Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).
Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).
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DOI：
10.1093/dnares/dsu046
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发表时间：
2015-04
期刊：
影响因子：
--
通讯作者：
Mohapatra T
中科院分区：
文献类型：
--
作者：
Kumar V;Singh A;Mithra SV;Krishnamurthy SL;Parida SK;Jain S;Tiwari KK;Kumar P;Rao AR;Sharma SK;Khurana JP;Singh NK;Mohapatra T
水稻的耐盐性是在盐碱地区保持生产的重要条件。它是一个复杂的数量性状，具有不同的组成部分，可以有效地解剖全基因组关联研究（GWAS）。在这里，我们实施GWAS来确定控制水稻耐盐性的基因座。一个定制设计的阵列基于6,000个单核苷酸多态性（SNPs）在尽可能多的压力响应基因，分布在12个水稻染色体上的平均物理间隔<100 kb，使用Infinium高通量测定基因型220水稻品种。在田间条件下，在生殖阶段与12个不同的性状记录在这些加入进行了遗传关联分析。我们发现20个SNPs（位点）显着相关的Na+/K+比，44个SNPs与其他性状在胁迫条件下观察。通过GWAS鉴定的各种盐度指数的位点解释了5-18%的表型方差。水稻1号染色体上控制水稻苗期耐盐性的主效数量性状位点Saltol与水稻生殖期Na+/K+比值存在主效关系。除Saltol外，我们还发现了代表第4、6和7染色体上新QTL的GWAS峰。目前的关联作图小组包含了大部分籼稻种质，可以作为新的耐盐基因和等位基因的来源。本研究中使用的基于基因的SNP阵列被发现具有成本效益和效率，在揭示基因组区域/候选基因调节水稻耐盐胁迫。
Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na+/K+ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na+/K+ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.
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DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
5.4
作者：
Cai, HW;Morishima, H
通讯作者：
Morishima, H
拟南芥中全基因组的关联映射确定了先前已知的开花时间和病原体抗性基因。
影响因子：
4.5
作者：
Aranzana MJ;Kim S;Zhao K;Bakker E;Horton M;Jakob K;Lister C;Molitor J;Shindo C;Tang C;Toomajian C;Traw B;Zheng H;Bergelson J;Dean C;Marjoram P;Nordborg M
通讯作者：
Nordborg M
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y