Journal articles: 'Polyploid Wheat'

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Krasileva, Ksenia V., Hans A. Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, et al. "Uncovering hidden variation in polyploid wheat." Proceedings of the National Academy of Sciences 114, no. 6 (January 17, 2017): E913—E921. http://dx.doi.org/10.1073/pnas.1619268114.

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Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35–40 mutations per kb in each population. With these mutation densities, we identified an average of 23–24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.

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Breiman, Adina, and Dan Graur. "WHEAT EVOLUTION." Israel Journal of Plant Sciences 43, no. 2 (May 13, 1995): 85–98. http://dx.doi.org/10.1080/07929978.1995.10676595.

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Many wild and cultivated wheat species are amphidiploid, i.e., they are polyploid species containing two or more distinct nuclear genomes, each with its own independent evolutionary history, but whose genetic behavior resembles that of diploids. Amphidiploidy has important evolutionary consequences in wheat. Since the beginning of this century different methods have been employed to identify the diploid donors of the coexisting genomes in the polyploids. To date, several of the genomic donors have been identified, and the search for the others has been narrowed down considerably. Molecular methodologies that are being increasingly used in studies aimed at reconstructing the evolutionary history of wheat species and their wild relatives have resolved many of the phylogenetic relationships among the various taxa.

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Kerby, K., and J. Kuspira. "The phylogeny of the polyploid wheats Triticum aestivum (bread wheat) and Triticum turgidum (macaroni wheat)." Genome 29, no. 5 (October 1, 1987): 722–37. http://dx.doi.org/10.1139/g87-124.

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The phylogeny of the polyploid wheats has been the subject of intense research and speculation during the past 70 years. Various experimental approaches have been employed to ascertain the diploid progenitors of these wheats. The species having donated the D genome to Triticum aestivum has been unequivocally identified as Aegilops squarrosa. On the basis of evidence from many studies, Triticum monococcum has been implicated as the source of the A genome in both Triticum turgidum and Triticum aestivum. However, numerous studies since 1968 have shown that Triticum urartu is very closely related to Triticum monococcum and that it also carries the A genome. These studies have prompted the speculation that Triticum urartu may be the donor of this chromosome set to the polyploid wheats. The donor of the B genome to Triticum turgidum and Triticum aestivum remains equivocal and controversial. Six different diploid species have been implicated as putative B genome donors: Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Aegilops speltoides, and Triticum urartu. Until recently, evidence presented by different researchers had not permitted an unequivocal identification of the progenitor of the B genome in polyploid wheats. Recent studies, involving all diploid and polyploid wheats and putative B genome donors, lead to the conclusion that Aegilops speltoides and Triticum urartu can be excluded as B genome donors and that Aegilops searsii is the most likely source of this chromosome set. The possibility of the B genome having arisen from an AAAA autotetraploid or having a polyphyletic origin is discussed. Key words: phylogeny; Triticum aestivum; Triticum turgidum; A, B, and D genomes.

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Talbert, L. E., G. Kimber, G. M. Magyar, and C. B. Buchanan. "Repetitive DNA variation and pivotal–differential evolution of wild wheats." Genome 36, no. 1 (February 1, 1993): 14–20. http://dx.doi.org/10.1139/g93-003.

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Several polyploid species in the genus Triticum contain a U genome derived from the diploid T. umbellulatum. In these species, the U genome is considered to be unmodified from the diploid based on chromosome pairing analysis, and it is referred to as pivotal. The additional genome(s) are considered to be modified, and they are thus referred to as differential genomes. The M genome derived from the diploid T. comosum is found in many U genome polyploids. In this study, we cloned three repetitive DNA sequences found primarily in the U genome and two repetitive DNA sequences found primarily in the M genome. We used these to monitor variation for these sequences in a large set of species containing U and M genomes. Investigation of sympatric and allopatric accessions of polyploid species did not show repetitive DNA similarities among sympatric species. This result does not support the idea that the polyploid species are continually exchanging genetic information through introgression. However, it is also possible that repetitive DNA is not a suitable means of addressing the question of introgression. The U genomes of both diploid and polyploid U genome species were similar regarding hybridization patterns observed with U genome probes. Much more variation was found both among diploid T. comosum accessions and polyploids containing M genomes. The observed variation supports the cytogenetic evidence that the M genome is more variable than the U genome. It also raises the possibility that the differential nature of the M genome may be due to variation within the diploid T. comosum, as well as among polyploid M genome species and accessions.Key words: wheat, molecular, evolution, introgression.

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Bento, Miguel, J. Perry Gustafson, Wanda Viegas, and Manuela Silva. "Size matters in Triticeae polyploids: larger genomes have higher remodeling." Genome 54, no. 3 (March 2011): 175–83. http://dx.doi.org/10.1139/g10-107.

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Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid species are excellent models to study polyploids evolution, particularly the wheat–rye hybrid triticale, which includes various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome size homogenization, diploidization establishment, and stabilization of polyploid species is discussed.

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Blake, Nancy K., Ben R. Lehfeldt, Matt Lavin, and Luther E. Talbert. "Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: The B genome of wheat." Genome 42, no. 2 (April 1, 1999): 351–60. http://dx.doi.org/10.1139/g98-136.

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Study of bread wheat (Triticum aestivum) may help to resolve several questions related to polyploid evolution. One such question regards the possibility that the component genomes of polyploids may themselves be polyphyletic, resulting from hybridization and introgression among different polyploid species sharing a single genome. We used the B genome of wheat as a model system to test hypotheses that bear on the monophyly or polyphyly of the individual constituent genomes. By using aneuploid wheat stocks, combined with PCR-based cloning strategies, we cloned and sequenced two single-copy-DNA sequences from each of the seven chromosomes of the wheat B genome and the homologous sequences from representatives of the five diploid species in section Sitopsis previously suggested as sister groups to the B genome. Phylogenetic comparisons of sequence data suggested that the B genome of wheat underwent a genetic bottleneck and has diverged from the diploid B genome donor. The extent of genetic diversity among the Sitopsis diploids and the failure of any of the Sitopsis species to group with the wheat B genome indicated that these species have also diverged from the ancestral B genome donor. Our results support monophyly of the wheat B genome.Key words: wheat evolution, phylogenetics, DNA sequencing.

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Liu, B., C. L. Brubaker, G. Mergeai, R. C. Cronn, and J. F. Wendel. "Polyploid formation in cotton is not accompanied by rapid genomic changes." Genome 44, no. 3 (June 1, 2001): 321–30. http://dx.doi.org/10.1139/g01-011.

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Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22 000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.Key words: polyploidy, genome evolution, cotton, Gossypium, amplified fragment length polymorphism (AFLP).

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Faris, J., B. Friebe, and B. Gill. "Wheat Genomics: Exploring the Polyploid Model." Current Genomics 3, no. 6 (December 1, 2002): 577–91. http://dx.doi.org/10.2174/1389202023350219.

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9

Ramírez-González, R. H., P. Borrill, D. Lang, S. A. Harrington, J. Brinton, L. Venturini, M. Davey, et al. "The transcriptional landscape of polyploid wheat." Science 361, no. 6403 (August 16, 2018): eaar6089. http://dx.doi.org/10.1126/science.aar6089.

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The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world’s major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.

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Muterko, Alexandr, and Elena Salina. "VRN1-ratio test for polyploid wheat." Planta 250, no. 6 (September 16, 2019): 1955–65. http://dx.doi.org/10.1007/s00425-019-03279-z.

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11

Feldman, Moshe, Bao Liu, Gregorio Segal, Shahal Abbo, Avraham A. Levy, and Juan M. Vega. "Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes." Genetics 147, no. 3 (November 1, 1997): 1381–87. http://dx.doi.org/10.1093/genetics/147.3.1381.

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To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, lowcopy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.

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De Bustos, A., R. Pérez, A. Cuadrado, and N. Jouve. "The MRN complex of wheat." Czech Journal of Genetics and Plant Breeding 47, Special Issue (October 20, 2011): S35—S38. http://dx.doi.org/10.17221/3251-cjgpb.

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The MRN complex is formed by the interaction of the products of the Mre11, Rad50 and Nbs1 genes. This complex plays a central role on repair of double-strand breaks (DSBs) and acts in a great number of cellular processes. In this study we have performed the analysis of the MRN complex in diploid and polyploid species of wheat. The molecular characterization was carried out in the diploid T. monococcum (genome A) and Ae. tauschii (genome D) and in the tetraploid T. turgidum (genomes A and B). The results obtained showed that in all cases the genes presented the main characteristics previously described in other species. A modified FISH protocol was used to locate the Rad50, Mre11 and the Nbs1 genes on the homoeologous chromosomes 5, 2 and 1, respectively. Analysis of expression showed that the hexaploid T. aestivum was the species with the higher level of expression whereas the rest of the species analysed showed no relation with its ploidy. Also, quantification of the expression of each homoeologous gene in the polyploid species evidenced in some cases a process of silencing after polyploidization. The study of the interaction between the proteins demonstrated that the interaction of proteins was not restricted to each genome, detecting interaction between proteins belonging to different genomes.

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Thomas, Gregg W. C., S. Hussain Ather, and Matthew W. Hahn. "Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events." Systematic Biology 66, no. 6 (April 28, 2017): 1007–18. http://dx.doi.org/10.1093/sysbio/syx044.

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Abstract Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids—autopolyploids and allopolyploids—differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]

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Yaakov, Beery, and Khalil Kashkush. "Methylation, Transcription, and Rearrangements of Transposable Elements in Synthetic Allopolyploids." International Journal of Plant Genomics 2011 (May 15, 2011): 1–7. http://dx.doi.org/10.1155/2011/569826.

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Transposable elements (TEs) constitute over 90% of the wheat genome. It was suggested that “genomic stress” such as hybridity or polyploidy might activate transposons. Intensive investigations of various polyploid systems revealed that allopolyploidization event is associated with widespread changes in genome structure, methylation, and expression involving low- and high-copy, coding and noncoding sequences. Massive demethylation and transcriptional activation of TEs were also observed in newly formed allopolyploids. Massive proliferation, however, was reported for very limited number of TE families in various polyploidy systems. The aim of this review is to summarize the accumulated data on genetic and epigenetic dynamics of TEs, particularly in synthetic allotetraploid and allohexaploid wheat species. In addition, the underlying mechanisms and the potential biological significance of TE dynamics following allopolyploidization are discussed.

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Zhao, Na, Qianli Dong, Brian D. Nadon, Xiaoyang Ding, Xutong Wang, Yuzhu Dong, Bao Liu, Scott A. Jackson, and Chunming Xu. "Evolution of Homeologous Gene Expression in Polyploid Wheat." Genes 11, no. 12 (November 25, 2020): 1401. http://dx.doi.org/10.3390/genes11121401.

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Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.

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Dvorak, Jan, Patrick E. McGuire, and Brandt Cassidy. "Apparent sources of the A genomes of wheats inferred from polymorphism in abundance and restriction fragment length of repeated nucleotide sequences." Genome 30, no. 5 (October 1, 1988): 680–89. http://dx.doi.org/10.1139/g88-115.

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Four hundred random DNA fragment clones of wild diploid wheat Triticum monococcum ssp. aegilopoides (syn. T. baeoticum) were screened for clones of repeated nucleotide sequences. Seven DNA fragments were isolated that were more abundant by one order of magnitude or more in the genome of diploid T. monococcum ssp. aegilopoides (genome A) than in the genome of diploid Triticum speltoides (genome BS). These clones were then used to determine which of the two wild diploid wheats, T. m. ssp. aegilopoides or T. urartu, was the ancestor of domesticated diploid wheat T. m. ssp. monococcum, wild tetraploid wheats T. turgidum ssp. dicoccoides and T. timopheevii ssp. araraticum, domesticated tetraploid wheat T. turgidum, and hexaploid bread wheat T. aestivum. Three of the seven cloned repeated nucleotide sequences differentiated the genome of T. m. ssp. aegilopoides from that of T. urartu in repeated sequence abundance, restriction fragment length polymorphism, or both. The same distinctions were observed between the A genome of T. m. ssp. aegilopoides and the A genomes of polyploid wheats. From this it was concluded that the species from which T. m. ssp. monococcum was domesticated was T. m. ssp. aegilopoides but that the A genomes of the polyploid wheats are equivalent to that of T. urartu. The results presented here demonstrate the utility of polymorphism in repeated nucleotide sequences in the investigation of the origin of genomes in polyploid plants.Key words: RFLP, Triticum, wheat phylogeny.

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Kantar, Melda, Bala Anı Akpınar, Miroslav Valárik, Stuart J. Lucas, Jaroslav Doležel, Pilar Hernández, and Hikmet Budak. "Subgenomic analysis of microRNAs in polyploid wheat." Functional & Integrative Genomics 12, no. 3 (May 17, 2012): 465–79. http://dx.doi.org/10.1007/s10142-012-0285-0.

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Miller, T. E., and S. M. Reader. "Polyploid meiocytes in wheat—a heritable trait." Caryologia 44, no. 3-4 (January 1991): 293–99. http://dx.doi.org/10.1080/00087114.1991.10797194.

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Brandolini, A., P. Vaccino, G. Boggini, H. Özkan, B. Kilian, and F. Salamini. "Quantification of genetic relationships among A genomes of wheats." Genome 49, no. 4 (April 1, 2006): 297–305. http://dx.doi.org/10.1139/g05-110.

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The genetic relationships of A genomes of Triticum urartu (Au) and Triticum monococcum (Am) in polyploid wheats are explored and quantified by AFLP fingerprinting. Forty-one accessions of A-genome diploid wheats, 3 of AG-genome wheats, 19 of AB-genome wheats, 15 of ABD-genome wheats, and 1 of the D-genome donor Ae. tauschii have been analysed. Based on 7 AFLP primer combinations, 423 bands were identified as potentially A genome specific. The bands were reduced to 239 by eliminating those present in autoradiograms of Ae. tauschii, bands interpreted as common to all wheat genomes. Neighbour-joining analysis separates T. urartu from T. monococcum. Triticum urartu has the closest relationship to polyploid wheats. Triticum turgidum subsp. dicoccum and T. turgidum subsp. durum lines are included in tightly linked clusters. The hexaploid spelts occupy positions in the phylogenetic tree intermediate between bread wheats and T. turgidum. The AG-genome accessions cluster in a position quite distant from both diploid and other polyploid wheats. The estimates of similarity between A genomes of diploid and polyploid wheats indicate that, compared with Am, Au has around 20% higher similarity to the genomes of polyploid wheats. Triticum timo pheevii AG genome is molecularly equidistant from those of Au and Am wheats.Key words: A genome, Triticum, genetic relationships, AFLP.

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Sallares, Robert, and Terence A. Brown. "PCR-based analysis of the intergenic spacers of the Nor loci on the A genomes of Triticum diploids and polyploids." Genome 42, no. 1 (February 1, 1999): 116–28. http://dx.doi.org/10.1139/g98-102.

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We present DNA sequence data showing population variation in the intergenic spacer (IGS) regions of the ribosomal DNAs (rDNAs) on the A genomes of 27 diploid and polyploid wheats. PCRs (polymerase chain reactions) specific for the Am genome gave products with five populations of Triticum monococcum but did not give products with AABB or AABBDD wheats. PCRs specific to the Au genome of T. urartu gave products with all the AABB and AABBDD polyploids that were tested, but not with T. monococcum. AAGG tetraploids gave products only with the Au-specific primers, but the AAAAGG hexaploid T. zhukovskyi gave products with both the Au and Am primers. Phylogenetic analysis showed a substantial degree of IGS divergence for both the Am and Au genomes in diploids and polyploids compared with other genomes of Triticum and Aegilops. The rate of evolution of the IGS is much greater than previously reported for the internal transcribed region of the rDNAs but the view that the IGS only gives random noise is rejected, the IGS sequences presented here reflecting the general evolutionary trends affecting the wheat genome as a whole.Key words: wheat, ribosomal DNA, intergenic spacer, polymerase chain reaction.

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Belyayev, Alexander, Olga Raskina, Abraham Korol, and Eviatar Nevo. "Coevolution of A and B genomes in allotetraploid Triticum dicoccoides." Genome 43, no. 6 (December 1, 2000): 1021–26. http://dx.doi.org/10.1139/g00-060.

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Data is presented on the coevolution of A and B genomes in allotetraploid wheat Triticum dicoccoides (2n = 4x = 28, genome AABB) obtained by genomic in situ hybridization (GISH). Probing chromosomes of T. dicoccoides with DNA from the proposed A/B diploid genome ancestors shows evidence of enriching A-genome with repetitive sequences of B-genome type. Thus, ancestral S-genome sequences have spread throughout the AB polyploid genome to a greater extent than have ancestral A-genome sequences. The substitution of part of the A-genome heterochromatin clusters by satellite DNA of the B genome is detected by using the molecular banding technique. The cause may be interlocus concerted evolution and (or) colonization. We propose that the detected high level of intergenomic invasion in old polyploids might reflect general tendencies in speciation and stabilization of the allopolyploid genome.Key words: Triticum, polyploid, evolution, genomic in situ hybridization, repetitive sequences.

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Wazuddin, M., and C. J. Driscoll. "Chromosome constitution of polyploid wheats: Introduction of diploid wheat chromosome 4." Proceedings of the National Academy of Sciences 83, no. 11 (June 1, 1986): 3870–74. http://dx.doi.org/10.1073/pnas.83.11.3870.

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Harrington, Sophie A., Anna E. Backhaus, Ajit Singh, Keywan Hassani-Pak, and Cristobal Uauy. "The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat." G3: Genes|Genomes|Genetics 10, no. 10 (August 3, 2020): 3675–86. http://dx.doi.org/10.1534/g3.120.401436.

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Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

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LIMIN, A. E., and D. B. FOWLER. "COLD HARDINESS IN Triticum AND Aegilops SPECIES." Canadian Journal of Plant Science 65, no. 1 (January 1, 1985): 71–77. http://dx.doi.org/10.4141/cjps85-010.

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A total of 237 Triticum and Aegilops accessions were cold-acclimated and screened for cold hardiness. These included 90 A genome accessions (T. monococcum L. and T. beoticum Boiss.), 26 AG genome accessions of T. timopheevi (Zhuk.) Zhuk., 44 D genome accessions of Ae. squarrosa L., and 77 accessions made from 22 Aegilops species. The greatest degree of cold hardiness was found in the polyploid Aegilops species; particularly Ae. cylindrica Host (CD genome). One Ae. cylindrica accession was equal to the hardy winter wheat cultivar Norstar (T. aestivum L., ABD genome). Triticum timopheevi accessions possessed only poor levels of cold hardiness. Two of the diploid progenitor species of common wheat, T. monococcum and Ae. squarrosa, had poor to intermediate levels of cold hardiness. The D genome species was, on average, more hardy than the A genome species. Several polyploids have achieved a level of cold hardiness greater than that found in any of the diploid species. It is speculated that these hardiness levels have been achieved, in part, by the chance incorporation of hardy diploids in the original hybridization. However, the evolution of new genie forms or an integrated genetic system between the genomes of the polyploid was probably equally important to the development of highly cold hardy types. The utility of related species for the improvement of cold hardiness in common wheat is discussed.Key words: Triticum, Aegilops, cold hardiness, winter wheat, interspecific hybridization

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Saintenac, Cyrille, Dayou Jiang, Shichen Wang, and Eduard Akhunov. "Sequence-Based Mapping of the Polyploid Wheat Genome." G3: Genes|Genomes|Genetics 3, no. 7 (May 11, 2013): 1105–14. http://dx.doi.org/10.1534/g3.113.005819.

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Romanov, B. V., K. I. Pimonov, I. Yu Sorokina, G. А. Kozlechkov, and S. V. Pasko. "GENOME INFLUENCE ON THE SYNTHESIZED POLYPLOID WHEAT PHENOTYPE." Vestnik of the Russian agricultural science, no. 2 (April 11, 2018): 27–30. http://dx.doi.org/10.30850/vrsn/2018/2/27-30.

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Presents the results of a study of the effect of genomes on the formation of phenotypes synthesized polyploid species of wheat forms. As objects of study were samples synthesized tetraploid T. erebuni Gandil. AuD, T. palmovae G. Ivanov DAb, hexaploid T. kiharae Dorof. et Migusch. AbGD and diploid carriers of the original genomes: T. urartu Tum. ex Gandil Au T. boeoticum Boiss Ab, Aegilops tauschii subsp strangulate D, and tetraploid T. timopheevii, on the basis of which was created the above tetra - and hexaploid species. A detailed examination of artificially synthesized polyploid wheat, with the involvement of the original sources of the genomes, shows the obvious influence of genomes on the formation of their phenotypic characteristics, including formation of public production of signs. So in the phenotype in artificially created tetraploidtion Triticum erebuni AuAuDD well enough to see the influence of the genome of original diploid wheat T. urartu AuAu. The phenotype of T. palmovae AbAbDD, on the contrary in a greater degree dominante features of a source genome Aegilops tau-schii DD. This allows you to make water that at first as mother plants were used diploid wheat, and T. palmovae - Ae. tauschii. However, this production characteristic as the number of glosses in the ear they were largely under the control of his father's plants. So T. erebuni, the number of spikelets per spike level per se Ae. tauschii, and T. palmovae, on the contrary, closer to the rate of diploid wheat T. boeoticum AbAb. At the hexaploid T. kiharae AbAbGGDD, in contrast to the tetraploid T. erebuni AuAuDD, the phenotype is not observed the corresponding dominance of the signs of the wheat T. timopheevii and the number of ears he's closer to the source of the DD genome. The results of the evaluation of the influence of the genome on the phenotypic features of the synthesized forms provide an opportunity to more thoroughly and effectively suited to the process of creating polyploid forms.

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Gardiner, Laura-Jayne, Ryan Joynson, Jimmy Omony, Rachel Rusholme-Pilcher, Lisa Olohan, Daniel Lang, Caihong Bai, et al. "Hidden variation in polyploid wheat drives local adaptation." Genome Research 28, no. 9 (August 9, 2018): 1319–32. http://dx.doi.org/10.1101/gr.233551.117.

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Daud, Hassan Mat, and J. P. Gustafson. "Molecular evidence for Triticum speltoides as a B-genome progenitor of wheat (Triticum aestivum)." Genome 39, no. 3 (June 1, 1996): 543–48. http://dx.doi.org/10.1139/g96-069.

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In polyploid wheat, the origin of the B-genome donor has remained relatively unknown in spite of a number of investigations attempting to identify the parental species. A project was designed to isolate and clone a genome-specific DNA sequence from Triticum speltoides L. to determine if that species could be the B-genome donor. A cloning scheme involving the prescreening of 1-kb fragments followed by colony, dot blot, and Southern blot hybridization screenings was used to isolate a speltoides-specific sequence (pSp89.XI). The methods used allowed for rapid isolation of a genome-specific sequence when screened against total DNA from closely related species. Subsequent analyses showed that the sequence was barely detected in any of the other genomes of the annual Sitopsis section. The results of dot blot and Southern blot analyses established that (i) the sequence pSP89.XI, specific to T. speltoides relative to the other species of the Sitopsis section, was present in the genomes of tetraploid and hexaploid wheat, (ii) the relative abundance of pSp89.XI seemed to decrease from the diploid to the polyploid wheats, and (iii) the existence of a related, but modified B genome in polyploid wheat compared with that in modern T. speltoides was probable. Key words : genome-specific, DNA.

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Chen, Shisheng, Joshua Hegarty, Tao Shen, Lei Hua, Hongna Li, Jing Luo, Hongyu Li, Shengsheng Bai, Chaozhong Zhang, and Jorge Dubcovsky. "Stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal translocation of Triticum monococcum chromosome 5AmL into common wheat." Theoretical and Applied Genetics 134, no. 7 (March 31, 2021): 2197–211. http://dx.doi.org/10.1007/s00122-021-03816-z.

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AbstractKey messageThe stripe rust resistance geneYr34 was transferred to polyploid wheat chromosome 5AL from T. monococcumand has been used for over two centuries.Wheat stripe (or yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently among the most damaging fungal diseases of wheat worldwide. In this study, we report that the stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal segment of the cultivated Triticum monococcum subsp. monococcum chromosome 5AmL translocated to chromosome 5AL in polyploid wheat. The diploid wheat species Triticum monococcum (genome AmAm) is closely related to T. urartu (donor of the A genome to polyploid wheat) and has good levels of resistance against the stripe rust pathogen. When present in hexaploid wheat, the T. monococcum Yr34 resistance gene confers a moderate level of resistance against virulent Pst races present in California and the virulent Chinese race CYR34. In a survey of 1,442 common wheat genotypes, we identified 5AmL translocations of fourteen different lengths in 17.5% of the accessions, with higher frequencies in Europe than in other continents. The old European wheat variety “Mediterranean” was identified as a putative source of this translocation, suggesting that Yr34 has been used for over 200 years. Finally, we designed diagnostic CAPS and sequenced-based markers that will be useful to accelerate the deployment of Yr34 in wheat breeding programs to improve resistance to this devastating pathogen.

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Soares, Nina Reis, Marcelo Mollinari, Gleicy K. Oliveira, Guilherme S. Pereira, and Maria Lucia Carneiro Vieira. "Meiosis in Polyploids and Implications for Genetic Mapping: A Review." Genes 12, no. 10 (September 27, 2021): 1517. http://dx.doi.org/10.3390/genes12101517.

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Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.

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Saintenac, Cyrille, Wenjun Zhang, Andres Salcedo, Matthew N. Rouse, Harold N. Trick, Eduard Akhunov, and Jorge Dubcovsky. "Identification of Wheat Gene Sr35 That Confers Resistance to Ug99 Stem Rust Race Group." Science 341, no. 6147 (June 27, 2013): 783–86. http://dx.doi.org/10.1126/science.1239022.

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Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating disease that can cause severe yield losses. A previously uncharacterized Pgt race, designated Ug99, has overcome most of the widely used resistance genes and is threatening major wheat production areas. Here, we demonstrate that the Sr35 gene from Triticum monococcum is a coiled-coil, nucleotide-binding, leucine-rich repeat gene that confers near immunity to Ug99 and related races. This gene is absent in the A-genome diploid donor and in polyploid wheat but is effective when transferred from T. monococcum to polyploid wheat. The cloning of Sr35 opens the door to the use of biotechnological approaches to control this devastating disease and to analyses of the molecular interactions that define the wheat-rust pathosystem.

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Gornicki, Piotr, Huilan Zhu, Junwei Wang, Ghana S. Challa, Zhengzhi Zhang, Bikram S. Gill, and Wanlong Li. "The chloroplast view of the evolution of polyploid wheat." New Phytologist 204, no. 3 (July 24, 2014): 704–14. http://dx.doi.org/10.1111/nph.12931.

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33

Arumugam, S., and V. R. K. Reddy. "ROLE OF DIFFERENT GENOME COMBINATIONS ON STABILITY PARAMETERS IN WHEAT AND TRITICALE." Acta Agronomica Hungarica 49, no. 1 (May 1, 2001): 53–58. http://dx.doi.org/10.1556/aagr.49.2001.1.6.

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The role of the different genome combinations in a polyploid on phenotypic stability was analysed in wheat and triticale. Twelve genotypes with four genome combinations (AABB, AABBDD, AABBRR and AABBDDRR) were raised in eight artificially created environments. The data on grains per spike, 100-grain weight and grain yield per plant were recorded and analysed following the models of Perkins and Jinks (1968) and Eberhart and Russell (1966). The results revealed that in polyploid species the genes for stability were not uniformly distributed in different genomes. It was therefore inferred that stability may largely depend on the gene combination rather than on the genome combination.

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34

Lloyd, James R. "The A to B of starch granule formation in wheat endosperm." Journal of Experimental Botany 71, no. 1 (October 21, 2019): 1–3. http://dx.doi.org/10.1093/jxb/erz414.

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This article comments on: Chia T, Chirico M, King R et al. 2019. A carbohydrate-binding protein, B-granule content 1 influences starch granule-size distribution in a dose dependent manner in polyploid wheat. Journal of Experimental Botany 70, 105–115.

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Rees, Hannah, Rachel Rusholme-Pilcher, Paul Bailey, Joshua Colmer, Benjamen White, Connor Reynolds, Sabrina Jaye Ward, et al. "Circadian regulation of the transcriptome in a complex polyploid crop." PLOS Biology 20, no. 10 (October 13, 2022): e3001802. http://dx.doi.org/10.1371/journal.pbio.3001802.

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The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

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Rayburn, A. Lane, and B. S. Gill. "Molecular evidence for the origin and evolution of chromosome 4A in polyploidy wheats." Canadian Journal of Genetics and Cytology 27, no. 2 (April 1, 1985): 246–50. http://dx.doi.org/10.1139/g85-036.

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The chromosomes of polyploid Triticum species and the putative donor diploid species were analyzed by in situ hybridization with a repeated DNA sequence clone pSc 119 isolated from rye and also found in wheat. In Triticum aestivum cv. Chinese Spring, chromosome 4A showed one terminal site in the short arm and one terminal and two interstitial sites of hybridization in the long arm. Triticum turgidum contained a 4A chromosome identical to 'Chinese Spring' with respect to hybridization sites. Chromosome 4A of the timopheevi wheats differed from 4A of 'Chinese Spring' in that the site of the sequence on the short arm was subterminal rather than terminal. Of the A-, B-, and D-genome progenitor species, only potential B-genome donors Aegilops speltoides and Aegilops sharonensis each showed a chromosome with hybridization sites similar to 4A. This suggested that 4A belongs to the B genome. Moreover, with regard to this sequence, chromosome 4A has undergone only minor changes during the evolution of the polyploid wheats.Key words: wheat evolution, in situ hybridization, biotin labeling.

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37

Tsujimoto, H., and B. S. Gill. "Repetitive DNA sequences from polyploid Elymus trachycaulus and the diploid progenitor species: detection and genomic affinity of Elymus chromatin added to wheat." Genome 34, no. 5 (October 1, 1991): 782–89. http://dx.doi.org/10.1139/g91-122.

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A set of four repetitive DNA clones, pEt1, pEt2, pCb1, and pCb3, were isolated from SH-genome polyploid Elymus trachycaulus and H-genome diploid Critesion bogdanii. The clone Et1 represents a tandemly arranged telomeric sequence. Et2 represents tandem repeats interspersed along the entire length of individual chromosomes. The Cb1 sequence was more evenly dispersed. The Et1 clone shared homology with a 350 base pair family of rye sequences. The Cb3 sequence was evenly distributed in S- and H-genome species. All the repetitive DNA sequences were excellent markers for the specific detection and genomic affinity of Elymus chromatin added to wheat. All clones showed intragenomic variation in copy number and chromosomal location. Based on the analysis of this variation, we conclude that E. trachycaulus most probably originated from putative diploid H- and S-genome species resembling Critesion californicum and Pseudoroegneria spicata, respectively.Key words: wheatgrass, wheat–Elymus hybrid, addition lines, polyploidy, restriction fragment length polymorphism.

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38

Sun, Congwei, Zhongdong Dong, Lei Zhao, Yan Ren, Ning Zhang, and Feng Chen. "The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat." Plant Biotechnology Journal 18, no. 6 (March 10, 2020): 1354–60. http://dx.doi.org/10.1111/pbi.13361.

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39

Wright, Christine S., and Natasha Raikhel. "Sequence variability in three wheat germ agglutinin isolectins: Products of multiple genes in polyploid wheat." Journal of Molecular Evolution 28, no. 4 (April 1989): 327–36. http://dx.doi.org/10.1007/bf02103429.

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40

Caldwell, Katherine S., Jan Dvorak, Evans S. Lagudah, Eduard Akhunov, Ming-Cheng Luo, Petra Wolters, and Wayne Powell. "Sequence Polymorphism in Polyploid Wheat and Their D-Genome Diploid Ancestor." Genetics 167, no. 2 (June 2004): 941–47. http://dx.doi.org/10.1534/genetics.103.016303.

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41

Muterko, A. F., and E. A. Salina. "Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat." Vavilov Journal of Genetics and Breeding 21, no. 3 (January 1, 2017): 323–33. http://dx.doi.org/10.18699/vj16.19-o.

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Borrill, Philippa, Nikolai Adamski, and Cristobal Uauy. "Genomics as the key to unlocking the polyploid potential of wheat." New Phytologist 208, no. 4 (June 24, 2015): 1008–22. http://dx.doi.org/10.1111/nph.13533.

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43

Su, Handong, Yalin Liu, Chang Liu, Qinghua Shi, Yuhong Huang, and Fangpu Han. "Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes." Plant Cell 31, no. 9 (July 16, 2019): 2035–51. http://dx.doi.org/10.1105/tpc.19.00133.

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44

Yan, L., M. Helguera, K. Kato, S. Fukuyama, J. Sherman, and J. Dubcovsky. "Allelic variation at the VRN-1 promoter region in polyploid wheat." Theoretical and Applied Genetics 109, no. 8 (October 6, 2004): 1677–86. http://dx.doi.org/10.1007/s00122-004-1796-4.

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45

Cai, Xiwen, Steven S. Xu, and Xianwen Zhu. "Mechanism of haploidy-dependent unreductional meiotic cell division in polyploid wheat." Chromosoma 119, no. 3 (February 2, 2010): 275–85. http://dx.doi.org/10.1007/s00412-010-0256-y.

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46

Bomblies, Kirsten. "When everything changes at once: finding a new normal after genome duplication." Proceedings of the Royal Society B: Biological Sciences 287, no. 1939 (November 18, 2020): 20202154. http://dx.doi.org/10.1098/rspb.2020.2154.

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Whole-genome duplication (WGD), which leads to polyploidy, is implicated in adaptation and speciation. But what are the immediate effects of WGD and how do newly polyploid lineages adapt to them? With many studies of new and evolved polyploids now available, along with studies of genes under selection in polyploids, we are in an increasingly good position to understand how polyploidy generates novelty. Here, I will review consistent effects of WGD on the biology of plants, such as an increase in cell size, increased stress tolerance and more. I will discuss how a change in something as fundamental as cell size can challenge the function of some cell types in particular. I will also discuss what we have learned about the short- to medium-term evolutionary response to WGD. It is now clear that some of this evolutionary response may ‘lock in’ traits that happen to be beneficial, while in other cases, it might be more of an ‘emergency response’ to work around physiological changes that are either deleterious, or cannot be undone in the polyploid context. Yet, other traits may return rapidly to a diploid-like state. Polyploids may, by re-jigging many inter-related processes, find a new, conditionally adaptive, normal.

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Wang, Meiyue, Zijuan Li, Yu’e Zhang, Yuyun Zhang, Yilin Xie, Luhuan Ye, Yili Zhuang, et al. "An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses." Plant Cell 33, no. 4 (February 2, 2021): 865–81. http://dx.doi.org/10.1093/plcell/koab028.

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Abstract Wheat (Triticum aestivum) has a large allohexaploid genome. Subgenome-divergent regulation contributed to genome plasticity and the domestication of polyploid wheat. However, the specificity encoded in the wheat genome determining subgenome-divergent spatio-temporal regulation has been largely unexplored. The considerable size and complexity of the genome are major obstacles to dissecting the regulatory specificity. Here, we compared the epigenomes and transcriptomes from a large set of samples under diverse developmental and environmental conditions. Thousands of distal epigenetic regulatory elements (distal-epiREs) were specifically linked to their target promoters with coordinated epigenomic changes. We revealed that subgenome-divergent activity of homologous regulatory elements is affected by specific epigenetic signatures. Subgenome-divergent epiRE regulation of tissue specificity is associated with dynamic modulation of H3K27me3 mediated by Polycomb complex and demethylases. Furthermore, quantitative epigenomic approaches detected key stress responsive cis- and trans-acting factors validated by DNA Affinity Purification and sequencing, and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Together, this study provides a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat.

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Tian, Geng, Guoqing Li, Yanling Liu, Qinghua Liu, Yanxia Wang, Guangmin Xia, and Mengcheng Wang. "Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat." PLOS ONE 15, no. 11 (November 19, 2020): e0242624. http://dx.doi.org/10.1371/journal.pone.0242624.

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Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants, SCUB. Its effect on organellar genes has not, however, been widely addressed. The present analysis targeted the chloroplast genomes of two leading polyploid crop species, namely cotton and bread wheat. The frequency of codons in the chloroplast genomes ending in either adenosine (NNA) or thymine (NNT) proved to be higher than those ending in either guanidine or cytosine (NNG or NNC), and this difference was conserved when comparisons were made between polyploid and diploid forms in both the cotton and wheat taxa. Preference for NNA/T codons was heterogeneous among genes with various numbers of introns and was also differential among the exons. SCUB patterns distinguished tetraploid cotton from its diploid progenitor species, as well as bread wheat from its diploid/tetraploid progenitor species, indicating that SCUB in the chloroplast genome partially mirrors the formation of polyploidies.

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Terashima, Akihiro, and Shigeo Takumi. "Allopolyploidization reduces alternative splicing efficiency for transcripts of the wheat DREB2 homolog, WDREB2." Genome 52, no. 1 (January 2009): 100–105. http://dx.doi.org/10.1139/g08-101.

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The wheat DREB2 homolog, WDREB2, encodes an EREBP/AP2-type transcription factor that activates downstream Cor/Lea genes and plays important roles in abiotic stress responses. WDREB2 expression is posttranscriptionally regulated by alternative splicing. In this study, the alternative splicing patterns of WDREB2 transcripts were compared among wheats of different ploidy levels. In diploid progenitors, alternative splicing rapidly produced functional forms from the WDREB2 transcripts and the levels of the nonfunctional form gradually decreased in response to drought stress; however, in hexaploid wheat lines, including both cultivars and synthetic lines, the nonfunctional form failed to decrease. The accumulation levels of the three spliced forms in synthetic allopolyploids were not equal to the sum of those in the parental lines. These results indicated that allopolyploidization during wheat polyploid evolution inhibited efficient alternative splicing of WDREB2 transcripts.

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Glémin, Sylvain, Celine Scornavacca, Jacques Dainat, Concetta Burgarella, Véronique Viader, Morgane Ardisson, Gautier Sarah, Sylvain Santoni, Jacques David, and Vincent Ranwez. "Pervasive hybridizations in the history of wheat relatives." Science Advances 5, no. 5 (May 2019): eaav9188. http://dx.doi.org/10.1126/sciadv.aav9188.

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Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

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Journal articles on the topic 'Polyploid Wheat'

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