Background

Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited.

Results

Here, an F_2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F_2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress.

Conclusion

These results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).

中文翻译：

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使用QTL-Seq和RNA-Seq鉴定水稻（Oryza sativa L.）芽爆发期的主要QTL和耐盐性候选基因分析。

背景

盐胁迫是限制全球水稻产量的主要非生物胁迫之一。在直接播种栽培模型中，芽爆发期的水稻耐盐性直接影响幼苗的成活率和最终产量。然而，关于芽胞爆发期耐盐性的数量性状基因座（QTL）作图和基于图谱的克隆的报道是有限的。

结果

在这里，使用基于全基因组测序的QTL-Q，从IR36（对盐敏感）和Weiguo（对盐敏感）之间杂交得到的F _2：3种群用于鉴定芽萌芽期的耐盐QTL间隔。 seq包含40个极端耐盐和40个极端耐盐的个体。使用ΔSNP索引算法和欧几里德距离（ED）算法在7号染色体上检测到与相对芽长（RSL）相关的主要QTL qRSL7。根据父母之间的单核苷酸多态性（SNPs），等位基因特异的25 Kompetitive PCR（KASP）标记物附近开发qRSL7，以及使用个人199从F进行区域QTL作图_2：3的人口。然后我们确认并缩小范围qRSL7至222 kb基因组间隔。此外，盐胁迫和控制条件在芽爆发阶段后36小时，对IR36和Weiguo进行了RNA测序（RNA-seq），并在候选区域中检测到5个差异表达基因（DEG）。qRT-PCR结果显示与RNA-seq数据相同的表达模式。此外，序列分析揭示了IR36和Weiguo之间的Os07g0569700（OsSAP16）有1 bp的Indel差异。OsSAP16编码一种与压力相关的蛋白质，其表达在干旱胁迫下会增加。

结论

这些结果表明，OsSAP16是的候选基因qRSL7。该结果对于qRSL7的基因克隆和通过标记辅助选择（MAS）提高水稻品种的耐盐性是有用的。