Genome-wide association studies of 14 agronomic traits in rice landraces

Huang, Xuehui; Wei, Xinghua; Su, Tao; Zhao, Qiang; Feng, Qi; Zhao, Yan; Li, Canyang; Zhu, Chuanrang; Lu, Tingting; Zhang, Zhiwu; Li, Meng; Fan, Danlin; Guo, Yunli; Wang, Ahong; Wang, Lu; Deng, Liuwei; Li, Wenjun; Lu, Yiqi; Weng, Qijun; Liu, Kunyan; Huang, Tao; Zhou, Tong; Jing, Yufeng; Li, Wei; Lin, Zhang; Buckler, Edward S.; Qian, Qian; Zhang, Qifa; Li, Jiayang; Han, Bin

doi:10.1038/ng.695

Cited by 1,832 publications

(1,554 citation statements)

References 39 publications

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“…In the soybean landraces and improved cultivars, LD increased to 83 kb and 133 kb, respectively (Fig. 2a), similar to that of cultivated rice (123 kb and 167 kb in indica and japonica, respectively) 18 but much higher than cultivated maize (30 kb) 5 . All three populations had low background LD values, but wild soybean had a relatively higher value (Supplementary Fig.…”

Section: Genomic Variationmentioning

confidence: 55%

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

et al. 2015

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Section: Genomic Variationmentioning

confidence: 55%

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

et al. 2015

View full text Add to dashboard Cite

“…4). The level of population differentiation, F ST , was estimated at 0.18 among the groups of O. rufipogon, which is much lower than that of O. sativa (,0.55 on average 21 ). The differentiation was not evenly distributed across the rice genome ( Supplementary Fig.…”

Section: Analysis Of Wild Rice Populationsmentioning

confidence: 79%

“…We found that the decay rate of linkage disequilibrium in O. rufipogon, expressed as r 2 , dropped to half of its maximum value at ,20 kilobases (kb) on average ( Supplementary Fig. 6), which is much more rapid than that in O. sativa (,123 kb and ,167 kb in indica and japonica, respectively) 21 . To perform GWAS in O. rufipogon, we used the k-nearest neighbour algorithm for data imputation (Supplementary Table 6), and phenotyped the O. rufipogon population for two traits, leaf sheath colour and tiller angle.…”

Section: Analysis Of Wild Rice Populationsmentioning

confidence: 89%

A map of rice genome variation reveals the origin of cultivated rice

Huang

Kurata

Wei

et al. 2012

Nature

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Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

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“…Although bi-parental mapping populations are a good method for gene cloning, limitation of genetic diversity and long time period with less resolution are the shortcoming for discovering more new genes (Pradhan et al 2016). The genome-wide association study (GWAS) method has proved to be very useful for dissecting complicated quantitative traits based on a linkage disequilibrium mapping approach (Huang et al 2010(Huang et al , 2012b(Huang et al , 2016. Recently, several studies have used GWAS to explore cold tolerance in rice.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

Zhang

et al. 2018

Plant Cell Rep

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Key message A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Abstract Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.

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Genome-wide association studies of 14 agronomic traits in rice landraces

Cited by 1,832 publications

References 39 publications

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

A map of rice genome variation reveals the origin of cultivated rice

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

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