DNA-segment copy number variations (DSCNVs), such as deletions and duplications, are important sources of genomic structural variation. However, types and sizes of DSCNVs in wheat, as well as their genome-wide distribution and potential functions are poorly known. Here, we identified 198,985 DSCNVs by investigating 491 genomes of common wheat, which accounted for 20% of the entire genome. Interestingly, approximately 38% of genes were linked to DSCNVs. The number of DSCNVs within each accession ranged between 47,366 to 96,342, with a total size varying from 421.3 to 1267.9 Mb. Furthermore, we found that 957 and 1,304 DSCNVs had been favored by breeders in China and the United States, respectively. By conducting DSCNVs-based genome-wide association studies for the principal component of plant development and yield component traits, 34 loci were identified to be directly or indirectly involved in controlling multiple traits formation. Notably, a newly discovered DSCNVs covering TaFT-D1 exhibited a significant association with flowering time and other agronomic traits. Overall, our findings highlight the potential of DSCNVs in driving fundamental discoveries in plant science. The comprehensive DSCNVs map and DSCNV-associated genes should also facilitate future research efforts to improve wheat yield, quality and adaption.
Keywords: Common wheat; DNA-segment copy number variation; GWAS; flowering time; whole-genome resequencing.
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