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

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

doi:10.3389/fpls.2016.01801

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.

Highlights

Rice is one of the most important staple foods and plays an important role to ensure food safety
Plant height, panicle length, panicle neck length, seed-setting rate, spikelet numbers per panicle, and grain yield per plant were significantly reduced in the mutant plants under drought stress conditions (Figure 8). These results demonstrate that OsRLK5 is responsible for the GY under drought stress
Drought stress can occur at any crop growth stage and can affect productivity to variable degrees depending on the onset time, duration, and intensity of drought

Summary

Introduction

Rice is one of the most important staple foods and plays an important role to ensure food safety. Rice production consumes copious amounts of fresh water. In China, 49% of all fresh water resources are used for rice production (Zhang, 2007). GWAS for Drought Resistance in Rice grain production (Pennisi, 2008). Throughout Asia, 20% of all rice production areas are affected by drought per year (Gowda et al, 2011). This strengthens the disparity between supply and demand of rice production. Enhancing the drought resistance of rice is vital to reduce the effect of drought on rice production

Methods

Results

Conclusion