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Genome-wide association mapping of aluminum toxicity tolerance and fine mapping of a candidate gene for Nratl in rice

文献类型： 外文期刊

作者： Tao, Yonghong 1 ; Niu, Yanan 1 ; Wang, Yun 1 ; Chen, Tianxiao 1 ; Naveed, Shahzad Amir 1 ; Zhang, Jian 2 ; Xu, Jianlon 1 ;

作者机构： 1.Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, Beijing, Peoples R China

2.Beijing Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Beijing, Peoples R China

3.Chinese Acad Agr Sci, Shenzhen Inst Breeding & Innovat, Shenzhen, Peoples R China

4.Chinese Acad Agr Sci, Shenzhen Inst Breeding & Innovat, S

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2018 年 13 卷 6 期

页码：

收录情况： SCI

摘要： Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on combined haplotype analysis and functional annotation, and the most likely candidate gene(s) for each important QTL were also discussed. Also a candidate gene Nratl on chromosome 2 was further fine-mapped using BSA-seq and linkage analysis in the F2 population derived from the cross of Al tolerant accession CC105 and super susceptible accession CC180. A new non-synonymous SNP variation was observed at Nratl between CC105 and CC180, which resulted in an amino-acid substitution from Ala (A) in CC105 to Asp (D) in CC180. Haplotype analysis of Nratl using 327 3K RGP accessions indicated that minor allele variations in aus and indica subpopulations decreased Al toxicity tolerance in rice. The candidate genes identified in this study provide valuable information for improvement of Al toxicity tolerance in rice. Our research indicated that minor alleles are important for QTL mapping and its application in rice breeding when natural gene resources are used.

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