Salinity stress is the most prominent stress impacting rice productivity worldwide. In the past, several quantitative trait loci (QTLs) for salinity tolerance had been identified in rice, however their utilization in rice breeding programs is largely confounded due to the unwanted linkage drag associated with the QTL region. Thus, it is strongly desirable to delimit the QTL region to a least possible chromosomal interval minimising any unwanted association. Addressing this, we have evaluated 68 recombinant inbred lines (RILs) derived from a cross between a salinity tolerant parent ‘Kolajoha’ and a salinity sensitive parent ‘Ranjit’ for identification of QTL(s) involved in imparting salinity tolerance at seedling stage. Genotyping by sequencing approach (GBS) was followed for SNP identification at genome wide scale. Around 3649 SNPs were identified by GBS method initially at 20% minor allele frequency. After filtering of SNPs with polymorphism with less than 10–15% of missing data, a total of 1248 SNPs were mapped to 1247 recombination points and the genetic map was constructed with a total map length of 1201.21 cM and resolution of 0.95 cM between markers. For 10 traits, a total of 23 additive QTLs were identified of which only 1 was a major QTL and 22 were minor QTLs. The average QTL interval size is about 2945 kb. Epistatic QTL mapping had identified one pair of QTLs that contribute significantly in the phenotypic variation of traits among the RILs. Total 1895 genes were identified in the QTL intervals, majority of them are located in Chr1 of rice genome between 22.09 and 38.29 Mb region. Although, this region is not very narrow, some of the genes falling in this region can be utilized for validation of QTLs in future. One differentially methylated region was found to be colocalized within the QTL intervals determined in Chr2 which indicates their potential role in epigenetic modifications in improving stress tolerance in rice.

中文翻译：

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印度阿萨姆邦传统芳香短粒水稻地方品种科拉乔哈（Oryza sativa L.）苗期耐盐性的数量性状基因座（QTL）和上位QTL的鉴定和定位

盐分胁迫是影响全球水稻产量的最突出的胁迫。过去，已经在水稻中鉴定了几个耐盐性的数量性状位点 (QTL)，但是由于与 QTL 区域相关的不需要的连锁阻力，它们在水稻育种计划中的应用在很大程度上受到了混淆。因此，强烈希望将 QTL 区域限定在尽可能少的染色体间隔内，从而最大限度地减少任何不需要的关联。为了解决这个问题，我们评估了来自耐盐亲本“Kolajoha”和盐度敏感亲本“Ranjit”之间杂交的 68 个重组自交系 (RIL)，用于鉴定涉及在幼苗阶段赋予耐盐性的 QTL。通过测序方法 (GBS) 进行基因分型，用于在全基因组范围内进行 SNP 鉴定。最初通过 GBS 方法以 20% 的次要等位基因频率鉴定了大约 3649 个 SNP。过滤掉缺失数据小于10%~15%的多态性SNPs后，共有1248个SNPs被定位到1247个重组点，构建的遗传图谱总长为1201.21cM，标记间分辨率为0.95cM。对于10个性状，共鉴定出23个附加QTL，其中只有1个是主要QTL，22个是次要QTL。平均 QTL 间隔大小约为 2945 kb。上位 QTL 定位确定了一对 QTL，它们对 RIL 之间性状的表型变异有显着贡献。在QTL区间共鉴定出1895个基因，其中大部分位于水稻基因组Chr1的22.09-38.29 Mb区域。虽然这个区域不是很窄，落入该区域的一些基因将来可用于验证 QTL。发现一个差异甲基化区域共定位在 Chr2 中确定的 QTL 区间内，这表明它们在表观遗传修饰中可能在提高水稻胁迫耐受性方面发挥作用。