野生稻萌发期耐冷性 QTL 定位与候选基因鉴定

QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice.

机构信息

Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.

Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.

出版信息

Genes Genomics. 2023 Jul;45(7):867-885. doi: 10.1007/s13258-023-01394-6. Epub 2023 May 20.

DOI:10.1007/s13258-023-01394-6

PMID:37209287

Abstract

BACKGROUND

Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe.

OBJECTIVE

This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment.

METHODS

A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage.

RESULTS

A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11.

CONCLUSIONS

This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

摘要

背景

寒害胁迫显著影响水稻生长（发芽和幼苗），并在全球温带和高海拔地区造成严重的产量损失。

目的

本研究旨在探索水稻的耐寒性（CT）基因座，并创造新的耐寒种质资源。我们通过对表型在冷处理下的 CSSL 进行全基因组重测序，构建了一个具有强 CT 的染色体片段替换系（CSSL），并精细定位了与 CT 相关的数量性状位点（QTL）。

方法

利用耐寒野生稻 Y11（Oryza rufipogon Griff.）与感寒品种 GH998 杂交产生的 271 个 CSSL 系，构建了一个用于在发芽阶段定位 CT 相关 QTL 的染色体 CSSL。对 CSSL 进行全基因组重测序，以定位与发芽阶段 CT 相关的 QTL。

结果

利用 1484 个 bin 的全基因组重测序构建了 CSSL 的高密度连锁图谱。利用 615466 个单核苷酸多态性（SNP）进行 QTL 分析，在第 8 号染色体（qCTG-8）和第 11 号染色体（qCTG-11）上鉴定出 2 个与低温下发芽率相关的 QTL。qCTG-8 和 qCTG-11 分别解释了总表型变异的 14.55%和 14.31%。我们将 qCTG-8 和 qCTG-11 分别缩小到 195.5 和 78.83-kb 区域。根据 qCTG-8 和 qCTG-11 冷诱导表达分析中的基因序列，鉴定了不同组织中重要候选基因的表达模式以及 CSSL 的 RNA-seq。在 qCTG-8 中鉴定出 LOC_Os08g01120 和 LOC_Os08g01390 为候选基因，在 qCTG-11 中鉴定出 LOC_Os11g32880 为候选基因。