QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management

Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, ‘Attila’ and ‘CDC Go’, and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management. Here, we evaluated 167 RILs for number of tillers (tillering), flowering time, maturity, plant height, test weight (grain volume weight), 1000 kernel weight, grain yield, and grain protein content at seven conventionally managed environments from 2008 to 2014. Using inclusive composite interval mapping (ICIM) on phenotypic data averaged across seven environments and a subset of 1203 informative markers (1200 SNPs and 3 gene specific markers), we identified a total of 14 QTLs associated with flowering time (1), maturity (2), plant height (1), grain yield (1), test weight (2), kernel weight (4), tillering (1) and grain protein content (2). Each QTL individually explained from 6.1 to 18.4% of the phenotypic variance. Overall, the QTLs associated with each trait explained from 9.7 to 35.4% of the phenotypic and from 22.1 to 90.8% of the genetic variance. Three chromosomal regions on chromosomes 2D (61–66 cM), 4B (80–82 cM) and 5A (296–297 cM) harbored clusters of QTLs associated with two to three traits. The coincidental region on chromosome 5A harbored QTL clusters for both flowering and maturity time, and mapped about 2 cM proximal to the Vrn-A1 gene, which was in high linkage disequilibrium (0.70 ≤ r2 ≤ 0.75) with SNP markers that mapped within the QTL confidence interval. Six of the 14 QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each) were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision) for organic management.本研究前期以两个春小麦（Triticum aestivum L.）栽培品种‘Attila’与‘CDC Go’杂交构建的重组自交系（recombinant inbred lines, RILs）群体为材料，利用小麦90K单核苷酸多态性（single nucleotide polymorphic, SNP）芯片及3个基因特异性标记（Ppd-D1、Vrn-A1和Rht-B1），探究了其对有机管理下3个环境中8个农艺性状数量性状位点（quantitative trait loci, QTL）检测的影响。本研究的目标为：采用与有机管理试验相同的标记集，探究常规栽培管理对同一作图群体QTL检测的影响，并将结果与有机管理条件下的结果进行对比。 本研究于2008至2014年间，在7个常规管理环境下对167个RILs的分蘖数、抽穗期、成熟期、株高、容重（籽粒体积重量）、千粒重、籽粒产量及籽粒蛋白质含量进行了表型鉴定。基于7个环境的平均表型数据及1203个有效标记（1200个SNP与3个基因特异性标记），利用完备复合区间作图法（inclusive composite interval mapping, ICIM）进行分析，本研究共鉴定到14个与目标性状相关的QTL：其中抽穗期1个、成熟期2个、株高1个、籽粒产量1个、容重2个、千粒重4个、分蘖数1个、籽粒蛋白质含量2个。单个QTL可解释6.1%~18.4%的表型变异；针对各性状的QTL集合总体可解释9.7%~35.4%的表型变异与22.1%~90.8%的遗传变异。在2D染色体（61~66 cM区间）、4B染色体（80~82 cM区间）与5A染色体（296~297 cM区间）上共存在3个QTL簇区间，每个区间内的QTL可关联2~3个目标性状。其中5A染色体上的重合区间同时包含抽穗期与成熟期的QTL簇，其定位位置距Vrn-A1基因约2 cM的近端区域；该基因与QTL置信区间内的SNP标记存在较高的连锁不平衡（0.70 ≤ r² ≤ 0.75）。在14个QTL中，有6个（抽穗期与株高各1个、成熟期与千粒重各2个）在常规管理与有机管理体系中均被检测到，这表明直接基于常规管理条件下的基因发掘结果开展有机生产体系的精细化选择（决策）存在一定局限性。