Wyatt, Robert; Odrzykoski, Ireneusz J.; Stoneburner, Ann; Bass, Henry W.; Galau, Glenn A.
Bryophytes are thought to be unique among land plants in lacking the important evolutionary process of allopolyploidy, which involves interspecific hybridization and chromosome doubling. Electrophoretic data show, however, that the polyploid moss Plagiomnium medium is an allopolyploid derivative of Plagiomnium ellipticum and Plagiomnium insigne, that P. medium has originated more than once from these progenitors, and that cross-fertilization results in interlocus genetic recombination. Evidence from restriction fragment length polymorphisms in chloroplast DNA implicates P. insigne as the female parent in interspecific hybridizations with P. ellipticum. Contrary to prevailing views, it appears that those evolutionary processes responsible for genetic differentiation and speciation in other land plants occur in the bryophytes as well. Images PMID:16593968
Worthington, Margaret; Heffelfinger, Christopher; Bernal, Diana; Quintero, Constanza; Zapata, Yeny Patricia; Perez, Juan Guillermo; De Vega, Jose; Miles, John; Dellaporta, Stephen; Tohme, Joe
Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR-BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR-BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR-BBML as candidate genes for the apomictic function of parthenogenesis. Copyright © 2016 by the Genetics Society of America.
Worthington, Margaret; Heffelfinger, Christopher; Bernal, Diana; Quintero, Constanza; Zapata, Yeny Patricia; Perez, Juan Guillermo; De Vega, Jose; Miles, John; Dellaporta, Stephen; Tohme, Joe
Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis. PMID:27206716
Neiva, João; Serrão, Ester A; Anderson, Laura; Raimondi, Peter T; Martins, Neusa; Gouveia, Licínia; Paulino, Cristina; Coelho, Nelson C; Miller, Kathy Ann; Reed, Daniel C; Ladah, Lydia B; Pearson, Gareth A
Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome. Here, using a congeneric phylogeographic approach, we investigated two monotypic and geographically complementary sister genera of north-east Pacific intertidal seaweeds (Hesperophycus and Pelvetiopsis), for which preliminary molecular tests revealed unexpected conflicts consistent with unrecognized cryptic diversity and hybridization. The three recovered mtDNA clades did not match a priori species delimitations. H. californicus was congruent, whereas widespread P. limitata encompassed two additional narrow-endemic species from California - P. arborescens (here genetically confirmed) and P. hybrida sp. nov. The congruence between the genotypic clusters and the mtDNA clades was absolute. Fixed heterozygosity was apparent in a high proportion of loci in P. limitata and P. hybrida, with genetic analyses showing that the latter was composed of both H. californicus and P. arborescens genomes. All four inferred species could be distinguished based on their general morphology. This study confirmed additional diversity and reticulation within NE Pacific Hesperophycus/Pelvetiopsis, including the validity of the much endangered, modern climatic relict P. arborescens, and the identification of a new, stable allopolyploid species (P. hybrida) with clearly discernable ancestry (♀ H. californicus x ♂ P. arborescens), morphology, and geographical distribution. Allopolyploid speciation is otherwise completely unknown in brown seaweeds, and its unique occurrence within this genus (P. limitata possibly representing a second example) remains enigmatic. The taxonomic separation of Hesperophycus and Pelvetiopsis is not supported and the genera should be synonymized; we retain only the latter. The transitional coastline between Point Conception and Monterey Bay represented a diversity hotspot for the genus and the likely sites of extraordinary evolutionary events of allopolyploid speciation at sympatric range contact zones. This study pinpoints how much diversity (and evolutionary processes) potentially remains undiscovered even on a conspicuous seaweed genus from the well-studied Californian intertidal shores let alone in other, less studied marine groups and regions/depths.
Díaz-Pérez, A J; Sharifi-Tehrani, M; Inda, L A; Catalán, P
The fine-leaved Loliinae is one of the temperate grass lineages that is richest in number of evolutionary switches from perennial to annual life-cycle, and also shows one of the most complex reticulate patterns involving distinct diploid and allopolyploid lineages. Eight distinct annual lineages, that have traditionally been placed in the genus Vulpia and in other fine-leaved ephemeral genera, have apparently emerged from different perennial Festuca ancestors. The phenotypically similar Vulpia taxa have been reconstructed as polyphyletic, with polyploid lineages showing unclear relationships to their purported diploid relatives. Interspecific and intergeneric hybridization is, however, rampant across different lineages. An evolutionary analysis based on cloned nuclear low-copy GBSSI (Granule-Bound Starch Synthase I) and multicopy ITS (Internal Transcribed Spacer) sequences has been conducted on representatives of most Vulpia species and other fine-leaved lineages, using Bayesian consensus and agreement trees, networking split graphs and species tree-based approaches, to disentangle their phylogenetic relationships and to identify the parental genome donors of the allopolyploids. Both data sets were able to reconstruct a congruent phylogeny in which Vulpia was resolved as polyphyletic from at least three main ancestral diploid lineages. These, in turn, participated in the origin of the derived allopolyploid Vulpia lineages together with other Festuca-like, Psilurus-like and some unknown genome donors. Long-distance dispersal events were inferred to explain the polytopic origin of the Mediterranean and American Vulpia lineages. Copyright © 2014 Elsevier Inc. All rights reserved.
Ferreira de Carvalho, Julie; Boutte, Julien; Bourdaud, Pierre; Chelaifa, Houda; Ainouche, Kader; Salmon, Armel; Ainouche, Malika
Allopolyploidy is a peculiar process entailing the cohabitation of two (or more) divergent genomes. Consequences on plant genomes are varied and can utlimately alter gene expression and regulatory interactions. Most studies have explored polyploid expression evolution in experimental controlled
Zozomová-Lihová, J.; Krak, Karol; Mandáková, T.; Shimizu, K. K.; Španiel, S.; Vít, Petr; Lysák, M. A.
Roč. 113, č. 5 (2014), s. 817-830 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : allopolyploidy * hybridization * microsatellites Subject RIV: EF - Botanics Impact factor: 3.654, year: 2014
Hemleben, V.; Kovařík, Aleš; Torres-Ruiz, R.A.; Volkov, R.A.; Beridze, T.
Roč. 5, č. 3 (2007), s. 277-289 ISSN 1477-2000 R&D Projects: GA ČR(CZ) GA521/04/0775 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : satellite DNA * evolution * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 2.818, year: 2007
Húska, Dalibor; Leitch, I. J.; de Carvalho, J.F.; Leitch, A.R.; Salmon, A.; Ainouche, M.; Kovařík, Aleš
Roč. 18, č. 8 (2016), s. 2137-2151 ISSN 1387-3547 R&D Projects: GA ČR(CZ) GA13-10057S Institutional support: RVO:68081707 Keywords : Spartina * Allopolyploidy * Cytotypes Subject RIV: BO - Biophysics Impact factor: 2.473, year: 2016
Introduction. The key role of polyploidy in the evolution of plants has been long recognized by biologists. (see Matsuoka et al. 2014 for a review). Allopolyploidy consists in two major events starting with the hybridization of two or more divergent genomes into a single nucleus, followed by polyploidization (Stebbins 1971).
Marcussen, T.; Jakobsen, K. S.; Danihelka, Jiří; Ballard, H. E.; Blaxland, K.; Brysting, A. K.; Oxelman, B.
Roč. 61, č. 1 (2012), s. 107-126 ISSN 1063-5157 R&D Projects: GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : allopolyploidy * BEAST * homoeolog loss Subject RIV: EF - Botanics Impact factor: 12.169, year: 2012
Bendiksby, M.; Tribsch, A.; Borgen, L.; Trávníček, Pavel; Brysting, A. K.
Roč. 191, č. 4 (2011), s. 1150-1167 ISSN 0028-646X Institutional research plan: CEZ:AV0Z60050516 Keywords : allopolyploidy * Galeopsis * molecular phylogenentics Subject RIV: EF - Botanics Impact factor: 6.645, year: 2011
Książczyk, T.; Kovařík, Aleš; Eber, F.; Huteau, V.; Crhák Khaitová, Lucie; Tesaříková, Zuzana; Coriton, O.; Chevre, A.-M.
Roč. 120, č. 6 (2011), s. 557-571 ISSN 0009-5915 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * ribosomal RNA * expression Subject RIV: BO - Biophysics Impact factor: 3.847, year: 2011
Leitch, I.J.; Hanson, L.; Lim, K.Y.; Kovařík, Aleš; Chase, M.W.; Clarkson, J.J.; Leitch, A.R.
Roč. 101, č. 6 (2008), s. 805-814 ISSN 0305-7364 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : genome size * allopolyploidy * evolution-Nicotiana Subject RIV: BO - Biophysics Impact factor: 2.755, year: 2008
Krak, Karol; Vít, Petr; Belyayev, Alexander; Douda, Jan; Hreusová, Lucia; Mandák, Bohumil
Roč. 11, č. 8 (2016), s. 1-22, č. článku e0161063. E-ISSN 1932-6203 R&D Projects: GA ČR GA13-02290S Institutional support: RVO:67985939 Keywords : Chenopodium * allopolyploidy * evolution Subject RIV: EF - Botanics Impact factor: 2.806, year: 2016
Nov 24, 2017 ... Journal of Genetics, Vol. 96, No. 5, November 2017, pp. 753–763. © Indian Academy .... some studies, allopolyploidy in Primula, and. Darwinian fitness? Here Haldane neatly con- joins Darwin ... Haldane's interest in genetics went back to his child- hood, and he was one of the first to report linkage (though.
Renny-Byfield, S.; Chester, M.; Kovařík, Aleš; Le Comber, S.C.; Grandbastien, M.-A.; Deloger, M.; Nichols, R.A.; Macas, Jiří; Novák, Petr; Chase, M.W.; Leitch, A.R.
Roč. 28, č. 10 (2011), s. 2843-2854 ISSN 0737-4038 R&D Projects: GA MŠk(CZ) OC10037 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z50510513 Keywords : allopolyploidy * evolution * genome structure Subject RIV: BO - Biophysics Impact factor: 5.550, year: 2011
Kovařík, Aleš; Nešpor Dadejová, Martina; Lim, Y.K.; Chase, M.W.; Clarkson, J.J.; Knapp, S.; Leitch, A.R.
Roč. 101, č. 6 (2008), s. 815-823 ISSN 0305-7364 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : rDNA * allopolyploidy * evolution-Nicotiana Subject RIV: BO - Biophysics Impact factor: 2.755, year: 2008
Lim, K.Y.; Soltis, D.E.; Soltis, P.S.; Tate, J.; Matyášek, Roman; Šrubařová, Hana; Kovařík, Aleš; Pires, J.Ch.; Xiong, Z.; Leitch, A.R.
Roč. 3, č. 10 (2008), s. 1-13 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * chromosomes * evolution Subject RIV: BO - Biophysics
Full Text Available The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy, is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH and genomic in situ hybridisation (GISH have been applied to: 1 studies of interspecific hybridisation and polyploidy in nature, 2 analyses of phylogenetic relationships between species, 3 genetic mapping and 4 analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
Matyášek, Roman; Tate, J. A.; Lim, Y.K.; Šrubařová, Hana; Koh, J.; Leitch, A.R.; Soltis, D.E.; Soltis, P.S.; Kovařík, Aleš
Roč. 176, č. 4 (2007), s. 2509-2519 ISSN 0016-6731 R&D Projects: GA ČR(CZ) GA204/05/0687; GA ČR(CZ) GA521/07/0116; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : rDNA silencing * nucleolar dominance * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 4.001, year: 2007
Lim, K.Y.; Matyášek, Roman; Kovařík, Aleš; Leitch, A.
Roč. 100, č. 2 (2007), s. 219-224 ISSN 0305-7364 R&D Projects: GA ČR(CZ) GA521/07/0116; GA ČR(CZ) GA204/05/0687; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * evolution * rDNA * Iris Subject RIV: BO - Biophysics Impact factor: 2.939, year: 2007
Kovařík, Aleš; Pires, J. C.; Leitch, A. R.; Lim, K. Y.; Sherwood, A.M.; Matyášek, Roman; Rocca, J.; Soltis, D. E.; Soltis, P. S.
Roč. 169, č. 2 (2005), s. 931-944 ISSN 0016-6731 R&D Projects: GA ČR(CZ) GA521/04/0775; GA ČR(CZ) GA204/05/0687; GA AV ČR(CZ) IBS5004010 Institutional research plan: CEZ:AV0Z50040507 Keywords : rDNA * genes homogenization * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 4.289, year: 2005
Matyášek, Roman; Fulneček, Jaroslav; Leitch, A.R.; Kovařík, Aleš
Roč. 192, č. 3 (2011), s. 747-759 ISSN 0028-646X R&D Projects: GA ČR(CZ) GA206/09/1751; GA ČR(CZ) GAP501/10/0208; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA-curvature * subtelomeric satellite repeats * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 6.645, year: 2011
Petit, M.; Guidat, C.; Daniel, J.; Montoriol, E.; Bui, Q.T.; Lim, K.Y.; Kovařík, Aleš; Leitch, A.R.; Grandbastien, M.-A.; Mhiri, C.
Roč. 186, č. 1 (2010), s. 135-147 ISSN 0028-646X R&D Projects: GA MŠk(CZ) MEB020823; GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * evolution * retrotransposition Subject RIV: AQ - Safety, Health Protection, Human - Machine Impact factor: 6.516, year: 2010
Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes
Fulneček, Jaroslav; Matyášek, Roman; Kovařík, Aleš
Roč. 281, č. 4 (2009), s. 407-420 ISSN 1617-4615 R&D Projects: GA ČR(CZ) GA204/06/1432; GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : cytosine methylation * DNA (cytosine-5) methyltransferase * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 2.579, year: 2009
Ramsey, Justin; Ramsey, Tara S
Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions-as achieved from divergence of physiological and life-history traits-but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910 s-1930 s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930 s-1950 s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940 s and 1950 s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s-1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990 s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical
Karlin, Eric F; Boles, S B; Ricca, M; Temsch, E M; Greilhuber, J; Shaw, A J
This paper documents the occurrence of allotriploidy (having three differentiated genomes) in gametophytes of two Southern Hemisphere Sphagnum species (S. australe, S. falcatulum). The pattern of microsatellite alleles indicates that both species are composed of a complex of allodiploid and allotriploid gametophytes, with the latter resulting from two allopolyploidization events. No haploid (n = x) gametophytes were found for either species. The ploidal levels suggested by the pattern of microsatellite alleles were confirmed by flow cytometry and Feulgen DNA image densitometry. For both S. australe and S. falcatulum, the respective allodiploid plants (or their ancestors) are one of the parent species of the allotriploid plants. This is the first report of triploidy in Sphagnum gametophytes occurring in nature and also the first report of the presence of three differentiated genomes in any bryophyte. It is also the first report of intersectional allopolyploidy in Sphagnum, with S. australe appearing to have parental species from Sphagnum sections Rigida and Sphagnum, and S. falcatulum having parental species from Sphagnum sections Cuspidata and Subsecunda. In both species, the allotriploid cytotypes were the most prevalent cytotype on the South Island of New Zealand. The pattern of microsatellite alleles shows the presence of two genetically distinct populations of allodiploid S. australe, possibly indicating multiple origins of polyploidy for that allodiploid cytotype. Morphological evidence is also highly indicative of recurrent polyploidy in the allotriploid cytotype of S. falcatulum. Allopolyploidy has clearly played a major evolutionary role in these two Southern Hemisphere taxa. This study, in conjunction with other recent research, indicates that allopolyploidy is a common, if not the predominant, form of polyploidy in Sphagnum.
The role of cytogenetics in plant domestication is not as direct as that of plant breeding, agronomy or crop botany. Five major areas of cytogenetic interest in plant domestication are distinguished: analysis of the genetic structure of the species and its relation with other species, including genome analysis; monitoring of chromosomal, including meiotic, consequences of drastic genetic alterations such as artificial mutations (including somaclonal variation) and interspecific hybridization (including complete and partial protoplast fusion); induction, monitoring and adjustment of auto- and allopolyploidy; introduction of alien chromosome segments by meiotic manipulation and translocation; adjustment of the genetic transmission system, such as the construction of systems for hybrid varieties, allopolyploidization of (partial) autopolyploids or non-functional allopolyploids and permanent complex translocation heterozygotes. It is concluded that the last three areas are of interest only in the context of large programmes with sufficient and guaranteed input and continuity. (author). 23 refs
F. Douglas Wilson
Full Text Available Hibiscus section Furcaria is a natural group of plants that presently includes 109 recognized taxa. Taxa are found in subsaharan Africa, India, southeastern Asia, Malesia, Australia, islands of the Pacific basin, the Caribbean, North, Central, and South America. The basic chromosome number is x = 18. In nature, ploidy levels range from diploid to decaploid. The taxa exhibit a remarkable amount of genome diversity. At least 13 genomes have been identified, some distributed widely and others with more restricted distributions. No modern taxonomic monograph ofHibiscus section Furcaria exists, but a number of regional studies have appeared that are essentially global in extent. Also, a number of studies of chromosome numbers and genome relationships have been published. The present paper includes a census of all the presently accepted taxa, the geographical distribution of each taxon, and chromosome numbers and genome designations of the 49 taxa for which the information is available. Important mechanisms of speciation include genome divergence at the diploid level, followed by hybridization and allopolyploidy, significant species radiation at the tetraploid and hexaploid levels, and the development of even higher levels of allopolyploids.
Scott, Alison Dawn; Stenz, Noah W M; Ingvarsson, Pär K; Baum, David A
Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.
Won, Hyosig; Renner, Susanne S
We analyze the structure of the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA in the gymnosperm Gnetum, using a phylogenetic framework derived mainly from an intron in the nuclear low-copy LEAFY gene. Gnetum comprises 25-35 species in South America, Africa, and Asia, of which we sampled 16, each with two to six clones. Criteria used to assess ITS functionality were highly divergent nucleotide substitution, GC content, secondary structure, and incongruent phylogenetic placement of presumed paralogs. The length of ITS1 ranged from 225 to 986 bp and that of ITS2 from 259 to 305 bp, the largest ranges so far reported from seed plants. Gnetum ITS1 contains two informative sequence motifs, but different from other gymnosperms, there are only few and short (7-13 bp) tandem repeats. Gnetum ITS2 contains two structural motifs, modified in different clades by shortening of stems and loops. Conspecific sequences grouped together except for two recombinant pseudogenes that had ITS1 of one clade and ITS2 of another. Most of the pseudogenic ITS copies, paralogs, and putative chimeras occurred in a clade that according to a fossil-calibrated chloroplast-DNA clock has an age of a few million years. Based on morphology and chromosome numbers, the most plausible causes of the observed high levels of ITS polymorphism are hybridization, allopolyploidy, and introgression.
Coughlan, J M; Han, S; Stefanović, S; Dickinson, T A
Range and niche expansion are commonly associated with transitions to asexuality, polyploidy and hybridity (allopolyploidy) in plants. The ability of asexual polyploids to colonize novel habitats may be due to widespread generalist clones, multiple ecologically specialized clones, or may be a neutral by-product of multiple, independent origins of asexual polyploids throughout the range. We have quantified niche size and divergence for hawthorns of the Pacific Northwest using data from herbarium vouchers with known cytotypes. We find that all polyploid niches diverge from that of the diploid range, and allopolyploids have the broadest niches. Allotetraploids have the largest niche and the widest geographic distribution. We then assessed the genetic mechanism of range expansion by surveying the ecological and geographic distribution of genotypes within each cytotype from sites in which fine-scale habitat assessments were completed. We find no isolation by either geographic or ecological distance in allopolyploids, suggesting high dispersal and colonization ability. In contrast, autotriploids and diploids show patterns of isolation by geographic distance. We also compared the geographic and ecological distributions of clonal genotypes with those of randomly drawn sites of the most widespread cytotype. We found that most clones are geographically widespread and occur in a variety of habitats. We interpret these findings to suggest that patterns of range and niche expansion in Pacific Northwest Hawthorns may stem from these widespread, ecologically generalist clones of hybrid origin. © 2017 John Wiley & Sons Ltd.
Feldman, Moshe; Levy, Avraham A.
The wheat group has evolved through allopolyploidization, namely, through hybridization among species from the plant genera Aegilops and Triticum followed by genome doubling. This speciation process has been associated with ecogeographical expansion and with domestication. In the past few decades, we have searched for explanations for this impressive success. Our studies attempted to probe the bases for the wide genetic variation characterizing these species, which accounts for their great adaptability and colonizing ability. Central to our work was the investigation of how allopolyploidization alters genome structure and expression. We found in wheat that allopolyploidy accelerated genome evolution in two ways: (1) it triggered rapid genome alterations through the instantaneous generation of a variety of cardinal genetic and epigenetic changes (which we termed “revolutionary” changes), and (2) it facilitated sporadic genomic changes throughout the species’ evolution (i.e., evolutionary changes), which are not attainable at the diploid level. Our major findings in natural and synthetic allopolyploid wheat indicate that these alterations have led to the cytological and genetic diploidization of the allopolyploids. These genetic and epigenetic changes reflect the dynamic structural and functional plasticity of the allopolyploid wheat genome. The significance of this plasticity for the successful establishment of wheat allopolyploids, in nature and under domestication, is discussed. PMID:23135324
Christopher G Love
Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.
Herklotz, V; Ritz, C M
Polyploidy and hybridization are important factors for generating diversity in plants. The species-rich dog roses ( Rosa sect. Caninae ) originated by allopolyploidy and are characterized by unbalanced meiosis producing polyploid egg cells (usually 4 x ) and haploid sperm cells (1 x ). In extant natural stands species hybridize spontaneously, but the extent of natural hybridization is unknown. The aim of the study was to document the frequency of reciprocal hybridization between the subsections Rubigineae and Caninae with special reference to the contribution of unreduced egg cells (5 x ) producing 6 x offspring after fertilization with reduced (1 x ) sperm cells. We tested whether hybrids arose by independent multiple events or via a single or few incidences followed by a subsequent spread of hybrids. Population genetics of 45 mixed stands of dog roses across central and south-eastern Europe were analysed using microsatellite markers and flow cytometry. Hybrids were recognized by the presence of diagnostic alleles and multivariate statistics were used to display the relationships between parental species and hybrids. Among plants classified to subsect. Rubigineae , 32 % hybridogenic individuals were detected but only 8 % hybrids were found in plants assigned to subsect. Caninae . This bias between reciprocal crossings was accompanied by a higher ploidy level in Rubigineae hybrids, which originated more frequently by unreduced egg cells. Genetic patterns of hybrids were strongly geographically structured, supporting their independent origin. The biased crossing barriers between subsections are explained by the facilitated production of unreduced gametes in subsect. Rubigineae . Unreduced egg cells probably provide the highly homologous chromosome sets required for correct chromosome pairing in hybrids. Furthermore, the higher frequency of Rubigineae hybrids is probably influenced by abundance effects because the plants of subsect. Caninae are much more abundant
Triplett, Jimmy K; Wang, Yunjing; Zhong, Jinshun; Kellogg, Elizabeth A
Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum) and common or Proso millet (P. miliaceum). Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels.
Gou, Xiaowan; Bian, Yao; Zhang, Ai; Zhang, Huakun; Wang, Bin; Lv, Ruili; Li, Juzuo; Zhu, Bo; Gong, Lei; Liu, Bao
Whereas a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole genome duplication (WGD) has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, i.e., involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that (i) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual; (ii) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations; (iii) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint; (iv) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization; and (v) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that WGD enhances organismal evolvability. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular
Background All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont. Results The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote. Conclusions The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes. Reviewers This article was reviewed by: Eugene Koonin, William Martin
Jimmy K Triplett
Full Text Available Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum and common or Proso millet (P. miliaceum. Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels.
A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy.
Winkler, Manuela; Escobar García, Pedro; Gattringer, Andreas; Sonnleitner, Michaela; Hülber, Karl; Schönswetter, Peter; Schneeweiss, Gerald M
Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished. © 2016 John Wiley & Sons Ltd.
Powell, Adrian F; Doyle, Jeff J
Previous studies have shown that polyploidy can alter biotic interactions, and it has been suggested that these effects may contribute to the increased ability for colonization of new habitats shown by many allopolyploids. Little is known, however, about the effects of allopolyploidy, which combines hybridity and genome doubling, on symbiotic interactions with rhizobial bacteria. We examined interactions of the allopolyploid Glycine dolichocarpa (designated T2) with novel rhizobial partners, such as might occur in a context of colonization, and compared these with the responses of its diploid progenitors, G. tomentella (D3) and G. syndetika (D4). We assessed root hair response, nodule formation, nodule mass, nodule number, and plant biomass. The allopolyploid (T2) showed a greater root hair deformation response when exposed to rhizobia, compared with either diploid. T2 had a greater probability of forming nodules with NGR234 compared with diploid D4, and greater total nodule mass per nodulated plant compared with diploid D3. T2 also had greater plant biomass responses to nitrogen and when exposed to NGR234. The allopolyploid is characterized by transgressive responses to rhizobia for some variables, while also combining certain parental diploid responses such that its capacity for interactions with rhizobia appears to be greater than for either diploid progenitor. This overall enhanced nodulation capacity and the ability to make greater gains from exposure to both rhizobia and additional nitrogen indicate a greater potential of the allopolyploid to benefit from these factors both generally and in a context of colonization. © 2016 Botanical Society of America.
Full Text Available How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional ''diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression. Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5. Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock
Full Text Available Abstract Background Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (Gossypium spp., including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (G. herbaceum, G. raimondii or allotetraploid (G. hirsutum, G. barbadense cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton. Results We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs for members of the PHYA, PHYB/D, PHYC and PHYE gene sub-families from A- and D-genome diploid and AD-genome allotetraploid Gossypium species. We identified two paralogous PHYA genes (designated PHYA1 and PHYA2 in diploid cottons, the result of a Malvaceae-specific PHYA gene duplication that occurred approximately 14 million years ago (MYA, before the divergence of the A- and D-genome ancestors. We identified a single gene copy of PHYB, PHYC, and PHYE in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four PHYA genes and two genes encoding PHYB, PHYC and PHYE in the AD-genomes. We did not identify a PHYD gene in any cotton genomes examined. Conclusions Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for
Frajman, Božo; Rešetnik, Ivana; Niketić, Marjan; Ehrendorfer, Friedrich; Schönswetter, Peter
Polyploidy is one of the most important evolutionary pathways in flowering plants and has significantly contributed to their diversification and radiation. Due to the prevalence of reticulate evolution spanning three ploidy levels, Knautia is considered one of the taxonomically most intricate groups in the European flora. On the basis of ITS and plastid DNA sequences as well as AFLP fingerprints obtained from 381 populations of almost all species of the genus we asked the following questions. (1) Where and when did the initial diversification in Knautia take place, and how did it proceed further? (2) Did Knautia undergo a similarly recent (Pliocene/Pleistocene) rapid radiation as other genera with similar ecology and overlapping distribution? (3) Did polyploids evolve within the previously recognised diploid groups or rather from hybridisation between groups? The diversification of Knautia was centred in the Eastern Mediterranean. According to our genetic data, the genus originated in the Early Miocene and started to diversify in the Middle Miocene, whereas the onset of radiation of sect. Trichera was in central parts of the Balkan Peninsula, roughly 4 Ma. Extensive spread out of the Balkans started in the Pleistocene about 1.5 Ma. Diversification of sect. Trichera was strongly fostered by polyploidisation, which occurred independently many times. Tetraploids are observed in almost all evolutionary lineages whereas hexaploids are rarer and restricted to a few phylogenetic groups. Whether polyploids originated via autopolyploidy or allopolyploidy is unclear due to the weak genetic separation among species. In spite of the complexity of sect. Trichera, we present nine AFLP-characterised informal species groups, which coincide only partly with former traditional groups. Knautia sect. Trichera is a prime example for rapid diversification, mostly taking place during Pliocene and Pleistocene. Numerous cycles of habitat fragmentation and subsequent reconnections likely
Nagy Ervin D
Full Text Available Abstract Background Cultivated peanut (Arachis hypogaea is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago
Grant, Joshua N; Burris, Jason N; Stewart, C Neal; Lenaghan, Scott C
Panicum hallii Vasey (Hall's panicgrass) is a compact, perennial C 4 grass in the family Poaceae, which has potential to enable bioenergy research for switchgrass (Panicum virgatum L.). Unlike P. hallii, switchgrass has a large genome, allopolyploidy, self-incompatibility, a long life cycle, and large stature-all suboptimal traits for rapid genetics research. Herein we improved tissue culture methodologies for two inbred P. hallii populations: FIL2 and HAL2, to enable further development of P. hallii as a model C 4 plant. The optimal seed-derived callus induction medium was determined to be Murashige and Skoog (MS) medium supplemented with 40 mg L -1 L-cysteine, 300 mg L -1 L-proline, 3% sucrose, 1 g L -1 casein hydrolysate, 3 mg L -1 2,4-dichlorophenoxyacetic acid (2,4-D), and 45 μg L -1 6-benzylaminopurine (BAP), which resulted in callus induction of 51 ± 29% for FIL2 and 81 ± 19% for HAL2. The optimal inflorescence-derived callus induction was observed on MP medium (MS medium supplemented with 2 g L -1 L-proline, 3% maltose, 5 mg L -1 2,4-D, and 500 μg L -1 BAP), resulting in callus induction of 100 ± 0.0% for FIL2 and 84 ± 2.4% for HAL2. Shoot regeneration rates of 11.5 ± 0.8 shoots/gram for FIL2 and 11.3 ± 0.6 shoots/gram for HAL2 were achieved using seed-induced callus, whereas shoot regeneration rates of 26.2 ± 2.6 shoots/gram for FIL2 and 29.3 ± 3.6 shoots/gram for HAL2 were achieved from inflorescence-induced callus. Further, cell suspension cultures of P. hallii were established from seed-derived callus, providing faster generation of callus tissue compared with culture using solidified media (1.41-fold increase for FIL2 and 3.00-fold increase for HAL2). Aside from abbreviated tissue culture times from callus induction to plant regeneration for HAL2, we noted no apparent differences between FIL2 and HAL2 populations in tissue culture performance. For both populations, the cell suspension cultures