Weed competitive ability (WCA) is vital for the improvement of grain yield under direct-seeded and aerobic rice ecosystems where weeds are a major limiting factor. Early seed germination (ESG) and early seedling vigor (ESV) are the crucial traits for WCA. This study attempted to map the quantitative trait loci (QTLs) and hotspot regions governing ESG and ESV traits. A total of 167 BC1F5 selective introgression lines developed from an early backcross population involving Weed Tolerant Rice 1 (WTR-1) as the recipient parent and Y-134 as the donor parent were phenotyped for ESG and ESV traits. Analysis of variance revealed significant differences in ESG-related traits except for root length and in ESV-related traits except for plant height at 7 days after sowing. A total of 677-high quality single nucleotide polymorphism (SNP) markers were used to analyze the marker-trait association from a 6 K SNP genotyping array. Forty-three QTLs were identified on all chromosomes, except on chromosomes 4 and 8. Thirty QTLs were contributed by a desirable allele from Y-134, whereas 13 QTLs were from WTR-1. Twenty-eight of the identified genetic loci associated with ESG and ESV traits were novel. Two QTL hotspot regions were mapped on chromosomes 11 and 12. The genomic regions of QTL hotspots were fine-tuned and a total of 13 putative candidate genes were discovered on chromosomes 11 and 12 collectively. The mapped QTLs will be useful in advancing the marker aided-selection schemes and breeding programs for the development of rice cultivars with WCA traits. Electronic supplementary material The online version of this article (10.1007/s10681-020-02694-8) contains supplementary material, which is available to authorized users.

中文翻译：

---

水稻早期发芽和与杂草竞争能力相关的幼苗活力性状数量性状位点的鉴定


在杂草是主要限制因素的直播和好氧水稻生态系统中，杂草竞争能力（WCA）对于提高粮食产量至关重要。早期种子发芽 (ESG) 和早期幼苗活力 (ESV) 是 WCA 的关键性状。本研究试图绘制控制 ESG 和 ESV 性状的数量性状基因座 (QTL) 和热点区域。总共 167 个 BC1F5 选择性基因渗入系由早期回交群体发育而成，其中耐杂草水稻 1 (WTR-1) 作为受体亲本，Y-134 作为供体亲本，对 ESG 和 ESV 性状进行了表型分析。方差分析显示，播种后 7 天，除根长外的 ESG 相关性状和除株高外的 ESV 相关性状存在显着差异。总共 677 个高质量单核苷酸多态性 (SNP) 标记用于分析 6 K SNP 基因分型阵列中的标记-性状关联。除 4 号和 8 号染色体外，所有染色体上均鉴定出 43 个 QTL。其中 30 个 QTL 由 Y-134 的理想等位基因贡献，而 13 个 QTL 来自 WTR-1。已识别的与 ESG 和 ESV 性状相关的基因位点中有 28 个是新的。在11号和12号染色体上定位了两个QTL热点区域。对QTL热点基因组区域进行微调，在11号和12号染色体上总共发现了13个假定的候选基因。定位的 QTL 将有助于推进标记辅助选择方案和育种计划，以开发具有 WCA 性状的水稻品种。电子补充材料 本文的在线版本 (10.1007/s10681-020-02694-8) 包含补充材料，可供授权用户使用。