Identification and verification of grain shape QTLs by SNP array in rice.

Junxiao Chen,Aiqing You,Wenjun Zha,Kai Liu,Sanhe Li,Pingli Chen,Lei Zhou,Zhijun Chen,Ming Li,Guocai Yang,Peide Li,Huashan Xu,Zhukuan Cheng

doi:10.1371/journal.pone.0260133

Abstract

Grain shape strongly influences the economic value and grain yield of rice. Thus, identifying quantitative trait loci (QTLs) for grain shape has been a longstanding goal in rice genetic research and breeding programs. Single nucleotide polymorphism (SNP) markers are ubiquitous in the rice genome and are more abundant and evenly distributed on the 12 rice chromosomes than traditional markers. An F2 population was genotyped using the RICE6K SNP array to elucidate the mechanisms governing grain shape. Thirty-five QTLs for grain shape were detected on 11 of 12 chromosomes over 2 years. The major QTL cluster qGS7 was detected in both years and displayed strong genetic effects on grain length and width, showing consistency with GL7/GW7. Some minor QTLs were also detected, and the effects of four QTLs on seed size were then validated using BC1F6 populations with residual heterozygous lines in each QTL region. Our findings provide insights into the molecular basis of grain shape as well as additional resources and approaches for producing hybrid high-yield rice varieties.

Highlights

It is critical to increase crop productivity through efficient breeding to meet the challenge of feeding a rapidly growing world population in a smaller area [1]
Grain shape in rice is controlled by a combination of grain length, grain width, and grain thickness and is a major determinant of grain yield and grain appearance quality [2]
It is essential to explore the genetic basis of grain shape and identify new quantitative trait loci (QTLs) for the improvement of grain yield and quality

Summary

Introduction

It is critical to increase crop productivity through efficient breeding to meet the challenge of feeding a rapidly growing world population in a smaller area [1]. Grain shape in rice is controlled by a combination of grain length, grain width, and grain thickness and is a major determinant of grain yield and grain appearance quality [2]. It is essential to explore the genetic basis of grain shape and identify new quantitative trait loci (QTLs) for the improvement of grain yield and quality. Most QTLs influence grain shape by regulating cell division or proliferation, and several major QTLs have been cloned and functionally characterized. GS3, the first cloned gene for grain shape, encodes a putative transmembrane protein and function as a negative regulator of grain length [3, 4]. The QTL qGL3/qGL3.1 encodes a protein phosphatase with a Kelch-like repeat domain and negatively controls grain length [5].

Methods

Results

Conclusion