Zhao Jiajia, Li Xiaohua, Qiao Ling, Zheng Xingwei, Wu Bangbang, Guo Meijun, Feng Meichen, Qi Zengjun, Yang Wude, Zheng Jun
College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China.
Institute of Wheat Research, Shanxi Agricultural University, Linfen, China.
Theor Appl Genet. 2023 Mar 10;136(3):37. doi: 10.1007/s00122-023-04283-4.
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
结构变异在植物基因组中很常见，影响小麦的减数分裂重组和分离畸变。存在/缺失变异会显著影响小麦的耐旱性。干旱是限制小麦产量的主要非生物胁迫。普通小麦具有复杂的基因组，由三个亚基因组组成，其中存在大量结构变异（SVs）。SVs在理解植物驯化的遗传贡献和表型可塑性方面起着关键作用，但对其基因组特征及其对耐旱性的影响了解甚少。在本研究中，构建了180个双单倍体（DHs）的高分辨率核型。涉及亲本之间信号多态性，与分布在21条染色体的7条（2A、4A、5A、7A、3B、7B和2D）上的8个串联重复序列（TR）的存在/缺失变异（PAVs）有关。其中，2D染色体上的PAV表现出分离畸变，其他的在群体中以1:1的分离比例正常传递；并且在2A染色体上发生了PAV重组。对不同水分条件下PAV与表型性状进行关联分析，我们发现4A、5A和7B染色体上的PAV对粒长（GL）和粒宽（GW）有负面影响；7A染色体上的PAV对粒厚（GT）和穗长（SL）有相反影响，不同水分条件下对性状的影响不同。连锁群2A、4A、7A、2D和7B上的PAV与耐旱系数（DTCs）相关，在7B染色体上的PAV对抗旱值（D值）有显著负面影响。此外，使用90K SNP芯片对与表型性状相关的数量性状位点（QTL）分析表明，4A染色体上与DTCs和粒相关性状的QTL，以及5A、3B染色体上的QTL共定位于PAVs的差异区域。这些PAVs可导致SNP目标区域的分化，可通过标记辅助选择（MAS）育种用于干旱胁迫下农艺性状的遗传改良。
