Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Abstract

Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known “green revolution” gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process.

Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents

“…The first group included genes encoding enzymes such as Acc-1 ( Chalupska et al , 2008 ), Acc-2 ( Chalupska et al , 2008 ), CAC3 ( Ke et al , 2000 ), starch synthase I gene ( Li et al , 1999 ), UBA1 ( Hatfield et al , 1990 ), and waxy gene (Takeuchi T, Sato M, Suzuki T, Yoshimura Y, Nakamichi K, Kobayashi S, Nishimura T, Ikenaga M and Sato N. unpublished). The second group included genes encoding regulatory proteins such as vp1D ( McKibbin et al , 2002 ), Rht-A ( Wu et al , 2013 ), Rht-B ( Wu et al. , 2013 ), VRN3 ( Yan et al , 2006 ), VRN-A1 ( Ivanicova et al , 2016 ), VRN-B1 (Guedira M, Xiong M, Johnson J, Marshall D and Brown-Guedira G. unpublished), and PRR73 ( Cockram et al , 2012 ).…”