Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

Yano, Kenji; Yamamoto, Eiji; Aya, Koichiro; Takeuchi, Hideyuki; Lo, Pei Ching; Li, Hu; Yamasaki, Mariko; Yoshida, Shigeo; Kitano, Hidemi; Hirano, Ken; Matsuoka, Makoto

doi:10.1038/ng.3596

Cited by 522 publications

(381 citation statements)

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“…Although recently, some GWAS involved over a million SNP markers (Huang et al 2015), given the extent of linkage disequilibrium in both panels, the genome coverage should have been sufficient to detect most of the loci involved in rice blast resistance. The drawback is that the resolution power of GWAS should be limited as many candidate genes may be detected in a same LD block (Yano et al 2016). Still, a higher density of markers may allow localizing with more precision causative genes and polymorphisms.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, GWAS may not be able to detect the phenotypic effects of rare alleles (present at very low frequencies in the populations studied) and GWAS detection power may decrease in the case of loci involving multiple allelic variants (Morris and Kaplan 2002), which may explain why GWAS have only unraveled a small portion of phenotypic variance (Zuk et al 2014). Despite these constraints, GWAS have been successfully used to dissect complex traits in many crop species including maize (Buckler et al 2009), sorghum (Morris et al 2013) and rice (Huang et al 2010; Zhao et al 2011; Huang et al 2012; Courtois et al 2013; Huang et al 2015; Si et al 2016; Yano et al 2016). Incorporation of GWAS information in genomic selection models has also proved able to improve the accuracy of predictions and should consequently be used in rice breeding programs (Spindel et al 2015; Spindel et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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Association mapping of resistance to rice blast in upland field conditions

Raboin

Ballini

Tharreau

et al. 2016

Rice

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BackgroundRice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers.ResultsThe contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance.ConclusionsIt was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0131-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Association mapping of resistance to rice blast in upland field conditions

Raboin

Ballini

Tharreau

et al. 2016

Rice

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“…Two of the three genes involved in microtubule-based process, and another one associated with glycolytic pathway and expressed in response to abiotic stress. Recently, many novel genes have been cloned as a result of GWAS (Duan et al 2017, Si et al 2016Yano et al 2016). However, in our study, because the genotype was from the 5K SNPs array, the SNPs density was insufficient to cover every gene.…”

Section: Identification Of Candidate Gene Controlling Cold Tolerancementioning

confidence: 92%

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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“…Compared to QTL analysis, GWAS is based on natural populations, and can detect multiple alleles at the same site (Flint-Garcia et al, 2003). GWAS have widely been used in human genetic studies as well as in plants, such as Arabidopsis , maize, sorghum, and rice (Atwell et al, 2010; Huang et al, 2011; Tian et al, 2011; Li et al, 2012; Riedelsheimer et al, 2012; Morris et al, 2013; Chen et al, 2014; Wen et al, 2014; Yang et al, 2014, 2015; Wang et al, 2015; Yano et al, 2016). Identification of the allelic variation underpinning the phenotypic diversity in rice will result in enormous practical implications for rice breeding.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Fěng

Wei

et al. 2016

Front. Plant Sci.

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Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.

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Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

Cited by 522 publications

References 78 publications

Association mapping of resistance to rice blast in upland field conditions

Association mapping of resistance to rice blast in upland field conditions

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

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

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