Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections.

Fangxi Wu,Jianguo Li,Yidong Wei,Xi Luo,Lingqiang Wang,Huaan Xie,Guosheng Xie,Jianfu Zhang

doi:10.3390/plants10040812

Abstract

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

Highlights

Rice (Oryza sativa L.) is one of the staple crops worldwide
Our results indicate that pyramiding of superior alleles of these genes for seed storability will lead to new varieties with improved seed longevity and storage in the future
The superior haplotype with qSS1-2, qSS8-1, and qSS11-1 displayed a higher average germination percentage than the superior haplotype with qSS1-1, qSS1-2, qSS8-1, and qSS11-1 in japonica subspecies. These results indicated that pyramiding of quantitativepopulations trait loci (QTLs) superior alleles of these seed storability-associated genes would be essential for breeding a new rice variety with improved storability

Summary

Introduction

Rice (Oryza sativa L.) is one of the staple crops worldwide. In recent years, nearly 3%of the average annual rice grain, namely 15 billion kg, has been lost due to seed aging during storage [1]. The loss of seed viability due to seed deterioration has been a great challenge to the crop production industry [3]. The improvement of seed storability is of great significance to assurance storage safety of grain and seeds in rice. Seed storability is defined as the longevity of seeds after storage. It is an important agronomic trait for the preservation of seed fitness after harvest [4]. Recent researches have demonstrated that seed storability varies greatly among different rice accessions, and seed storability of indica subspecies is better than that of japonica subspecies [5,6,7], suggesting that there are different genetic mechanism and interaction network for seed storability between indica and japonica subspecies

Results

Discussion

Conclusion