. Structural characterization and expression pattern analysis of 10 ZmRCI2s (Zea mays RCI2 genes) were subsequently determined. Sequence and phylogenetic analyses indicated that ZmRCI2s are highly conserved, and most of them could be grouped with their orthologues from other organisms. Chromosomal location analysis indicated that ZmRCI2s were distributed unevenly on seven chromosomes with two segmental duplication events, suggesting that maize RCI2 gene family is an evolutionarily conserved family. Putative stress-responsive cis-elements were detected in the 2-kb promoter regions of the 10 ZmRCI2s. In addition, the 10 ZmRCI2s showed different expression patterns in maize development based on transcriptome analysis. Further, microarray and quantitative real-time PCR (qRT-PCR) analysis showed that each maize RCI2 genes were responsive to drought stress, suggesting their important roles in drought stress response. The results of this work provide a basis for future cloning and application studies of maize RCI2 genes.
Full Text Available Cadmium (Cd is a heavy metal and is highly toxic to all plant species. However, the underlying molecular mechanism controlling the effects of auxin on the Cd stress response in maize is largely unknown. In this study, the transcriptome produced by maize ‘Zheng 58’ root responses to Cd stress was sequenced using Illumina sequencing technology. In our study, six RNA-seq libraries yielded a total of 244 million clean short reads and 30.37 Gb of sequence data. A total of 6342 differentially expressed genes (DEGs were grouped into 908 Gene Ontology (GO categories and 198 Kyoto Encyclopedia of Genes and Genomes terms. GO term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Comparison of the transcript abundances for auxin biosynthesis, transport, and downstream response genes revealed a universal expression response under Cd treatment. Furthermore, our data showed that free indole-3-acetic acid (IAA levels were significantly reduced; but IAA oxidase activity was up-regulated after Cd treatment in maize roots. The analysis of Cd activity in maize roots under different Cd and auxin conditions confirmed that auxin affected Cd accumulation in maize seedlings. These results will improve our understanding of the complex molecular mechanisms underlying the response to Cd stress in maize roots.
Martínez-Romero, Esperanza; Silva-Sanchez, Jesús; Barrios, Humberto; Rodríguez-Medina, Nadia; Martínez-Barnetche, Jesús; Téllez-Sosa, Juan; Gómez-Barreto, Rosa Elena; Garza-Ramos, Ulises
Three endophytic Klebsiella variicola isolates-T29A, 3, and 6A2, obtained from sugar cane stem, maize shoots, and banana leaves, respectively-were used for whole-genome sequencing. Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes contain plant colonization and cellulases genes. This study will help toward understanding the genomic basis of K. variicola interaction with plant hosts.
Cooper, Mark; Gho, Carla; Leafgren, Roger; Tang, Tom; Messina, Carlos
Germplasm, genetics, phenotyping, and selection, combined with a clear definition of product targets, are the foundation of successful hybrid maize breeding. Breeding maize hybrids with superior yield for the drought-prone regions of the US corn-belt involves integration of multiple drought-specific technologies together with all of the other technology components that comprise a successful maize hybrid breeding programme. Managed-environment technologies are used to enable scaling of precision phenotyping in appropriate drought environmental conditions to breeding programme level. Genomics and other molecular technologies are used to study trait genetic architecture. Genetic prediction methodology was used to breed for improved yield performance for drought-prone environments. This was enabled by combining precision phenotyping for drought performance with genetic understanding of the traits contributing to successful hybrids in the target drought-prone environments and the availability of molecular markers distributed across the maize genome. Advances in crop growth modelling methodology are being used to evaluate the integrated effects of multiple traits for their combined effects and evaluate drought hybrid product concepts and guide their development and evaluation. Results to date, lessons learned, and future opportunities for further improving the drought tolerance of maize for the US corn-belt are discussed.
Full Text Available Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6,004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.
Genotyping breeding materials is now relatively inexpensive but phenotyping costs have remained the same. One method to increase gene mapping power is to use genome-wide genetic markers to combine existing phenotype data for multiple populations into a unified analysis. We combined data from 15 bipa...
L. Cavallarin; Antoniazzi, S.; E. Tabacco; G. Borreani
Whole-plant maize silage, stored in horizontal silos, is the main diet source of lactating dairy cows in Italy. Mycotoxin contamination of maize grain has widely been described (Hussein and Brasel, 2001), while limited information is available on mycotoxins in maize silage (Oldenburg, 1991).
Krakowsky, M D; Lee, M; Coors, J G
Maize silage is a significant energy source for animal production operations, and the efficiency of the conversion of forage into animal mass is an important consideration when selecting cultivars for use as feed. Fiber and lignin are negatively correlated with digestibility of feed, so the development of forage with reduced levels of these cell-wall components (CWCs) is desirable. While variability for fiber and lignin is present in maize germplasm, traditional selection has focused on the yield of the ear rather than the forage quality of the whole plant, and little information is available concerning the genetics of fiber and lignin. The objectives of this study were to map quantitative trait loci (QTLs) for fiber and lignin in the maize stalk and compare them with QTLs from other populations. Stalk samples were harvested from 191 recombinant inbred lines (RILs) of B73 (an inbred line with low-to-intermediate levels of CWCs) x De811 (an inbred line with high levels of CWCs) at two locations in 1998 and one in 1999 and assayed for neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL). The QTLs were detected on nine chromosomes, mostly clustered in concordance with the high genetic correlations between NDF and ADF. Adjustment of NDF for ADF and ADF for ADL revealed that most of the variability for CWCs in this population is in ADF. Many of the QTLs detected in this study have also been detected in other populations, and several are linked to candidate genes for cellulose or starch biosynthesis. The genetic information obtained in this study should be useful to breeding efforts aimed at improving the quality of maize silage.
Christie, Nanette; Myburg, Alexander A; Joubert, Fourie; Murray, Shane L; Carstens, Maryke; Lin, Yao-Cheng; Meyer, Jacqueline; Crampton, Bridget G; Christensen, Shawn A; Ntuli, Jean F; Wighard, Sara S; Van de Peer, Yves; Berger, Dave K
We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for susceptibility to GLS. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defence responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.
Assem, Shireen K
Maize (Zea mays L.) is the third most important food crop globally after wheat and rice. In sub-Saharan Africa, tropical maize has traditionally been the main staple of the diet; 95 % of the maize grown is consumed directly as human food and as an important source of income for the resource-poor rural population. The biotechnological approach to engineer biotic and abiotic traits implies the availability of an efficient plant transformation method. The production of genetically transformed plants depends both on the ability to integrate foreign genes into target cells and the efficiency with which plants are regenerated. Maize transformation and regeneration through immature embryo culture is the most efficient system to regenerate normal transgenic plants. However, this system is highly genotype dependent. Genotypes adapted to tropic areas are difficult to regenerate. Therefore, transformation methods used with model genotypes adapted to temperate areas are not necessarily efficient with tropical lines. Agrobacterium-mediated transformation is the method of choice since it has been first achieved in 1996. In this report, we describe a transformation method used successfully with several tropical maize lines. All the steps of transformation and regeneration are described in details. This protocol can be used with a wide variety of tropical lines. However, some modifications may be needed with recalcitrant lines.
Defense response genes in higher plant species are involved in a variety of signal tranaduction pathways and biochemical reactions to counterattack invading pathogens. In this study, a total of 366 non-redundant defense response gene homologs (DRHs), Including 124 unigenes/expressed sequence tags, 226 tentative consensuses, and 16 DRH contigs have been identified by mining the Maize Genetics and Genomics and The Institute for Genomic Research maize databases using 35 essential defense response genes. Of 366 DRHs, 202 are mapped to 152 loci across ten maize chromosomes via both the genetic and in silico mapping approaches. The mapped DRHs seem to cluster together rather than be evenly distributed along the maize genome. Approximately half of these DHRs are located in regions harboring either major resistance genes or quantitative trait loci(QTL). Therefore, this comprehensive DRH linkage map will provide reference sequences to Identify either positional candidate genes for resistance genes and/or QTLs or to develop makers for fine-mapping and marker-assisted selection of resistance genes and/or QTLs.
Ranum, Peter; Peña-Rosas, Juan Pablo; Garcia-Casal, Maria Nieves
Maize (Zea mays), also called corn, is believed to have originated in central Mexico 7000 years ago from a wild grass, and Native Americans transformed maize into a better source of food. Maize contains approximately 72% starch, 10% protein, and 4% fat, supplying an energy density of 365 Kcal/100 g and is grown throughout the world, with the United States, China, and Brazil being the top three maize-producing countries in the world, producing approximately 563 of the 717 million metric tons/year. Maize can be processed into a variety of food and industrial products, including starch, sweeteners, oil, beverages, glue, industrial alcohol, and fuel ethanol. In the last 10 years, the use of maize for fuel production significantly increased, accounting for approximately 40% of the maize production in the United States. As the ethanol industry absorbs a larger share of the maize crop, higher prices for maize will intensify demand competition and could affect maize prices for animal and human consumption. Low production costs, along with the high consumption of maize flour and cornmeal, especially where micronutrient deficiencies are common public health problems, make this food staple an ideal food vehicle for fortification.
Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public
REN Zhen-jing; CAO Gao-yi; ZHANG Yu-wen; LIU Yan; LIU Yun-jun
It has previously been shown that a bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene AM79 aroA can be a candidate gene to develop glyphosate-tolerant transgenic crops (Cao et al. 2012). In this study, AM79 aroA was redesigned using the plant biased codons and eliminating the motifs which would lead to the instability of mRNA, to create a synthetic gene that would be expressed highly in plant cel s. The redesigned and artiifcial y synthesized gene, named as mAM79, was cloned into plant expression vector pM3301UbiSpAM79, where mAM79 is fused with signal peptide sequence of pea rib-1,5-bisphospate carboxylase (rbcS) smal subunit and control ed by ubiquitin promoter. The plasmid was transformed into maize (Zea mays) immature embryos using Agrobacterium-mediated transformation method. Total 74 regenerated plants were obtained and PCR analysis showed that these transgenic plants had the integration of mAM79. Southern blot analysis was performed on the genomic DNA from four transgenic lines, and the result showed that one or two copies of mAM79 were integrated into maize genome. RT-PCR analysis result indicated that mAM79 was highly transcribed in transgenic maize plants. When sprayed with glyphosate, transgenic maize line AM85 and AM72 could tolerate 4-fold of commercial usage of glyphosate;however, al the non-transgenic maize plants were kil ed by glyphosate. The results in this study conifrmed that mAM79 could be used to develop glyphosate-tolerant maize, and the obtained transgenic maize lines could be used for the breeding of glyphosate-tolerant maize.
YANG Hua; YANG Junpin; RONG Tingzhao; TAN Jun; QIU Zhenggao
The genetic linkage map has been constructed with 125 SSR markers based on BC1:2 population consisting of 322 lines derived from the combination of (CML270×478) ×CML270 in maize (Zea mays L.), covering 1939.0 cM of maize genome. The average mapping distance was about 15.5 cM. Three major QTLs of the relative resistant index of resistance to maize sheath blight (Rhizoctonia solani) had been located on chromosomes 1, 7 by composite interval mapping (CIM). 7 QTLs of the plant height have been located on chromosomes 3, 4, 5, 6. Five QTLs of ear height have been located on chromosomes 3, 4, 6. The resistance to the sheath blight is shown to be not relative to plant height and ear height genetically. Inbred line CML270 was used for molecular assisted selection and cloning the genes.
Martin, D P; Willment, J A; Billharz, R; Velders, R; Odhiambo, B; Njuguna, J; James, D; Rybicki, E P
Full genomic sequences were determined for 12 Maize streak virus (MSV) isolates obtained from Zea mays and wild grass species. These and 10 other publicly available full-length sequences were used to classify a total of 66 additional MSV isolates that had been characterized by PCR-restriction fragment length polymorphism and/or partial nucleotide sequence analysis. A description is given of the host and geographical distribution of the MSV strain and subtype groupings identified. The relationship between the genotypes of 21 fully sequenced virus isolates and their virulence in differentially MSV-resistant Z. mays genotypes was examined. Within the only MSV strain grouping that produced severe symptoms in maize, highly virulent and widely distributed genotypes were identified that are likely to pose the most serious threat to maize production in Africa. Evidence is presented that certain of the isolates investigated may be the products of either intra- or interspecific recombination.
Full Text Available Zea stands for ‘sustaining life’ and Mays stands for ‘life giver’. Zea mays is one of the oldest and most dynamic crop species, which has gained popularity in modern world too, due to its applications in diverse dishes. Corn is produced in every continent of the world with the exception of Antarctica. It is an annual monoecious sunny plant, surviving perfectly in nutrient rich, well-drained soil. Each and every part of the corn, from husk to corn silk is beneficial for the society. There are more than 3,500 different uses for corn products. Corn does much more than feed people and livestock. The plant contains alkaloids, flavonoids, saponins, maizenic acid, vitamins B1, K and minerals like potassium, phosphorous and zinc. Traditionally, Maize is used as an analgesic, anti-diarrheal, anti-prostatitic, anti-lithiasis, anti-tumor, anti-hypertensive, anti-diabetic, anti-hyperlipidemic, anti-inflammatory and anti-oxidant. In this review article, we have narrated miscellaneous uses of corn varieties and described the pharmacological activities, phytoconstituents, nutritional value and traditional uses of maize. The maize has assorted uses like culinary, medicinal and industrial. Corn dishes like corn-meal, corn-flakes, popcorn, “makki ki roti” and corn soup highlight its dominance all over the world. Therefore, maize has become a craze among modern youth.
Full Text Available A novel virus, tentatively named Maize Yellow Mosaic Virus (MaYMV, was identified from the field-grown maize plants showing yellow mosaic symptoms on the leaves collected from the Yunnan Province of China by the deep sequencing of small RNAs. The complete 5642 nucleotide (nt-long genome of the MaYMV shared the highest nucleotide sequence identity (73% to Maize Yellow Dwarf Virus-RMV. Sequence comparisons and phylogenetic analyses suggested that MaYMV represents a new member of the genus Polerovirus in the family Luteoviridae. Furthermore, the P0 protein encoded by MaYMV was demonstrated to inhibit both local and systemic RNA silencing by co-infiltration assays using transgenic Nicotiana benthamiana line 16c carrying the GFP reporter gene, which further supported the identification of a new polerovirus. The biologically-active cDNA clone of MaYMV was generated by inserting the full-length cDNA of MaYMV into the binary vector pCB301. RT-PCR and Northern blot analyses showed that this clone was systemically infectious upon agro-inoculation into N. benthamiana. Subsequently, 13 different isolates of MaYMV from field-grown maize plants in different geographical locations of Yunnan and Guizhou provinces of China were sequenced. Analyses of their molecular variation indicate that the 3′ half of P3–P5 read-through protein coding region was the most variable, whereas the coat protein- (CP- and movement protein- (MP-coding regions were the most conserved.
崔小雯; 高波; 许斐斐; 李向东; 张春庆; 苗洪芹
Totally 11 maize samples showing dwarf mosaic symptoms were collected from Chengde, Hebei Province. The 3'-terminal 2.1 kb genomic fragments were amplified with degenerate primers for Sugarcane mosaic virus (SCMV) and Pennisetum mosaic virus (PenMV) and then sequenced. The Blast results showed that eight samples were infected with PenMV. The cloned genome of these eight isolates were all 2 135 nucleo-tides (nt) long, including partial Nib gene (985 nt), complete CP gene (909 nt) and the 3'-UTR (241 nt). The CP gene and 3'- UTR shared nt identities of 89.8% -93.4% and 95.9% -97.9% , respectively, with the corresponding PenMV sequences available in the GenBank. In the phylogenetic trees constructed with the 3'-terminal 2 135 nt sequence and CP gene, all the PenMV isolates were divided into two groups; Shanxi group (SX) and Chengde group (CD). Recombination event was detected in the CP gene of isolate CD9.%采自河北承德11个表现矮花叶症状的玉米样品,用甘蔗花叶病毒(Sugarcane mosaic virus,SCMV)和白草花叶病毒(Pennisetum mosaic virus,PenMV)简并引物扩增了基因组3’端约2.1kb的片段并进行测序.Blast结果表明其中8个样品含有PenMV.扩增到的PenMV序列均为2 135 nt,包括部分NIb基因(985 nt)、完整的CP基因(909 nt)和3’-UTR(241nt).这8个分离物CP基因和3’-UTR与GenBank上其他PenMV分离物相应序列的核苷酸一致率分别为89.8％～93.4％和95.9％～97.9％.根据扩增的2 135nt序列和CP基因序列构建系统发育树,8个分离物与GenBank上其他PenMV分离物都分为2个组:山西组和承德组.重组分析表明CD9的CP基因存在重组.
A field experiment was conducted during winter seasons of 2003-04 and 2004-05 at Kanpur, India to study the effect of winter maize (Zea mays L.) based intercropping systems on maize yield, associated weeds and economics under irrigated condition of central Uttar Pradesh. Thirteen maize-based cropping systems such as maize sole, potato (Solanum tuberosum L.) sole, mustard [Brassica juncea (L.) Czernj. & Cosson] sole, toria (Brassica campestris var. toria) sole, pea (Pisum sativum L.) sole, lin...
Buddhi Bahadur Achhami; Santa Bahadur BK; Ghana Shyam Bhandari
Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and the average plant damage per...
Buddhi Bahadur Achhami; Santa Bahadur BK; Ghana Shyam Bhandari
Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and the average plant damage...
WANG YueBing; LANG Zhihong; ZHANG Jie; HE KangLai; SONG FuPing; HUANG DaFang
The cry1Ah gone was one of novel insecticidal genes cloned from Bacillus thuringiensis isolate BT8. Two plant expression vectors containing cry1Ah gone were constructed. The first intron of maize ubiqutin1 gone was inserted between the maize Ubiquitin promoter and cry1Ah gone in one of the plant expressing vectors (pUUOAH). The two vectors were introduced into maize immature embryonic calli by microprojectile bombardment, and the reproductively plants were acquired. PCR and Southern blot analysis showed that foreign genes had been integrated into maize genome and inherited to the next generation stably. The ELISA assay to T1 and T2 generation plants showed that the expression of Cry1Ah protein in the construct containing the ubi1 intron (pUUOAH) was 20% higher than that of the intronless construct (pUOAH). Bioassay results showed that the transgenic maize harboring cry1Ah gone had high resistance to the Asian corn borers and the insecticidal activity of the transgenic maize containing the ubi1 intron was higher than that of the intronless construct. These results indicated that the maize ubil intron can enhance the expression of the Bt cry1Ah gone in transgenic maize efficiently
Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Htl, Htnl and Ht2, Helminthosporium maydis Nisik resistance genes Rhml and Rhm2,maize dwarf mosaic virus resistance gene Mdml, wheat streak mosaic virus resistance gene Wsml, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2. 1 of tomato, and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i. e. , chromosomesl, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3. 25) except for genes Rhml, Rhm2, Mdml and Wsml which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.
The paper assesses the effects of maize yields just prior to birth (in utero), in the first and the second years of life on adult life productivity and efficiency of maize farmers born between 1984 and 1995 in rural Malawi. To ensure that early life maize yields are not confounded by omitted local chacteristics, they are transformed into relative maize yields by using a cumulative gamma distribution. I find that maize yield just prior to birth significantly increases maize output in a farmer'...
Antonio Turrent Fernández; Timothy A. Wise; Elise Garvey
Rising agricultural prices, combined with growing import dependence, have driven Mexico’s food import bill over $20 billion per year and increased its agricultural trade deficit. Mexico imports one-third of its maize, overwhelmingly from the United States, but three million producers grow most of the country’s white maize, which is used primarily for tortillas and many other pluricultural products for human consumption. Yield gaps are large among the country’s small to medium-scale maize farm...
Downs, Gregory S; Bi, Yong-Mei; Colasanti, Joseph; Wu, Wenqing; Chen, Xi; Zhu, Tong; Rothstein, Steven J; Lukens, Lewis N
Here, we present a genome-wide overview of transcriptional circuits in the agriculturally significant crop species maize (Zea mays). We examined transcript abundance data at 50 developmental stages, from embryogenesis to senescence, for 34,876 gene models and classified genes into 24 robust coexpression modules. Modules were strongly associated with tissue types and related biological processes. Sixteen of the 24 modules (67%) have preferential transcript abundance within specific tissues. One-third of modules had an absence of gene expression in specific tissues. Genes within a number of modules also correlated with the developmental age of tissues. Coexpression of genes is likely due to transcriptional control. For a number of modules, key genes involved in transcriptional control have expression profiles that mimic the expression profiles of module genes, although the expression of transcriptional control genes is not unusually representative of module gene expression. Known regulatory motifs are enriched in several modules. Finally, of the 13 network modules with more than 200 genes, three contain genes that are notably clustered (P < 0.05) within the genome. This work, based on a carefully selected set of major tissues representing diverse stages of maize development, demonstrates the remarkable power of transcript-level coexpression networks to identify underlying biological processes and their molecular components.
Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.
Li, Chuxi; Liu, Changlin; Qi, Xiantao; Wu, Yongchun; Fei, Xiaohong; Mao, Long; Chen, Beijiu; Li, Xinhai; Xie, Chuanxiao
The RNA-guided Cas9 system is a versatile tool for genome editing. Here, we established a RNA-guided endonuclease (RGEN) system as an in vivo desired-target mutator (DTM) in maize to reduce the linkage drag during breeding procedure, using the LIGULELESS1 (LG1) locus as a proof-of-concept. Our system showed 51.5% to 91.2% mutation frequency in T0 transgenic plants. We then crossed the T1 plants stably expressing DTM with six diverse recipient maize lines and found that 11.79% to 28.71% of the plants tested were mutants induced by the DTM effect. Analysis of successive F2 plants indicated that the mutations induced by the DTM effect were largely heritable. Moreover, DTM-generated hybrids had significantly smaller leaf angles that were reduced more than 50% when compared with that of the wild type. Planting experiments showed that DTM generated maize plants can be grown with significantly higher density and hence greater yield potential. Our work demonstrate that stably expressed RGEN could be implemented as an in vivo DTM to rapidly generate and spread desired mutations in maize through hybridization and subsequent backcrossing, and hence bypassing the linkage drag effect in convention introgression methodology. This proof-of-concept experiment can be a potentially much more efficient breeding strategy in crops employing the RNA-guided Cas9 genome editing. This article is protected by copyright. All rights reserved.
Brenner, Everton A; Zein, Imad; Chen, Yongsheng
Background OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover. Results Variation in genomic sequences codi...
The 10 k zein gene of maize was under control of patatin class ⅠPromoter of potato and transferred into potato genome by the leaf-disc method.The expression of 10 ku zein was determined in the tuber of transgenic plants by RT-PCR.Furthermore,the sulphur-containing amino acids in transgenic tuber increase remarkably.
Yi Zhou; Yingjia Han; Zhigang Li; Yang Fu; Zhiyuan Fu; Shutu Xu; Jiansheng Li; Jianbing Yan; Xiaohong Yang
α-carotene is one of the important components of pro-vitamin A,which is able to be converted into vitamin A in the human body.One maize (Zea mays L.) ortholog of carotenoid hydroxylases in Arabidopsis thaliana,ZmcrtRB3,was cloned and its role in carotenoid hydrolyzations was addressed.ZmcrtRB3 was mapped in a quantitative trait locus (QTL) cluster for carotenoid-related traits on chromosome 2 (bin 2.03) in a recombinant inbred line (RIL) population derived from By804 and B73.Candidate-gene association analysis identified 18 polymorphic sites in ZmcrtRB3 significantly associated with one or more carotenoid-related traits in 126 diverse yellow maize inbred lines.These results indicate that the enzyme ZmcrtRB3 plays a role in hydrolyzing both α- andβ-carotenes,while polymorphisms in ZmcrtRB3 contributed more variation in α-carotene than that inβ-carotene.Two single nucleotide polymorphisms (SNPs),SNP1343 in 5'untranslated region and SNP2172 in the second intron,consistently had effects on α-carotene content and composition with explained phenotypic variations ranging from 8.7％ to 34.8％.There was 1.7- to 3.7-fold change between the inferior and superior haplotype for α-carotene content and composition.Thus,SNP1343 and SNP2172 are potential polymorphic sites to develop functional markers for applying marker-assisted selection in the improvement of pro-vitamin A carotenoids in maize kernels.
Full Text Available Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs, we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.
Xin, Mingming; Yang, Ruolin; Li, Guosheng; Chen, Hao; Laurie, John; Ma, Chuang; Wang, Dongfang; Yao, Yingyin; Larkins, Brian A; Sun, Qixin; Yadegari, Ramin; Wang, Xiangfeng; Ni, Zhongfu
In angiosperms, the endosperm provides nutrients for embryogenesis and seed germination and is the primary tissue where gene imprinting occurs. To identify the imprintome of early developing maize (Zea mays) endosperm, we performed high-throughput transcriptome sequencing of whole kernels at 0, 3, and 5 d after pollination (DAP) and endosperms at 7, 10, and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal transcripts in 3- and 5-DAP kernels. In 7-DAP endosperm, the majority of the genes tested reached a 2:1 maternal versus paternal ratio, suggesting that paternal genes are nearly fully activated by 7 DAP. A total of 116, 234, and 63 genes exhibiting parent-specific expression were identified at 7, 10, and 15 DAP, respectively. The largest proportion of paternally expressed genes was at 7 DAP, mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP and were primarily attributed to sharply increased expression levels compared with the other stages. Gene ontology enrichment analysis of the imprinted genes suggested that 10-DAP endosperm-specific MEGs are involved in nutrient uptake and allocation and the auxin signaling pathway, coincident with the onset of starch and storage protein accumulation.
Zhang, Yikai; Chen, Fanjun; Li, Long; Chen, Yanhua; Liu, Bingran; Zhou, Yuling; Yuan, Lixing; Zhang, Fusuo; Mi, Guohua
Interspecific root/rhizosphere interactions affect phosphorus (P) uptake and the productivity of maize/faba bean and maize/wheat intercropping systems. The aim of these experiments was to determine whether manipulation of maize root growth could improve the productivity of the two intercropping systems. Two near isogenic maize hybrids (the larger-rooted T149 and smaller-rooted T222) were intercropped with faba bean and wheat, under conditions of high- and low-P availability. The larger-rooted T149 showed greater competitive ability than the smaller-rooted T222 in both maize/faba bean and maize/wheat intercropping systems. The higher competitive ability of T149 improved the productivity of the maize/faba bean intercropping system in P-sufficient conditions. In maize/wheat intercropping systems, root growth, shoot biomass, and P uptake of maize were inhibited by wheat, regardless of the P-supply. Compared with T222, the larger-rooted T149 suffered less in the intercropping systems. The total biomass of the maize/wheat intercropping system was higher for wheat/T149 than for wheat/T222 under low-P conditions. These data suggested that genetic improvement of maize root size could enhance maize growth and its ability to compete for P resources in maize/faba bean and maize/wheat intercropping systems. In addition, depending on the P availability, larger maize roots could increase the productivity of intercropping systems.
LI Xiu-ying; LANG Zhi-hong; ZHANG Jie; HE Kang-lai; ZHU Li; HUANG Da-fang
A novel insecticidal gene cry1Ah was cloned from Bacillus thuringiensis isolate BT8 previously for plant genetic engineering improvement. Truncated active Cry1Ah toxin has a toxicity level similar to that of the full-length Cry1Ah toxin. In this study, plant expression vector pMhGM harboring truncated cry1Ah gene was transformed into maize (Zea mays L.) immature embryos by Agrobacterium tumefaciens-mediated transformation at which maize alcohol dehydrogenase matrix attachment regions (madMARs) were incorporated on both sides of the gene expression cassette to improve gene expression. A total of 23 PCR positive events were obtained with a transformation efifciency of 5%around. Bioassay results showed that events 1-4 and 1-5 exhibited enhanced resistance to the Asian corn borer (Ostrinia furnacalis). These two events were further conifrmed by molecular analysis. Southern blot suggested that a single copy of the cry1Ah gene was successfully integrated into the maize genome. Western blot and ELISA showed that the foreign gene cry1Ah was expressed stably at high level in maize and could be inherited stably over generations. The results of a bioassay of T1-T4 transgenic maize plants indicated that the transgenic plants were highly toxic to the Asian corn borer and their resistance could be inherited stably from generation to generation. Thus, events 1-4 and 1-5 are good candidates for the breeding of insect-resistant maize.
Full Text Available Abstract Background In-depth sequencing analysis has not been able to determine the overall complexity of transcriptional activity of a plant organ or tissue sample. In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs, although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure for validating gene prediction and estimating overall gene coverage. This approach could be very valuable for complex plant genomes. In addition, little emphasis has been given to efforts aiming at an estimation of the overall transcriptional universe found in a multicellular organism at a specific developmental stage. Results To explore, in depth, the transcriptional diversity in an ancient maize landrace, we developed a protocol to optimize the sequencing of cDNAs and performed 4 consecutive GS20–454 pyrosequencing runs of a cDNA library obtained from 2 week-old Palomero Toluqueño maize plants. The protocol reported here allowed obtaining over 90% of informative sequences. These GS20–454 runs generated over 1.5 Million reads, representing the largest amount of sequences reported from a single plant cDNA library. A collection of 367,391 quality-filtered reads (30.09 Mb from a single run was sufficient to identify transcripts corresponding to 34% of public maize ESTs databases; total sequences generated after 4 filtered runs increased this coverage to 50%. Comparisons of all 1.5 Million reads to the Maize Assembled Genomic Islands (MAGIs provided evidence for the transcriptional activity of 11% of MAGIs. We estimate that 5.67% (86,069 sequences do not align with public ESTs or annotated genes, potentially representing new maize transcripts. Following the assembly of 74.4% of the reads in 65,493 contigs, real-time PCR of selected genes confirmed a predicted correlation between the abundance of GS20–454 sequences and corresponding levels of gene expression. Conclusion A protocol was developed that significantly
The classical maize mutant iojap (Iodent japonica) has variegated green and white leaves. Green sectors have cells with normal chloroplasts whereas white sectors have cells where plastids fail to differentiate. These mutant plastids, when transmitted through the female gametophyte, do not recover in the presence of wild type Iojap. We cloned the Ij locus, and we have investigated the mechanism of epigenetic inheritance and phenotypic expression. More recently, a modifier of this type of variegation, ''Inhibitor of striate'', has also been cloned. Both the iojap and inhibitor of striate proteins have homologs in bacteria and are members of ancient conserved families found in multiple species. These tools can be used to address fundamental questions of inheritance and variegation associated with this classical conundrum of maize genetics. Since the work of Rhoades there has been considerable speculation concerning the nature of the Iojap gene product, the origin of leaf variegation and the mechanism behind the material inheritance of defective plastids. This has made Iojap a textbook paradigm for cytoplasmic inheritance and nuclear-organellar interaction for almost 50 years. Cloning of the Iojap gene in maize, and homologs in other plants and bacteria, provides a new means to address the origin of heteroplastidity, variegation and cytoplasmic inheritance in higher plants.
[目的]构建玉米胚芽鞘负向重力生长时期的酵母双杂交文库,并对其进行评价.[方法]以玉米骨干自交系B73为材料,利用Trizol试剂提取玉米胚芽鞘在负向生长时期所表达的总RNA,再利用SMART技术构建酵母双杂交文库,并转化进酵母Y187中.[结果]试验得到的原始文库库容量高达1×106个单克隆；文库中插入的片段集中在0.5～1.5 kb,平均插入长度为800 bp.[结论]试验构建得到了高质量的米胚芽鞘酵母双杂交文库,为研究胚芽鞘的负向重力反应机制奠定了基础.%[Objective] The aim was to construct and appraise the yeast two hybrid library of maize coleoptile during its negative-gravitropic growth. [ Method] Using maize inbred line B73 as materials, the total RNA which expressed during negative-gravitropic growth period of maize coleoptile was extracted by Trizol, and the yeast two hybrid library was constructed by SMART technology and transformed into yeast Y187. [ Result] The results showed that the library contained 1 × 106 monoclones and the predominant size of inserted fragments in library was 0.5-1.5 kb, average size was 800 bp. [ Conclusion ] High-quailty yeast two hybrid library of maize coleoptile was constructed and it prepared the ground for the study of negative-gravitropic reaction mechanism of coleoptile.
王凯; 朱小蓬; 钟兰; 陈润生
Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.
Tropical maize is an alternative energy crop being considered as a feedstock for bioethanol production in the North Central and Midwest United States. Tropical maize is advantageous because it produces large amounts of soluble sugars in its stalks, creates a large amount of biomass, and requires lo...
Full Text Available Maize (Zea mays is a major food and animal feed worldwide and occupies a relevant place in the world economy and trade as an industrial grain crop. Currently more than 70% of maize production is used for food and feed; therefore, knowledge of genes involved in grain structure and chemical is important for improving the nutritional and food-making properties of maize. It is a good source of carbohydrates, fats, proteins, vitamins and minerals but deficient in two essential amino acids, Viz., lysine and tryptophan. To overcome this problem and to improve the above quality characters the maize breeders have followed different strategies like opaque 2, QPM and development of transgenic maize with improved quality characters. Finally we can conclude that the conventional breeding techniques and now plant biotechnology are helping meet the growing demand for food production, nutrition security while preserving our environment for future generations
Vega, Juan M; Yu, Weichang; Han, Fangpu; Kato, Akio; Peters, Eric M; Zhang, Zhanyuan J; Birchler, James A
The Cre/loxP site-specific recombination system has been applied in various plant species including maize (Zea mays) for marker gene removal, gene targeting, and functional genomics. A BIBAC vector system was adapted for maize transformation with a large fragment of genetic material including a herbicide resistance marker gene, a 30 kb yeast genomic fragment as a marker for fluorescence in situ hybridization (FISH), and a 35S-lox-cre recombination cassette. Seventy-five transgenic lines were generated from Agrobacterium-mediated transformation of a maize Hi II line with multiple B chromosomes. Eighty-four inserts have been localized among all 10 A chromosome pairs by FISH using the yeast DNA probe together with a karyotyping cocktail. No inserts were found on the B chromosomes; thus a bias against the B chromosomes by the Agrobacterium-mediated transformation was revealed. The expression of a cre gene was confirmed in 68 of the 75 transgenic lines by a reporter construct for cre/lox mediated recombination. The placement of the cre/lox site-specific recombination system in many locations in the maize genome will be valuable materials for gene targeting and chromosome engineering.
Latré, J; Dewitte, K; Derycke, V; De Roo, B; Haesaert, G
Integrated pest management has been implemented as a general practice by EU legislation. As weed control actually is the most important crop protection measure in maize for Western Europe, the new legislation will have its impact. The question is of course which systems can be successfully implemented in practice with respect to labour efficiency and economical parameters. During 3 successive growing seasons (2007, 2008, 2009) weed control in maize was evaluated, the main focus was put on different techniques of integrated weed control and was compared with chemical weed control. Additionally, during 4 successive growing seasons (2011, 2012, 2013 and 2014) two objects based on integrated weed control and two objects based on mechanical weed control were compared to about twenty different objects of conventional chemical weed control. One of the objects based on mechanical weed control consisted of treatment with the flex-tine harrow before and after emergence in combination with chemical weed control at a reduced rate in 3-4 leave stage. The second one consisted of broadcast mechanical treatments before and after emergence followed by a final in-row application of herbicides and an inter-row cultivation at 6-7(8) leave stage. All trials were conducted on the Experimental farm of Bottelare HoGent-UGent on a sandy loam soil. Maize was growing in 1/3 crop rotation. The effect on weed growth as well as the economic impact of the different applications was evaluated. Combining chemical and mechanical weed control is a possible option in conventional farming but the disadvantages must be taken into account. A better planned weed control based on the real present weed-population in combination with a carefully thought-out choice of herbicides should also be considered as an IPM--approach.
Wang, Wei; Zhou, Hongxian; Yang, Hong; Zhao, Siming; Liu, Youming; Liu, Ru
The objective of this study was to evaluate the effects of salts on the gelatinization and retrogradation of maize and waxy maize starch. Experimental results showed that the salting-out or structure-making ions, such as F(-) and SO4(2-), decreased the swelling power, solubility and transparency of both starches, but increased the gelatinization temperature, enthalpy, and syneresis, due to the tendency of these ions to protect the hydrogen bond links among starch molecules. On the other hand, the salting-in or structure-breaking ions, such as I(-) and SCN(-), exhibited the opposite effects. Microscopic observations confirmed such effects of salts on both starches. Furthermore, the effects of salts were more significant on waxy maize and on normal maize starch. Generally, salts could significantly influence on the gelatinization and retrogradation of maize and waxy maize starch, following the order of the Hofmeister series.
Full Text Available Abstract Background The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD, which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation. Results Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only. Conclusion Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein
Lehoczky, E; Kismányoky, A; Nagy, P; Németh, T
Our study was carried out in Hungary at Keszthely, in 2007. The effect of different cultivation methods: no-till drill, disk tillage, conventional tillage (ploughing) and five increasing N doses were studied on the weediness. The bi-factorial trial was arranged in split plot design with four replications. Crop rotation: winter wheat-winter wheat-maize-maize. The seeding of maize was 23rd of April in 2007. The weed survey was made with Balázs-Ujvárosi coenological method on the 17th of May. In the experiment were found 21 weed species. We collected all plants of every weed species by plots. The sample area was 1 m2. Furthermore five maize plants per plot were sampled on the 22nd of May. Maize was at 3-4 leaves stage. For reason of competition studies no herbicides were applied on sampling sites. The aerial parts of weeds and maize plants were collected, and the fresh and dry matter weight was measured. We analyzed in detail, the occurrence of weed species, and the biomass production of weeds in comparison with maize. The effect of different cultivation methods markedly demonstrated the weed cover, the number of perennial and annual weeds and the number of occurring weed species.
Dooner, Hugo K; He, Limei
Nucleotide diversity is greater in maize than in most organisms studied to date, so allelic pairs in a hybrid tend to be highly polymorphic. Most recombination events between such pairs of maize polymorphic alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. To investigate whether gene conversion at the bz locus is polarized, two large diallel crossing matrices involving mutant sites spread across the bz gene were performed and more than 2,500 intragenic recombinants were scored. In both diallels, around 90% of recombinants could be accounted for by gene conversion. Furthermore, conversion exhibited a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene. The implications of these findings are discussed with reference to recent data from genome-wide studies in other plants.
Full Text Available BACKGROUND: Members of the homeodomain-leucine zipper (HD-Zip gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.. METHODS AND FINDINGS: In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55 were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR. All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution. CONCLUSIONS: Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.
XIONG Zhiyong; GAO Yuan; HE Guanyuan; GU Mingguang; GUO Lequn; SONG Yunchun
Knob-associated tandem repeats, 180-bp repeats and TR-1 elements, together with 45S rDNA were located on mitotic chromosomes of Zea diploperennis (DP),maize inbred line F102 and their hybrid. In DP, knobs on the short arm of chromosomes 1 and 4 and on the long arm of the chromosomes 4 and 5 are composed predominantly of the 180-bp repeats. In addition, 180-bp repeats existed together with TR-1 elements were also detected on the short arm of chromosomes 2 and 5 and on the long arm of the chromosomes 2, 6, 7, 8 and 9. In maize inbred line F102, 180-bp repeats were present in chromosomes 7S and one homologue of chromosomes 8L. TR-1 elements appeared on satellite of chromosome 6 and no detectable hybridization site co-located with 180-bp repeats was observed in maize F102. Polymorphism of size, number, and distribution of 180-bp and TR-1 signals were revealed among different chromosomes in these two species and heteromorphism existed between some homologous chromosomes in the same species.Using these excellent landmarks, the interspecific hybrid of maize and DP were identified. The results suggest that comparative analysis of 180-bp repeats and TR-1 elements may help understand the genome organization and the evolution in Zea.
Zhaoyu Wang; Kewei Zhang; Xiaofen Sun; Kexuan Tang; Juren Zhang
In order to enhance the resistance to pests, transgenic maize (Zea mays L.) plants from elite inbred lines containing the gene encoding snowdrop lectin (Galanthus nivalis L. agglutinin; GNA) under control of a phloemspecific promoter were generated through the Agrobacterium tumefaciens-mediated method. The toxicity of GNA-expressing plants to aphids has also been studied. The independently derived plants were subjected to molecular analyses. Polymerase chain reaction (PCR) and Southern blot analyses confirmed that the gna gene was integrated into maize genome and inherited to the following generations. The typical Mendelian patterns of inheritance occurred in most cases. The level of GNA expression at 0.13%–0.28% of total soluble protein was observed in different transgenic plants. The progeny of nine GNA-expressing independent transformants that were derived separately from the elite inbred lines DH4866, DH9942, and 8902, were selected for examination of resistance to aphids. These plants synthesized GNA at levels above 0.22% total soluble protein, and enhanced resistance to aphids was demonstrated by exposing the plants to corn leaf aphid (Rhopalosiphum maidis Fitch) under greenhouse conditions. The nymph production was significantly reduced by 46.9% on GNA-expressing plants. Field evaluation of the transgenic plants supported the results from the inoculation trial. After a series of artificial self-crosses, some homozygous transgenic maize lines expressing GNA were obtained. In the present study, we have obtained new insect-resistant maize material for further breeding work.
Wang, Zhaoyu; Zhang, Kewei; Sun, Xiaofen; Tang, Kexuan; Zhang, Juren
In order to enhance the resistance to pests, transgenic maize (Zea mays L.) plants from elite inbred lines containing the gene encoding snowdrop lectin (Galanthus nivalis L. agglutinin; GNA) under control of a phloem-specific promoter were generated through the Agrobacterium tumefaciens-mediated method. The toxicity of GNA-expressing plants to aphids has also been studied. The independently derived plants were subjected to molecular analyses. Polymerase chain reaction (PCR) and Southern blot analyses confirmed that the gna gene was integrated into maize genome and inherited to the following generations. The typical Mendelian patterns of inheritance occurred in most cases. The level of GNA expression at 0.13%-0.28% of total soluble protein was observed in different transgenic plants. The progeny of nine GNA-expressing independent transformants that were derived separately from the elite inbred lines DH4866, DH9942, and 8902, were selected for examination of resistance to aphids. These plants synthesized GNA at levels above 0.22% total soluble protein, and enhanced resistance to aphids was demonstrated by exposing the plants to corn leaf aphid (Rhopalosiphum maidis Fitch) under greenhouse conditions. The nymph production was significantly reduced by 46.9% on GNA-expressing plants. Field evaluation of the transgenic plants supported the results from the inoculation trial. After a series of artificial self-crosses, some homozygous transgenic maize lines expressing GNA were obtained. In the present study, we have obtained new insect-resistant maize material for further breeding work.
Fox, Glen; Manley, Marena
Maize is a highly important crop to many countries around the world, through the sale of the maize crop to domestic processors and subsequent production of maize products and also provides a staple food to subsistance farms in undeveloped countries. In many countries, there have been long-term research efforts to develop a suitable hardness method that could assist the maize industry in improving efficiency in processing as well as possibly providing a quality specification for maize growers, which could attract a premium. This paper focuses specifically on hardness and reviews a number of methodologies as well as important biochemical aspects of maize that contribute to maize hardness used internationally. Numerous foods are produced from maize, and hardness has been described as having an impact on food quality. However, the basis of hardness and measurement of hardness are very general and would apply to any use of maize from any country. From the published literature, it would appear that one of the simpler methods used to measure hardness is a grinding step followed by a sieving step, using multiple sieve sizes. This would allow the range in hardness within a sample as well as average particle size and/or coarse/fine ratio to be calculated. Any of these parameters could easily be used as reference values for the development of near-infrared (NIR) spectroscopy calibrations. The development of precise NIR calibrations will provide an excellent tool for breeders, handlers, and processors to deliver specific cultivars in the case of growers and bulk loads in the case of handlers, thereby ensuring the most efficient use of maize by domestic and international processors. This paper also considers previous research describing the biochemical aspects of maize that have been related to maize hardness. Both starch and protein affect hardness, with most research focusing on the storage proteins (zeins). Both the content and composition of the zein fractions affect
Full Text Available The main pathogen of maize are fungi of the genus Fusarium. Besides phytopathogenic Fusarium, Ustilago maydis is another fungal genus affecting maize yields, causing lesions, known as smut. The objective of the study was evaluation of the cytotoxicity of Ustilago maydis isolated from maize. Nine Ustilago maydis strains were selected to a detailed evaluation of their cytotoxicity using a 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT test. Ustilago maydis strains showed medium and high cytotoxicity compared to control. High levels of cytotoxicity of Ustilago maydis may be indicative of their toxigenic potential.
Achhami, Buddhi Bahadur; Santa Bahadur BK; Bhandari, GhanaShyam
Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and...
LI Xia; DING Zaisong; LI Lianlu; WANG Meiyun; ZHAO Ming
Four maize inbred lines with different photosyn-thetic rates and their two hybrids were used as test materials,and the diurnal variations of their photosynthesis parameters in the silking stage were measured to study the heterosis of photosynthetic performance.Results showed that net photo-synthetic rate (In),transpiration rate (Tr) and stomatal conductance (Gs) all presented an obvious single-peaked curve in a day,with the peak values occurring at 10:00-12:00,12:00,10:00-12:00 a.m.,respectively,while water use efficiency (WUE) had a"V"type variant trend,with the lowest value appearing at 12:00.The diurnal variation of Pn and Tr was correlated markedly with Gs,suggesting that Gs played an important role in regulating the diurnal variation of Pn and Tr,and Pn,Tr and Gs had a higher heterosis in the afternoon than in the morning,while the WUE was in reverse,indicating that maize hybrid had higher resistance to the high temperature and dehydration in the afternoon,which provided a new path to select varieties with a high net photosynthetic rate.
Zhang, Jisen; Boualem, Adnane; Bendahmane, Abdelhafid; Ming, Ray
Sex determination is a major switch in the evolutionary history of angiosperm, resulting 11% monoecious and dioecious species. The genomic sequences of papaya sex chromosomes unveiled the molecular basis of recombination suppression in the sex determination region, and candidate genes for sex determination. Identification and analyses of sex determination genes in cucurbits and maize demonstrated conservation of sex determination mechanism in one lineage and divergence between the two systems. Epigenetic control and hormonal influence of sex determination were elucidated in both plants and animals. Intensive investigation of potential sex determination genes in model species will improve our understanding of sex determination gene network. Such network will in turn accelerate the identification of sex determination genes in dioecious species with sex chromosomes, which are burdensome due to no recombination in sex determining regions. The sex determination genes in dioecious species are crucial for understanding the origin of dioecy and sex chromosomes, particularly in their early stage of evolution.
The maize DNA fragments was successfully incorporated into rice by Associate Prof WAN Wenju's research team at Hunan Agricultural College, Changsha, China. The new gene transferring rice is named Genetic Engineered Rice (GER) line.
Cristian Forestan; Serena Varotto
In plants,proper seed development and the continuing post-embryonic organogenesis both require that different cell types are correctly differentiated in response to internal and external stimuli.Among internal stimuli,plant hormones and particularly auxin and its polar transport(PAT)have been shown to regulate a multitude of plant physiological processes during vegetative and reproductive development.Although our current auxin knowledge is almost based on the results from researches on the eudicot Arabidopsis thaliana,during the last few years,many studies tried to transfer this knowledge from model to crop species,maize in particular.Applications of auxin transport inhibitors,mutant characterization,and molecular and cell biology approaches,facilitated by the sequencing of the maize genome,allowed the identification of genes involved in auxin metabolism,signaling,and particularly in polar auxin transport.PIN auxin efflux carriers have been shown to play an essential role in regulating PAT during both seed and post-embryonic development in maize.In this review,we provide a summary of the recent findings on PIN-mediated polar auxin transport during maize development.Similarities and differences between maize and Arabidopsis are analyzed and discussed,also considering that their different plant architecture depends on the differentiation of structures whose development is controlled by auxins.
Wang, Xiao-Chun; Yang, Wen-Yu; Deng, Xiao-Yan; Zhang, Qun; Yong, Tai-Wen; Liu, Wei-Guo; Yang, Feng; Mao, Shu-Ming
A large amount of nitrogen (N) fertilizers poured into the fields severely pollute the environment. Reasonable application of N fertilizer has always been the research hotpot. The effects of N management on maize N utilization and residual nitrate N in soil under maize/soybean and maize/ sweet potato relay strip intercropping systems were reported in a field experiment in southwest China. It was found that maize N accumulation, N harvest index, N absorption efficiency, N contribution proportion after the anthesis stage in maize/soybean relay strip intercropping were increased by 6.1%, 5.4%, 4.3%, and 15.1% than under maize/sweet potato with an increase of 22.6% for maize yield after sustainable growing of maize/soybean intercropping system. Nitrate N accumulation in the 0-60 cm soil layer was 12.9% higher under maize/soybean intercropping than under maize/sweet potato intercropping. However, nitrate N concentration in the 60-120 cm soil layer when intercropped with soybean decreased by 10.3% than when intercropped with sweet potato, indicating a decrease of N leaching loss. Increasing of N application rate enhanced N accumulation of maize and decreased N use efficiency and significantly increased nitrate concentration in the soil profile except in the 60-100 cm soil layer, where no significant difference was observed with nitrogen application rate at 0 to 270 kg · hm(-2). Further application of N fertilizer significantly enhanced nitrate leaching loss. Postponing N application increased nitrate accumulation in the 60-100 cm soil layer. The results suggested that N application rates and ratio of base to top dressing had different influences on maize N concentration and nitrate N between maize/soybean and maize/sweet potato intercropping. Maize N concentration in the late growing stage, N harvest index and N use efficiency under maize/soybean intercropping increased (with N application rate at 180-270 kg · hm(-2) and ratio of base to top dressing = 3:2:5) and
LI Qing; LI Lin; DAI JingRui; LI JianSheng; YAN JianBing
Transposable elements (TEs)-mediated gene sequence movement is thought to play an important role in genome expansion and origin of genes with novel functions. In this study, a gene, HGGT, involved in vitamin E synthesis was used in a case study to discover and characterize transposons carrying gene fragments in maize. A total of 69 transposons that are distributed across the 10 chromosomes and have an average length of 3689 bp were identified from the maize sequence database by using the BLAST search algorithm. Three of these carry gene fragments from the progenitor HGGT gene, while the rest (66) contain gene fragments from other cellular genes. Nine of the 69 transposons contain fragments derived from two locations in the genome. By querying the maize Expressed Sequence Tag (EST) da-tabase, we found that at least thirteen out of the 69 TEs had corresponding transcripts. More interest-ingly, two transposons that carry gene fragments from two different chromosomal loci could be ex-pressed as chimeric transcripts.
Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG
The development of genomics and bioinfor-matics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available, using the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them were clustered on chromosomes 3 and 6. By using the method of meta-analysis, we identified one "consensus QTL" on chromosome 3 covering a genetic distance of 6.44 cM, and two on chromosome 6 covering genetic distances of 16 cM and 27.48 cM, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via the strategy of comparative genomics. These results suggest that application of a combination of meta-analysis within a species with sequence homology comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provide useful information for iden-tifying and cloning the major gene(s) conferring resistance to SCMV in maize.
孙峰成; 冯勇; 赵瑞霞; 苏二虎; 张来厚; 刘志雄; 石海波
为明确玉米群体的遗传变异性，利用SSR分子标记技术，采用12株叶片混合、每个群体5个混合样本提取DNA的最优取样方法，对12个玉米群体及6个对照自交系进行遗传多样性分析，试验筛选出86对SSR适宜引物，共扩增出391条多态性带，每个位点上的等位基因数为2～11条，平均5．67条，以GD值0．67为基准，划分为6个类群。蒙A群、蒙B群、中综5号、黄早4为第一类，蒙C群、蒙群1、掖478为第二类，蒙群2、蒙群4、C群1、C群2、Mo17为第三类，蒙群3、C群3、中综7号、B73为第四类，丹340和齐319各单独为一类，该结果与产量SCA效应分析划分结果基本一致。%The widely genetic diversity in maize population is the important basis for maize breeding .To clear the genetic basis and genetic diversity is very important for germplasm enhancement and improvement of maize .In this research,SSR molecular marker technology and the best sampling method ,which DNA was extracted from five samples in each maize population and mixture of leaves of 12 plants, was adopted .The genetic diversity from 12 maize populations and 6 control inbred lines were analysed .86 pairs SSR primers were filtered in this experiment , 391 polymorphic bands were gained .The number of alleles ranged from 2 to 11,the average is 5.76.The studied 12 maize populations and 6 control inbred lines could be partitioned into 6 class groups on the basis of 0 .67 for the GD value.Meng A,Meng B,Zhongzong 5 and Huangzao 4 are belonged to one group ,Meng C,Mengqun 1 and Ye 478 are belonged to the second group ,Mengqun 2,Mengqun 4,C Qun 1,C Qun 2 and Mo17 are belonged to the third group,Mengqun 3,C Qun 3,Zhongzong 7 and B73 are belonged to the fourth group ,Dan 340 and Qi 319 are belonged to the fifth and sixth group ,respectively .The partition is similar with the partition based on the yield SCA effect .
Nereu Augusto Streck
Full Text Available The objective of this work was to simulate maize leaf development in climate change scenarios at Santa Maria, RS, Brazil, considering symmetric and asymmetric increases in air temperature. The model of Wang & Engel for leaf appearance rate (LAR, with genotype-specific coefficients for the maize variety BRS Missões, was used to simulate tip and expanded leaf accumulated number from emergence to flag leaf appearance and expansion, for nine emergence dates from August 15 to April 15. LAR model was run for each emergence date in 100-year climate scenarios: current climate, and +1, +2, +3, +4 and +5°C increase in mean air temperature, with symmetric and asymmetric increase in daily minimum and maximum air temperature. Maize crop failure due to frost decreased in elevated temperature scenarios, in the very early and very late emergence dates, indicating a lengthening in the maize growing season in warmer climates. The leaf development period in maize was shorter in elevated temperature scenarios, with greater shortening in asymmetric temperature increases, indicating that warmer nights accelerate vegetative development in maize.
Xu, Hong; Twine, Tracy E; Girvetz, Evan
Climate is changing across the world, including the major maize-growing state of Iowa in the USA. To maintain crop yields, farmers will need a suite of adaptation strategies, and choice of strategy will depend on how the local to regional climate is expected to change. Here we predict how maize yield might change through the 21st century as compared with late 20th century yields across Iowa, USA, a region representing ideal climate and soils for maize production that contributes substantially to the global maize economy. To account for climate model uncertainty, we drive a dynamic ecosystem model with output from six climate models and two future climate forcing scenarios. Despite a wide range in the predicted amount of warming and change to summer precipitation, all simulations predict a decrease in maize yields from late 20th century to middle and late 21st century ranging from 15% to 50%. Linear regression of all models predicts a 6% state-averaged yield decrease for every 1°C increase in warm season average air temperature. When the influence of moisture stress on crop growth is removed from the model, yield decreases either remain the same or are reduced, depending on predicted changes in warm season precipitation. Our results suggest that even if maize were to receive all the water it needed, under the strongest climate forcing scenario yields will decline by 10-20% by the end of the 21st century.
Yuanzeng Zhao; Xiaomin Lu; Chaoxian Liu; Haiying Guan; Mei Zhang; Zhongfeng Li; Hongwei Cai; Jinsheng Lai
rhm1 is a major recessive disease resistance locus for Southern corn leaf blight (SCLB).To further narrow down its genetic position,F2 population and BC1F1 population derived from the cross between resistant (H95rhm) and susceptible parents (H95) of maize (Zea mays) were constructed.Using newly developed markers,rhm1 was initially delimited within an interval of 2.5 Mb,and then finally mapped to a 8.56 kb interval between InDel marker IDP961-503 and simple sequence repeat (SSR) marker A194149-1.Three polymorphic markers IDP961-504,IDP B2-3 and A194149-2 were shown to be co-segregated with the rhm1 locus.Sequence analysis of the 8.56 kb DNA fragment revealed that it contained only one putative gene with a predicted amino acid sequence identical to lysine histidine transporter 1 (LHT1).Comparative sequence analysis indicated that the LHT1 in H95rhm harbors a 354 bp insertion in its third exon as compared with that of susceptible alleles in B73,H95 and Mo17.The 354 bp insertion resulted in a truncation of the predicted protein of candidate resistance allele (LHT1-H95rhm).Our results strongly suggest LHT1 as the candidate gene for rhm1 against SCLB.The tightly linked molecular markers developed in this study can be directly used for molecular breeding of resistance to Southern corn leaf blight in maize.
Peng, Hua [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130 (China); Sichuan Tourism College, Chengdu, 610000, Sichuan (China); He, Xiujing [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130 (China); Gao, Jian [Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing (China); Ma, Haixia; Zhang, Zhiming; Shen, Yaou [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130 (China); Pan, Guangtang, E-mail: email@example.com [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130 (China); Lin, Haijian, E-mail: firstname.lastname@example.org [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130 (China)
The heavy metal cadmium (Cd), acts as a widespread environmental contaminant, which has shown to adversely affect human health, food safety and ecosystem safety in recent years. However, research on how plant respond to various kinds of heavy metal stress is scarcely reported, especially for understanding of complex molecular regulatory mechanisms and elucidating the gene networks of plant respond to Cd stress. Here, transcriptomic changes during Mo17 and B73 seedlings development responsive to Cd pollution were investigated and comparative RNAseq-based approach in both genotypes were performed. 115 differential expression genes (DEGs) with significant alteration in expression were found co-modulated in both genotypes during the maize seedling development; of those, most of DGEs were found comprised of stress and defense responses proteins, transporters, as well as transcription factors, such as thaumatin-like protein, ZmOPR2 and ZmOPR5. More interestingly, genotype-specific transcriptional factors changes induced by Cd stress were found contributed to the regulatory mechanism of Cd sensitivity in both different genotypes. Moreover, 12 co-expression modules associated with specific biological processes or pathways (M1 to M12) were identified by consensus co-expression network. These results will expand our understanding of complex molecular mechanism of response and defense to Cd exposure in maize seedling roots. - Highlights: • Transcriptomic changes responsive to Cd pollution using comparative RNAseq-based approach. • 115 differential expression genes (DEGs) were found co-modulated in both genotypes. • Most of DGEs belong to stress and defense responses proteins, transporters, transcription factors. • 12 co-expression modules associated with specific biological processes or pathways. • Genotype-specific transcriptional factors changes induced by Cd stress were found.
Li, Zhao; Hu, Guanghui; Liu, Xiangfeng; Zhou, Yao; Li, Yu; Zhang, Xu; Yuan, Xiaohui; Zhang, Qian; Yang, Deguang; Wang, Tianyu; Zhang, Zhiwu
Originating in a tropical climate, maize has faced great challenges as cultivation has expanded to the majority of the world's temperate zones. In these zones, frost and cold temperatures are major factors that prevent maize from reaching its full yield potential. Among 30 elite maize inbred lines adapted to northern China, we identified two lines of extreme, but opposite, freezing tolerance levels—highly tolerant and highly sensitive. During the seedling stage of these two lines, we used RNA-seq to measure changes in maize whole genome transcriptome before and after freezing treatment. In total, 19,794 genes were expressed, of which 4550 exhibited differential expression due to either treatment (before or after freezing) or line type (tolerant or sensitive). Of the 4550 differently expressed genes, 948 exhibited differential expression due to treatment within line or lines under freezing condition. Analysis of gene ontology found that these 948 genes were significantly enriched for binding functions (DNA binding, ATP binding, and metal ion binding), protein kinase activity, and peptidase activity. Based on their enrichment, literature support, and significant levels of differential expression, 30 of these 948 genes were selected for quantitative real-time PCR (qRT-PCR) validation. The validation confirmed our RNA-Seq-based findings, with squared correlation coefficients of 80% and 50% in the tolerance and sensitive lines, respectively. This study provided valuable resources for further studies to enhance understanding of the molecular mechanisms underlying maize early freezing response and enable targeted breeding strategies for developing varieties with superior frost resistance to achieve yield potential. PMID:27774095
Li Li-jia; Song Yun-chun
Cytogenetic maps of four clusters of disease resistance genes were generated by ISH of the two RFLP markers tightly linked to and flanking each of maize resistance genes and the cloned resistance genes from other plant species onto maize chromosomes, combining with data published before. These genes include Helminthosporium turcium Pass resistance genes Ht1, Htn1 and Ht2, Helminthosporium maydis Nisik resistance genes Rhm1 and Rhm2, maize dwarf mosaic virus resistance gene Mdm1, wheat streak mosaic virus resistance gene Wsm1, Helminthosporium carbonum ULLstrup resistance gene Hml and the cloned Xanthomonas oryzae pv. Oryzae resistance gene Xa21 of rice, Cladosporium fulvum resistance genes Cf-9 and Cf-2.1 of tomato,and Pseudomonas syringae resistance gene RPS2 of Arabidopsis. Most of the tested disease resistance genes located on the four chromosomes, i.e., chromosomes1, 3, 6 and 8, and they closely distributed at the interstitial regions of these chromosomal long arms with percentage distances ranging 31.44(±3.72)-72.40(±3.25) except for genes Rhm1, Rhm2, Mdm1 and Wsm1 which mapped on the satellites of the short arms of chromosome6. It showed that the tested RFLP markers and genes were duplicated or triplicated in maize genome. Homology and conservation of disease resistance genes among species, and relationship between distribution features and functions of the genes were discussed. The results provide important scientific basis for deeply understanding structure and function of disease resistance genes and breeding in maize.
QIN Hui-juan; PAN Hong; FAN Xian-wei; WU Qiao; LI You-zhi
Maize (Zea mays L.) is one of the world’s major food crops, and often suffers from tremendous yield loss caused by abiotic stresses. The MADS-box genes are known to play versatile roles in plants, controlling plant responses to multiple abiotic stresses. However, understanding of regulation of their expressions by the conventional loss-of-function approach is very dififcult. So far, regulation of MADS-box gene expression is little known. The best approach to retrieve expression regulation of this category of genes is to characterize expression of their promoters. In this study, the promoter of a homolog (GenBank accession no. EC864166) of maize MADS-box gene m18 was cloned by way of genome-walking PCR, named Pro66. Predicative analysis indicated that Pro66 contains more than one TATA box and multiple cis-acting environmental conditions-responsive elements (ECREs). Pro66 could drive expression of theβ-glucuronidase (GUS)-encoding gene in maize, and heterologous expression of GUS in red pepper stressed by water deifcit, salt, copper, iron deifciency, heat, cold, and grown under short and long photoperiods, echoing predicative ECREs. Conclusively, maize MADS-box gene m18 likely plays versatile functions in maize response to multiple abiotic stresses due to the promoter with multiple cis-acting elements. The complex arrangement of multiple cis-acting elements in the promoter features meticulously regulated expression of m18. The results give informative clues for heterologous utilisation of the promoters in monocot and dicot species. The copy of the ECREs and heterologous expression of the promoter in dicot species are also discussed.
He, Min; Song, Dan; Jia, Hong C; Zheng, Yongquan
To study the dissipation rates and final residual levels of chlorantraniliprole and thiamethoxam in maize straw, maize, and soil, two independent field trials were conducted during the 2014 cropping season in Beijing and Anhui Provinces of China. A 40% wettable powder (20% chlorantraniliprole + 20% thiamethoxam) was sprayed onto maize straw and soil at an application rate of 118 g of active ingredient per hectare (g a.i.ha(-1)). The residual concentrations were determined by ultra-high-performance liquid chromatography-tandem mass spectrometry. The chlorantraniliprole half-lives in maize straw and soil were 9.0-10.8 and 9.5-21.7 days, respectively. The thiamethoxam half-lives in maize straw and soil were 8.4-9.8 and 4.3-11.7 days, respectively. The final residues of chlorantraniliprole and thiamethoxam in maize straw, maize, and soil were measured after the pesticides had been sprayed two and three times with an interval of 7 days using 1 and 1.5 times the recommended rate (72 g a.i. ha(-1) and 108 g a.i. ha(-1), respectively). Representative maize straw, maize, and soil samples were collected after the last treatment at pre-harvest intervals of 7, 14, and 28 days. The chlorantraniliprole residue was below 0.01 mg kg(-1) in maize, between 0.01 and 0.31 mg kg(-1) in maize straw, and between 0.03 and 1.91 mg kg(-1) in soil. The thiamethoxam residue concentrations in maize, maize straw, and soil were <0.01, <0.01, and 0.01-0.03 mg kg(-1), respectively. The final pesticide residues on maize were lower than the maximum residue limit (MRL) of 0.02 mg kg(-1) after a 14-day pre-harvest interval. Therefore, a dosage of 72 g a.i. ha(-1) was recommended, as it can be considered safe to human beings and animals.
张宏; 王国英; 谢友菊; 戴景瑞; 许宁; 赵南明; 李太源; 田颖川; 乔利亚; 莽克强
An insecticidal protein gene isolated from Bacillus thuringiensis was transferred into maize by using ultrasonication. The fertile transgenic plants and their progeny were obtained. The Southern hybridization results indi-cated that the foreign gene had integrated into the maize genome. It has been found that the acoustic intensity and the duration of treatment are the important parameters influencing transformation efficiency by ultrasonication. The maxi-mum relative transformation frequency of 34. 1 % was achieved after 30 min of sonication at 0. 5 W/cm2 acoustic inten-sity. With appropriate parameters the ultrasonication ran make a number of micropores formed on the cell surface and minimize the treatment damage to the foreign DNA molecules, thus facilitating the DNA molecules to enter the cells.
Xin, Mingming; Yang, Ruolin; Li, Guosheng; Chen, Hao; Laurie, John; Ma, Chuang; Wang, Dongfang; Yao, Yingyin; Larkins, Brian A.; Sun, Qixin; Yadegari, Ramin; Wang, Xiangfeng; Ni, Zhongfu
In angiosperms, the endosperm provides nutrients for embryogenesis and seed germination and is the primary tissue where gene imprinting occurs. To identify the imprintome of early developing maize (Zea mays) endosperm, we performed high-throughput transcriptome sequencing of whole kernels at 0, 3, and 5 d after pollination (DAP) and endosperms at 7, 10, and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal transcripts in 3- and 5-DAP kernels. In 7-DAP endosperm, the majority of the genes tested reached a 2:1 maternal versus paternal ratio, suggesting that paternal genes are nearly fully activated by 7 DAP. A total of 116, 234, and 63 genes exhibiting parent-specific expression were identified at 7, 10, and 15 DAP, respectively. The largest proportion of paternally expressed genes was at 7 DAP, mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP and were primarily attributed to sharply increased expression levels compared with the other stages. Gene ontology enrichment analysis of the imprinted genes suggested that 10-DAP endosperm-specific MEGs are involved in nutrient uptake and allocation and the auxin signaling pathway, coincident with the onset of starch and storage protein accumulation. PMID:24058158
Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genet...
Full Text Available Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb stress. Therefore, in this study, we aimed to compare DNA methylation profiles during the dynamic development of maize roots following Pb treatment to identify candidate genes involved in the response to Pb stress. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq was used to investigate the genome-wide DNA methylation patterns in maize roots under normal condition (A1 and 3 mM Pb(NO32 stress for 12 h (K2, 24 h (K3 and 48 h (K4. The results showed that the average methylation density was the highest in CpG islands (CGIs, followed by the intergenic regions. Within the gene body, the methylation density of the introns was higher than those of the UTRs and exons. In total, 3857 methylated genes were found in 4 tested samples, including 1805 differentially methylated genes for K2 versus A1, 1508 for K3 versus A1, and 1660 for K4 versus A1. Further analysis showed that 140 genes exhibited altered DNA methylation in all three comparisons, including some well-known stress-responsive transcription factors and proteins, such as MYB, AP2/ERF, bZIP, serine-threonine/tyrosine-proteins, pentatricopeptide repeat proteins, RING zinc finger proteins, F-box proteins, leucine-rich repeat proteins and tetratricopeptide repeat proteins. This study revealed the genome-scale DNA methylation patterns of maize roots in response to Pb exposure and identified candidate genes that potentially regulate root dynamic development under Pb stress at the methylation level.
Xia, Zihao; Zhao, Zhenxing; Chen, Ling; Li, Mingjun; Zhou, Tao; Deng, Congliang; Zhou, Qi; Fan, Zaifeng
The co-infection of Maize chlorotic mottle virus (MCMV) and Sugarcane mosaic virus (SCMV) can cause maize lethal necrosis. However, the mechanism underlying the synergistic interaction between these two viruses remains elusive. In this study, we found that the co-infection of MCMV and SCMV increased the accumulation of MCMV. Moreover, the profiles of virus-derived siRNAs (vsiRNAs) from MCMV and SCMV in single- and co-infected maize plants were obtained by high-throughput sequencing. Our data showed that synergistic infection of MCMV and SCMV increased remarkably the accumulation of vsiRNAs from MCMV, which were mainly 22 and 21 nucleotides in length. The single-nucleotide resolution maps of vsiRNAs revealed that vsiRNAs were almost continuously but heterogeneously distributed throughout MCMV and SCMV genomic RNAs, respectively. Moreover, we predicted and annotated dozens of host transcript genes targeted by vsiRNAs. Our results also showed that maize DCLs and several AGOs RNAs were differentially accumulated in maize plants with different treatments (mock, single or double inoculations), which were associated with the accumulation of vsiRNAs. Our findings suggested possible roles of vsiRNAs in the synergistic interaction of MCMV and SCMV in maize plants. PMID:26864602
Wang, Hongzhen; Cheng, Jun; Cheng, Yanping; Zhou, Xioafu
It has been paid more and more attention on maize tissue culture as it is a basic work in maize genetic transformation, especially huge breakthrough has been made in maize tissue culture utilizing mature embryos as explants in the recent years. This paper reviewed the study progress on maize tissue culture and plant regeneration utilizing mature embryos as explants from callus induction, subculture, plant regeneration and browning reduction and so on.
Larson,Donald W.; Mbowa, Swaibu
Strategic marketing issues and challenges face maize seed marketing firms as farmers increasingly adopt hybrid varieties in a modernizing third world country such as Uganda. The maize seed industry of Uganda has changed dramatically from a government owned, controlled, and operated industry to a competitive market oriented industry with substantial private firm investment and participation. The new maize seed industry is young, dynamic, growing and very competitive. The small maize seed marke...
Corn is the cereal with the highest production worldwide and is used for human consumption, livestock feed, and fuel. Various food technologies are currently used for processing industrially produced maize flours and corn meals in different parts of the world to obtain precooked refined maize flour, dehydrated nixtamalized flour, fermented maize flours, and other maize products. These products have different intrinsic vitamin and mineral contents, and their processing follows different pathwa...
Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops
Ali, M.; Cone, J.W.; Hendriks, W.H.; Struik, P.C.
The degradation of starch largely determines the feeding value of maize (Zea mays L.) for dairy cows. Normally, maize kernels are dried and ground before chemical analysis and determining degradation characteristics, whereas cows eat and digest fresh material. Drying the moist maize kernels (consist
Hoof, van W.C.H.
Mixed cropping of groundnuts and maize in East Java was studied by means of a survey of farming practice and by field experiments. The influence of different sowing times and plant density of maize on the development and yield of groundnuts and maize were the main topics in this thesis. Plant arrang
Continuous maize yields are limited by the release of phytotoxic compounds as the previous year’s maize residue decomposes. We tested the hypothesis that soil biochar applications could help mitigate maize autotoxicity and the associated yield depression. Eighteen small field plots (23.7 m2) were es...
Panfeng Zhao; Guobin Zhang; Xiaojun Wu; Na Li; Dianyi Shi; Dengfeng Zhang; Chunfang Ji
Southern rust (Puccinia polysora Underw.) is a major disease that can cause severe yield losses in maize (Zea mays L.).In our previous study,a major gene RppP25 that confers resistance to southern rust was identified in inbred line P25.Here,we report the fine mapping and candidate gene analysis of RppP25from the near-isogenic line F939,which harbors RppP25 in the genetic background of the susceptible inbred line F349.The inheritance of resistance to southern rust was investigated in the BC1F1 and BC3F1 populations,which were derived from a cross between F939 and F349 (as the recurrent parent).The 1:1 segregation ratio of resistance to susceptible plants in these two populations indicated that the resistance is controlled by a single dominant gene.Ten markers,including three simple sequence repeat (SSR) markers and seven insertion/deletion (InDel) markers,were developed in the RppP25 region.RppP25 was delimited to an interval between P091 and M271,with an estimated length of 40 kb based on the physical map of B73.In this region,a candidate gene was identified that was predicted to encode a putative nucleotide-binding site leucine-rich repeat (NBS-LRR) protein.Two co-segregated markers will aid in pyramiding diverse southern rust resistance alleles into elite materials,and thereby improve southern rust resistance worldwide.
Susca, Antonia; Moretti, Antonio; Stea, Gaetano; Villani, Alessandra; Haidukowski, Miriam; Logrieco, Antonio; Munkvold, Gary
non-producing strains distributed among the clades: A. welwitschiae, A. niger group 1 and A. niger group 2, confirming the potential of Aspergillus sect. Nigri species to contribute to total fumonisin contamination of maize. A higher percentage of A. niger isolates (72.0%) produced FB2 compared to A. welwitschiae (36.6%). The percentage of FB2-producing A. niger strains was similar in the USA and Italian populations; however, the predominance of A. niger in the USA population suggests a higher potential for fumonisin production. Some strains with fum8 present in the genome did not produce FB2in vitro, confirming the ineffectiveness of fum8 presence as a predictor of FB2 production.
Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong
De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads . However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.
Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong
De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads . However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.
Bakan, B; Melcion, D; Richard-Molard, D; Cahagnier, B
Fungi of the genus Fusarium are common fungal contaminants of maize and are also known to produce mycotoxins. Maize that has been genetically modified to express a Bt endotoxin has been used to study the effect of insect resistance on fungal infection of maize grains by Fusarium species and their related mycotoxins. Maize grain from Bt hybrids and near-isogenic traditional hybrids was collected in France and Spain from the 1999 crop, which was grown under natural conditions. According to the ergosterol level, the fungal biomass formed on Bt maize grain was 4-18 times lower than that on isogenic maize. Fumonisin B(1) grain concentrations ranged from 0.05 to 0.3 ppm for Bt maize and from 0.4 to 9 ppm for isogenic maize. Moderate to low concentrations of trichothecenes and zearalenone were measured on transgenic as well as on non-transgenic maize. Nevertheless, significant differences were obtained in certain regions. The protection of maize plants against insect damage (European corn borer and pink stem borer) through the use of Bt technology seems to be a way to reduce the contamination of maize by Fusarium species and the resultant fumonisins in maize grain grown in France and Spain.
Kilonzo, Robert M; Imungi, Jasper K; Muiru, William M; Lamuka, Peter O; Njage, Patrick M Kamau
Aflatoxicosis has repeatedly affected Kenyans, particularly in the eastern region, due to consumption of contaminated maize. However, save for the cases of acute toxicity, the levels of sub-lethal exposure have not been adequately assessed. It is believed that this type of exposure does exist even during the seasons when acute toxicity does not occur. This study, therefore, was designed to assess the exposure of households to aflatoxins through consumption of maize and maize products. Twenty samples each of maize kernels, muthokoi and maize meal were randomly sampled from households in Kibwezi District of Makueni County in Eastern Kenya and analysed for aflatoxin contamination. The samples were quantitatively analysed for aflatoxin contamination using HPLC. The uncertainty and variability in dietary exposure was quantitatively modelled in Ms Excel using Monte Carlo simulation in @Risk software. Aflatoxins were found in 45% of maize kernels at between 18 and 480 μg kg⁻¹, 20% of muthokoi at between 12 and 123 μg kg⁻¹, and 35% of maize meal at between 6 and 30 μg kg⁻¹. The mean dietary exposure to aflatoxin in maize kernels was 292 ± 1567 ng kg⁻¹ body weight day⁻¹, while the mean dietary exposure to aflatoxin in maize meal and muthokoi were 59 ± 62 and 27 ± 154 ng kg⁻¹ body weight day⁻¹ respectively. The results showed that the amount and frequency of consumption of the three foods is the more important contributing factor than the mean aflatoxin concentration levels, to the risk of dietary exposure to aflatoxins.
Sun, Wei; Chen, Hao; Wang, Juan; Sun, Hong Wei; Yang, Shu Ke; Sang, Ya Lin; Lu, Xing Bo; Xu, Xiao Hui
Mitogen-activated protein kinases (MAPKs) play important roles in stress responses and development in plants. Maize (Zea mays), an important cereal crop, is a model plant species for molecular studies. In the last decade, several MAPKs have been identified in maize; however, their functions have not been studied extensively. Genome-wide identification and expression analysis of maize MAPK genes could provide valuable information for understanding their functions. In this study, 20 non-redundant maize MAPK genes (ZmMPKs) were identified via a genome-wide survey. Phylogenetic analysis of MAPKs from maize, rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), and tomato (Solanum lycopersicum) classified them into four major classes. ZmMPKs in the same class had similar domains, motifs, and genomic structures. Gene duplication investigations suggested that segmental duplications made a large contribution to the expansion of ZmMPKs. A number of cis-acting elements related to plant development and response to stress and hormones were identified in the promoter regions of ZmMPKs. Furthermore, transcript profile analysis in eight tissues and organs at various developmental stages demonstrated that most ZmMPKs were preferentially expressed in reproductive tissues and organs. The transcript abundance of most ZmMPKs changed significantly under salt, drought, cold, or abscisic acid (ABA) treatments, implying that they might participate in abiotic stress and ABA signaling. These expression analyses indicated that ZmMPKs might serve as linkers between abiotic stress signaling and plant reproduction. Our data will deepen our understanding of the complexity of the maize MAPK gene family and provide new clues to investigate their functions.
Ana Mariana Dincu
Full Text Available In this work, was calculated and the level of profitability for several levels of production for grain maize cultivation. We chose corn because it is one of the most important forage crops, we could say even the largest, occupying third place among cultivated plants worldwide. Along with wheat and barley, the food is the biggest part of the population in the world, directly or converted to animal products. Maize can be used in animal feed in various forms. The most used is corn grain, which is characterized by a very high nutritional value, this product is properly regarded as a feed concentrate. Culture of maize have been designed two levels of production: 4000 kg / ha and 6000 kg / ha.
Elena Corina Popescu
Full Text Available Maize, rice, wheat and potato are the main sources of starches which differ significantly in composition, morphology,thermal, rheological and retrogradation properties. Starch has unique thermal properties and functionality that havepermitted its wide use in food products and industrial applications.The structure of the starch granule results from the physical arrangement of amylose and amylopectin. Amylose contentof starches from different maize types ranged between 15.3% and 25.1%. Amylopectin is considered responsible for thecrystalline structure of starch granules.The morphological and physicochemical characteristics of maize starch are related to the enzymes involved in itsbiosynthesis.The surface of the starch granule plays a fundamental rôle as the first barrier to processes such as granule hydration,enzyme attack, and chemical reaction with modifying agents. Major parameters describing the solid surface are:specific surface area, total pore volume, mean pore radius (diameter and pore volume distribution in relation to poreradius (diameter.
Knowledge of the identities and characteristics of genes that govern the dramatic phenotypic differences between cultivated plants and their wild ancestors has greatly enhanced our understanding of the domestication process. In this issue of Molecular Ecology, Sigmon & Vollbrecht report the discovery of a new maize domestication gene, ramosa1, which encodes a putative transcription factor in the ramosa developmental pathway. Ramosa1 appears to be instrumental in determining the straightness of kernel rows on the maize cob. The key domestication alleles at ramosa1 are prevalent in landraces of maize. These results reinforce findings from previous studies of crop evolution by highlighting the importance of standing genetic variation and changes in transcriptional regulators in domestication. The evolutionary genetics of domestication also provides a framework for predicting the evolutionary response of organisms to strong human-induced selection pressures over limited time intervals.
El Baidouri, Moaine; Panaud, Olivier
Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.
Trifa, Youssef; Zhang, David
PCR-based techniques are the most widely used methods for the quantification of genetically modified organisms (GMOs) through the determination of the ratio of transgenic DNA to total DNA. It is shown that the DNA content per mass unit is significantly different among 10 maize cultivars. The DNA contents of endosperms, embryos, and teguments of individual kernels from 10 maize cultivars were determined. According to our results, the tegument's DNA ratio reaches at maximum 3.5% of the total kernel's DNA, whereas the endosperm's and the embryo's DNA ratios are nearly equal to 50%. The embryo cells are diploid and made of one paternal and one maternal haploid genome, whereas the endosperm is constituted of triploid cells made of two maternal haploid genomes and one paternal haploid genome. Therefore, it is shown, in this study, that the accuracy of the GMO quantification depends on the reference material used as well as on the category of the transgenic kernels present in the mixture.
Full Text Available Chloroplast genomes in land plants contain approximately 100 genes, the majority of which reside in polycistronic transcription units derived from cyanobacterial operons. The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photosynthetic progenitors. In C4 plants, the partitioning of photosynthesis between two cell types, bundle sheath and mesophyll, adds an additional layer of complexity. We used ribosome profiling and RNA-seq to generate a comprehensive description of chloroplast gene expression at four stages of chloroplast differentiation, as displayed along the maize seedling leaf blade. The rate of protein output of most genes increases early in development and declines once the photosynthetic apparatus is mature. The developmental dynamics of protein output fall into several patterns. Programmed changes in mRNA abundance make a strong contribution to the developmental shifts in protein output, but output is further adjusted by changes in translational efficiency. RNAs with prioritized translation early in development are largely involved in chloroplast gene expression, whereas those with prioritized translation in photosynthetic tissues are generally involved in photosynthesis. Differential gene expression in bundle sheath and mesophyll chloroplasts results primarily from differences in mRNA abundance, but differences in translational efficiency amplify mRNA-level effects in some instances. In most cases, rates of protein output approximate steady-state protein stoichiometries, implying a limited role for proteolysis in eliminating unassembled or damaged proteins under non-stress conditions. Tuned protein output results from gene-specific trade-offs between translational efficiency and mRNA abundance, both of which span a large dynamic range. Analysis of ribosome footprints at sites of RNA editing showed that the chloroplast translation machinery
Chotewutmontri, Prakitchai; Barkan, Alice
Chloroplast genomes in land plants contain approximately 100 genes, the majority of which reside in polycistronic transcription units derived from cyanobacterial operons. The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photosynthetic progenitors. In C4 plants, the partitioning of photosynthesis between two cell types, bundle sheath and mesophyll, adds an additional layer of complexity. We used ribosome profiling and RNA-seq to generate a comprehensive description of chloroplast gene expression at four stages of chloroplast differentiation, as displayed along the maize seedling leaf blade. The rate of protein output of most genes increases early in development and declines once the photosynthetic apparatus is mature. The developmental dynamics of protein output fall into several patterns. Programmed changes in mRNA abundance make a strong contribution to the developmental shifts in protein output, but output is further adjusted by changes in translational efficiency. RNAs with prioritized translation early in development are largely involved in chloroplast gene expression, whereas those with prioritized translation in photosynthetic tissues are generally involved in photosynthesis. Differential gene expression in bundle sheath and mesophyll chloroplasts results primarily from differences in mRNA abundance, but differences in translational efficiency amplify mRNA-level effects in some instances. In most cases, rates of protein output approximate steady-state protein stoichiometries, implying a limited role for proteolysis in eliminating unassembled or damaged proteins under non-stress conditions. Tuned protein output results from gene-specific trade-offs between translational efficiency and mRNA abundance, both of which span a large dynamic range. Analysis of ribosome footprints at sites of RNA editing showed that the chloroplast translation machinery does not generally
Gelsolin is a representative of a type of actin-binding proteins (ABPs) universally found in eukaryotes. It plays role in nucleation, capping and severing of actin filaments in vitro. In our experiment, gelsolin was purified from pig plasma and the polyclonal antibodies against it were prepared. The crude extracts of maize pollen were immunodetected by Western-blotting with polyclonal antibody and monoclonal antibody respectively. The immunodetection results show that gelsolin exists in maize pollen and its molecular weight is about 91 ku, similar to that of gelsolin found in animal tissues.
Ghareeb, Hassan; Drechsler, Frank; Löfke, Christian; Teichmann, Thomas; Schirawski, Jan
The biotrophic fungus Sporisorium reilianum causes head smut of maize (Zea mays) after systemic plant colonization. Symptoms include the formation of multiple female inflorescences at subapical nodes of the stalk because of loss of apical dominance. By deletion analysis of cluster 19-1, the largest genomic divergence cluster in S. reilianum, we identified a secreted fungal effector responsible for S. reilianum-induced loss of apical dominance, which we named SUPPRESSOR OF APICAL DOMINANCE1 (SAD1). SAD1 transcript levels were highly up-regulated during biotrophic fungal growth in all infected plant tissues. SAD1-green fluorescent protein fusion proteins expressed by recombinant S. reilianum localized to the extracellular hyphal space. Transgenic Arabidopsis (Arabidopsis thaliana)-expressing green fluorescent protein-SAD1 displayed an increased number of secondary rosette-leaf branches. This suggests that SAD1 manipulates inflorescence branching architecture in maize and Arabidopsis through a conserved pathway. Using a yeast (Saccharomyces cerevisiae) two-hybrid library of S. reilianum-infected maize tissues, we identified potential plant interaction partners that had a predicted function in ubiquitination, signaling, and nuclear processes. Presence of SAD1 led to an increase of the transcript levels of the auxin transporter PIN-FORMED1 in the root and a reduction of the branching regulator TEOSINTE BRANCHED1 in the stalk. This indicates a role of SAD1 in regulation of apical dominance by modulation of branching through increasing transcript levels of the auxin transporter PIN1 and derepression of bud outgrowth.
Full Text Available Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis. In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.
Liu, Zhengbin; Garcia, Arturo; McMullen, Michael D; Flint-Garcia, Sherry A
Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays) kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis). In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL) for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.
Paternò, Annalisa; Marchesi, Ugo; Gatto, Francesco; Verginelli, Daniela; Quarchioni, Cinzia; Fusco, Cristiana; Zepparoni, Alessia; Amaddeo, Demetrio; Ciabatti, Ilaria
The comparison of five real-time polymerase chain reaction (PCR) methods targeted at maize ( Zea mays ) endogenous sequences is reported. PCR targets were the alcohol dehydrogenase (adh) gene for three methods and high-mobility group (hmg) gene for the other two. The five real-time PCR methods have been checked under repeatability conditions at several dilution levels on both pooled DNA template from several genetically modified (GM) maize certified reference materials (CRMs) and single CRM DNA extracts. Slopes and R(2) coefficients of all of the curves obtained from the adopted regression model were compared within the same method and among all of the five methods, and the limit of detection and limit of quantitation were analyzed for each PCR system. Furthermore, method equivalency was evaluated on the basis of the ability to estimate the target haploid genome copy number at each concentration level. Results indicated that, among the five methods tested, one of the hmg-targeted PCR systems can be considered equivalent to the others but shows the best regression parameters and a higher repeteability along the dilution range. Thereby, it is proposed as a valid module to be coupled to different event-specific real-time PCR for maize genetically modified organism (GMO) quantitation. The resulting practicability improvement on the analytical control of GMOs is discussed.
Walaa Kamel Mousa
Full Text Available Wild maize (teosinte has been reported to be less susceptible to pests than their modern maize (corn relatives. Endophytes, defined as microbes that inhabit plants without causing disease, are known for their ability to antagonize plant pests and pathogens. We hypothesized that the wild relatives of modern maize may host endophytes that combat pathogens. Fusarium graminearum is the fungus that causes Gibberella Ear Rot (GER in modern maize and produces the mycotoxin, deoxynivalenol (DON. In this study, 215 bacterial endophytes, previously isolated from diverse maize genotypes including wild teosintes, traditional landraces and modern varieties, were tested for their ability to antagonize F. graminearum in vitro. Candidate endophytes were then tested for their ability to suppress GER in modern maize in independent greenhouse trials. The results revealed that three candidate endophytes derived from wild teosintes were most potent in suppressing F. graminearum in vitro and GER in a modern maize hybrid. These wild teosinte endophytes could suppress a broad spectrum of fungal pathogens of modern crops in vitro. The teosinte endophytes also suppressed DON mycotoxin during storage to below acceptable safety threshold levels. A fourth, less robust anti-fungal strain was isolated from a modern maize hybrid. Three of the anti-fungal endophytes were predicted to be Paenibacillus polymyxa, along with one strain of Citrobacter. Microscopy studies suggested a fungicidal mode of action by all four strains. Molecular and biochemical studies showed that the P. polymyxa strains produced the previously characterized anti-Fusarium compound, fusaricidin. Our results suggest that the wild relatives of modern crops may serve as a valuable reservoir for endophytes in the ongoing fight against serious threats to modern agriculture. We discuss the possible impact of crop evolution and domestication on endophytes in the context of plant defense.
HUASHENG ZHU; JIANDONG WU; YINGLI JIANG; JING JIN; WEI ZHOU; YU WANG; GUOMIN HAN; YANG ZHAO; BEIJIU CHENG
Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro–exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka / Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize
Full Text Available Abstract Background Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations. Results Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill. Conclusion We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.
Leaf area development of six tropical maize cultivars grown in 1995 and 1996 in several tropical environments in Mexico (both favourable and moisture-and N-limited) was observed and analysed. First, the validity of a bell-shaped curve describing the area of individual leaves as a function of leaf nu
Mulder, Christian; Wouterse, Marja; Raubuch, Markus; Roelofs, Willem; Rutgers, Michiel
The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical gu
Torres, A.F.; Noordam-Boot, C.M.M.; Dolstra, Oene; Weijde, van der Tim; Combes, Eliette; Dufour, Philippe; Vlaswinkel, Louis; Visser, R.G.F.; Trindade, L.M.
Genetic studies are ideal platforms for assessing the extent of genetic diversity, inferring the genetic architecture, and evaluating complex trait interrelations for cell wall compositional and bioconversion traits relevant to bioenergy applications. Through the characterization of a forage maiz
Meiosis, particularly meiotic recombination, is a major factor affecting yield and breeding of plants. To gain insight into the transcriptome landscape during early initiation steps of meiotic recombination, we profiled early prophase I meiocytes from maize using RNA-seq. Our analyses of genes prefe...
Eli J. Borrego
Full Text Available Of the over 600 oxylipins present in all plants, the phytohormone jasmonic acid (JA remains the best understood in terms of its biosynthesis, function and signaling. Much like their eicosanoid analogues in mammalian system, evidence is growing for the role of the other oxylipins in diverse physiological processes. JA serves as the model plant oxylipin species and regulates defense and development. For several decades, the biology of JA has been characterized in a few dicot species, yet the function of JA in monocots has only recently begun to be elucidated. In this work, the synthesis and function of JA in maize is presented from the perspective of oxylipin biology. The maize genes responsible for catalyzing the reactions in the JA biosynthesis are clarified and described. Recent studies into the function of JA in maize defense against insect herbivory, pathogens and its role in growth and development are highlighted. Additionally, a list of JA-responsive genes is presented for use as biological markers for improving future investigations into JA signaling in maize.
Aspergillus flavus is an opportunistic fungal pathogen that colonizes maize seeds and contaminates them with aflatoxin. The fungus is localized in the endosperm and aleurone. To investigate the plant microbe interaction, we conducted histological and molecular studies to characterize the internal co...
Jolokhava, Tamar; Kenchiashvili, Naira; Tarkhnishvili, Maia; Ghambashidze, Giorgi
Maize remains to be the most important cereal crop in Georgia. Total area of arable land under cereal crops production equals to 184 thousands hectares (FAO statistical yearbook, 2014), from which maize takes the biggest share. Leading position of maize among other cereal crops is caused by its dual purpose as food and feed product. In Spite of a relatively high production of maize to other cereals there is still a high demand on it, especially as feed for animal husbandry. The same tendency is seen in organic production, where producers of livestock and poultry products require organically grown maize, the average yield of which is much less than those produced conventionally. Therefore, it is important to increase productivity of maize in organic farms. Current study aimed to improve maize yield using locally produced organic fertilizers and to compare them to the effect of mineral fertilizers. The study was carried out in Eastern Georgia under dry subtropical climate conditions on local hybrid of maize. This is the first attempt to use hybrid maize (developed with organic plant breeding method) in organic field trials in Georgia. The results shown, that grain yield from two different types of organic fertilizers reached 70% of the yields achieved with industrial mineral fertilizers. As on farm level differences between organic and conventional maize production are much severe, the results from the field trials seems to be promising for future improvement of organic cereal crop production.
Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun
Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949
Full Text Available Waxy maize (Zea mays L. var. certaina Kulesh, with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F* were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.
Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner
Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...
Cui Yu; Zhang Ai-hong; Ren Ai-jun; Miao Hong-qin
There are a total of more than 40 reported maize viral diseases worldwide. Five of them have reportedly occurred in China. They are maize rough dwarf disease, maize dwarf mosaic disease, maize streak dwarf disease, maize crimson leaf disease, maize wallaby ear disease and corn lethal necrosis disease. This paper reviewed their occurrence and distribution as well as virus identification techniques in order to provide a basis for virus identification and diagnosis in corn production.
Full Text Available Maize enterprise profitability is essential for sustainable maize production in smallholder farming. In Zimbabwe a lot of factors including several policy measures implemented in the past are believed to be influencing current maize profitability trends. Literature to confirm some of the crucial factors is limited especially in the smallholder farming sector. In this study we analyze profitability of smallholder maize farmers in Mazowe District of Zimbabwe. We estimate maize enterprise profitability using gross margin analysis, factors driving profitability using linear regression analysis and the influence of tobacco farming adoption on maize enterprise profitability using propensity score matching. We relied on both primary and secondary data from the study area. Results did not show robust outcomes on maize enterprises profitability. Maize profitability was found to be influenced positively by age of household head and selling produce to private buyers and negatively by fertilizer, chemical, and transport costs. Tobacco farming adoption was found to have a positive influence on maize profitability. Based on the results the study recommends the government through its various programs targeting agricultural development and food security to focus on smallholder maize production and marketing with the aim of improving its profitability.
LIU Wenting; GAO Youjun; TENG Feng; SHI Qing; ZHENG Yonglian
A total of 26718 M1 plants were obtained by crossing the active mutator transposon donor parents (Q105, WW51, 115F, V26-2 and 919J)with the recipient parents (Hz85,W328 with Bz gene and S-Mo17Rf3Rf3). The phenotypes of M1 plants were observed in the field. M1 plants were self-pollinated to develop the mutator insertion-mutagenized M2 seeds. The transposition frequency of the mutator in the genome was calculated based on the spotted aleurone phenotype of the M2 seeds. The results showed that: (1) the mutation frequency of M1 phenotypes in the field was 0.07 in the population of W328×Mu; (2) the mutation frequency of spotted aleurone seeds on the M2 ears was 0.122 in the population of W328×Mu; (3) five S-cytoplasm male-sterile plants were found among 22500 M1 plants of S-Mo17Rf3Rf3×Mu, with the transposition frequency about 2.2×10-4 per locus. 99 flanking sequences of mutator transposition were amplified by the modified MuTAIL-PCR, and 59 non-redundant sequences with length around 400 bp were obtained.After bioinformatic analysis, 27 sequences of them could be annotated, using non-redundant nucleotide database of maize, rice, and Arabidopsis. 36 sequences of them were located on the genetic map of maize by comparative genomics, and several flanking sequences of mutator insertion were mapped on the single marker locus. Hotspot sequences of mutator transposition were revealed by comparing the homologies between the 9-bp target site duplication of the mutator insertion. The putative functions of 8 flanking sequences of rnutator transposition had identity with the functions of their corresponding marker. The constructed mutator insertion mutant population in maize will facilitate the new gene discovery and functional genomics study in maize.
Manevski, Kiril; Børgesen, Christen Duus; Andersen, Mathias Neumann
effects on the maize systems. Results Intercropped maize had 15–37 % lower N leaching than monocrop maize. Maize intercropping following a maize crop was achieved without yield loss at the standard N rate or higher, while red fescue offset N leaching. Maize intercropping following grass-clover needed less...... N, thereby greatly reducing the N leaching. Conclusions The hypothesis that maize intercropping with fertilizer N rates applicable to monocrop maize decreases N leaching without significant yield loss was largely supported given the effect of cropping history and soil type. The applicability...
Jie Xu; Tingzhao Rong; Yaxi Liu; Jian Liu; Moju Cao; Jing Wang; Hai Lan; Yunbi Xu; Yanli Lu; Guangtang Pan
The control of flowering is not only important for reproduction,but also plays a key role in the processes of domestication and adaptation.To reveal the genetic architecture for flowering time and photoperiod sensitivity,a comprehensive evaluation of the relevant literature was performed and followed by meta analysis.A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development.Besides,a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits.Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.).Our results suggest that the combination of literature review,meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering.Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection,such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.
Picard, Christine; Bosco, Marco
By comparing the distribution of two genomic markers among Pseudomonas strains recovered from the rhizosphere of two maize hybrids with those of strains recovered from the rhizosphere of their four respective parental lines, we showed that both hybrids supported more elite probiotic strains than the parents. Elite Pseudomonas strains showed genomic potential for both an appropriate in vitro 2,4-diacetylphloroglucinol (DAPG) productivity, and a superior root-colonization ability. The actual biocontrol and root-colonization abilities of these strains were confirmed by bioassays on five fungal strains and on axenic maize plants. Furthermore, results on the abundance and genetic diversity of resident DAPG+ Pseudomonas strains indicated that each hybrid was able to select its own specific DAPG+ population, whereas the four parental lines were not. The evidence that heterozygosis can drive maize plants to select elite probiotic rhizospheric DAPG+ Pseudomonas strains opens the way to a new strategy in the set up of plant breeding for low-input and organic agriculture.
JIANG Hui-ming; GU Li-li
Jilin Province is one of the main grain-producing provinces of China, which has dominant position in maize production, by the view of its advantages in policy, location, breed and market. And after entering WTO,some measures have been taken to enhance maize competitive ability. But there are some difficulties in concentrating production to maize advantaged areas. This paper expounds the basis that Jilin Province becomes the advantage area of maize, analyzes the problems and puts forward the supporting policy. Some strategic measures are proposed,as developing comparable advantages, carrying out the strategy of un-equilibrium development and cultivating advantaged product areas of maize to rapidly improve the international competitive ability and productivity of maize in Jilin Province, cast the agricultural predicament off and promote the agricultural development into a new stage.
Gwirtz, Jeffrey A; Garcia-Casal, Maria Nieves
Corn is the cereal with the highest production worldwide and is used for human consumption, livestock feed, and fuel. Various food technologies are currently used for processing industrially produced maize flours and corn meals in different parts of the world to obtain precooked refined maize flour, dehydrated nixtamalized flour, fermented maize flours, and other maize products. These products have different intrinsic vitamin and mineral contents, and their processing follows different pathways from raw grain to the consumer final product, which entail changes in nutrient composition. Dry maize mechanical processing creates whole or fractionated products, separated by anatomical features such as bran, germ, and endosperm. Wet maize processing separates by chemical compound classification such as starch and protein. Various industrial processes, including whole grain, dry milling fractionation, and nixtamalization, are described. Vitamin and mineral losses during processing are identified and the nutritional impacts outlined. Also discussed are the vitamin and mineral contents of corn. PMID:24329576
Mohammed A. Ahmed
Full Text Available An experiment was conducted to study the nutritional value of yellow maize when it substitutes sorghum grain as source of energy at levels 0, 25, 50, 75 and 100% in broiler rations. One hundred and forty unsexed one day old (Ross broiler chicks were randomly assigned to five approximately isocaloric and isonitrogenous diets labeled as follows: Diet (S0 containing sorghum 100% (control, 60% of the diet, diet (S1 75% sorghum 25% maize, diet (S2 50% sorghum 50% maize, diet (S3 25% sorghum 75% maize and diet (S4 maize (100% (without sorghum. Each treatment had four replicates with 7 birds/replicate. The experiment lasted for 6 weeks. Feed intake and body weight gain had been recorded weekly. The results showed significant increase (P 0.05 effect on cold carcass dressing percentage, liver and abdominal fat weights, serum cholesterol, serum calcium and inorganic phosphorus levels. The cost of production decreased by increasing level of maize.
Gwirtz, Jeffrey A; Garcia-Casal, Maria Nieves
Corn is the cereal with the highest production worldwide and is used for human consumption, livestock feed, and fuel. Various food technologies are currently used for processing industrially produced maize flours and corn meals in different parts of the world to obtain precooked refined maize flour, dehydrated nixtamalized flour, fermented maize flours, and other maize products. These products have different intrinsic vitamin and mineral contents, and their processing follows different pathways from raw grain to the consumer final product, which entail changes in nutrient composition. Dry maize mechanical processing creates whole or fractionated products, separated by anatomical features such as bran, germ, and endosperm. Wet maize processing separates by chemical compound classification such as starch and protein. Various industrial processes, including whole grain, dry milling fractionation, and nixtamalization, are described. Vitamin and mineral losses during processing are identified and the nutritional impacts outlined. Also discussed are the vitamin and mineral contents of corn.
Zhu, Qi-Bing; Feng, Zhao-Li; Huang, Min; Zhu, Xiao
The sufficiency of feature extraction and the rationality of classifier design are two key issues affecting the accuracy of maize seed recognition. In the present study, the hyperspectral images of maize seeds were acquired using hyperspectral image system, and the image entropy of maize seeds for each wavelength was extracted as classification features. Then, support vector data description (SVDD) algorithm was used to develop the classifier model for each variety of maize seeds. The SVDD models yielded 94.14% average test accuracy for known variety samples and 92.28% average test accuracy for new variety samples, respectively. The simulation results showed that the proposed method implemented accurate identification of maize seeds and solved the problem of misclassification by the traditional classification algorithm for new variety maize seeds.
Purugganan, M D; Wessler, S R
The magellan transposable element is responsible for a spontaneous 5.7-kb insertion in the maize wx-M allele. This element has the sequence and structural characteristics of a Ty3/gypsy-like retrotransposon. The magellan element is present in all Zea species and Tripsacum andersonii; it is absent, however, in the genomes of all other Tripsacum species analyzed. The genetic distances between magellan elements suggest that this retrotransposon is evolving faster than other Zea nuclear loci. The phylogeny of magellan within Zea and T. andersonii also reveals a pattern of interspecies transfers, resulting in the movement of magellan subfamilies between different species genomes. Interspecific hybridization may be a major mechanism by which this retrotransposon invades and establishes itself in new taxa.
Skovgård, Henrik; Päts, Peeter
The effects of maize-cowpea intercropping on three lepidopteran stemborers (Chilo partellus (Swinhoe) C. orichalcociliellus (Strand) and Sesamia calamistis Hampson) and their natural enemies were studied in Kenya. Oviposition was not affected by intercropping, but significantly fewer larvae...... and wandering spiders, were not augmented by intercropping, but an inverse relationship in abundance was found between these two predator groups. It is concluded that maize intercropped with cowpea has only limited potential as a method of controlling the key pests in maize....
de Herrera, Adys Pereira; Sain, Gustavo
An aggressive research and validation program launched in 1984 in Azuero, Panama, yielded a recommendation advocating zero tillage for maize production. Ten years later, maize farmers in Azuero used three land preparation methods: conventional tillage, zero tillage, and minimum tillage (an adaptation of the zero tillage technology). This study aimed to quantify the adoption of zero and minimum tillage for maize in Azuero; identify factors influencing adoption of the different land preparation...
Full Text Available This study was conducted to analyze the acreage response of maize with respect to price and non-price factors in Khyber Pakhtunkhwa. The time-series data for the period of 35 years (1976-2010 pertaining to, maize area, maize price, rice price, maize yield, average rainfall were collected from various published sources. Nerlovian adjustment lag model and Vector Auto Regression (VAR technique of estimation was employed for analyzing acreage response of maize. The model explained more than 90 percent of variation in the dependent variable. The expected maize price was unlikely found to be negative and statistically insignificant. The regression coefficients for lag rice price and lag maize yield also appeared insignificant. Area under maize in lagged year was found to be an important variable influencing farmer’s decision on acreage allocation. Among the short run and long run elasticities with respect to lag area that is 0.7155 and 2.5149, long run elasticity was more, signaling that acreage adjustment would normally take place in the long run. The coefficient of lag rainfall was found to be negative and significant indicating a negative relation between maize acreage and rainfall. The short run elasticity of maize area with respect to lag rainfall during the study period has been calculated at -0.0894 while the long run elasticity comes to be -0.3142, indicate its inelastic nature and little effect on the decision of farmers regarding allocation of land to maize. Small area adjustment coefficient (0.2845 revealed low rate of farmers’ area adjustment to desired level because of more institutional and technological constraints. Based upon the findings of this study it can be concluded that farmers allocate land to maize crop mainly basing on their previous allocation pattern rather than relative crop prices.
Cutts, Michela; Hassan, Rashid M.
In almost all of the Southern Africa Development Community (SADC) countries maize is cropped on a commercial basis except in Mauritius and Seychelles. Maize meal is the most important food staple in Southern and Eastern Africa. This is one of the main reason many governments in the region implement various policies to protect the maize sector. With adoption of the Uruguay Round Agreement on Agriculture (URAA) in the late 1990s, there has been a wave of market liberalization in the region. Mai...
This paper explores the effects of maize processing on the carbonization and preservation of maize kernels in the archaeological record. The shift to processing maize with lime (known as hominy production in the Eastern Woodlands and nixtamalization in Mesoamerica) in ancient times had the effect of making maize more nutritious through increasing the availability of calcium, niacin, dietary fiber, and essential amino acids. Less understood is how this process of cooking maize in a lime solut...
Schaefer, Robert J; Briskine, Roman; Springer, Nathan M; Myers, Chad L
Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB), which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.
Robert J Schaefer
Full Text Available Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB, which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.
Green, Jason M; Harnsomburana, Jaturon; Schaeffer, Mary L; Lawrence, Carolyn J; Shyu, Chi-Ren
Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php.
Steven R Eichten
Full Text Available DNA methylation is a chromatin modification that is sometimes associated with epigenetic regulation of gene expression. As DNA methylation can be reversible at some loci, it is possible that methylation patterns may change within an organism that is subjected to environmental stress. In order to assess the effects of abiotic stress on DNA methylation patterns in maize (Zea mays, seeding plants were subjected to heat, cold, and UV stress treatments. Tissue was later collected from individual adult plants that had been subjected to stress or control treatments and used to perform DNA methylation profiling to determine whether there were consistent changes in DNA methylation triggered by specific stress treatments. DNA methylation profiling was performed by immunoprecipitation of methylated DNA followed by microarray hybridization to allow for quantitative estimates of DNA methylation abundance throughout the low-copy portion of the maize genome. By comparing the DNA methylation profiles of each individual plant to the average of the control plants it was possible to identify regions of the genome with variable DNA methylation. However, we did not find evidence of consistent DNA methylation changes resulting from the stress treatments used in this study. Instead, the data suggest that there is a low-rate of stochastic variation that is present in both control and stressed plants.
Lisson, Ralph; Hellert, Jan; Ringleb, Malte; Machens, Fabian; Kraus, Josef; Hehl, Reinhard
The maize Activator/Dissociation (Ac/Ds) transposable element system was introduced into sugar beet. The autonomous Ac and non-autonomous Ds element excise from the T-DNA vector and integrate at novel positions in the sugar beet genome. Ac and Ds excisions generate footprints in the donor T-DNA that support the hairpin model for transposon excision. Two complete integration events into genomic sugar beet DNA were obtained by IPCR. Integration of Ac leads to an eight bp duplication, while integration of Ds in a homologue of a sugar beet flowering locus gene did not induce a duplication. The molecular structure of the target site indicates Ds integration into a double strand break. Analyses of transposase transcription using RT-PCR revealed low amounts of alternatively spliced mRNAs. The fourth intron of the transposase was found to be partially misspliced. Four different splice products were identified. In addition, the second and third exon were found to harbour two and three novel introns, respectively. These utilize each the same splice donor but several alternative splice acceptor sites. Using the SplicePredictor online tool, one of the two introns within exon two is predicted to be efficiently spliced in maize. Most interestingly, splicing of this intron together with the four major introns of Ac would generate a transposase that lacks the DNA binding domain and two of its three nuclear localization signals, but still harbours the dimerization domain.
Farhan Ali; Jianbing Yan
Diseases are a potential threat to global food security but plants have evolved an extensive array of methodologies to cope with the invading pathogens.Non-host resistance and quantitative resistance are broad spectrum forms of resistance,and all kinds of resistances are controlled by extremely diverse genes called “R-genes”.R-genes follow different mechanisms to defend plants and PAMP-induced defenses in susceptible host plants are referred to as basal resistance.Genetic and phenotypic diversity are vital in maize (Zea mays L.); as such,genome wide association study (GWAS)along with certain other methodologies can explore the maximum means of genetic diversity.Exploring the complete genetic architecture to manipulate maize genetically reduces the losses from hazardous diseases.Genomic studies can reveal the interaction between different genes and their pathways.By confirming the specific role of these genes and protein-protein interaction (proteomics) via advanced molecular and bioinformatics tools,we can shed a light on the most complicated and abstruse phenomena of resistance.
Hauck, Andrew L; Novais, Joana; Grift, Tony E; Bohn, Martin O
The mature root system is a vital plant organ, which is critical to plant performance. Commercial maize (Zea mays L.) breeding has resulted in a steady increase in plant performance over time, along with noticeable changes in above ground vegetative traits, but the corresponding changes in the root system are not presently known. In this study, roughly 2500 core root systems from field trials of a set of 10 diverse elite inbreds formerly protected by Plant Variety Protection plus B73 and Mo17 and the 66 diallel intercrosses among them were evaluated for root traits using high throughput image-based phenotyping. Overall root architecture was modeled by root angle (RA) and stem diameter (SD), while root complexity, the amount of root branching, was quantified using fractal analysis to obtain values for fractal dimension (FD) and fractal abundance (FA). For each trait, per se line effects were highly significant and the most important contributor to trait performance. Mid-parent heterosis and specific combining ability was also highly significant for FD, FA, and RA, while none of the traits showed significant general combining ability. The interaction between the environment and the additive line effect was also significant for all traits. Within the inbred and hybrid generations, FD and FA were highly correlated (rp ≥ 0.74), SD was moderately correlated to FD and FA (0.69 ≥ rp ≥ 0.48), while the correlation between RA and other traits was low (0.13 ≥ rp ≥ -0.40). Inbreds with contrasting effects on complexity and architecture traits were observed, suggesting that root complexity and architecture traits are inherited independently. A more comprehensive understanding of the maize root system and the way it interacts with the environment will be useful for defining adaptation to nutrient acquisition and tolerance to stress from drought and high plant densities, critical factors in the yield gains of modern hybrids.
Buddhi Bahadur Achhami
Full Text Available Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and the average plant damage percentage by stem borer was up to 18.11%. Length of the feeding tunnel in maize stem was significantly higher in January than July. In case of exit holes made by borer counted more than four holes per plant that were planted in the month of January. All in all, except the tunnel length measurement per plant, we observed similar pattern in other borer damage parameters such as exit whole counts and plant damage percentage within the tested varieties. Stem borer damage was not significantly affect on grain yield.
Odgaard, Mette Vestergaard; Bøcher, Peder Klith; Dalgaard, Tommy;
It is expected that the ongoing anthropogenic climate change will drive changes in agricultural production and its geographic distribution. Here, we assess the extent to which climate change is already driving spatiotemporal dynamics in maize production in Denmark. We use advanced spatial...... regression modeling with multi-model averaging to assess the extent to which the recent spatiotemporal dynamics of the maize area in Denmark are driven by climate (temperature as represented by maize heating units [MHU] and growing-season precipitation), climate change and non-climatic factors (cattle...... density [in Denmark, maize is mainly grown for ensilage to feed livestock], and sandy soil [facilitates maize growing in cold areas due to higher soil temperature than loamy soils]). Our results indicate that there has been a geographical expansion of maize in Denmark from 1999 to 2008, with a strong link...
Raun, Birgitte Marie Løvendahl; Kristensen, Niels Bastian
The objective of the present study was to investigate the prevalence maize silage containing propanol, the seasonal variation in propanol content of maize silage, and correlations between propanol and other fermentation products in maize silage collected from 20 randomly selected Danish dairy farms...... farms, the maize silage had ≥5 g propanol/kg DM. The present study indicates that dairy cows in Denmark are commonly exposed to propanol and that approximately 20% of the dairy cows will have an intake in the range of 75-100 g propanol/d under common feeding conditions....
Zbigniew PODKÓWKA; Lucyna PODKÓWKA
Sweet sorghum (Sorghum saccharatum) silage, maize (Zea mays) silage, and sorghum and maize (1:1) silage were investigated. The silages were analysed for chemical composition, quality and aerobic stability. Dry matter was the lowest (20.88%) in sorghum silage and the highest (37.45%) in maize silage. In sorghum silage, the concentration of crude ash and crude fibre was higher, and that of crude protein, crude fat and N-free extractives lower compared to maize silage. Neutral detergent fibre an...
Zhiming Xie; Ri Song; Hongbo Shao; Fengbin Song; Hongwen Xu; Yan Lu
The research aimed to determine the effects of Si application on photosynthetic characteristics of maize on saline-alkaline soil, including photosynthetic rate (P n ), stomatal conductance (g s ), transpiration rate (E), and intercellular CO2 concentration (C i ) of maize in the field with five levels (0, 45, 90, 150, and 225 kg·ha−1) of Si supplying. Experimental results showed that the values of P n , g s , and C i of maize were significantly enhanced while the values of E of maize were dra...
Meissle, Michael; Romeis, Jörg; Bigler, Franz
The European corn borer (Ostrinia nubilalis), the Mediterranean corn borer (Sesamia nonagrioides) and the western corn rootworm (Diabrotica virgifera virgifera) are the main arthropod pests in European maize production. Practised pest control includes chemical control, biological control and cultural control such as ploughing and crop rotation. A pest control option that is available since 1996 is maize varieties that are genetically engineered (GE) to produce insecticidal compounds. GE maize varieties available today express one or several genes from Bacillus thuringiensis (Bt) that target corn borers or corn rootworms. Incentives to growing Bt maize are simplified farm operations, high pest control efficiency, improved grain quality and ecological benefits. Limitations include the risk of resistance evolution in target pest populations, risk of secondary pest outbreaks and increased administration to comply with licence agreements. Growers willing to plant Bt maize in the European Union (EU) often face the problem that authorisation is denied. Only one Bt maize transformation event (MON810) is currently authorised for commercial cultivation, and some national authorities have banned cultivation. Spain is the only EU member state where Bt maize adoption levels are currently delivering farm income gains near full potential levels. In an integrated pest management (IPM) context, Bt maize can be regarded as a preventive (host plant resistance) or a responsive pest control measure. In any case, Bt maize is a highly specific tool that efficiently controls the main pests and allows combination with other preventive or responsive measures to solve other agricultural problems including those with secondary pests.
Schirawski, Jan; Mannhaupt, Gertrud; Münch, Karin; Brefort, Thomas; Schipper, Kerstin; Doehlemann, Gunther; Di Stasio, Maurizio; Rössel, Nicole; Mendoza-Mendoza, Artemio; Pester, Doris; Müller, Olaf; Winterberg, Britta; Meyer, Elmar; Ghareeb, Hassan; Wollenberg, Theresa; Münsterkötter, Martin; Wong, Philip; Walter, Mathias; Stukenbrock, Eva; Güldener, Ulrich; Kahmann, Regine
Biotrophic pathogens, such as the related maize pathogenic fungi Ustilago maydis and Sporisorium reilianum, establish an intimate relationship with their hosts by secreting protein effectors. Because secreted effectors interacting with plant proteins should rapidly evolve, we identified variable genomic regions by sequencing the genome of S. reilianum and comparing it with the U. maydis genome. We detected 43 regions of low sequence conservation in otherwise well-conserved syntenic genomes. These regions primarily encode secreted effectors and include previously identified virulence clusters. By deletion analysis in U. maydis, we demonstrate a role in virulence for four previously unknown diversity regions. This highlights the power of comparative genomics of closely related species for identification of virulence determinants.
Wang, Wen; Zheng, Hongkung; Fan, Chuanzhu;
and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons...
Truter, J; Van Hamburg, H; Van Den Berg, J
The biodiversity of an agroecosystem is not only important for its intrinsic value but also because it influences ecological functions that are vital for crop production in sustainable agricultural systems and the surrounding environment. A concern about genetically modified (GM) crops is the potential negative impact that such crops could have on diversity and abundance of nontarget organisms, and subsequently on ecosystem functions. Therefore, it is essential to assess the potential environmental risk of the release of a GM crop and to study its effect on species assemblages within that ecosystem. Assessment of the impact of Bt maize on the environment is hampered by the lack of basic checklists of species present in maize agroecosystems. The aims of the study were to compile a checklist of arthropods that occur on maize in South Africa and to compare the diversity and abundance of arthropods and functional groups on Bt maize and non-Bt maize. Collections of arthropods were carried out during two growing seasons on Bt maize and non-Bt maize plants at two localities. Three maize fields were sampled per locality during each season. Twenty plants, each of Bt maize and non-Bt maize, were randomly selected from the fields at each site. The arthropods collected during this study were classified to morphospecies level and grouped into the following functional groups: detritivores, herbivores, predators, and parasitoids. Based on feeding strategy, herbivores and predators were further divided into sucking herbivores or predators (piercing-sucking mouthparts) and chewing herbivores or predators (chewing mouthparts). A total of 8,771 arthropod individuals, comprising 288 morphospecies and presenting 20 orders, were collected. Results from this short-term study indicated that abundance and diversity of arthropods in maize and the different functional guilds were not significantly affected by Bt maize, either in terms of diversity or abundance.
R-r controls the production of anthocyanin pigment in plant parts and the aleurone layer of seeds through the production of a family of transcriptional activating proteins of the helix-loop-helix type. A series of mutant derivatives of R-r which have lost portions of the complex through unequal crossing over or intrachromosomal rearrangements have been examined to elucidate the molecular structure of the complex. The complex comprises a series of repeated, homologous components arranged in both direct and inverted orientations. These include the (P) component which causes pigmentation of plant parts and consists of a simple R gene; the (Q) component which is a truncated and, therefore, an inactive R gene, and the (S) subcomplex which consists of two functional R components that pigment the aleurone. The identity of each functional component was confirmed by microprojectile bombardment of intact maize tissues with cloned genomic DNA. Analysis of high molecular weight DNA has shown that the R-r complex spans more than 250 kb of DNA with the (P) component separated from the others by 190 kb, and the (Q) component separated from the (S) subcomplex by 20 kb. Sequence analysis shows that the R-r elements, (Q), (Sl) and (S2) were derived through the rearrangement of a simple (P)-like progenitor element. We present molecular evidence that the complex arose through a series of transposon-mediated rearrangements.
R-r controls the production of anthocyanin pigment in plant parts and the aleurone layer of seeds through the production of a family of transcriptional activating proteins of the helix-loop-helix type. A series of mutant derivatives of R-r which have lost portions of the complex through unequal crossing over or intrachromosomal rearrangements have been examined to elucidate the molecular structure of the complex. The complex comprises a series of repeated, homologous components arranged in both direct and inverted orientations. These include the (P) component which causes pigmentation of plant parts and consists of a simple R gene; the (Q) component which is a truncated and, therefore, an inactive R gene, and the (S) subcomplex which consists of two functional R components that pigment the aleurone. The identity of each functional component was confirmed by microprojectile bombardment of intact maize tissues with cloned genomic DNA. Analysis of high molecular weight DNA has shown that the R-r complex spans more than 250 kb of DNA with the (P) component separated from the others by 190 kb, and the (Q) component separated from the (S) subcomplex by 20 kb. Sequence analysis shows that the R-r elements, (Q), (Sl) and (S2) were derived through the rearrangement of a simple (P)-like progenitor element. We present molecular evidence that the complex arose through a series of transposon-mediated rearrangements.
Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization
Full Text Available Plant leaves are inhabited by a diverse group of microorganisms that are important contributors to optimal growth. Biotic and abiotic effects on plant growth are usually studied in controlled settings examining response to variation in single factors and in field settings with large numbers of variables. Multi-factor experiments with combinations of stresses bridge this gap, increasing our understanding of the genotype-environment-phenotype functional map for the host plant and the affiliated epiphytic community. The maize inbred B73 was exposed to single and combination abiotic and the biotic stress treatments: low nitrogen fertilizer and high levels of infection with southern leaf blight (causal agent Cochliobolus heterostrophus. Microbial epiphyte samples were collected at the vegetative early-season phase and species composition was determined using 16S ribosomal intergenic spacer analysis. Plant traits and level of southern leaf blight disease were measured late-season. Bacterial diversity was different among stress treatment groups (P< 0.001. Lower species richness—alpha diversity--was correlated with increased severity of southern leaf blight disease when disease pressure was high. Nitrogen fertilization intensified the decline in bacterial alpha diversity. While no single bacterial ribotype was consistently associated with disease severity, small sets of ribotypes were good predictors of disease levels. Difference in leaf bacterial-epiphyte diversity early in the season were correlated with plant disease severity, supporting further tests of microbial epiphyte-disease correlations for use in predicting disease progression.
Bodnar, Anastasia L; Proulx, Amy K; Scott, M Paul; Beavers, Alyssa; Reddy, Manju B
Maize ( Zea mays ) is an important staple crop in many parts of the world but has low iron bioavailability, in part due to its high phytate content. Hemoglobin is a form of iron that is highly bioavailable, and its bioavailability is not inhibited by phytate. It was hypothesized that maize hemoglobin is a highly bioavailable iron source and that biofortification of maize with iron can be accomplished by overexpression of maize globin in the endosperm. Maize was transformed with a gene construct encoding a translational fusion of maize globin and green fluorescent protein under transcriptional control of the maize 27 kDa γ-zein promoter. Iron bioavailability of maize hemoglobin produced in Escherichia coli and of stably transformed seeds expressing the maize globin-GFP fusion was determined using an in vitro Caco-2 cell culture model. Maize flour fortified with maize hemoglobin was found to have iron bioavailability that is not significantly different from that of flour fortified with ferrous sulfate or bovine hemoglobin but is significantly higher than unfortified flour. Transformed maize grain expressing maize globin was found to have iron bioavailability similar to that of untransformed seeds. These results suggest that maize globin produced in E. coli may be an effective iron fortificant, but overexpressing maize globin in maize endosperm may require a different strategy to increase bioavailable iron content in maize.
Chitra Bahadur Kunwar
Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.
Ana Luisa Martínez-López
Full Text Available The laccase induced gelation of maize bran arabinoxylans at 2.5% (w/v in the presence of insulin or β-lactoglobulin at 0.1% (w/v was investigated. Insulin and β-lacto-globulin did not modify either the gel elasticity (9 Pa or the cross-links content (0.03 and 0.015 mg di- and triferulic acids/mg arabinoxylan, respectively. The protein release capability of the gel was also investigated. The rate of protein release from gels was dependent on the protein molecular weight. The apparent diffusion coefficient was 0.99 × 10-7 and 0.79 × 10-7 cm2/s for insulin (5 kDa and β-lactoglobulin (18 kDa, respectively. The results suggest that maize bran arabinoxylan gels can be potential candidates for the controlled release of proteins.
Full Text Available Genetic progress depends on germplasm quality and breeding methods. Twelve maize populations and their crosses were evaluated to estimate combining ability and potential to be included as source populations in breeding programs. Plant height, point of insertion of the first ear, number of ears per plant, number of grains per ear, root and stalk lodging and grain yield were studied in two locations in Brazil, during the 1997/98 season. Genotype sum of squares was divided into general (GCA and specific (SCA combining ability. Results indicated the existence of genetic divergence for all traits analyzed, where additive effects were predominant. The high heterosis levels observed, mainly in Xanxerê, suggested the environmental influence on the manifestation of this genetic phenomenon. Populations revealed potential to be used in breeding programs; however, those more intensively submitted to selection could provide larger genetic progress, showing the importance of population improvement for the increment of the heterosis in maize.
Gottlieb, Andrea; Müller, Hans-Georg; Massa, Alicia N; Wanjugi, Humphrey; Deal, Karin R; You, Frank M; Xu, Xiangyang; Gu, Yong Q; Luo, Ming-Cheng; Anderson, Olin D; Chan, Agnes P; Rabinowicz, Pablo; Devos, Katrien M; Dvorak, Jan
Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.
Full Text Available Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.
Fernandes, Telmo J R; Oliveira, M Beatriz P P; Mafra, Isabel
Broa is a maize bread highly consumed and appreciated, especially in the north and central zones of Portugal. In the manufacturing of broa, maize flour and maize semolina might be used, besides other cereals such as wheat and rye. Considering the needs for genetically modified organism (GMO) traceability in highly processed foods, the aim of this work was to assess DNA degradation, DNA amplification and GMO quantification along breadmaking process of broa. DNA degradation was noticed by its decrease of integrity after dough baking and in all parts of bread sampling. The PCR amplification results of extracted DNA from the three distinct maize breads (broa 1, 2 and 3) showed that sequences for maize invertase gene and for events MON810 and TC1507 were easily detected with strong products. Real-time PCR revealed that quantification of GMO was feasible in the three different breads and that sampling location of baked bread might have a limited influence since the average quantitative results of both events after baking were very close to the actual values in the case of broa 1 (prepared with maize semolina). In the other two maize breads subjected to the same baking treatment, the contents of MON810 maize were considerably underestimated, leading to the conclusion that heat-processing was not the responsible parameter for that distortion, but the size of particle and mechanical processing of raw maize play also a major role in GMO quantification.
Full Text Available maize Zea mays Zea_mays_L.png Zea_mays_NL.png Zea_mays_S.png Zea_mays_NS.png http://biosciencedbc.jp/taxonom...y_icon/icon.cgi?i=Zea+mays&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Zea...+mays&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Zea+mays&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Zea+mays&t=NS ...
Kifle, Medhin H.; Laing, Mark D.
Laboratory, greenhouse, and field experiments were conducted at the University of KwaZulu-Natal, Pietermaritzburg, South Africa in the 2010/2011 and 2011∖2012 seasons to study the effects of eight strains of diazotrophic bacteria on the growth and yield of maize. Maize seeds were treated with Bacillus megaterium (V16), Pseudomonas sp. (StB5, A3, A6, and A61), Burkholderia ambifaria (V9), Enterobacter cloacae (L1) and Pantoea ananatis (LB5), aiming to stimulate plant growth, and maintain or increase yields while reducing the need for N fertilization. All the diazotrophic bacteria increased germination of maize seed, and Pseudomonas sp. (StB5) and B. megaterium (V16) significantly increased shoot length. Pseudomonas sp. (StB5), B. megaterium (V16), E. cloacae (L1), B. ambifaria (V9), and Pseudomonas sp. (A3) very significantly increased root length and seed vigor index. Under greenhouse conditions, plants treated with diazotrophic bacteria developed more leaf chlorophyll and greater dry weight, albeit not significantly (n.s.). In a field trial in 2010/2011, application of the best five diazotrophic bacteria, with or without 33% N-fertilizer, had no significant effect on germination, grain yield, dry weight, plant height and leaf chlorophyll. In the 2011/2012 growing season, at 60 days after planting (DAP), all the diazotrophic bacteria increased plant dry weights to equal that of the fertilized control (33%N-fertilizer) (n.s.). After inoculation with the diazotrophs alone increased plant heights (n.s.), and chlorophyll contents (n.s.). With the addition of 33%N-fertilizer at planting, the diazotrophs still caused increases of chlorophyll content relative to the control with 33%N (n.s.). It may be concluded that the tested diazotrophs alone may be beneficial for use on maize growth. PMID:27713756
Medhin Hadish Kifle
Full Text Available Laboratory, greenhouse, and field experiments were conducted at the University of KwaZulu-Natal, Pietermaritzburg, South Africa in the 2010 2011 and 2011 2012 seasons to study the effects of eight strains of diazotrophic bacteria on the growth and yield of maize. Maize seeds were treated with Bacillus megaterium (V16, Pseudomonas sp. (StB5, A3, A6, and A61, Burkholderia ambifaria (V9, Enterobacter cloacae (L1 and Pantoea ananatis (LB5, aiming to stimulate plant growth, and maintain or increase yields while reducing the need for N fertilization. All the diazotrophic bacteria increased germination of maize seed, and Pseudomonas sp. (StB5 and B. megaterium (V16 significantly increased shoot length. Pseudomonas sp. (StB5, B. megaterium (V16, E. cloacae (L1, B. ambifaria (V9 and Pseudomonas sp. (A3 very significantly increased root length and seed vigor index. Under greenhouse conditions, plants treated with diazotrophic bacteria developed more leaf chlorophyll and greater dry weight, albeit not significantly (n.s.. In a field trial in 2010/2011, application of the best five diazotrophic bacteria, with or without 33% N-fertilizer, had no significant effect on germination, grain yield, dry weight, plant height and leaf chlorophyll. In the 2011/2012 growing season, at 60 days after planting (DAP, all the diazotrophic bacteria increased plant dry weights to equal that of the fertilized control (33%N-fertilizer(n.s.. After inoculation with the diazotrophs alone increased plant heights (n.s., and chlorophyll contents (n.s.. With the addition of 33%N-fertilizer at planting, the diazotrophs still caused increases of chlorophyll content relative to the control with 33%N (n.s.. It may be concluded that the tested diazotrophs alone may be beneficial for use on maize growth.
Bentivenha, J P F; Baldin, E L L; Hunt, T E; Paula-Moraes, S V; Blankenship, E E
The western bean cutworm Striacosta albicosta (Smith), the fall armyworm Spodoptera frugiperda (J. E. Smith), and the corn earworm Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) are among the major lepidopteran pests of maize in the United States, belonging to the same guild and injuring the reproductive tissues of this crop. Here, intraguild competition of these lepidopterans on non-Bt maize was evaluated through survival analysis of each species under laboratory and field conditions. Competition scenarios were carried out in arenas containing maize silk or ear tissue, using larvae on different stadium of development. Fitness cost competition studies were conducted to examine the influence of intraguild competition and cannibalism and predation rates on larval development. The survival of S. albicosta competing with the other species was significantly lower than in intraspecific competition, even when the larvae were more developed than the competitor. For S. frugiperda, survival remained high in the different competition scenarios, except when competing in a smaller stadium with H. zea Larvae of H. zea had a high rate of cannibalism, higher survival when competing against S. albicosta than S. frugiperda, and reduced survival when the H. zea larvae were at the same development stadium or smaller than the competitors. Based on fitness cost results, the absence of a competitor for the feeding source may confer an advantage to the larval development of S. frugiperda and H. zea Our data suggest that S. frugiperda has a competitive advantage against the other species, while S. albicosta has the disadvantage in the intraguild competition on non-Bt maize.
Full Text Available Maize stem borer (MSB, Chilo partellus Swinhoe, Lepidoptera: Pyralidae is one of the most important insect pest of maize in Nepal. Host plant resistance is the cost-effective, ecologically sound and stable approach to reduce damage by stem borers. Forty four maize genotypes were screened for resistance to maize stem borer at the research field of National Maize Research Program, Rampur during spring seasons (March to June of two consecutive years 2013 and 2014. The maize genotypes were evaluated in randomized complete block design with three replications and data were collected on foliar damage rating, tunnel length and number of exit holes made by the borer. The foliar damage and tunnel length damage were significant for genotypes for both the years. The exit holes were not significant in 2013 but significant in 2014 ranging from 2-6 scale. The foliar rating ranged from 2 to 5.5 in 2013 and 1.1 to 4.5 in 2014 on a 1-9 rating scale. The highly resistant genotypes (10 cm scale. The least susceptible genotypes (<5 cm were RampurSO3F8, RampurSO3FQ02 and RampurS10F18. The genotypes having least exit holes (2.0 in 2014 were RampurSO3F8, RampurSO3FQ02, RampurS10F18. Thus less damage parameters were observed in R-POP-2, RML-5/RML-8, RampurSO3F8, RampurSO3FQ02 and RampurS10F18 and therefore they can be used as parents or as sources of resistance in breeding program.
W. Paul Williams
Full Text Available Aflatoxins, produced by the fungus Aspergillus flavus, occur naturally in maize. Contamination of maize grain with aflatoxin is a major food and feed safety problem and greatly reduces the value of the grain. Plant resistance is generally considered a highly desirable approach to reduction or elimination of aflatoxin in maize grain. In this investigation, a diallel cross was produced by crossing 10 inbred lines with varying degrees of resistance to aflatoxin accumulation in all possible combinations. Three lines that previously developed and released as sources of resistance to aflatoxin accumulation were included as parents. The 10 parental inbred lines and the 45 single crosses making up the diallel cross were evaluated for aflatoxin accumulation in field tests conducted in 2013 and 2014. Plants were inoculated with an A. flavus spore suspension seven days after silk emergence. Ears were harvested approximately 60 days later and concentration of aflatoxin in the grain determined. Parental inbred lines Mp717, Mp313E, and Mp719 exhibited low levels (3–12 ng/g of aflatoxin accumulation. In the diallel analysis, both general and specific combining ability were significant sources of variation in the inheritance of resistance to aflatoxin accumulation. General combining ability effects for reduced aflatoxin accumulation were greatest for Mp494, Mp719, and Mp717. These lines should be especially useful in breeding for resistance to aflatoxin accumulation. Breeding strategies, such as reciprocal recurrent selection, would be appropriate.
Wu, Felicia; Guclu, Hasan
Worldwide, food supplies often contain unavoidable contaminants, many of which adversely affect health and hence are subject to regulations of maximum tolerable levels in food. These regulations differ from nation to nation, and may affect patterns of food trade. We soughtto determine whether there is an association between nations' food safety regulations and global food trade patterns, with implications for public health and policymaking. We developed a network model of maize trade around the world. From maize import/export data for 217 nations from 2000-2009, we calculated basic statistics on volumes of trade; then examined how regulations of aflatoxin, a common contaminant of maize, are similar or different between pairs of nations engaging in significant amounts of maize trade. Globally, market segregation appears to occur among clusters of nations. The United States is at the center of one cluster; European countries make up another cluster with hardly any maize trade with the US; and Argentina, Brazil, and China export maize all over the world. Pairs of nations trading large amounts of maize have very similar aflatoxin regulations: nations with strict standards tend to trade maize with each other, while nations with more relaxed standards tend to trade maize with each other. Rarely among the top pairs of maize-trading nations do total aflatoxin standards (standards based on the sum of the levels of aflatoxins B(1), B(2), G(1), and G(2)) differ by more than 5 µg/kg. These results suggest that, globally, separate maize trading communities emerge; and nations tend to trade with other nations that have very similar food safety standards.
Full Text Available Agricultural development policy in Kenya has emphasised the use of incentives towards increased production and therefore self-sufficiency in maize which is a basic staple for most households. The channels used to provide incentives to maize farmers over the years include setting higher producer prices; subsidisation of inputs; provision of agricultural credit, research and extension services; construction and maintenance of roads, development of irrigation and water systems; legislative, institutional and macroeconomic reforms. Despite these efforts outputof maize has remained below domestic requirements in most years and the country continues to rely on imports to meet the deficits. Studies have assessed the responsiveness of maize to output price and reported inelastic responses and have recommended policies targeting non-price incentives to complement prices for the required increased production of maize. The studies, however, did not analyse the influence of the non-price incentives on the production of the crop. The findings of those studies are therefore deficient in explaining the relative importance of different non-price incentives and how they complement prices in influencing maize production in Kenya. This study investigated the response of maize production to both price and non-price incentives. The aim of this study was to ascertain the relative importance of non-price factors in influencing production of the crops as well as complementarity between price and non-price incentives. The findings show that maize production responds positively to its output price, development expenditures in agriculture, maize sales to marketing boards, growth in per capita GDP, liberalisation and governance reforms. However, maize production responds negatively to fertiliser price and unfavourable weather conditions. The response of maize output to its price is lower with rising inflation and grain market liberalisation.
Wu, Felicia; Guclu, Hasan
Worldwide, food supplies often contain unavoidable contaminants, many of which adversely affect health and hence are subject to regulations of maximum tolerable levels in food. These regulations differ from nation to nation, and may affect patterns of food trade. We soughtto determine whether there is an association between nations' food safety regulations and global food trade patterns, with implications for public health and policymaking. We developed a network model of maize trade around the world. From maize import/export data for 217 nations from 2000–2009, we calculated basic statistics on volumes of trade; then examined how regulations of aflatoxin, a common contaminant of maize, are similar or different between pairs of nations engaging in significant amounts of maize trade. Globally, market segregation appears to occur among clusters of nations. The United States is at the center of one cluster; European countries make up another cluster with hardly any maize trade with the US; and Argentina, Brazil, and China export maize all over the world. Pairs of nations trading large amounts of maize have very similar aflatoxin regulations: nations with strict standards tend to trade maize with each other, while nations with more relaxed standards tend to trade maize with each other. Rarely among the top pairs of maize-trading nations do total aflatoxin standards (standards based on the sum of the levels of aflatoxins B1, B2, G1, and G2) differ by more than 5 µg/kg. These results suggest that, globally, separate maize trading communities emerge; and nations tend to trade with other nations that have very similar food safety standards. PMID:23049773
Burger, H-M; Shephard, G S; Louw, W; Rheeder, J P; Gelderblom, W C A
Mycotoxin contamination of maize and maize-based food and feed products poses a health risk to humans and animals if not adequately controlled and managed. The current study investigates the effect of dry milling on the reduction of fumonisins (FB), deoxynivalenol (DON) and zearalenone (ZEA) in maize. Five composite samples, constructed to represent different mycotoxin contamination levels were degermed yielding degermed maize and the germ. The degermed maize was milled under laboratory conditions and four major milling fractions (SPECIAL, SUPER, semolina (SEM) and milling hominy feed) collected. The whole maize, degermed maize and total hominy feed (germ+milling hominy feed) were reconstructed to ensure homogenous samples for mycotoxin analyses. For comparison, commercial dry milling fractions (whole maize, SPECIAL, SUPER and total hominy feed), collected from three South African industrial mills, were analysed for the same mycotoxins and hence a more accurate assessment of the distribution between the different milling fractions. The distribution of the mycotoxins during the experimental dry milling of the degermed maize differs, with FB mainly concentrated in the SPECIAL, DON in the SEM whereas ZEA was equally distributed between the two milling fractions. Distribution of mycotoxins between the fractions obtained during commercial dry milling generally provided similar results with the total hominy feed containing the highest and the SUPER milling fractions the lowest mycotoxin levels although variations existed. Although milling is an effective way to reduce mycotoxins in maize, kernel characteristics and resultant fungal colonisation may impact on the distribution of specific mycotoxins among the different milling fractions. Differences in industrial dry milling practices and problems encountered in sampling bulk maize remain a large problem in assessing mycotoxin contamination in milling fractions intended for human consumption.
Full Text Available Worldwide, food supplies often contain unavoidable contaminants, many of which adversely affect health and hence are subject to regulations of maximum tolerable levels in food. These regulations differ from nation to nation, and may affect patterns of food trade. We soughtto determine whether there is an association between nations' food safety regulations and global food trade patterns, with implications for public health and policymaking. We developed a network model of maize trade around the world. From maize import/export data for 217 nations from 2000-2009, we calculated basic statistics on volumes of trade; then examined how regulations of aflatoxin, a common contaminant of maize, are similar or different between pairs of nations engaging in significant amounts of maize trade. Globally, market segregation appears to occur among clusters of nations. The United States is at the center of one cluster; European countries make up another cluster with hardly any maize trade with the US; and Argentina, Brazil, and China export maize all over the world. Pairs of nations trading large amounts of maize have very similar aflatoxin regulations: nations with strict standards tend to trade maize with each other, while nations with more relaxed standards tend to trade maize with each other. Rarely among the top pairs of maize-trading nations do total aflatoxin standards (standards based on the sum of the levels of aflatoxins B(1, B(2, G(1, and G(2 differ by more than 5 µg/kg. These results suggest that, globally, separate maize trading communities emerge; and nations tend to trade with other nations that have very similar food safety standards.
Zhang, Zhongbao; Li, Xianglong; Zhang, Chun; Zou, Huawen; Wu, Zhongyi
NUCLEAR FACTOR-Y (NF-Y) has been shown to play an important role in growth, development, and response to environmental stress. A NF-Y complex, which consists of three subunits, NF-YA, NF-YB, and, NF-YC, binds to CCAAT sequences in a promoter to control the expression of target genes. Although NF-Y proteins have been reported in Arabidopsis and rice, a comprehensive and systematic analysis of ZmNF-Y genes has not yet been performed. To examine the functions of ZmNF-Y genes in this family, we isolated and characterized 50 ZmNF-Y (14 ZmNF-YA, 18 ZmNF-YB, and 18 ZmNF-YC) genes in an analysis of the maize genome. The 50 ZmNF-Y genes were distributed on all 10 maize chromosomes, and 12 paralogs were identified. Multiple alignments showed that maize ZmNF-Y family proteins had conserved regions and relatively variable N-terminal or C-terminal domains. The comparative syntenic map illustrated 40 paralogous NF-Y gene pairs among the 10 maize chromosomes. Microarray data showed that the ZmNF-Y genes had tissue-specific expression patterns in various maize developmental stages and in response to biotic and abiotic stresses. The results suggested that ZmNF-YB2, 4, 8, 10, 13, and 16 and ZmNF-YC6, 8, and 15 were induced, while ZmNF-YA1, 3, 4, 6, 7, 10, 12, and 13, ZmNF-YB15, and ZmNF-YC3 and 9 were suppressed by drought stress. ZmNF-YA3, ZmNF-YA8 and ZmNF-YA12 were upregulated after infection by the three pathogens, while ZmNF-YA1 and ZmNF-YB2 were suppressed. These results indicate that the ZmNF-Ys may have significant roles in the response to abiotic and biotic stresses.
Full Text Available This paper explores the effects of maize processing on the carbonization and preservation of maize kernels in the archaeological record. The shift to processing maize with lime (known as hominy production in the Eastern Woodlands and nixtamalization in Mesoamerica in ancient times had the effect of making maize more nutritious through increasing the availability of calcium, niacin, dietary fiber, and essential amino acids. Less understood is how this process of cooking maize in a lime solution affects the archaeological preservation of maize; if there is a clear difference in the archaeological signature of maize remains that are and are not processed this way, then this process may be identifiable in the archaeological record. To this end, an experiment was constructed analyzing the variation in size between dried and alkali processed maize kernels before and after carbonization. Results indicate that alkali processed maize kernels are less likely to fragment during carbonization.
YAN Jian-bing; TANG Hua; HUANG Yi-qin; SHI Yong-gang; ZHENG Yong-lian; LI Jian-sheng
Plant height has become one of important agronomic traits with the increase of planting densityrecently and the rapid developments of molecular markers have provided powerful tools to localize importantagronomic QTL at the genomic level. The purposes of this investigation are to map plant height QTL with mo-lecular markers and to analyze their genetic effects in maize. An F2:3 population from an elite combination(Zong3 × 87-1) was utilized for evaluating plant height in two locations, Wuhan and Xiangfan, with a ran-domized complete block design. The mapping population included 266 F2:3 family lines. A genetic linkagemap, containing 150 SSR and 24 RFLP markers, was constructed, spanning a total of 2 531.6 cm with an av-erage interval of 14.5 cm. Totally 10 QTL affecting plant height were mapped on six different chromosomeswith the composite interval mapping. Seven of 10 QTL were detected in two locations. The contributions tophenotypic variations for the single QTL varied between 5.3 and 17.1%. Additive, partial dominance, domi-nance, and overdominance actions existed among all detected QTL affecting plant heights. A large number ofdigenic interactions for plant height were detected by two-way analyses of variance. 107 and 98 two-locus com-binations were found to be significant at a 0.01 probability level in two locations respectively. 23 of them weresimultaneously detected in both locations. They accounted for phenotypic variations of 4.5 -11%. It was no-ticed that a locus, umc1122, had digenic interactive effects with other four different loci for plant height,which distributed on three chromosomes. A few of plant height QTL was involved in significant digenic inter-actions, but most significant interactions occurred between markers that are not adjacent to mapped QTL.These results demonstrated that epistatic interactions might play an equal importance role as the single-locuseffects in determining plant height of maize.
The vasculature of plants act as a channel for transport of signal(s) that facilitate long-distance intraplant communication. In maize, Maize insect resistance1-Cysteine Protease (Mir1-CP), which has homology to papain-like proteases, provides defense to different feeding guilds of insect pests. Fur...
Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared to maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic ...
Effects of four coating formulations on maize production were studied. The results showec that all coating formulations had some effects on improving maize seedlings, strengthening the resistance againt diseases and pests and increasing the yields in dtifferent degrees, especially Paxil which increased the com yield by 12.0%, significantly higher than the control.
Lichota, J.; Grasser, Klaus D.
maize HMGA and five different HMGB proteins with mononucleosomes (containing approx. 165 bp of DNA) purified from micrococcal nuclease-digested maize chromatin. The HMGB proteins interacted with the nucleosomes independent of the presence of the linker histone H1, while the binding of HMGA...
Developmental changes occur in maize (Zea mays L.) as it transitions from juvenile stages to the mature plant. Changes also occur as newly formed cells mature into adult cells. Maize leaf blades, including the midribs and sheaths, undergo cell wall changes as cells transition to fully mature cell ty...
Maize is by quantity the most important C4 cereal crop in the US; however, future climate changes are expected to increase maize susceptibility to mycotoxigenic fungal pathogens and reduce productivity. While rising atmospheric [CO2] is a driving force behind the warmer temperatures and drought, whi...
The natural history of maize began nine thousand years ago when Mexican farmers started to collect the seeds of the wild grass, teosinte. Invaluable as a food source, maize permeated Mexican culture and religion. Its domestication eventually led to its adoption as a model organism, aided in large pa...
Full Text Available Sweet sorghum (Sorghum saccharatum silage, maize (Zea mays silage, and sorghum and maize (1:1 silage were investigated. The silages were analysed for chemical composition, quality and aerobic stability. Dry matter was the lowest (20.88% in sorghum silage and the highest (37.45% in maize silage. In sorghum silage, the concentration of crude ash and crude fibre was higher, and that of crude protein, crude fat and N-free extractives lower compared to maize silage. Neutral detergent fibre and acid detergent fibre were the highest in sorghum silage and the lowest in maize silage. The silages were dominated by lactic acid, with trace amounts of butyric acid. Maize silage was higher lactic acid and higher total acids than others. All silages were of very good quality according to Flieg-Zimmer scale. Silage pH ranged from 4.20 to 4.31. Sorghum silage was characterized by higher aerobic stability (81h compared to the other silages from maize (74h and sorghum and maize 1:1 (69h.
DONG Jian-nan; MA Yong-qiang; LIU Feng-mao; JIANG Nai-wen; JIAN Qiu
A rapid and reliable method was developed for analysis of ethephon residues in maize, in combination with the investigation of its dissipation in ifeld condition and stabilities during the sample storage. The residue analytical method in maize plant, maize kernel and soil was developed based on the quantiifcation of ethylene produced from the derivatization of ethephon residue by adding the saturated potassium hydroxide solution to the sample. The determination was carried out by using the head space gas chromatography with lfame ionization detector (HS-GC-FID). The limit of quantiifcation (LOQ) of the method for maize plant was 0.05, 0.02 mg kg–1 for maize kernel and 0.05 mg kg–1 for soil, respectively. The fortiifed recoveries of the method were from 84.6–102.6%, with relative standard deviations of 7.9–3.8%. Using the methods, the dissipation of ephethon in maize plant or soil was investigated. The half life of ethephon degradation was from 0.6 to 3.3 d for plant and 0.7 to 5.7 d for soil, respectively. The storage stabilities of ethephon residues were determined in fresh and dry kernels with homogenization and without homogenization process. And the result showed that ethephon residues in maize kernels were stable under –18°C for 6 mon. The results were helpful to monitor the residue dissipation of ethephon in the maize ecosystem for further ecological risk assessment.
Suverkropp, B.P.; Bigler, F.; Lenteren, van J.C.
Glue-sprayed maize plants were used to study dispersal behaviour of the egg parasitoid Trichogramma brassicae Bezdenko (Hymenoptera Trichogrammatidae) in maize fields. To estimate the distance covered during an initial flight, T. brassicae were studied in a field cage with 73 glue-sprayed plants. Mo
Lausser, Andreas; Kliwer, Irina; Srilunchang, Kanok-orn; Dresselhaus, Thomas
Pollen tube germination, growth, and guidance (progamic phase) culminating in sperm discharge is a multi-stage process including complex interactions between the male gametophyte as well as sporophytic tissues and the female gametophyte (embryo sac), respectively. Inter- and intra-specific crossing barriers in maize and Tripsacum have been studied and a precise description of progamic pollen tube development in maize is reported here. It was found that pollen germination and initial tube growth are rather unspecific, but an early, first crossing barrier was detected before arrival at the transmitting tract. Pollination of maize silks with Tripsacum pollen and incompatible pollination of Ga1s/Ga1s-maize silks with ga1-maize pollen revealed another two incompatibility barriers, namely transmitting tract mistargeting and insufficient growth support. Attraction and growth support by the transmitting tract seem to play key roles for progamic pollen tube growth. After leaving transmitting tracts, pollen tubes have to navigate across the ovule in the ovular cavity. Pollination of an embryo sac-less maize RNAi-line allowed the role of the female gametophyte for pollen tube guidance to be determined in maize. It was found that female gametophyte controlled guidance is restricted to a small region around the micropyle, approximately 50-100 microm in diameter. This area is comparable to the area of influence of previously described ZmEA1-based short-range female gametophyte signalling. In conclusion, the progamic phase is almost completely under sporophytic control in maize.
... 19 Customs Duties 1 2010-04-01 2010-04-01 false Certified seed potatoes, and seed corn or maize... Provisions Potatoes, Corn, Or Maize § 10.57 Certified seed potatoes, and seed corn or maize. Claim for classification as seed potatoes under subheading 0701.10.00, as seed corn (maize) under subheading...
Fourteen inbreds of maize were tested for the tolerance to chlorsulfuron with the method of seedling wa- ter culter. Significant difference existed in the tolerance of different type maize when tested with 1 and 2 μg/ kg of chlorsulfuron. The tolerance in different type maize wa dent＞flint＞sugar＞midiem＞super sugar pop. The tolerance of different inbred maize was negative correlated with the concentration concentration of chorsulfuron. The tolerance of hybrids might have some relation with their parent lines because in this test the hybrids response to chlorsulfuron showed significant positive correlation with that of tits female parent which suggented some maternal in inheritance and was not controlled by nuclear. It was possible that toler- ance of maize to chlorsulfuron was cytoplasm inheritance.
Full Text Available Maize is becoming more and more important crop for dairy farming as forage and as substrate for biogas production. The mycotoxin producing fungi can spoil feed, reduce cattle productivity and cause health problems. The aim of this research was to study the mycoflora of maize grains in order to clarify the fungal composition and verify the presence of potential mycotoxin producing fungi. The grain samples were collected from different maize hybrid performance trial in Research and Study farm “Vecauce” of Latvia University of Agriculture in 2014. The fungi from 14 genera were isolated from surface sterilized grains. The most abundant were Alternaria, Fusarium and Penicillium spp. Mycotoxin producing fungi are present in maize grain mycoflora, and there is a risk that maize production can contain mycotoxins.
Full Text Available Cowpea growth and yield performance when intercropped with maize was studied for 3 consecutive seasons under three spatial arrangements, i. e., maize planted at 90 x 30, 100 x 27, and 120 x 22.5 cm, with 2 rows of cowpea between the maize rows. Growth and yield of cowpea was improved significantly by widening maize intra-row distances as compared to the 90 x 30 cm spacing. Hence, intercropped cowpea needs to be sown where maize rows are wide apart, but the maize rows should not be too wide as this would lower the grain yield of maize.
Full Text Available In the course of a project aimed to isolate transfer cells-specific genes in maize endosperm we have identified the BETL9 gene. BETL9 encodes for a small protein very similar in sequence to the product of the barley transfer cell-specific gene end-1. Both BETL9 and END-1 proteins are lipid transfer proteins, but their function is currently unknown. In situ hybridization analysis confirms that the BETL9 gene is exclusively transcribed in the basal endosperm transfer cell layer during seed development since 10 days after pollination. However, immunolocalization data indicates that the BETL9 protein accumulates in the maternal placento-chalaza cells located just beside the transfer cell layer. This suggests that the BETL9 protein should be transported to the maternal side to exert its, still unknown, function. In addition, we have identified a second maize gene very similar in sequence to BETL9 and we have named it BETL9like. In situ hybridization shows that BETL9like is also specifically transcribed in the developing maize endosperm within the same time frame that BETL9, but in this case it is exclusively expressed in the aleurone cell layer. Consequently, the BETL9 and BETL9like genes are transcribed in a non-overlapping pattern on the outer surface of the maize endosperm. The BETL9 and BETL9like promoter sequences, fused to the GUS reporter gen, accurately reflected the expression pattern observed for the genes in maize. Finally, we have identified in the Arabidopsis genome a set of four genes orthologous to BETL9 and BETL9like and analysed the activity of their promoters in Arabidopsis transgenic plants carrying fusions of their promoter sequences to the GUS reporter. As in the case of the maize genes, the Arabidopsis orthologs showed highly complementary expression patterns.
In September 2011, high incidence of a new maize (Zea mays L.) disease was reported at lower elevations (1900 masl) in the Longisa division of Bomet County, Southern Rift Valley of Kenya. Later the disease was noted in Bomet Central division, spreading into the neighboring Chepalungu and Narok South...
LI Zhao-hui; GUO Xing-qi; YE Bao-hua; GUO Yan-kui
The ultrastruetural alteration of maize plants infected with the maize rough dwarf virus (MRDV) was studied with transmission electron microscopy. The results revealed that aggregates of virus particles, with a diameter of 60nm, were found in the root cell, and always distributed near the vacuole membrane. However, no such particles were checked in leaf cells. Moreover, no virus was observed in choroplasts,mitochondria nuclei, plasmodesmata or intercellular canal of all kinds of infected cells of maize, either.Structures of various organelles changed in the infected leaf and root cells of maize. An inward collapse and localized splitting of the tonoplast were observed, the chloropoast structure was destroyed by MRDV, and the number of destroyed or dysplasia chloroplast in leaf cells with serious symptoms was more than that in leaves without symptoms. The matrix of mitochondria in cells infected by MRDV decreased and some of them expanded and destructed. Nuclei was abnormal and the nuclear membrane was broken, In addition, the infected cells were characterized by a voluminous cytoplasm containing hypertrophied endoplasmic reticulum, with rich ribosome content and lots of starch grain.
Full Text Available A strain of maize dwarf mosaic virus related to sugarcane mosaic virus has been isolated from maize in Burundi. The properties (including electron microscopy and serology of the virus are described, and elements for a control strategy are reviewed.
杨宗举; 闫蕾; 宋梅芳; 苏亮; 孟凡华; 李红丹; 白建荣; 郭林; 杨建平
processes, phytochromes play pivotal roles in regulations of seed germination, plant height, flowering time, and shade-avoidance. In the grasses, three subfamilies are present:PHYA,PHYB andPHYC. In maize, an ancient genome duplication has increased the family member to six:PHYA1, PHYA2,PHYB1,PHYB2,PHYC1, andPHYC2. Phytochrome A facilitates the inhibition of hypocotyl elongation, opening of the api-cal hook, expansion of cotyledons, accumulation of anthocyanin and blocking of greening by continuous FR (FRc) light. In order to evaluate the light response capability and difference of transcription abundance betweenZmPHYA1 andZmPHYA2, we employed quantitative real-time PCR (qRT-PCR) assay to investigate the expression patterns ofZmPHYA1 andZmPHYA2 in the inbred line B73 and Mo17 with different light treatments. The results indicated that both ZmPHYA1 andZmPHYA2 had a high expression level in leaf and silk, and the transcription abundance ofZmPHYA1 was 2–8 times higher than that ofZmPHYA2. Inbred lines of both B73 and Mo17 possessed longer mesocotyls in dark, far-red and blue light conditions than in red or white light conditions. BothZmPHYA1 and ZmPHYA2 had a high expression level in far-red and blue lights and rapidly responded to dark-to-far-red and dark-to-blue transitions. ZmPHYA1 was more important under far-red light, so wasZmPHYA2 in blue light. Both of the genes could rapidly respond to transi-tions from dark to red or white light with similar expression pattern. The both genes also respond to long-day or short-day treatments, however the transcription abundance ofZmPHYA1was 2–5 times higher than that ofZmPHYA2during the treatments. All the results suggested that the transcription of bothZmPHYA1 andZmPHYA2 could rapidly responded to different light treatments;ZmPHYA1 might be more effective thanZmPHYA2 in crop improvement. Our results provide a theoretical basis for the function study and evaluation of light response ability for bothZmPHYA1 andZmPHYA2.
Jovanović Petar Lj.
Full Text Available Maize germ was obtained by wet-milling laboratory processing of domestic high-oil maize hybrids. After separation, the germ was subjected to extraction of maize oil. Fatty acid composition of maize germ oil was determined by gas chromatography. The results showed very high levels of unsaturated fatty acids and a constant sum of oleic and linoleic acids in oils of different maize hybrids.
Santiago, Rogelio; Cao, Ana; Butrón, Ana
Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects. PMID:26308050
Brandenburg, Jean-Tristan; Mary-Huard, Tristan; Rigaill, Guillem; Corti, Hélène; Vitte, Clémentine; Charcosset, Alain; Tenaillon, Maud I.
Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans. PMID:28301472
Messina, Carlos D; Podlich, Dean; Dong, Zhanshan; Samples, Mitch; Cooper, Mark
The effectiveness of breeding strategies to increase drought resistance in crops could be increased further if some of the complexities in gene-to-phenotype (G → P) relations associated with epistasis, pleiotropy, and genotype-by-environment interactions could be captured in realistic G → P models, and represented in a quantitative manner useful for selection. This paper outlines a promising methodology. First, the concept of landscapes was extended from the study of fitness landscapes used in evolutionary genetics to the characterization of yield-trait-performance landscapes for agricultural environments and applications in plant breeding. Second, the E(NK) model of trait genetic architecture was extended to incorporate biophysical, physiological, and statistical components. Third, a graphical representation is proposed to visualize the yield-trait performance landscape concept for use in selection decisions. The methodology was demonstrated at a particular stage of a maize breeding programme with the objective of improving the drought tolerance of maize hybrids for the US Western Corn-Belt. The application of the framework to the genetic improvement of drought tolerance in maize supported selection of Doubled Haploid (DH) lines with improved levels of drought tolerance based on physiological genetic knowledge, prediction of test-cross yield within the target population of environments, and their predicted potential to sustain further genetic progress with additional cycles of selection. The existence of rugged yield-performance landscapes with multiple peaks and intervening valleys of lower performance, as shown in this study, supports the proposition that phenotyping strategies, and the directions emphasized in genomic selection can be improved by creating knowledge of the topology of yield-trait performance landscapes.
CHEN Xuqing; ZHANG Xiaodong; LIANG Rongqi; ZHANG Liquan; YANG Fengping; CAO Mingqing
Maize intact C4-pepc gene was amplified through LA-PCR and successfully sub-cloned into modified vector pGreen0029 to form a stable expression construct named as Pbac214 (12 kb), which contains CaMV 35S promoter driven bar gene as selection marker. Comparing the cloned DNA sequences (6.7 kb) with published maize C4-pepc gene (GenBank accession E17154) sequences, the identity of DNA sequence alignment is 98.96%. There are only 49 differences between these two intact DNA sequences, of which 13 occur in the region of promoter, 18 in introns, and 18 in exons. The homology of Mrna sequence alignment is 99.38%, and the putative amino acids sequence identity is 99.38%. There are only 15 differences between these two Mrna, and these differences bring 4 sites mutant on the putative amino acids of PEPC protein. Through biolistic bombardment of PDS1000/He system, expression vector Pbac214 has been transformed into winter wheat. Southern blotting results show that the intact C4-pepc gene has been integrated into genome of winter wheat. SDS-PAGE analysis of leaf soluble protein in transgenic wheat showed that the intact C4-pepc gene was well transcribed, spliced and translated as in maize. The enzyme activity of leaf PEPC in transgenic wheat has been detected. The activities of leaf PEPC increased over 3-5 times in some transgenic plants. The data of photosynthesis rate and transpiration rate of transgenic wheat flag leaves showed that the C4-pepc gene can increase the photosynthesis rate and transpiration rate of transgenic wheat.
Fábia Giovana do Val de Assis
Full Text Available The objective of this study was to evaluate the effect of bacterial inoculants at two inoculation rates on chemical and biological characteristics of maize silage. The treatments consisted of two inoculating rates (5 and 6 log cfu g-1 of forage for each strain of lactic acid bacteria (LAB identified as Lactobacillus buchneri, L. hilgardii, or L. plantarum. The maize was ensiled in experimental PVC silos. Samples were taken for the determination of the contents of dry matter (DM, crude protein (CP, neutral detergent fiber (NDF, water-soluble carbohydrates (WSC, organic acids and alcohols, for the evaluation of the populations of lactic acid bacteria, yeasts, filamentous fungi, and for the determination of pH values during ensilage and after 30 or 90 days of fermentation. The doses of inoculants did not promote significant differences on the evaluated characteristics. There was effect of inoculants on acetic acid, 1.2-propanediol, LAB population, filamentous fungi, and pH value. No significant influence of the treatments with inoculants was observed in the variables DM, WSC, CP, lactic acid concentrations, or ethanol. The maximum temperature, i.e., the time to achieve the maximum temperature (TMT and aerobic stability (AS, was not influencied by treatments. However, a decrease in maximum temperature, an increase in TMT, and improvement in the AS were observed after 90 days of fermentation. These results proved the advantage of microbial inoculation. The treatments influenced LAB populations and filamentous fungi, but no effect was observed on the yeast population. The best inoculation dose is 6 cfu g-1 of forage because it provides higher reduction of filamentous fungi in maize silage, thereby decreasing the aerobic deterioration by these microorganisms.
Full Text Available In sSome filamentous fungi, the pathways related to the oxidative stress and oxylipins production are involved both in the process of host-recognition of the host that and in the pathogenic phase. In fact, recent studies have shown that the production of oxylipins in filamentous fungi, yeasts and chromists is also related to the development of the organism itself and to mechanisms of communication with the host at the cellular level. The oxylipins, also involved produced in by the host during defense reactions, are able to induce sporulation and to modulate regulate the biosynthesis of mycotoxins in numerous several pathogenic fungi, apparently replacing the endogenous ones. In A. flavus, the oxylipins play a crucial role as signals for the regulation regulatingof the biosynthesis of aflatoxins, the conidiogenesis and the formation of sclerotia.To investigate the involvement of the an oxylipins based cross-talk into Z. mays and A. flavus interaction, we analyzed the oxylipins profile of the wild type strain and of three mutants of A. flavus that are deleted at the Aflox1 gene level also during maize kernel invasion; Aflox1 encodes for a manganese lipoxygenase.A lipidomic approach has been addressed through the use of LC-ToF-MS, followed by a statistical analysis of the principal components (PCA. The results showed the existence of a difference between the oxylipins profile generated by the WT and the mutants onto challenged maize. In relation to this, aflatoxin synthesis which is largely hampered in vitro, is intriguingly restored. These results highlight the important role of maize oxylipin in driving secondary metabolism in A. flavus.
Joseph A Bedell
Full Text Available Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis.
Bedell, Joseph A; Budiman, Muhammad A; Nunberg, Andrew; Citek, Robert W; Robbins, Dan; Jones, Joshua; Flick, Elizabeth; Rholfing, Theresa; Fries, Jason; Bradford, Kourtney; McMenamy, Jennifer; Smith, Michael; Holeman, Heather; Roe, Bruce A; Wiley, Graham; Korf, Ian F; Rabinowicz, Pablo D; Lakey, Nathan; McCombie, W Richard; Jeddeloh, Jeffrey A; Martienssen, Robert A
Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis.
Zhang, Han; Dawe, R Kelly
It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat-maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.
Using maize(B73)seedlings as experimental materials,the photosynthetic efficiency and activities of SOD,POD and CAT of leaves were investigated under salt stress. The results showed that the low concentration of NaCl(100 mmol/L)had little impact on the photosynthetic efficiency of maize seedling leaves,but high concentrations of NaCl stress(200 mmol/L or more)could significantly affect on the photosynthetic efficiency. At the same time,the activity of antioxidant enzymes displayed a synthetic positively correlation. However,in response to high concentration of NaCl stress,the antioxidant enzyme system(SOD,POD and CAT)activity showed a decreasing trend after the first rise.%以玉米品种B73幼苗为试验材料，研究盐胁迫对其光合荧光和抗氧化酶活性的影响。结果表明：低浓度的盐胁迫（100 mmol/L）对玉米幼苗叶片的光合效率影响不大，但是高浓度的盐胁迫（200 mmol/L以上）对玉米幼苗叶片的光合效率影响明显，且随着时间的延长不断加剧。同时，体内叶片抗氧化酶的活性变化同光合作用成正相关，说明在盐胁迫情况下，玉米幼苗可以通过启动抗氧化酶的活性来应答盐胁迫。此外，在应答盐胁迫时，玉米幼苗体内抗氧化保护酶系统（SOD、POD、CAT）活性会呈现出先升高后降低的趋势。
Vargas, Walter A; Sanz-Martín, José M; Rech, Gabriel E; Armijos-Jaramillo, Vinicio D; Rivera, Lina P; Echeverria, María Mercedes; Díaz-Mínguez, José M; Thon, Michael R; Sukno, Serenella A
Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host's nucleus, as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein, identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems, and roots. Genetic, molecular, and biochemical studies confirmed that this effector targets the host's nucleus and defines a novel class of double-stranded DNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process, with evidence for episodes of positive selection. We detected CgEP1 homologs in several species of a grass-infecting lineage of Colletotrichum spp., suggesting that its function may be conserved across a large number of anthracnose pathogens. Our results demonstrate that effectors targeted to the host nucleus may be key elements for disease development and aid in the understanding of the genetic basis of anthracnose development in maize plants.
Full Text Available Postemergence applications of nicosulfuron can cause great damage to certain maize inbred lines and hybrids. Variation among different responses to nicosulfuron may be attributed to differential rates of herbicide metabolism. We employed RNA-Seq analysis to compare transcriptome responses between nicosulfuron-treated and untreated in both tolerant and susceptible maize plants. A total of 71.8 million paired end Illumina RNA-Seq reads were generated, representing the transcription of around 40,441 unique reads. About 345,171 gene ontology (GO term assignments were conducted for the annotation in terms of biological process, cellular component and molecular function categories, and 6413 sequences with 108 enzyme commission numbers were assigned to 134 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG metabolic pathways. Digital gene expression profile (DGE analysis using Solexa sequencing was performed within the susceptible and tolerant maize between the nicosulfuron-treated and untreated conditions, 13 genes were selected as the candidates most likely involved in herbicide metabolism, and quantitative RT-PCR validated the RNA-Seq results for eight genes. This transcriptome data may provide opportunities for the study of sulfonylurea herbicides susceptibility emergence of Zea mays.
Ghareeb, Hassan; Löfke, Christian; Teichmann, Thomas; Schirawski, Jan
The biotrophic fungus Sporisorium reilianum causes head smut of maize (Zea mays) after systemic plant colonization. Symptoms include the formation of multiple female inflorescences at subapical nodes of the stalk because of loss of apical dominance. By deletion analysis of cluster 19-1, the largest genomic divergence cluster in S. reilianum, we identified a secreted fungal effector responsible for S. reilianum-induced loss of apical dominance, which we named SUPPRESSOR OF APICAL DOMINANCE1 (SAD1). SAD1 transcript levels were highly up-regulated during biotrophic fungal growth in all infected plant tissues. SAD1-green fluorescent protein fusion proteins expressed by recombinant S. reilianum localized to the extracellular hyphal space. Transgenic Arabidopsis (Arabidopsis thaliana)-expressing green fluorescent protein-SAD1 displayed an increased number of secondary rosette-leaf branches. This suggests that SAD1 manipulates inflorescence branching architecture in maize and Arabidopsis through a conserved pathway. Using a yeast (Saccharomyces cerevisiae) two-hybrid library of S. reilianum-infected maize tissues, we identified potential plant interaction partners that had a predicted function in ubiquitination, signaling, and nuclear processes. Presence of SAD1 led to an increase of the transcript levels of the auxin transporter PIN-FORMED1 in the root and a reduction of the branching regulator TEOSINTE BRANCHED1 in the stalk. This indicates a role of SAD1 in regulation of apical dominance by modulation of branching through increasing transcript levels of the auxin transporter PIN1 and derepression of bud outgrowth. PMID:26511912
Kandianis, Catherine B; Michenfelder, Abigail S; Simmons, Susan J; Grusak, Michael A; Stapleton, Ann E
The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks.
Harrison, L.; Michaelsen, J.; Funk, C.; Husak, G.
We examined intraseasonal changes in maize phenology and heat stress exposure over the 1979-2008 period, using Mozambique meteorological station data and maize growth requirements in a growing degree-day model. Identifying historical effects of warming on maize growth is particularly important in Mozambique because national food security is highly dependent on domestic food production, most of which is grown in already warm to hot environments. Warming temperatures speed plant development, shortening the length of growth periods necessary for optimum plant and grain size. This faster phenological development also alters the timing of maximum plant water demand. In hot growing environments, temperature increases during maize pollination threaten to make midseason crop failure the norm. In addition to creating a harsher thermal environment, we find that early season temperature increases have caused the maize reproductive period to start earlier, increasing the risk of heat and water stress. Declines in time to maize maturation suggest that, independent of effects to water availability, yield potential is becoming increasingly limited by warming itself. Regional variations in effects are a function of the timing and magnitude of temperature increases and growing season characteristics. Continuation of current climatic trends could induce substantial yield losses in some locations. Farmers could avoid some losses through simple changes to planting dates and maize varietal types.
Terence Epule Epule
Full Text Available Climate projections in Sub-Saharan Africa (SSA forecast an increase in the intensity and frequency of droughts with implications for maize production. While studies have examined how maize might be affected at the continental level, there have been few national or sub-national studies of vulnerability. We develop a vulnerability index that combines sensitivity, exposure and adaptive capacity and that integrates agroecological, climatic and socio-economic variables to evaluate the national and spatial pattern of maize yield vulnerability to droughts in Uganda. The results show that maize yields in the north of Uganda are more vulnerable to droughts than in the south and nationally. Adaptive capacity is higher in the south of the country than in the north. Maize yields also record higher levels of sensitivity and exposure in the north of Uganda than in the south. Latitudinally, it is observed that maize yields in Uganda tend to record higher levels of vulnerability, exposure and sensitivity towards higher latitudes, while in contrast, the adaptive capacity of maize yields is higher towards the lower latitudes. In addition to lower precipitation levels in the north of the country, these observations can also be explained by poor soil quality in most of the north and socio-economic proxies, such as, higher poverty and lower literacy rates in the north of Uganda.
Meng, Qingfeng; Chen, Xinping; Lobell, David B.; Cui, Zhenling; Zhang, Yi; Yang, Haishun; Zhang, Fusuo
Climate change can reduce crop yields and thereby threaten food security. The current measures used to adapt to climate change involve avoiding crops yield decrease, however, the limitations of such measures due to water and other resources scarcity have not been well understood. Here, we quantify how the sensitivity of maize to water availability has increased because of the shift toward longer-maturing varieties during last three decades in the Chinese Maize Belt (CMB). We report that modern, longer-maturing varieties have extended the growing period by an average of 8 days and have significantly offset the negative impacts of climate change on yield. However, the sensitivity of maize production to water has increased: maize yield across the CMB was 5% lower with rainfed than with irrigated maize in the 1980s and was 10% lower (and even >20% lower in some areas) in the 2000s because of both warming and the increased requirement for water by the longer-maturing varieties. Of the maize area in China, 40% now fails to receive the precipitation required to attain the full yield potential. Opportunities for water saving in maize systems exist, but water scarcity in China remains a serious problem.
Full Text Available The research aimed to determine the effects of Si application on photosynthetic characteristics of maize on saline-alkaline soil, including photosynthetic rate (Pn, stomatal conductance (gs, transpiration rate (E, and intercellular CO2 concentration (Ci of maize in the field with five levels (0, 45, 90, 150, and 225 kg·ha−1 of Si supplying. Experimental results showed that the values of Pn, gs, and Ci of maize were significantly enhanced while the values of E of maize were dramatically decreased by certain doses of silicon fertilizers, which meant that Si application with proper doses significantly increased photosynthetic efficiency of maize in different growth stages under stressing environment of saline-alkaline soil. The optimal dose of Si application in this experiment was 150 kg·ha−1 Si. It indicated that increase in maize photosynthesis under saline-alkaline stress took place by Si application with proper doses, which is helpful to improve growth and yield of maize.
Xie, Zhiming; Song, Ri; Shao, Hongbo; Song, Fengbin; Xu, Hongwen; Lu, Yan
The research aimed to determine the effects of Si application on photosynthetic characteristics of maize on saline-alkaline soil, including photosynthetic rate (P n ), stomatal conductance (g s ), transpiration rate (E), and intercellular CO2 concentration (C i ) of maize in the field with five levels (0, 45, 90, 150, and 225 kg · ha(-1)) of Si supplying. Experimental results showed that the values of P n, g s, and C i of maize were significantly enhanced while the values of E of maize were dramatically decreased by certain doses of silicon fertilizers, which meant that Si application with proper doses significantly increased photosynthetic efficiency of maize in different growth stages under stressing environment of saline-alkaline soil. The optimal dose of Si application in this experiment was 150 kg · ha(-1) Si. It indicated that increase in maize photosynthesis under saline-alkaline stress took place by Si application with proper doses, which is helpful to improve growth and yield of maize.
Zaralis, K.; Nørgaard, P.; Helander, C.
Whole-crop maize silage as forage in diets of finishing cattle can promote high intakes and thus, enhances animal performance. In the present study we evaluated the effect of whole-crop maize maturity at harvest and the proportion of maize-silage in diets of finishing bulls, on feed intake...... of treatments, involving two maturity stages of maize at harvest (i.e. dough stage or dent stage) and two maize silage proportions (i.e. 100% maize silage or 50% maize and 50% grass silage). The diets were offered ad libitum as total mixed rations (TMRs) with inclusion of concentrates (i.e. rolled barley; dried...... distillers’ grain plus soluble; cold-pressed rapeseed cake) in a 40% proportion on DM basis. All animals were slaughtered at a target body weight of 630 kg. Bulls fed on diets containing maize silage as sole forage achieved higher live-weight gain (P
Fine mapping of Helminthosporium turcicum resistance gene Ht2 is extremely valuable for map-based cloning of the Ht2 gene, gaining a better knowledge of the distribution of resistance genes in maize genome and marker-assisted selection in maize breeding. An F2 mapping population was developed from a cross between a resistant inbred line 77Ht2 and a susceptible inbred line Huobai. With the aid of RFLP marker analyses, the Ht2 gene was mapped between the RFLP markers UMC89 and BNL2.369 on chromosome 8, with a genetic distance of 0.9 cM to BNL2.369. There was a linkage between SSR markers UMC1202, BNLG1152, UMC1149 and the Ht2 gene by SSR assay. Among the SSR markers, the genetic distance between UMC1149 and the Ht2 gene was 7.2 cM. By bulked segregant analysis 7 RAPD-amplified products which were probably linked to the Ht2 gene were selected after screening 450 RAPD primers and converted the single-copy ones into SCAR markers. Linkage analysis showed that the genetic distance between the SCAR marker SD-06633 and the Ht2 gene was 0.4 cM. From these results, a part of linkage map around the Ht2 gene was constructed.
Defang Gan; Fei Ding; Dan Zhuang; Haiyang Jiang; Tong Jiang; Suwen Zhu; Beijiu Cheng
Specific fragments of the sugarcane mosaic virus (SCMV) coat protein gene (cp) were amplified by reverse transcription-polymerase chain reaction and used to construct a marker free small interfering RNA complex expression vector against SCMV. In planta transformation was performed on maize (Zea mays) inbred line 8112 mediated by Agrobacterium tumefaciens. PCR and Southern blot analyses demonstrated successful integration of the cp segment into the 8112 genome. The in planta transformation frequency was 0.1%, and the cotransformed frequency with the cp and bar genes was 0.034%. Realtime quantitative PCR of samples from different transgenic plant organs showed that the expression of the cp gene fragment in transgenic plants was variable and that the highest expression level occurred in the tassels and leaves and the lowest expression occurred in the roots. Real-time quantitative PCR was also used to measure how gene expression in transgenic T2 generation plants inoculated with SCMV changes over time. The results showed that the hairpin RNA structure transcribed from the cp gene interfered with SCMV infection and transgenic maize lines were not equally effective in preventing SCMV infection. Our findings provide a valuable tool for controlling plant viruses using RNA interference and the posttranslational gene silencing approach.
Leonard, April; Holloway, Beth; Guo, Mei; Rupe, Mary; Yu, GongXin; Beatty, Mary; Zastrow-Hayes, Gina; Meeley, Robert; Llaca, Victor; Butler, Karlene; Stefani, Tony; Jaqueth, Jennifer; Li, Bailin
tassel-less1 (tls1) is a classical maize (Zea mays) inflorescence mutant. Homozygous mutant plants have no tassels or very small tassels, and ear development is also impaired. Using a positional cloning approach, ZmNIP3;1 (a NOD26-like intrinsic protein) was identified as the candidate gene for tls1. The ZmNIP3;1 gene is completely deleted in the tls1 mutant genome. Two Mutator-insertional TUSC alleles of ZmNIP3;1 exhibited tls1-like phenotypes, and allelism tests confirmed that the tls1 gene encodes ZmNIP3;1. Transgenic plants with an RNA interference (RNAi) construct to down-regulate ZmNIP3;1 also showed tls1-like phenotypes, further demonstrating that TLS1 is ZmNIP3;1. Sequence analysis suggests that ZmNIP3;1 is a boron channel protein. Foliar application of boron could rescue the tls1 phenotypes and restore the normal tassel and ear development. Gene expression analysis indicated that in comparison with that of the wild type or tls1 plants treated with boron, the transition from the vegetative to reproductive phase or the development of the floral meristem is impaired in the shoot apical meristem of the tls1 mutant plants. It is concluded that the tls1 mutant phenotypes are caused by impaired boron transport, and boron is essential for inflorescence development in maize.
Full Text Available Starch is an important reserve of carbon and energy in plants, providing the majority of calories in the human diet and animal feed. Its synthesis is orchestrated by several key enzymes, and the amount and structure of starch, affecting crop yield and quality, are determined mainly by starch synthase (SS activity. To date, five SS isoforms, including SSI-IV and Granule Bound Starch Synthase (GBSS have been identified and their physiological functions have been well characterized. Here, we report the identification of a new SS isoform in maize, designated SSV. By searching sequenced genomes, SSV has been found in all green plants with conserved sequences and gene structures. Our phylogenetic analysis based on 780 base pairs has suggested that SSIV and SSV resulted from a gene duplication event, which may have occurred before the algae formation. An expression profile analysis of SSV in maize has indicated that ZmSSV is mainly transcribed in the kernel and ear leaf during the grain filling stage, which is partly similar to other SS isoforms. Therefore, it is likely that SSV may play an important role in starch biosynthesis. Subsequent analysis of SSV function may facilitate understanding the mechanism of starch granules formation, number and structure.
Danilevskaya, Olga N; Meng, Xin; McGonigle, Brian; Muszynski, Michael G
The transition from vegetative to reproductive development is a critical turning point in a plant’s life cycle. It is now widely accepted that a leaf-borne signal, florigen, moves via the phloem from leaves to the shoot apical meristem to trigger its reprogramming to produce flowers. In part, the florigenic signal comprises a protein that belongs to the phosphatidylethanolamine-binding protein (PEBP) family that is present in all living organisms but displays diverse functions. The founding floral-promoting PEBP gene in Arabidopsis is FLOWERING LOCUS T (FT) whose functional homologs have been indentified in many flowering plants. We recently accumulated sufficient evidence to demonstrate the maize FT homolog ZCN8 has florigenic function. This task was particularly challenging due to the large number of FT-homologous genes in the maize genome. Here we show that ZCN8 function is more complex than simply regulating the floral transition. ZCN8 appears to play a pleiotropic role in the regulation of generalized growth of vegetative and reproductive tissues.
Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F
Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.
Yu, Xiaoming; Jiang, Lili; Wu, Rui; Meng, Xinchao; Zhang, Ai; Li, Ning; Xia, Qiong; Qi, Xin; Pang, Jinsong; Xu, Zheng-Yi; Liu, Bao
ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages. Independent ZmCHB101 RNA interference plant lines displayed abaxially curling leaf phenotype due to increase of bulliform cell numbers, and showed impaired development of tassel and cob. RNA-seq-based transcriptome profiling revealed that ZmCHB101 dictated transcriptional reprogramming of a significant set of genes involved in plant development, photosynthesis, metabolic regulation, stress response and gene expressional regulation. Intriguingly, we found that ZmCHB101 was required for maintaining normal nucleosome density and 45 S rDNA compaction. Our findings suggest that the SWI3 protein, ZmCHB101, plays pivotal roles in maize normal growth and development via regulation of chromatin structure.
Sánchez, Berta; Rasmussen, Anton; Porter, John Roy
and maize crop responses to temperature in different, but consistent, phenological phases and development stages. A literature review and data compilation of around 140 scientific articles have determined the key temperature thresholds and response to extreme temperature effects for rice and maize...... defined in all three crops. Anthesis and ripening are the most sensitive temperature stages in rice as well as in wheat and maize. We call for further experimental studies of the effects of transgressing threshold temperatures so such responses can be included into crop impact and adaptation models....
Xu, Jian; Thomsen, Mette Hedegaard; Thomsen, Anne Belinda
The potential of maize silage as a feedstock to produce bioethanol was evaluated in the present study. The hydrothermal pretreatment with five different pretreatment severity factors (PSF) was employed to pretreat the maize silage and compared in terms of sugar recovery, toxic test, and ethanol...... the liquors from the five conditions were not toxic to the Baker’s yeast. Pretreatment under 195°C for 7 min had the similar PSF with that of 185°C for 15 min, and both gave the higher ethanol concentration of 19.92 and 19.98 g/L, respectively. The ethanol concentration from untreated maize silage was only 7...
The maize R gene is said to show more phenotypic variation than any other locus in higher plants. The locus is organized on a modular basis. Individual units -- termed genic elements'' since they function as independent genes -- differ by regulating the presence, intensity and timing of anthocyanin pigmentation in different plant parts. A given allele may comprise only one genic element or, more commonly, an allele comprises a complex of elements, organized as a small gene family. Different numbers and combinations of even a few genic elements gives a large number of possible complexes. Following molecular cloning of R we concentrated effort initially on a genic element that confers strong pigmentation only to the kernel. The functional limits of this gene (R-sc:124) had been defined genetically by extensive mutagenesis with the transposable element Dissociation. Subsequently, a set of contiguous probes were prepared from a genomic clone of R-sc:124. This set of probes distinguishes among various R-genic elements, providing physical evidence on gene complexes whose overall organization had been determined genetically. Some surprises were in store, as detailed below. These same tools made it possible to analyze the effect of position of Ds insertion within R-sc:124 on spotting phenotype, germinal reversion rate and frequency of Ds excision. Furthermore, we are now able to address in much more detail some of the unique phenomena of R action, such as a difference in kernel phenotype when certain alleles are transmitted by ovules relative to sperm. The last category of objectives is discussed in the section entitled updated research plan.''
The maize R gene is said to show more phenotypic variation than any other locus in higher plants. The locus is organized on a modular basis. Individual units -- termed ``genic elements`` since they function as independent genes -- differ by regulating the presence, intensity and timing of anthocyanin pigmentation in different plant parts. A given allele may comprise only one genic element or, more commonly, an allele comprises a complex of elements, organized as a small gene family. Different numbers and combinations of even a few genic elements gives a large number of possible complexes. Following molecular cloning of R we concentrated effort initially on a genic element that confers strong pigmentation only to the kernel. The functional limits of this gene (R-sc:124) had been defined genetically by extensive mutagenesis with the transposable element Dissociation. Subsequently, a set of contiguous probes were prepared from a genomic clone of R-sc:124. This set of probes distinguishes among various R-genic elements, providing physical evidence on gene complexes whose overall organization had been determined genetically. Some surprises were in store, as detailed below. These same tools made it possible to analyze the effect of position of Ds insertion within R-sc:124 on spotting phenotype, germinal reversion rate and frequency of Ds excision. Furthermore, we are now able to address in much more detail some of the unique phenomena of R action, such as a difference in kernel phenotype when certain alleles are transmitted by ovules relative to sperm. The last category of objectives is discussed in the section entitled ``updated research plan.``
Valéria Aparecida Vieira Queiroz
Full Text Available The aim of this study was to characterize the Zn and Fe availability by phytic acid/Zn and phytic acid/Fe molar ratios, in 22 tropical maize inbred lines with different genetic backgrounds. The Zn and Fe levels were determined by atomic absorption spectrophotometry and the P through colorimetry method. Three screening methods for phytic acid (Phy analysis were tested and one, based on the 2,2'-bipyridine reaction, was select. There was significant variability in the contents of zinc (17.5 to 42 mg.kg-1, iron (12.2 to 36.7 mg.kg-1, phosphorus (230 to 400 mg.100 g-1, phytic acid (484 to 1056 mg.100 g-1, phytic acid P (140 to 293 mg.100 g-1 and available-P (43.5 to 199.5 mg.100 g-1, and in the available-P/total-P ratio (0.14 to 0.50, Phy/Zn (18.0 to 43.5 and Phy/Fe (16.3 to 45.5 molar ratios. Lines 560977, 560978 and 560982 had greater availability of Zn and lines 560975, 560977, 561010 and 5610111 showed better Fe availability. Lines 560975, 560977 and 560978 also showed better available-P/total-P ratio. Thus, the lines 560975, 560977 and 560978 were considered to have the potential for the development of cultivars of maize with high availability of Fe and/or Zn.
de Abreu, C S; Figueiredo, J E F; Oliveira, C A; Dos Santos, V L; Gomes, E A; Ribeiro, V P; Barros, B A; Lana, U G P; Marriel, I E
In the present study, we demonstrated the in vitro activity of endophytic phosphate-solubilizing bacteria (PSB). Fifty-five endophytic PSB that were isolated from sap, leaves, and roots of maize were tested for their ability to solubilize tricalcium phosphate and produce organic acid. Partial sequencing of the 16S rRNA-encoding gene showed that the isolates were from the genus Bacillus and different species of Enterobacteriaceae. The phosphate solubilization index on solid medium and phosphate solubilization in liquid medium varied significantly among the isolates. There was a statistically significant difference (P ≤ 0.05) for both, the values of phosphate-solubilizing activity and pH of the growth medium, among the isolates. Pearson correlation was statistically significant (P ≤ 0.05) between P-solubilization and pH (R = -0.38), and between the gluconic acid production and the lowering of the pH of the liquid medium at 6 (R = 0.28) and 9 days (R = 0.39). Gluconic acid production was prevalent in all the PSB studied, and Bacillus species were most efficient in solubilizing phosphate. This is the first report on the characterization of bacterial endophytes from maize and their use as potential biofertilizers. In addition, this may provide an alternative strategy for improving the phosphorus acquisition efficiency of crop plants in tropical soils.
Mendoza-Díaz, Sandra; Ortiz-Valerio, Ma del Carmen; Castaño-Tostado, Eduardo; Figueroa-Cárdenas, Juan de Dios; Reynoso-Camacho, Rosalía; Ramos-Gómez, Minerva; Campos-Vega, Rocio; Loarca-Piña, Guadalupe
Nixtamalization process is the first step to obtain maize based products, like tortillas; however, in both the traditional and commercial processes, white grain is generally preferred. Creole maize races, mainly pigmented varieties, have increasingly attention since these are rich in anthocyanins and carotenoids. The aim of this investigation was to evaluate the antioxidant and antimutagenic activity of rich anthocyanins and carotenoids extracts from creole maize races before (grain) and after (masa and tortilla) the nixtamalization process. Most anthocyanins and carotenoids were lost during nixtamalization. Before nixtamalization, blue and red genotypes contained either higher antioxidant capacity and anthocyanin contents (963 ± 10.0 and 212.36 ± 0.36 mg of cyanidin-3-glucoside eq/100 g, respectively) than the white and yellow genotypes. However, the highest carotenoid levels were displayed by red grains (1.01 ± 0.07 to 1.14 ± 0.08 μg of β-carotene eq/g extract). Anthocyanins losses were observed when the blue grains were processed into masa (83 %) and tortillas (64 %). Anthocyanins content correlated with antiradical activity (r = 0.57) and with 2-aminoanthracene -induced mutagenicity inhibition on TA98 and TA100 (r = -0.62 and r = -0.44, respectively). For white grains, nixtamalization also reduced carotenoids (53 to 56 %), but not antioxidant activity and 2-Aa-induced mutagenicity. Throughout the nixtamalization process steps, all the extracts showed antimutagenic activity against 2-aminoanthracene-induced mutagenicity (23 to 90 %), displaying higher potential to inhibit base changes mutations than frameshift mutations in the genome of the tasted microorganism (TA100 and TA98, respectively). The results suggest that even though there were pigment losses, creole maize pigments show antioxidant and antimutagenic activities after nixtamalization process.
O'Kennedy, Martha M; Stark, Hester C; Dube, Nosisa
Maize (Zea mays L.) is the most important cereal food crop in sub-Saharan Africa and Latin America, and a key feed crop in Asia, whereas pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food that supplies a major proportion of calories and protein to large segments of the populations living in the semi-arid tropical regions of Africa and Asia. The limitations of biological gene transfer with Agrobacterium tumefaciens specifically related to recalcitrant cereal crops, led to the development of alternative methods of which high-velocity microprojectiles, biolistic genetic transfer is the most successful and also the most widely employed. Agrobacterium facilitated transformation is the method of choice especially for deregulation of commercial transgenic food crop products, but biolistic-mediated transformation is still valid for proof of concept and functional genomics applications. Biolistic-mediated transformation and the production of transgenic plantlets via somatic embryogenesis of two maize strains viz. Hi-II (a laboratory strain) and M37W (a South African elite white maize genotype) as well as a pearl millet strain (842B) are described in this chapter. The stages described include: (1) proliferation of immature zygotic embryos for biolistic-mediated transformation, (2) induction and maintenance of transgenic embryogenic tissue on selection medium; (3) maturation (both morphological and physiological) of transgenic somatic embryos; and (4) germination of the somatic embryos to putative transgenic primary events. Maize and pearl millet cultures were regenerated via somatic embryogenesis as they are bipolar structures that shoot and root simultaneously. The culture media described in this chapter rarely induced or regenerated plantlets via organogenesis.
Haiping; Ding; Jian; Gao; Mao; Luo; Hua; Peng; Haijian; Lin; Guangsheng; Yuan; Yaou; Shen; Maojun; Zhao; Guangtang; Pan; Zhiming; Zhang
Given the important roles of miRNAs in post-transcriptional gene regulation, identification of differentially expressed miRNAs will facilitate the elucidation of molecular mechanisms underlying kernel development. In this study, we constructed a small RNA library to comprehensively represent the full complement of individual small RNAs and to characterize miRNA expression profiles in pooled ears of maize(Zea mays L.) at 10, 15,20, 22, 25 and 30 days after pollination(DAP). At least 21 miRNAs were differentially expressed. The differential expression of three of these miRNAs, i.e., miR528a, miR167a and miR160b, at each stage was verified by qRT-PCR. The results indicated that these miRNAs might be involved in kernel development. In addition, the predicted functions of target genes indicated that most of the target genes are involved in signal transduction and cell communication pathways, particularly the auxin signaling pathway. The expression of candidate germination-associated miRNAs was analyzed by hybridization to a maize genome microarray, and revealed differential expression of genes involved in plant hormone signaling pathways. This finding suggests that phytohormones play a critical role in the development of maize kernels. We found that in combination with other miRNAs, miR528a regulated a putative laccase, a Ring-H2 zinc finger protein and a MADS box-like protein, whereas miR167a and miR160b regulated multiple target genes,including ARF(auxin response factor), a member of the B3 transcription factor family. All three miRNAs are important for ear germination, development and physiology. The small RNA transcriptomes and mRNA obtained in this study will help us gain a betterunderstanding of the expression and function of small RNAs in the development of maize kernel.
GUAN Yi-Xin; WANG Bao-hua; FENG Yan; LI Ping
Humankind has been through different periods of agricultural improvement aiming at enhancing our food supply and the performance of food crops. In recent years, whole genome sequencing and deep understanding of genetic and epigenetic mechanisms have facilitated new plant breeding approaches to meet the chalenge of growing population, dwindling re-sources, and changing climate. Here we proposed a simple and fast molecular breeding method, marker-assisted reverse breeding (MARB), which wil revert any maize hybrid into inbred lines with any level of required similarity to its original parent lines. Since al the pericarp DNA of a hybrid is from the maternal parent, whereas one half of the embryo DNA is from the maternal parent and the other half from the paternal parent, so we ifrstly extract DNA from seed embryo and pericarp of a selected elite hybrid separately and then we derived the genotypes of the two parents with high-density single nucleotide polymorphism (SNP) chips. The folowing marker-assisted selection was performed based on an Ilumina low-density SNP chip designed with 192 SNPs polymorphic between the two parental genotypes, which were uniformly distributed on 10 maize chromosomes. This method has the advantages of fast speed, ifxed heterotic mode, and quick recovery of beneifcial parental genotypes compared to traditional pedigree breeding using elite hybrids. Meanwhile, MARB has the advantage of not requiring sophisticated transformation and double haploid (DH) technologies over RNA interference (RNAi)-mediated reverse breeding. In addition, MARB can also be used with feed corn harvested from big farms, which is often similar to F2 populations, and the relevant transgenes in the population can be eliminated by marker-assisted selection. As a result, the whole global commercial maize hybrids can be utilized as germplasm for breeding with MARB technology. Starting with an F2 population derived from an elite hybrid, our experiment indicates that with three
Full Text Available Drought is one of the most important factors contributing to crop yield loss. In order to develop maize varieties with drought tolerance, it is necessary to explore the genetic basis. Mapping quantitative trait loci (QTL that control the yield and associate agronomic traits is one way of understanding drought genetics. QTLs associated with grain yield (GY, leaf width (LW3, LW4 plant height (PH, ear height (EH, leaf number (NL, tassel branch number (TBN and tassel length (TL were studied with composite interval mapping. A total of 43 QTLs were detected, distributed on all chromosomes, except chromosome 9. Phenotypic variability determined for the identified QTLs for all the traits was in the range from 20.99 to 87.24%. Mapping analysis identified genomic regions associated with two traits in a manner that was consistent with phenotypic correlation among traits, supporting either pleiotropy or tight linkage among QTLs.
赛吉庆; 康良仪; 黄忠; 史春霖; 田波; 谢友菊
The 3’-terminal 1 279 nucleotide sequence of maize dwarf mosaic virus (MDMV) genome has been determined. This sequence contains an open reading frame of 1023 nudeotides and a 3’ -non-coding region of 256 nucleotides. The open reading frame includes all of the coding regions for the viral capsid protein (CP) and part of the viral nuclear inclusion protein (Nib). The predicted viral CP consists of 313 amino acid residues with a calculated molecular weight of 35400. The amino acid sequence of the viral CP derived from MDMV cDNA shows about 47%-54% homology to that of 4 other potyviruses. The viral CP gene was constructed in frame with the lacZ gene in pUC19 plasmid and expressed in E. coli cells. The fusion polypeptide positively reacted in Western blot with an antiserum prepared against the native viral CP.
Zhang, R; Walker, J C
The extracellular of the putative receptor-like protein kinase, ZmPK1, is related to the self-incompatibility locus (S-locus) genes of Brassica. We have isolated and characterized a genomic DNA clone of ZmPK1 and three additional genes from maize that are highly related to ZmPK1. These three S-locus related genes do not appear to have the protein kinase catalytic domain that is found in ZmPK1. One or more of these genes are expressed specifically in the silks. This initial description of S-locus related genes in monocotyledonous plants suggests that the S-locus domain may be involved in several different cellular functions in a wide variety of plants.
Cabanes, Didier; Sousa, Sandra; Cossart, Pascale
The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.
Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne
Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....
GUO Xing-qi; ZHU Xiao-ping; ZHANG Jie-dao; GUO Yan-kui
Ultrastructural alterations in foliar cells were studied in leaves of resistant maize varietyLuyu16 and susceptible maize inbred line Luyuan92 infected by maize dwarf mosaic virus Shandong isolate(MDMV-SD), respectively. The results showed that marked cytopathological alterations were observed both inresistant plants and in susceptible plants, compared with that in healthy plants. However, some ultrastructur-al alterations, which observed in resistant plants, were different from those in susceptible plants. In resistantplants, which infected with the virus, the main organelles, including chloroplasts and mitochondria, wereslightly destroyed, the amount of mitochondria and peroxisome were increased. A few or no plasmodesmatawere observed. There were three kinds of inclusions including pinwheel, bundle and laminated aggregate, andthe virus particles in the cytoplasm. In susceptible plants, which infected with the virus, the chloroplasts wereheavily disrupted, including thylakoid swelling and envelope broking. The virus particles were more than thosein the resistant variety. Four kinds of inclusions including pinwheel, bundle, laminated aggregate and highelecton-dense body appeared in cytoplasm. Plasmodesmata and plasma membrane were abundant, and therewere frequent invaginations of the plasma membrane that led to the formation of vesicles and myelin-likestructures.
Nozoye, Tomoko; Nakanishi, Hiromi; Nishizawa, Naoko K
To acquire iron (Fe), graminaceous plants secrete mugineic acid family phytosiderophores (MAs) (Takagi, 1976 ) through the MAs efflux transporter TOM1 (Nozoye et al., 2011 ) and take up Fe in the form of Fe(III)-MAs complexes through the Fe(III)-MAs transporter YS1 (Curie et al., 2001 ). Yellow stripe 1 (ys1) and ys3 are recessive mutants of maize (Zea mays L.) that result in symptoms typical of Fe deficiency, i.e., interveinal chlorosis of the leaves. The ys1 mutant is defective in the YS1 transporter and is therefore unable to take up Fe(III)-MAs complexes. While the ys3 mutant has been shown to be defective in MA release, the causative gene has not been identified. The objective of the present work was to identify the genes responsible for the ys1 and ys3 phenotypes, so as to extend our understanding of Fe homeostasis in maize by qRT-PCR. In agreement with previous reports, the expression level of YS1 was decreased in the ys1 mutant. Moreover, we identified that the expression level of a homolog of TOM1 in maize (ZmTOM1) was significantly decreased in the ys3 mutant. Here described the quality control and analysis that were performed on the dataset. The data is publicly available through the GEO database with accession number GSE44557. The interpretation and description of these data are included in a manuscript (Nozoye et al., 2013 ).
Using antiserum against expressed aquaporin fusion protein, GST-RD28, the distribution of aquaporin in the plasma membrane of maize root protoplasts has been examined under confocal laser scanning microscopy by indirect fluorescence staining. Results indicate that there are abundant aquaporins in maize roots, which are distributed in plasma membrane unevenly. Western blotting analysis of total protein solubilized from maize root plasma membrane shows that antiserum against GST-RD28 can cross-react with one protein around 55 ku. Another 28 ku protein can also be detected when the concentration of SDS and DTT in SDS-PAGE sample buffer is increased. The 55 and 28 ku proteins may be dimeric and monomeric of aquaporin respectively. Functional experiments show that aquaporin blocker HgCl2 and aquaporin antiserum can suppress the swelling of maize root protoplasts in hypotonic solution, indicating that aquaporin in plasma membrane of protoplast facilitates rapid transmembrane water flow.
Colombo. N * , Presello, D.A. , Kandus M. , G.E. Eyherabide and J.C. Salerno
Full Text Available Cytoplasmic male sterility (CMS is maternally inherited in most of higher plants species. Together with nuclear restorer genes (Rf, CMS cytoplasms contribute significantly to the efficient production of hybrid seed. Three main types of male sterile cytoplasms are known in maize: T, S and C, which can be distinguished by crossing with specific restorer lines. Recently, PCR markers have been developed allowing the identification of different cytoplasms quickly and accurately. Our objective was to classify the cytoplasm type of maize inbred lines used in our breeding program and F1s obtained from crosses between CMS lines and elite maize lines using PCR multiplex. A multiplex PCR protocol was optimized for our conditions. We obtained the molecular classification of the analyzed cytoplasms. The optimized protocol is a valuable tool to trace male sterile cytoplasms and determine hybrid seed purity in our maize breeding program.
Mayer, Frédéric; Gerin, Patrick A; Noo, Anaïs; Foucart, Guy; Flammang, Jos; Lemaigre, Sébastien; Sinnaeve, Georges; Dardenne, Pierre; Delfosse, Philippe
A large set of maize silage samples was produced to assess the major traits influencing the biomethane production of this crop. The biomass yield, the volatile solids contents and the biochemical methane potential (BMP) were measured to calculate the biomethane yield per hectare (average=7266m(3)ha(-1)). The most influential factor controlling the biomethane yield was the cropping environment. The biomass yield had more impact than the anaerobic digestibility. Nevertheless, the anaerobic digestibility of maize silages was negatively affected by high VS content in mature maize. Late maturing maize varieties produced high biomass yield with high digestibility resulting in high biomethane yield per hectare. The BMP was predicted with good accuracy using solely the VS content.
Rasmussen, Rie Romme; Rasmussen, Peter Have; Larsen, Thomas Ostenfeld
Penicillium roqueforti, Penicillium paneum, Monascus ruber, Alternaria tenuissima, Fusarium graminearum, Fusarium avenaceum, Byssochlamys nivea and Aspergillus fumigatus have previously been identified as major fungal contaminants of Danish maize silage. In the present study their metabolite...
Augusto Samuel Jiménez-González
Full Text Available Maize heat shock protein of 101 KDa (HSP101 is essential for thermotolerance induction in this plant. The mRNA encoding this protein harbors an IRES element in the 5'UTR that mediates cap-independent translation initiation. In the current work it is demonstrated that hsp101 IRES comprises the entire 5'UTR sequence (150 nts, since deletion of 17 nucleotides from the 5' end decreased translation efficiency by 87% compared to the control sequence. RNA structure analysis of maize hsp101 IRES revealed the presence of three stem-loops toward its 5' end, whereas the remainder sequence contains a great proportion of unpaired nucleotides. Furthermore, HSP90 protein was identified by mass spectrometry as the protein preferentially associated with the maize hsp101 IRES. In addition, it has been found that eIFiso4G rather than eIF4G initiation factor mediates translation of the maize hsp101 mRNA.
Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen
by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...
Sato, Shusei; Andersen, Stig Uggerhøj
The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...
Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi
A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize, 3272. We first attempted to obtain genome DNA from this maize using a DNeasy Plant Maxi kit and a DNeasy Plant Mini kit, which have been widely utilized in our previous studies, but DNA extraction yields from 3272 were markedly lower than those from non-GM maize seeds. However, lowering of DNA extraction yields was not observed with GM quicker or Genomic-tip 20/G. We chose GM quicker for evaluation of the quantitative method. We prepared a standard plasmid for 3272 quantification. The conversion factor (Cf), which is required to calculate the amount of a genetically modified organism (GMO), was experimentally determined for two real-time PCR instruments, the Applied Biosystems 7900HT (the ABI 7900) and the Applied Biosystems 7500 (the ABI7500). The determined Cf values were 0.60 and 0.59 for the ABI 7900 and the ABI 7500, respectively. To evaluate the developed method, a blind test was conducted as part of an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSDr). The determined values were similar to those in our previous validation studies. The limit of quantitation for the method was estimated to be 0.5% or less, and we concluded that the developed method would be suitable and practical for detection and quantification of 3272.
Osondu L. C.; Ugwuoke E.C; Chikelu C. C.; Eze N.N; Ukwuani S.T
Abstract Drying under direct sunlight is one of the oldest techniques used by mankind to preserve Agriculture based food and non-food products. This paper focused on the use of solar dryer to reduce the moisture content of Agriculture produce such as maize. The experiment performed showed the moisture content of maize reduced from 20 to 13. It was also observed that the temperature increased with time. The assumed maximum temperature of the collector plate in the experiment was 100.
Williams, Paul; Kucheryavskiy, Sergey V.
NIR hyperspectral imaging was evaluated to classify maize kernels of three hardness categories: hard, medium and soft. Two approaches, pixel-wise and object-wise, were investigated to group kernels according to hardness. The pixel-wise classification assigned a class to every pixel from individual...... and specificity of 0.95 and 0.93). Both feature extraction methods can be recommended for classification of maize kernels on production scale....
The food/feed quality of a variety of genetically modified (GM) maize expressing Cry1Ab Bt-toxin was tested over the life-cycle of Daphnia magna, an arthropod commonly used as model organism in ecotoxicological studies. Demographic responses were compared between animals fed GM or unmodified (UM) near isogenic maize, with and without the addition of predator smell. Age-specific data on survival and birth rates were integrated and analysed using life tables and Leslie matrices. Survival, fecun...
© 2015, Springer Science+Business Media New York. Relatively little work has been reported about flour changes during microwave irradiation. For this reason, maize flours were treated by microwave radiation at 400 W for 0.5, 1, 2 and 4 min, and their microstructure and physicochemical characteristics (X-ray diffractometry, differential scanning calorimetry and pasting properties) were analysed. Micrographs showed that maize flour treated by microwave radiation displayed less compacted particl...
Alana Poloni; Jan Schirawski
Cereal crop plants such as maize and sorghum are constantly being attacked by a great variety of pathogens that cause large economic losses. Plants protect themselves against pathogens by synthesizing antimicrobial compounds, which include phytoalexins. In this review we summarize the current knowledge on phytoalexins produced by sorghum (luteolinidin, apigeninidin) and maize (zealexin, kauralexin, DIMBOA and HDMBOA). For these molecules, we highlight biosynthetic pathways, known intermediate...
Vinícius Soares Sturza
Full Text Available Brazil is among the world's biggest maize producers and fall armyworm, Spodoptera frugiperda (Smith (Lepidoptera: Noctuidae, is the main insect pest on this crop in the country. Despite the importance of its natural enemies, there still is a lack of information about parasitoids species that attack this insect-pest, such as larval parasitoids. This research reports Euplectrus furnius Walker (Hymenoptera: Eulophidae parasitizing S. fugiperda larvae on maize crop in Brazil.
Wu, Tong; Huang, Honglin; Zhang, Shuzhen
To investigate the accumulation and phytotoxicity of technical hexabromocyclododecane (HBCD) in maize, young seedlings were exposed to solutions of technical HBCD at different concentrations. The uptake kinetics showed that the HBCD concentration reached an apparent equilibrium within 96hr, and the accumulation was much higher in roots than in shoots. HBCD accumulation in maize had a positive linear correlation with the exposure concentration. The accumulation of different diastereoisomers followed the order γ-HBCD>β-HBCD>α-HBCD. Compared with their proportions in the technical HBCD exposure solution, the diastereoisomer contribution increased for β-HBCD and decreased for γ-HBCD in both maize roots and shoots with exposure time, whereas the contribution of α-HBCD increased in roots and decreased in shoots throughout the experimental period. These results suggest the diastereomer-specific accumulation and translocation of HBCD in maize. Inhibitory effects of HBCD on the early development of maize followed the order of germination rate>root biomass≥root elongation>shoot biomass≥shoot elongation. Hydroxyl radical (OH) and histone H2AX phosphorylation (γ-H2AX) were induced in maize by HBCD exposure, indicative of the generation of oxidative stress and DNA double-strand breaks in maize. An OH scavenger inhibited the expression of γ-H2AX foci in both maize roots and shoots, which suggests the involvement of OH generation in the HBCD-induced DNA damage. The results of this study will offer useful information for a more comprehensive assessment of the environmental behavior and toxicity of technical HBCD.
Mário Vanoli Scatolino
Full Text Available Agricultural residues are materials generated in large quantities in Brazil and can accumulate to such extent as to cause environmental problems. Among agricultural residues, maize cob is one worthy of notice, and an alternative use for maize cob would be to produce particleboard panels in association with wood particles. This study aimed to evaluate the feasibility of using maize cob for production of particleboard panels. The following maize cob percentages were used: 0%, 25%, 50%, 75% and 100%, in association with particles of Pinus oocarpa wood. Panels were made with 8% of urea formaldehyde and 1% of paraffin (based on dry weight of particles. For compressing the panels, a pressure of 3.92 MPa was applied at a temperature of 160º C, for 8 minutes. Increased replacement of pinewood by maize cob residue promoted significant improvements to the properties water absorption after two hours of immersion, thickness swelling after two and after twenty-four hours of immersion. Mechanical properties had a decreasing correlation with the maize cob percentage being incorporated.
Edema, Mojisola O; Sanni, Abiodun I
This paper focuses on the functional properties of maize sour-dough microflora selected and tested for their use as starter cultures for sour maize bread. Lactic acid bacteria and yeasts isolated from spontaneously fermented maize dough were selected based on dominance during fermentation and presence at the end of fermentation. Functional properties examined included acidification, leavening and production of some antimicrobial compounds in the fermenting matrix. The organisms previously identified as Lactobacillus plantarum, Lb. brevis, Lb. fermentum, Lb. acidophilus, Pediococcus acidilactici, Leuconostoc mesenteroides and Leuconostoc dextranicum and Saccharomyces cerevisiae were used singly and as mixed cultures in the fermentation (fermentation time: 12h at 28+/-2 degrees C) of maize meal (particle size >0.2mm). The pH fell from an initial value of 5.62-3.05 in maize meals fermented with Lb. plantarum; 4.37 in L. dextranicum+S. cerevisiae compared with the value for the control (no starter) of 4.54. Significant differences (P dough were confirmed by their abilities to inhibit the growth of Salmonella typhi, Escherichia coli, Staphylococcus aureus and Aspergillus flavus from an initial inoculum concentration of 7 log cfu ml(-1)) for test bacteria and zone of inhibition of up to 1.33 cm for aflatoxigenic A. flavus. The findings of this study form a database for further studies on the development of starter cultures for sour maize bread production as an alternative bread specialty.
Moming Zhao; Shuzhen Zhang; Sen Wang; Honglin Huang
Uptake,translocation and debromination of three polybrominated diphenyl ethers(PBDEs),BDE-28,-47 and-99,in maize were studied in a hydroponic experiment.Roots took up most of the PBDEs in the culture solutions and more highly brominated PBDEs had a stronger uptake capability.PBDEs were detected in the stems and leaves of maize after exposure but rarely detected in the blank control plants.Furthermore,PBDE concentrations decreased from roots to stems and then to leaves,and a very clear decreasing gradient was found in segments upwards along the stem.These altogether provide substantiating evidence for the acropetal translocation of PBDEs in maize.More highly brominated PBDEs were translocated with more difficulty.Radial translocation of PBDEs from nodes to sheath inside maize was also observed.Both acropetal and radial translocations were enhanced at higher transpiration rates,suggesting that PBDE transport was probably driven by the transpiration stream.Debromination of PBDEs occurred in all parts of the maize,and debromination patterns of different parent PBDEs and in different parts of a plant were similar but with some differences.This study for the first time provides direct evidence for the acropetal translocation of PBDEs within plants,elucidates the process of PBDE transport and clarifies the debromination products of PBDEs in maize.
Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus
The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...
Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;
, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...
Full Text Available Analysis of factors affecting adoption of hybrid and open pollinated maize varieties had not been taken yet in Nepal. Viewing this fact, this study was undertaken consisting of four purposively selected VDCs from two central Terai districts, Bara and Sarlahi, of Nepal. A total of 110 maize growers including 86 adopters and 24 non adopters of hybrid maize varieties (adopters of open pollinated maize varieties were interviewed with the help of structured questionnaire. Results of t-test showed that adopters of hybrid maize varieties had significantly larger farm size and, size of maize farm, were more experienced on maize farming, and used significantly higher amount of chemical fertilizers but lower amount of organic manures than the non-adopters. Further, more adopters used irrigation water, pesticides and hired labor than the non-adopters. The result showed that a substantial proportion of land area grown to maize was cultivated to hybrid maize varieties with an adoption rate of 81.9 % while the adoption rate for open pollinated varieties was estimated as 18.1%. The results of the binary logistic regression analysis showed that adoption of hybrid maize was positively influenced by farm size, irrigation availability, farmer’s attitude towards insect and disease tolerance characteristics of hybrid maize, male headed family and credit availability in the surveyed area. However, farming experience on maize was negatively associated with the adoption of hybrid maize varieties.
Full Text Available Six pure lines of maize were tested in a randomized complete block design with three replication under irrigated and rainfed conditions. Genetic variation was found between the genotypes for yield potential (Yp stress yield (Ys, tolerance index (TOL, geometric mean productivity (GMP, harmonic mean (HM and stress tolerance index (STI. Stress tolerance index was corrected using a correction coefficient (Ki and thus a modified stress tolerance index (MSTI was introduced as the optimal selection criterion for drought-tolerant genotypes. The results of three-D plotting indicated that the most desirable genotype for irrigated and rainfed conditions was the genotype K1515, for non-stressed conditions K18 and for stress conditions K104/3, K760/7 and K126/10.
Entringer, G C; Guedes, F L; Oliveira, A A; Nascimento, J P; Souza, J C
Among the many implications of climatic change on agriculture, drought is expected to continue to have a major impact on agribusinesses. Leaf curling is an anatomical characteristic that might be potentially used to enhance plant tolerance to water deficit. Hence, we aimed to study the genetic control of leaf curl in maize. From 2 contrasting inbred lines for the trait, generations F1, F2, and the backcrosses were obtained. All of these generations were evaluated in a randomized block design with 2 replicates. Leaf curl samples were collected from 3 leaves above the first ear at the tasseling stage, and quantified by dividing the width of the leaf blade with natural curling against its extended width. The mean and variance components were estimated by the weighted least square method. It was found that the trait studied has predominance of the additive effects, with genetic control being attributed to few genes that favor selection and exhibit minimal influence from the environment.
Mumme, Jan; Eckervogt, Lion; Pielert, Judith; Diakité, Mamadou; Rupp, Fabian; Kern, Jürgen
Hydrochars were prepared by hydrothermal carbonization (HTC) of maize silage previously treated at 55 °C in a two-stage solid-state reactor system. The HTC was carried out in a 1-L stirred pressure reactor with pH regulation by citric acid. The treated silage carbonized at relatively mild conditions (190 °C, 2 h), and the hydrochars showed mainly amorphous macro-size features with a carbon content of 59-79% (ash-free, dry) and a higher heating value of 25-36 MJ kg⁻¹. Temperature was the main influencing factor. The surface area according to Brunauer-Emmett-Teller (BET) analysis was highest at 190 °C (12.3 m²) g⁻¹). Based on these results, the hydrochars are potentially interesting for applications such as an alternative fuel or a soil conditioner.
Full Text Available The centromere is a specialized chromosomal region identified as the major constriction, upon which the kinetochore complex is formed, ensuring accurate chromosome orientation and segregation during cell division. The rapid evolution of centromere DNA sequence and the conserved centromere function are two contradictory aspects of centromere biology. Indeed, the sole presence of genetic sequence is not sufficient for centromere formation. Various dicentric chromosomes with one inactive centromere have been recognized. It has also been found that de novo centromere formation is common on fragments in which centromeric DNA sequences are lost. Epigenetic factors play important roles in centromeric chromatin assembly and maintenance. Nondisjunction of the supernumerary B chromosome early prophase of meiosis I requires an active centromere. This review discusses recent studies in maize about genetic and epigenetic elements regulating formation and maintenance of centromere chromatin, as well as centromere behavior in meiosis.
Full Text Available This paper focuses on the effect of the different injection moulding parameters and storing methods on injection moulded thermoplastic maize starch (TPS. The glycerol and water plasticized starch was processed in a twin screw extruder and then with an injection moulding machine to produce TPS dumbbell specimens. Different injection moulding set-ups and storing conditions were used to analyse the effects on the properties of thermoplastic starch. Investigated parameters were injection moulding pressure, holding pressure, and for the storage: storage at 50% relative humidity, and under ambient conditions. After processing the mechanical and shrinkage properties of the manufactured TPS were determined as a function of the ageing time. While conditioning, the characteristics of the TPS changed from a soft material to a rigid material. Although this main behaviour remained, the different injection moulding parameters changed the characteristics of TPS. Scanning electron microscope observations revealed the changes in the material on ageing.
Pre-harvest contamination of forage maize by mycotoxin producing Fusarium species was investigated in the UK in 2011 and 2012. A total of 15 Fusarium species were identified from a collection of 1,761 Fusarium isolates recovered from maize stalks and kernels. This study characterized the diversity of Fusarium species present in forage maize in the UK. The predominant species detected were F. graminearum (32.9%) and F. culmorum (34.1%). Along with those species; F. avenacem, F. cerealis, F. equiseti, F. langsethiae, F. napiforme, F. oxysporum, F. poae, F. proliferatum, F. scripi, F. solani, F. subglutinans, F. tricinctum and, F. verticillioides were occasionally isolated. The trichothecene genotypes for F. graminearum were determined to be 84.9% deoxynivalenol (DON) and 15.0% nivalenol (NIV) while F. culmorum isolates were determined to have 24.9% DON and 75.1% NIV genotypes. A Bayesian model-based clustering method with nine variable number of tandem repeat markers was used to evaluate the population genetic structure of 277 F. graminearum isolates from the maize and wheat in the UK. There were three genetic clusters detected which were DON in maize, NIV in maize and DON in wheat. There were high admixture probabilities for 14.1% of the isolates in the populations. In conclusion, increased maize production in the UK and the high admixture rates in a significant portion of F. graminearum populations in maize and wheat will contribute to a new pathogen population which will further complicate breeding strategies for tolerance or resistance to this pathogen in both crops.
Carolina da Silva Siqueira
Full Text Available ABSTRACT tenocarpella maydis is one of the main fungi associated with maize seeds, being a causative agent of stalk and ear rot, a disease which causes considerable losses for crop-producing regions in Brazil. The organism is considered to be a pest, subject to sanitary standardisation in current programs of seed certification in the country. The aim of this study was to evaluate the transmission rate of the fungus from infected maize seeds. Seeds were inoculated with two isolates using a method of physiological conditioning, in which the seeds are kept in contact with colonies of the fungus for 24 (P1, 48 (P2, 72 (P3 and 96 (P4 hours. Two cultivars were used, one susceptible (C1 and one moderately resistant (C2, and the trial carried out at two temperatures (20 ºC and 25 ºC. The inoculated seeds were distributed individually into plastic cups containing substrate. The plants were evaluated daily for stand and the appearance of post-emergent symptoms. Based on the number of dead seeds, transmission rates reached a maximum of 90.5% at the P4 inoculum potential, this rate being greater than transmission rates achieved for symptomatic and asymptomatic infection in emerged plants. For the total transmission rate, transmission of the pathogen was seen at all inoculum potentials; these values varying from 25% for cultivar C2 at potential P1 and a temperature of 20 ºC, to 93% for cultivar C2 at potential P3 and a temperature of 25 ºC.
Santi, Simonetta; Locci, Geraldine; Monte, Rossella; Pinton, Roberto; Varanini, Zeno
An investigation was carried out to assess the effect of nitrate supply on the root plasma membrane (PM) H+-ATPase of etiolated maize (Zea mays L.) seedlings grown in hydroponics. The treatment induced higher uptake rates of the anion and the expression of a putative high-affinity nitrate transporter gene (ZmNRT2.1), the first to be identified in maize. Root PM H+-ATPase activity displayed a similar time-course pattern as that of net nitrate uptake and investigations were carried out to determine which of the two isoforms reported to date in maize, MHA1 and 2, responded to the treatment. MHA1 was not expressed under the conditions analysed. Genome analysis revealed that MHA2, described as the most abundant form in all maize tissues, was not present in the maize hybrid investigated, but a similar form was found instead and named MHA3. A second gene (named MHA4) was also identified and partially sequenced. Both genes, classified as members of the PM H+-ATPase subfamily II, responded to nitrate supply, although to different degrees: MHA4, in particular, proved more sensitive than MHA3, with a greater up- and down-regulation in response to the treatment. Increased expression of subfamily II genes resulted in higher steady-state levels of the enzyme in the root tissues and enhanced ATP-hydrolysing activity. The results support the idea that greater proton-pumping activity is required when nitrate inflow increases and suggest that nitrate may be the signal triggering the expression of the two members of PM H+-ATPase subfamily II.
Heckmann, Lars-Henrik [National Environmental Research Institute, Department of Terrestrial Ecology, Vejlsovej 25, PO Box 314, DK-8600 Silkeborg (Denmark); Griffiths, Bryan S. [Scottish Crop Research Institute, Department of Soil Plant Dynamics, Invergowrie, Dundee DD2 5DA (United Kingdom); Caul, Sandra [Scottish Crop Research Institute, Department of Soil Plant Dynamics, Invergowrie, Dundee DD2 5DA (United Kingdom); Thompson, Jacqueline [Scottish Crop Research Institute, Department of Soil Plant Dynamics, Invergowrie, Dundee DD2 5DA (United Kingdom); Pusztai-Carey, Marianne [Case Western Reserve University, Cleveland, OH 44106 (United States); Moar, William J. [Auburn University, Department of Entomology and Plant Pathology, Auburn, AL 36849 (United States); Andersen, Mathias N. [Danish Institute of Agricultural Sciences, Research Centre Foulum, PO Box 50, DK-8830 Tjele (Denmark); Krogh, Paul Henning [National Environmental Research Institute, Department of Terrestrial Ecology, Vejlsovej 25, PO Box 314, DK-8600 Silkeborg (Denmark)]. E-mail: email@example.com
Studies on the effect of genetically modified Bacillus thuringiensis (Bt) crops on true soil dwelling non-target arthropods are scarce. The objective of this study was to assess the influence of a 4-week exposure to two Bt maize varieties (Cry1Ab) Cascade and MEB307 on the collembolan Protaphorura armata. For comparison three non-Bt maize varieties, Rivaldo (isogenic to Cascade), Monumental (isogenic to MEB307) and DK242, and two control diets based on baker's yeast (uncontaminated and contaminated with Bt toxin Cry1Ab) were also tested. Due to a lower C:N ratio, individuals reared on yeast performed significantly better in all of the measured endpoints than those reared on maize. P. armata performed equally well when reared on two Bt and three non-Bt maize varieties. Although there were no negative effects of Bt maize in this experiment, we recommend future studies on Bt crops to focus on species interactions in long-term, multi-species experiments. - Protaphorura armata performed equally well when reared on two Bt and three non-Bt maize varieties.
Full Text Available Growing seed-maize is more profitable than mercantile maize, but also riskier, especially under less favourable soil conditions because parents of maize hybrids are less tolerant than their progeny to environmental stress, including plant nutrition problems. For this reason, we conducted the field experiment with P and K fertilization and a range of maize genotypes (parents of seed-maize on soil with moderate P and K supplies. Following application of 382 kg P and 726 kg K ha-1 , maize grain yields increased from 1.93 t ha-1 to 2.86 t ha-1 (3-year means. High correlations were found between grain yields of maize genotypes and nutrient concentrations in ear-leaf at silking stage (r = 0.82** for P and r = 0.90** for K. Based on these results, we could recommend the higher P and K fertilization of seed-maize crops on soils of similar chemical properties.
Full Text Available Maize (Zea mays L. is a host to numerous pathogenic species that impose serious diseases to its ear and foliage, negatively affecting the yield and the quality of the maize crop. A considerable amount of research has been carried out to elucidate mechanisms of maize-pathogen interactions with a major goal to identify defense-associated proteins. In this review, we summarize interactions of maize with its agriculturally important pathogens that were assessed at the proteome level. Employing differential analyses, such as the comparison of pathogen-resistant and susceptible maize varieties, as well as changes in maize proteomes after pathogen challenge, numerous proteins were identified as possible candidates in maize resistance. We describe findings of various research groups that used mainly mass spectrometry-based, high through-put proteomic tools to investigate maize interactions with fungal pathogens Aspergillus flavus, Fusarium spp., and Curvularia lunata, and viral agents Rice Black-streaked Dwarf Virus and Sugarcane Mosaic Virus.
Full Text Available Unleavened flat bread (chapatti was prepared from wheat (Tritium aestivum and maize (Zea mays composite flour. The wheat flours from mill and grindstone were collected from local market and blended with maize flour in 100:0, 90:10, 80:20 proportions. Technological and rheological studies revealed that gluten, falling number and water absorption values decreased with increased maize proportion. Increased dough development time by addition of 20% maize flour for either flour types was observed. Decrease in dough stability was observed by increased maize proportion in grindstone flour but in mill flour decrease with 10% maize and increase with 20% maize is noted. Overall Farinographic quality was highest in 20% blend of maize in grindstone flour. Chapatties were prepared and subjected to organoleptic tests by a panel of trained judges and 20% blend get maximum acceptability.
Marisol Cruz Requena
Full Text Available Polyembryony is the formation of several embryos in a seed and is present in many plants, included maize. In the present study the chemical, physical and rheological properties of nixtamalized maize flour, masa and tortilla of maize kernel with high polyembryony levels and brachytic population were evaluated and compared to three control populations. The nixtamalized maize flour and tortillas of brachytic population were similar to the control population in most of the tests. The retrogradation in nixtamalized maize flour of brachytic population was lower than the control nixtamalized maize flour showed 191.77 RVU; the protein content of nixtamalized maize flour of brachytic population was greater and content of ash in tortilla was lower than the controls. The flour made from maize brachytic population is an option for the flour and tortilla industry.
... Nonregulated Status of Maize Genetically Engineered With Tissue- Selective Glyphosate Tolerance Facilitating... to glyphosate in order to facilitate the production of hybrid maize seed. The petition has been... Pests,'' regulate, among other things, the introduction (importation, interstate movement, or...
Kadjo, Didier; Ricker-Gilbert, Jacob; Alexander, Corinne
This paper uses household survey data from Benin to evaluate how grain quality affects maize prices in rural markets of sub-Saharan Africa. Stated preference methods reveal that a 10% increase in insect damage results in a 9% maize price discount. However, revealed preference results from farmers involved in past market transactions indicate that this discount is only 3 %. Evidence also suggests that this discount is larger in periods of maize abundance than in the lean periods when maize is ...
Alessandro de Lucca e Braccini; LILIAN GOMES DE MORAES DAN; GLEBERSON GUILLEN PICCININ; LEANDRO PAIOLA ALBRECHT; MAURO CEZAR BARBOSA; ALEX HENRIQUE TIENE ORTIZ
The inoculation of seeds with the bacterium Azospirillum has been carried out in maize culture and other grasses. The application of growth bio-regulators is another technology whose results in maize culture have yet to become more widespread. Current study evaluates the agronomic effectiveness of seed inoculation with Azospirillum brasilense in maize, associated with the use of the growth regulator Stimulate ®. Triple hybrid maize CD 304 underwent the following treatments: 1 - control withou...
Mertens, Anouk; Mondelaers, Koen; Claeys, Dakerlia; Lauwers, Ludwig; Buysse, Jeroen
This short poster paper presents ongoing research on the informal silage maize trade between specialised dairy farmers in Flanders, Belgium. We investigated the influence of transaction costs on the silage maize trade market. Additionally, we investigated the influence of the establishment of biogas plants on silage maize prices. The research indicates that with increasing transaction costs, trade between farmers declines. Furthermore, in the presence of a biogas plant, silage maize prices in...