Jizeng Jia;; Guangyao Zhao;; Danping Li;; Kai Wang;; Chuizheng Kong;; Pingchuan Deng;; Xueqing Yan;; Xueyong Zhang;; Zefu Lu;; Shujuan Xu;; Yuannian Jiao;; Kang Chong;; Xu Liu;; Dangqun Cui;; Guangwei Li;; Yijing Zhang;; Chunguang Du;; Liang Wu;; Tianbao Li;; Dong Yan; Kehui Zhan;; Feng Chen;; Zhiyong Wang;; Lichao Zhang;; Xiuying Kong;; Zhengang Ru;; Daowen Wang;; Lifeng Gao

Molecular Plant; 2023; IF 27.50

DOI:10.1016/j.molp.2023.10.015

ABSTRACT

Despite the progress made recently in crop genomics studies, the genomic changes brought by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding especially in the polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparisons between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes occurred in recent wheat varietal improvement. Furthermore, we explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based GWAS (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using the genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progenies, many of which could substantially improve wheat yield and related traits. We builded a website (available in https://triticeae.henau.edu.cn/aikang58/) in which data download of AK58 genome assembly sequence and annotation, blast analysis and Jbrowse could be performed. Our work enriches wheat genome resources, provides new insight into the genomic changes involved in modern wheat improvement, and suggests that efficient mining of elite HHs may contribute substantially to genomics-assisted breeding in common wheat and other polyploid crops.