Abstract
A Chinese wheat mini core collection was genotyped using the wheat 9 K iSelect SNP array. Total 2420 and 2396 polymorphic SNPs were detected on the A and the B genome chromosomes, which formed 878 haplotype blocks. There were more blocks in the B genome, but the average block size was significantly (P < 0.05) smaller than those in the A genome. Intense selection (domestication and breeding) had a stronger effect on the A than on the B genome chromosomes. Based on the genetic pedigrees, many blocks can be traced back to a well-known Strampelli cross, which was made one century ago. Furthermore, polyploidization of wheat (both tetraploidization and hexaploidization) induced revolutionary changes in both the A and the B genomes, with a greater increase of gene diversity compared to their diploid ancestors. Modern breeding has dramatically increased diversity in the gene coding regions, though obvious blocks were formed on most of the chromosomes in both tetraploid and hexaploid wheats. Tag-SNP markers identified in this study can be used for marker assisted selection using haplotype blocks as a wheat breeding strategy. This strategy can also be employed to facilitate genome selection in other self-pollinating crop species.
Highlights
St 2422–464 (St), was used to create 122 new varieties during 1970–1990 in China
Genotyping of the Chinese wheat mini core collections yielded a total of 5756 polymorphic SNPs, of which 5156 were mapped to a single chromosome location (Supplementary Table S1)
The analysis of haplotype blocks, haplotype-based association and evolution performed in this study, focused on the SNPs located on the A and the B genomes
Summary
St 2422–464 (St), was used to create 122 new varieties during 1970–1990 in China. This has provided us with very valuable information to reveal the formation and diversification of founder genotypes in historical wheat breeding in China. This study tracked the inheritance of haplotype blocks among common wheat cultivars of shared pedigree, and their formation in tetraploid and hexaploid in the A and the B genomes. We revealed the patterns of haplotype blocks in the founder genotypes and their impacts on the wheat breeding in China at different periods during the last century. The critical genomic regions controlling agronomic traits had stronger and larger haplotype blocks likely resulted from the conscious selection in both cultivated tetraploid and hexaploid wheat, but generally these blocks were formed earlier in the A genome than in the B genome. We found the A genome experienced stronger selection than the B genome in both domestication and breeding
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