New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses.

Xiaoqian Wang,Chunchao Wang,Zhikang Li,Yajun Zhu,Jianlong Xu,Kai Chen,Yunlong Pang,Congcong Shen,Jauhar Ali

doi:10.3389/fpls.2016.01998

Abstract

Appearance and milling quality are two crucial properties of rice grains affecting its market acceptability. Understanding the genetic base of rice grain quality could considerably improve the high quality breeding. Here, we carried out an association analysis to identify QTL affecting nine rice grain appearance and milling quality traits using a diverse panel of 258 accessions selected from 3K Rice Genome Project and evaluated in two environments Sanya and Shenzhen. Genome-wide association analyses using 22,488 high quality SNPs identified 72 QTL affecting the nine traits. Combined gene-based association and haplotype analyses plus functional annotation allowed us to shortlist 19 candidate genes for seven important QTL regions affecting the grain quality traits, including two cloned genes (GS3 and TUD), two fine mapped QTL (qGRL7.1 and qPGWC7) and three newly identified QTL (qGL3.4, qGW1.1, and qGW10.2). The most likely candidate gene(s) for each important QTL were also discussed. This research demonstrated the superior power to shortlist candidate genes affecting complex phenotypes by the strategy of combined GWAS, gene-based association and haplotype analyses. The identified candidate genes provided valuable sources for future functional characterization and genetic improvement of rice appearance and milling quality.

Highlights

As a major cereal crop, rice (Oryza sativa L.) is crucial to food security for more than half of the world’s population
Significant variations between SY and SZ were observed for degree of endosperm chalkiness (DEC), percentage of grain with chalkiness (PGWC), Tr, and head-milled rice rate (HMRR), but not for other traits (Figure 1A)
Positive correlations were observed between DEC, PGWC, and Tr, and they were negatively correlated with grain length (GL) and grain length to width ratio (GLWR), but positively correlated with grain width (GW)

Summary

Introduction

As a major cereal crop, rice (Oryza sativa L.) is crucial to food security for more than half of the world’s population. Rapid population growth coupled with the climate change creates an urgent need for rice varieties with high yield, high quality and stress tolerances. For rice breeders and consumers, rice grain quality is a foremost consideration which includes appearance, milling, cooking and eating, and nutritional quality. Grain appearance quality is a crucial factor affecting its market acceptability. Appearance quality indicates grain shape and chalkiness. Chalkiness is usually evaluated by the degree of endosperm chalkiness (DEC) and the percentage of grain with chalkiness (PGWC). Rice variety with PGWC more than 20% is not generally acceptable in most world markets (Chen et al, 2011). Milling quality is usually measured as brown rice rate (BRR), milled rice rate (MRR), and head-milled rice rate (HMRR)

Methods

Results

Discussion

Conclusion