Table_4_Identification and validation of two major QTLs for spikelet number per spike in wheat (Triticum aestivum L.).xlsx

The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019–2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43–47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97–34.43 Mb), explained 13.97%–45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis–exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.

小麦的总小穗数（total spikelets, TSPN）与可育小穗数（fertile spikelets, FSPN）会影响最终每小穗的籽粒数。本研究以小麦种质10-A与B39杂交得到的包含152个重组自交系（recombinant inbred lines, RIL）的群体为材料，利用55K单核苷酸多态性（single nucleotide polymorphism, SNP）芯片构建了高密度遗传图谱。基于2019-2021年10个环境下的表型数据，共定位到24个控制总小穗数的数量性状基因座（quantitative trait loci, QTL）以及18个控制可育小穗数的QTL。其中两个主效QTL：QTSPN/QFSPN.sicau-2D.4（物理区间34.43–47.43 Mb）与QTSPN/QFSPN.sicau-2D.5（物理区间32.97–34.43 Mb），可解释13.97%~45.90%的表型变异。随后利用竞争性等位基因特异性PCR（kompetitive allele-specific PCR, KASP）标记对这两个QTL进行了验证，结果显示在10-A×BE89（134个RIL）、10-A×川农16（192个RIL）以及四川小麦群体（233份种质）中，QTSPN.sicau-2D.4对总小穗数的调控效应弱于QTSPN.sicau-2D.5。携带QTSPN/QFSPN.sicau-2D.5的10-A等位基因与QTSPN.sicau-2D.4的B39等位基因的单倍型组合3，可获得最高的小穗数；与之相反，两个位点均携带B39等位基因的材料，其小穗数最低。通过集群分离分析-外显子捕获测序（bulk-segregant analysis–exon capture sequencing），在这两个QTL区间内共鉴定到6个SNP热点区域，包含31个候选基因。本研究还从B39中鉴定到Ppd-D1a等位型，从10-A中鉴定到Ppd-D1d等位型，并对小麦中的Ppd-D1变异进行了深入分析。本研究鉴定的位点与分子标记具备小麦育种应用潜力，同时为这两个位点的后续精细定位与克隆奠定了基础。