TaGW2, a Good Reflection of Wheat Polyploidization and Evolution

Hexaploid wheat consists of three subgenomes, namely, A, B, and D. These well-characterized ancestral genomes also exist at the diploid and tetraploid levels, thereby rendering wheat as a good model species for studying polyploidization. Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. Our results showed that genetic diversity of TaGW2 decreased with progression from the diploids to tetraploids and hexaploids. The strongest selection occurred in the promoter regions of TaGW2-6A and TaGW2-6B. Phylogenetic trees clearly indicated that Triticum urartu and Ae. speltoides were the donors of the A and B genomes in tetraploid and hexaploid wheats. Haplotypes detected among hexaploid genotypes traced back to the tetraploid level. Fst and π values revealed that the strongest selection on TaGW2 occurred at the tetraploid level rather than in hexaploid wheat. This infers that grain size enlargement, especially increased kernel width, mainly occurred in tetraploid genotypes. In addition, relative expression levels of TaGW2s significantly declined from the diploid level to tetraploids and hexaploids, further indicating that these genes negatively regulate kernel size. Our results also revealed that the polyploidization events possibly caused much stronger differentiation than domestication and breeding.

[1]  T. Naranjo,et al.  Homoeologous relationships of Aegilops speltoides chromosomes to bread wheat , 1998, Theoretical and Applied Genetics.

[2]  Chenyang Hao,et al.  Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.) , 2010, Theoretical and Applied Genetics.

[3]  R. Athwal,et al.  A reassessment of the course of evolution of wheat. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Xinhong Chen,et al.  TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield. , 2016, Plant biotechnology journal.

[5]  Qian Qian,et al.  Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm , 2011, Nature Genetics.

[6]  K. Tsunewaki,et al.  Wheat phylogeny determined by RFLP analysis of nuclear DNA. 2. Wild tetraploid wheats , 2004, Theoretical and Applied Genetics.

[7]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[8]  Bruce D. Smith,et al.  The Molecular Genetics of Crop Domestication , 2006, Cell.

[9]  Wei Huang,et al.  A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase , 2007, Nature Genetics.

[10]  P. Langridge,et al.  Cereal breeding takes a walk on the wild side. , 2008, Trends in genetics : TIG.

[11]  G. Stebbins,et al.  MORPHOLOGICAL EVIDENCE CONCERNING THE ORIGIN OF THE B GENOME IN WHEAT , 1956 .

[12]  G. Petersen,et al.  Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum). , 2006, Molecular phylogenetics and evolution.

[13]  P. Ronald,et al.  A Rapid DNA Minipreparation Method Suitable for AFLP and Other PCR Applications , 2004, Plant Molecular Biology Reporter.

[14]  Manuel Spannagl,et al.  Ancient hybridizations among the ancestral genomes of bread wheat , 2014, Science.

[15]  C. Hao,et al.  Global Selection on Sucrose Synthase Haplotypes during a Century of Wheat Breeding1[C][W] , 2014, Plant Physiology.

[16]  Y. Xing,et al.  Yield-related QTLs and their applications in rice genetic improvement. , 2012, Journal of integrative plant biology.

[17]  E. Lagudah,et al.  D genome of wheat: 60 years on from Kihara, Sears and McFadden , 2005 .

[18]  Xinhong Chen,et al.  A yield-associated gene TaCWI, in wheat: its function, selection and evolution in global breeding revealed by haplotype analysis , 2014, Theoretical and Applied Genetics.

[19]  K. Tsunewaki,et al.  Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Lijun Luo,et al.  Natural variation in GS5 plays an important role in regulating grain size and yield in rice , 2011, Nature Genetics.

[21]  Qifa Zhang,et al.  Genetic and molecular bases of rice yield. , 2010, Annual review of plant biology.

[22]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[23]  C. Hao,et al.  TEF-7A, a transcript elongation factor gene, influences yield-related traits in bread wheat (Triticum aestivum L.) , 2014, Journal of experimental botany.

[24]  Vandana Jaiswal,et al.  Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.) , 2015, PloS one.

[25]  M. Gore,et al.  Cloning and characterization of a putative GS3 ortholog involved in maize kernel development , 2009, Theoretical and Applied Genetics.

[26]  Catherine Ravel,et al.  Down-regulation of the TaGW 2 gene by RNA int rference results in decreased gr in size and weight in wheat , 2012 .

[27]  S. Glémin,et al.  Grinding up wheat: a massive loss of nucleotide diversity since domestication. , 2007, Molecular biology and evolution.

[28]  Longfei Chen,et al.  Transcript suppression of TaGW2 increased grain width and weight in bread wheat , 2014, Functional & Integrative Genomics.

[29]  Jianru Zuo,et al.  Molecular genetic dissection of quantitative trait loci regulating rice grain size. , 2014, Annual review of genetics.

[30]  K. Crandall,et al.  TCS: a computer program to estimate gene genealogies , 2000, Molecular ecology.

[31]  A. Brandolini,et al.  Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. , 2007, Molecular biology and evolution.

[32]  Qingxia Wu,et al.  SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight , 2012, Theoretical and Applied Genetics.

[33]  S. Kresovich,et al.  Molecular diversity, structure and domestication of grasses. , 2001, Genetical research.

[34]  Y. Xing,et al.  Natural variation and artificial selection in four genes determine grain shape in rice. , 2013, The New phytologist.

[35]  Jan Dvorak,et al.  Tempos of Gene Locus Deletions and Duplications and Their Relationship to Recombination Rate During Diploid and Polyploid Evolution in the Aegilops-Triticum Alliance , 2005, Genetics.

[36]  R. Haselkorn,et al.  Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[37]  J Dvorák,et al.  The evolution of polyploid wheats: identification of the A genome donor species. , 1993, Genome.

[38]  M. Feldman,et al.  Genomic asymmetry in allopolyploid plants: wheat as a model. , 2012, Journal of experimental botany.

[39]  Yuquan Wang,et al.  Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2 , 2014, BMC Plant Biology.

[40]  Cristobal Uauy,et al.  A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains , 2016, Theoretical and Applied Genetics.

[41]  A. Brandolini,et al.  A reconsideration of the domestication geography of tetraploid wheats , 2005, Theoretical and Applied Genetics.

[42]  H. Kihara.  Discovery of the DD-analyser, one of the ancestors of Triticum vulgare , 1944 .

[43]  Xiaohong Yang,et al.  Relationship, evolutionary fate and function of two maize co-orthologs of rice GW2 associated with kernel size and weight , 2010, BMC Plant Biology.

[44]  J Dvorák,et al.  Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.