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Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel
Frontiers in Plant Science ( IF 5.6 ) Pub Date : 2020-10-02 , DOI: 10.3389/fpls.2020.576479
Caijin Chen , Gareth J. Norton , Adam H. Price

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.



中文翻译:

利用孟加拉和阿萨姆邦研究小组进行的水培和土壤系统中水稻幼苗耐盐性的全基因组关联映射

盐分是一种主要的非生物胁迫,它抑制了许多国家(例如印度和孟加拉国)的沿海,干旱和半干旱地区的水稻生产。鉴定耐盐品种,数量性状位点(QTL)和基因对于育种耐盐水稻至关重要。的水稻亚群被认为主要起源于孟加拉国和印度,并且具有丰富的遗传多样性,在非生物胁迫抗性方面差异很大。这项研究的目的是鉴定QTL,然后使用来自并比较两种不同苗期筛选方法的结果。在控制和盐胁迫条件下,对在水培法和土壤法中生长的204种孟加拉和阿萨姆族人(BAAP)水稻品种进行了水稻幼苗期的耐盐性评估。测量了胁迫症状,植物生长以及钠和钾含量的十个盐相关性状。在两个系统中,三个品种BRRI dhan 47,Goria和T 1的耐盐性均高于耐性Pokkali。使用控制种群结构和亲缘关系的有效混合模型(EMMA)和显着性阈值对200万个SNP的盐指数特征进行了全基因组关联映射P<0.0001用于确定重要的SNP。分别确定了与水培和土壤系统性状相关的97个和74个QTL,包括在两个系统中鉴定的11个QTL。共发现65个候选基因,包括一个著名的主要基因OsHKT1; 5。在1号染色体上的40 Mb处检测到最显着的QTL,这与两个翻译后修饰的SUMOylation基因(OsSUMO1OsSUMO2),对此QTL进行了调查。此处鉴定的耐盐水稻品种和QTL /基因将为以后的遗传和耐盐水稻育种研究提供有用的信息。

更新日期:2020-10-28
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