López-Malvar Ana, Reséndiz-Ramirez Zoila, Butrón Ana, Jiménez-Galindo Jose Cruz, Revilla Pedro, Malvar Rosa Ana
Facultad, de Biología, Departamento de Biología Vegetal Y Ciencias del Suelo, Universidad de Vigo, Vigo, Spain.
Agrobiología Ambiental, Calidad de Suelos Y Plantas (UVIGO), Unidad Asociada a La MBG (CSIC), Vigo, Spain.
Front Plant Sci. 2024 Oct 22;15:1404881. doi: 10.3389/fpls.2024.1404881. eCollection 2024.
Validations of previously detected quantitative trait loci (QTLs) to assess their reliability are crucial before implementing breeding programs. The objective of this study was to determine the reliability and practical usefulness of previously reported QTLs for resistance to stem tunneling by the Mediterranean stem borer (MSB) and yield. These authors used approximately 600 recombinant inbred lines (RILs) from a multiparent advanced generation intercross (MAGIC) population to map QTL using a genome-wide association study (GWAS) approach.
We identified RILs situated at the extremes of resistance and yield distributions within the whole MAGIC, and those QTLs were evaluated and crossed to a tester (A638) using lattice designs. In each set, a significant single-nucleotide polymorphism (SNP) was considered validated if (1) the same SNP was associated with the trait with a -value < 0.02, or (2) within a ±2-Mbp interval, an SNP associated with the trait exhibited a -value < 0.02 and demonstrated linkage disequilibrium (2 > 0.2) with the SNPs previously reported.
The novel QTL validation approach was implemented using improved experimental designs that led to higher heritability estimates for both traits compared to those estimated with the whole MAGIC population. The procedure used allowed us to jointly validate several QTL and to ascertain their possible contribution to hybrid improvement. Specifically, nearly three-quarters of the QTLs for tunnel length were confirmed. Notably, QTLs located in the genomic region 6.05-6.07 were consistently validated across different sets and have been previously linked to resistance against stalk tunneling in various mapping populations. For grain yield, approximately 10 out of 16 QTLs were validated. The validation rate for yield was lower than for tunnel length, likely due to the influence of dominance and/or epistatic effects. Overall, 9 out of 21 QTLs for tunnel length and 6 out of 17 QTLs for grain yield identified in our previous research were validated across both validation sets, indicating a moderate genetic correlation between and testcross performance of inbred lines. These findings offer insights into the reliability of QTL and genomic predictions, both derived from assessments conducted on the entire MAGIC population. Genomic predictions for tunnel length based on inbred line evaluations could be useful to develop more resistant hybrids; meanwhile, genomic prediction for yield could only be valid in a homozygous background.
在实施育种计划之前，验证先前检测到的数量性状位点（QTL）以评估其可靠性至关重要。本研究的目的是确定先前报道的抗地中海茎螟（MSB）茎蛀和产量QTL的可靠性和实际实用性。这些作者使用来自多亲本高级世代杂交（MAGIC）群体的约600个重组自交系（RIL），采用全基因组关联研究（GWAS）方法绘制QTL图谱。
我们在整个MAGIC群体中确定了位于抗性和产量分布极端位置的RIL，并对这些QTL进行评估，并使用格子设计与一个测试品种（A638）杂交。在每组中，如果满足以下条件，则认为一个显著的单核苷酸多态性（SNP）得到验证：（1）同一个SNP与该性状相关，P值<0.02；或（2）在±2-Mbp区间内，与该性状相关的SNP的P值<0.02，并且与先前报道的SNP表现出连锁不平衡（r²>0.2）。
采用改进的实验设计实施了新的QTL验证方法，与使用整个MAGIC群体估计的结果相比，这两个性状的遗传力估计值更高。所使用的程序使我们能够联合验证多个QTL，并确定它们对杂种改良的可能贡献。具体而言，近四分之三的隧道长度QTL得到了确认。值得注意的是，位于基因组区域6.05-6.07的QTL在不同组中均得到一致验证，并且先前已与各种作图群体中的抗茎蛀性相关联。对于籽粒产量，16个QTL中约有10个得到了验证。产量的验证率低于隧道长度，可能是由于显性和/或上位性效应的影响。总体而言，我们先前研究中确定的21个隧道长度QTL中有9个以及17个籽粒产量QTL中有6个在两个验证组中均得到验证，表明近交系的测验种表现与性状之间存在中等程度的遗传相关性。这些发现为源自对整个MAGIC群体进行评估的QTL和基因组预测的可靠性提供了见解。基于近交系评估的隧道长度基因组预测对于培育更抗虫的杂种可能有用；同时，产量的基因组预测仅在纯合背景下才有效。
