Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran.
Cereal Department, Seed and Plant Improvement Institute, AREEO, Karaj, Iran, Karaj, Iran.
Sci Rep. 2022 Oct 25;12(1):17839. doi: 10.1038/s41598-022-22607-0.
Seed traits in bread wheat are valuable to breeders and farmers, thus it is important exploring putative QTLs responsible for key traits to be used in breeding programs. GWAS was carried out using 298 bread wheat landraces and cultivars from Iran to uncover the genetic basis of seed characteristics in both rain-fed and well-watered environments. The analyses of linkage disequilibrium (LD) between marker pairs showed that the largest number of significant LDs in landraces (427,017) and cultivars (370,359) was recorded in genome B, and the strongest LD was identified on chromosome 4A (0.318). LD decay was higher in the B and A genomes, compared to the D genome. Mapping by using mrMLM (LOD > 3) and MLM (0.05/m, Bonferroni) led to 246 and 67 marker-trait associations (MTAs) under rain-fed, as well as 257 and 74 MTAs under well-watered conditions, respectively. The study found that 3VmrMLM correctly detected all types of loci and estimated their effects in an unbiased manner, with high power and accuracy and a low false positive rate, which led to the identification of 140 MTAs (LOD > 3) in all environments. Gene ontology revealed that 10 and 10 MTAs were found in protein-coding regions for rain-fed and well-watered conditions, respectively. The findings suggest that landraces studied in Iranian bread wheat germplasm possess valuable alleles, which are responsive to water-limited conditions. MTAs uncovered in this study can be exploited in the genome-mediated development of novel wheat cultivars.
小麦种子特性对育种家和农民具有重要价值，因此探索负责关键特性的假定 QTL 并将其用于育种计划非常重要。本研究利用来自伊朗的 298 份小麦地方品种和栽培品种进行 GWAS，以揭示雨养和充分灌溉条件下种子特性的遗传基础。对标记对间连锁不平衡（LD）的分析表明，在地方品种（427017 个）和栽培品种（370359 个）中记录到最大数量的显著 LD，最强的 LD 位于 4A 染色体（0.318）上。与 D 基因组相比，B 和 A 基因组中的 LD 衰减更高。使用 mrMLM（LOD > 3）和 MLM（0.05/m，Bonferroni）进行作图导致在雨养条件下鉴定出 246 个和 67 个标记-性状关联（MTA），在充分灌溉条件下分别鉴定出 257 个和 74 个 MTA。研究发现，3VmrMLM 正确地以无偏的方式检测所有类型的位点并估计其效应，具有高功率和准确性以及低假阳性率，从而在所有环境中鉴定出 140 个 MTA（LOD > 3）。基因本体论揭示，在雨养和充分灌溉条件下，分别在蛋白质编码区发现了 10 个和 10 个 MTA。研究结果表明，在伊朗小麦种质中研究的地方品种具有响应水分限制条件的有价值等位基因。本研究中发现的 MTA 可用于新型小麦品种的基因组介导开发。
