Abstract
Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants.
Highlights
As an important and widely cultivated crop, bread wheat (Triticum aestivum L.) provides about 20% of the total calories in human food [1], and will need to increase its production by about 38% by 2050 to satisfy the increasing food requirements of a growing world population [2]
There were no significant differences found in gene numbers among the A, B and D subgenomes of wheat, but repeats and gene diversity was lower in the D subgenome [5]
The lower diversity of repeats and genes in the D subgenome may lead to a low chromosome recombination rate and mutation, which may be the main obstacle in effectively utilizing the genetic potential of the D genome in wheat breeding [10]
Summary
As an important and widely cultivated crop, bread wheat (Triticum aestivum L.) provides about 20% of the total calories in human food [1], and will need to increase its production by about 38% by 2050 to satisfy the increasing food requirements of a growing world population [2]. Due to a lack of knowledge about genome-scale genetic markers, yield and quality traits, genes and their homologous correspondence between wheat subgenomes, research has been limited to uncovering the underlying molecular mechanisms of crop characteristics, and the effective breeding of fine wheat cultivars to satisfy the increasing requirements of yield and quality. Based on the wheat draft shotgun sequence and the genes order between wheat and Brachypodium, the comparison of homologous genes is hard to extend to explore structure changes in the whole wheat genome [11], where the 551 homologous genes used to detect pericentric rearrangements in wheat chromosomes [12] are not sufficient for genome-scale investigation. Further investigation of genome-scale distribution and correspondence between homologous genes in wheat can help us to better understand the process of wheat polyploidization to develop more effective genetic markers, isolate genes of important crop traits and provide a springboard for meeting. This study provides a refined genome-scale reference of homologous genes for molecular research and wheat breeding, which may help to widen the application of the wheat genome and could be used as a template for the analysis of other polyploid plants
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