Chen Ling, Tao Yue, Song Chengxiang, Liu Yike, Tong Hanwen, Ning Qiang, Zou Juan, Fu Penghao, Zhang Yuqing, Gao Chunbao, Zhu Zhanwang
Institute of Food Crops, Hubei Academy of Agricultural Sciences/Central China Wheat Disease Biology Research Station of Ministry of Agriculture and Rural Affairs/Hubei Engineering and Technology Research Center of Wheat/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement/Key Laboratory of Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, 430064, China.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
BMC Plant Biol. 2025 Jul 29;25(1):973. doi: 10.1186/s12870-025-07039-y.
Pre-harvest sprouting (PHS) is a serious problem in wheat production globally. Grain color (GC) has a notable impact on PHS resistance, red grains typically show higher resistance compared to white grains. To understand the genetic factors influencing PHS and GC, a genome-wide association study (GWAS) was conducted on a natural population of 235 wheat cultivars using a 90 K single nucleotide polymorphism (SNP) arrays.
A strong correlation between PHS and GC was observed, with the highest correlation coefficient of 0.85 (P < 0.0001). Association mapping was performed using four different models (BLINK, FarmCPU, MMLM and MLM) in the GAPIT along with MLM model in the Tassel. The study identified twelve stable quantitative trait loci (QTLs) related to PHS resistance and another twelve stable QTLs associated with GC. Notably, six QTLs for PHS resistance were newly discovered, explaining 5.8-10.0% of the phenotypic variation. Additionally, four common QTLs were identified that are linked to both PHS resistance and GC. Among these, Qphs.hbaas-3B.2/Qgc.hbaas-3B.2 and Qphs.hbaas-3D/Qgc.hbaas-3D were recognized as major loci significantly affecting both traits, likely associated with the genes Tamyb-B1 and Tamyb-D1, respectively. The other two new QTLs on chromosome 2B explained 7.0-10.0% of phenotypic variation in PHS resistance and 4.7-7.4% of phenotypic variation in GC. Furthermore, six candidate genes associated with PHS resistance were predicted, warranting further investigation. Three KASP markers IACX5850, Tdurum_contig11028_236 and wsnp_Ex_c269_518324 linked to three QTLs (Qphs.hbaas-2B.2, Qphs.hbaas-2B.4, and Qphs.hbaas-7B.2) are applicable for marker-assisted selection in wheat breeding to enhance PHS resistance.
This study provides valuable genetic loci and KASP markers that can enhance PHS resistance in wheat breeding programs and offers insights for discovering PHS resistance genes.
收获前发芽（PHS）是全球小麦生产中的一个严重问题。籽粒颜色（GC）对PHS抗性有显著影响，通常红色籽粒比白色籽粒表现出更高的抗性。为了了解影响PHS和GC的遗传因素，利用90K单核苷酸多态性（SNP）芯片对235个小麦品种的自然群体进行了全基因组关联研究（GWAS）。
观察到PHS与GC之间存在强相关性，最高相关系数为0.85（P < 0.0001）。在GAPIT中使用四种不同模型（BLINK、FarmCPU、MMLM和MLM）以及在Tassel中使用MLM模型进行关联作图。该研究鉴定出12个与PHS抗性相关的稳定数量性状位点（QTL）和另外12个与GC相关的稳定QTL。值得注意的是，新发现了6个PHS抗性QTL，解释了5.8 - 10.0%的表型变异。此外，鉴定出4个与PHS抗性和GC均相关的共同QTL。其中，Qphs.hbaas - 3B.2/Qgc.hbaas - 3B.2和Qphs.hbaas - 3D/Qgc.hbaas - 3D被认为是显著影响这两个性状的主要位点，可能分别与Tamyb - B1和Tamyb - D1基因相关。2B染色体上的另外两个新QTL解释了PHS抗性中7.0 - 10.0%的表型变异和GC中4.7 - 7.4%的表型变异。此外，预测了6个与PHS抗性相关的候选基因，值得进一步研究。与三个QTL（Qphs.hbaas - 2B.2、Qphs.hbaas - 2B.4和Qphs.hbaas - 7B.2）连锁的三个KASP标记IACX5850、Tdurum_contig11028_236和wsnp_Ex_c269_518324可用于小麦育种中的标记辅助选择，以提高PHS抗性。
本研究提供了有价值的遗传位点和KASP标记，可在小麦育种计划中提高PHS抗性，并为发现PHS抗性基因提供了见解。
