Mekonnen Tilahun, Sneller Clay H, Haileselassie Teklehaimanot, Ziyomo Cathrine, Abeyo Bekele G, Goodwin Stephen B, Lule Dagnachew, Tesfaye Kassahun
Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
Biosciences Eastern and Central Africa (BecA), Nairobi, Kenya.
Front Plant Sci. 2021 Sep 24;12:671323. doi: 10.3389/fpls.2021.671323. eCollection 2021.
Septoria tritici blotch, caused by the fungus , poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant ( ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs ( = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.
由该真菌引起的小麦叶枯病，对埃塞俄比亚乃至全球的小麦种植构成了严重且持久的挑战。推广抗性品种是控制小麦叶枯病（STB）的主要组成部分。因此，本研究的目的是阐明由178个面包小麦基因型组成的关联群体中STB抗性的基因组结构。该关联群体在三个地点进行了为期2年的STB抗性、物候期、产量及产量相关性状的表型鉴定。该群体还使用测序分型（GBS）方法对单核苷酸多态性（SNP）标记进行了基因分型，后续分析共使用了7776个多态性SNP。还使用基因组关联和预测综合工具（GAPIT）计算了标记-性状关联。该研究随后发现，STB抗性的广义遗传力在个体水平和跨环境水平分别为0.58至0.97和0.72至0.81，表明关联群体中存在STB抗性等位基因。群体结构和主成分分析检测到两个混合程度较高的亚组。对338,125个标记对进行的连锁不平衡（LD）分析也检测到27.6%的标记对存在显著（≤0.01）连锁。具体而言，在所有染色体上，SNP之间的LD在2.26 - 105.62 Mbp范围内下降，总体平均值为31.44 Mbp。此外，关联分析确定了53个与STB抗性显著相关（错误发现率，FDR，<0.05）的位点，进一步指向33个假定的数量性状位点（QTL）。其中大多数与已发表的叶枯病抗性基因位于相似染色体上，这些基因分布在1B、1D、2A、2B、2D、3A、3B、3D、4A、5A、5B、6A、7A、7B和7D染色体上。然而，在1A、5D和6B染色体上鉴定出的5个假定QTL似乎是新的。在国际小麦基因组测序联盟（IWGSC）参考序列注释v2.1上剖析检测到的位点，发现在已鉴定的QTL区域存在与植物防御反应相关的抗病基因。这些假定的QTL解释了总表型变异的2.7 - 13.2%。7个STB抗性QTL（= 2.7 - 10.8%）也与农艺性状的标记-性状关联（MTA）共定位。总体而言，本分析报告了成株对STB抗性和一些重要农艺性状的假定QTL。已鉴定出先前报道的和新的QTL，表明通过标记辅助选择将QTL聚合有可能提高STB抗性。
