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. 2016 Nov 29:7:1801.
doi: 10.3389/fpls.2016.01801. eCollection 2016.

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

Xiaosong Ma  1 , Fangjun Feng  2 , Haibin Wei  2 , Hanwei Mei  2 , Kai Xu  2 , Shoujun Chen  2 , Tianfei Li  2 , Xiaohua Liang  2 , Hongyan Liu  2 , Lijun Luo  1
Affiliations

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

Xiaosong Ma et al. Front Plant Sci. .

Abstract

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.

Keywords: GWAS; candidate genes; drought resistance; grain yield; plant height.

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Figures

Figure 1
Figure 1
Genome-wide manhattan plots of association mapping for plant height. (A) plant height under normal water condition in 2011; (B) plant height under drought stress condition in 2011; (C) plant height under normal water condition in 2012; (D) plant height under drought stress condition in 2012.
Figure 2
Figure 2
Genome-wide manhattan plots of association mapping for grain yield per plant. (A) grain yield under normal water condition in 2011; (B) grain yield under drought stress condition in 2011; (C) grain yield under normal water condition in 2012; (D) grain yield under drought stress condition in 2012.
Figure 3
Figure 3
Genome-wide manhattan plots of association mapping for drought resistant coefficient. (A) DRC in 2011; (B) DRC in 2012.
Figure 4
Figure 4
Analysis of seeding height and root length for the mutant of OsGNA1. (A) seedling height in T0 mutant plants. (B) root length in T0 mutant plants. Values represent mean ± SD. Non-m, non-mutant (n = 13), He-m, heterozygous mutants (n = 4), Ho-m, homozygous mutants (n = 6). “**” represent significances at p < 0.01.
Figure 5
Figure 5
Cluster analysis of OsGNA1. Black font represents japonica, gray font represents indica, purple font represents aus. NIP = Nipponbare.
Figure 6
Figure 6
LD analysis of OsGNA1.
Figure 7
Figure 7
Water loss in the mutant of OsRLK5. Values represent mean ± SD, n = 5. “*” and “**” represent significances at p < 0.05, p < 0.01, respectively.
Figure 8
Figure 8
Drought resistance assay of OsRLK5 under drought stress condition. Plant height (A), tiller number (B), biomass (C), grain yield per plant (D), panicle length (E), panicle neck length (F), seed setting rate (G), and spikelet numbers per panicle (H) were measured under drought stress condition. (I), the panicle of wild-type Nipponbare (WT) and transgenic plant (Mutant). Values represent mean ± SD, n = 5. “*” and “**” represent significances at p < 0.05, p < 0.01, respectively.
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