Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole-genome resequencing (WGRS) based QTL-seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F₂), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late-flowering, and early-flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL-Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late-flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I-SP-383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties.

中文翻译：

---

使用 QTL-Seq 方法描绘控制扁豆 (Lens culinaris Medik.) 超早熟性状的基因座


开发早熟扁豆有可能最大限度地减少产量损失，尤其是在末期干旱期间。基于 QTL-seq 的全基因组重测序 (WGRS) 确定了控制扁豆早熟的基因座。成熟持续时间的遗传分析非常适合 3:1 分离 (F ₂ )，表明早熟是一种隐性性状。 Globe Mutant（晚亲本）、晚花和早花批量（来自 RIL）的 WGRS 分别生成了 1124.57、1052.24 百万个原始读数和干净读数。 QTL-Seq鉴定了3号染色体上的三个QTL（ LcqDTF3.1 、 LcqDTF3.2和LcqDTF3.3 ） ，具有246244个SNP和15577个插入/缺失（InDels）和13个开花途径基因。其中，11 个在批量和验证 (qPCR) 之间表现出序列变异，揭示了 9 个候选基因 ( LcGA20oxG 、 LcFRI 、 LcLFY 、 LcSPL13a 、 Lcu.2RBY.3g060720 、 Lcu.2RBY.3g062540 、 Lcu.2RBY.3g060720 、Lcu.2RBY.3g062540 、 Lcu.2RBY.3g060720和Lcu.2RBY.3g062540的表达存在显着差异。 3g062760 、 LcELF3a和LcEMF1 )。有趣的是， LcELF3a基因在晚花基因型中表现出显着较高的表达，并且在促进延迟方面表现出实质性参与。随后，从LcqDTF3开发出 InDel 标记（I-SP-383.9； LcELF3a基因）。 2 QTL 区域显示早熟性为 82.35% PVE（表型变异已解释）。对父母双方LcELF3a基因的克隆、测序和比较分析揭示了 23 个 SNP 和 InDels。 有趣的是，L4775 的LcELF3a基因中记录了 52 bp 的缺失，预计由于翻译过程中的移码，第 351 个氨基酸之外的 4 个错义氨基酸会导致蛋白质合成过早终止。鉴定出的 InDel 标记对于培育早熟扁豆品种具有巨大潜力。