Genome-wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions.

Hongyan Liu,Hongyan Liu,Junhui Zhan,Jindong Liu,Jindong Liu,Yamei Wang,Yamei Wang,Quanzhi Zhao,Xiang Lu,Jiaolong Li,Jiaolong Li,Guoyou Ye,Guoyou Ye,Guoyou Ye

doi:10.3390/genes11010049

Abstract

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.

Highlights

Rice (Oryza sativa) is one of the most important cereal crops grown worldwide
Mesocotyl length of 208 rice accessions were evaluated in water, sand and soil (2, 4 and 6 cm)
Continuous variation was observed across all environments, presenting a wide range of mesocotyl length and indicating that this diversity panel was ideal for conducting Genome-wide association study (GWAS) (Figure 1)

Summary

Introduction

Rice (Oryza sativa) is one of the most important cereal crops grown worldwide. Dry direct-seeded rice refers to the process of establishing the crop from seeds sown on non-puddled and unsaturated soil; in contrast, seedlings from nursery are transplanted into puddled or submerged soil in transplanted rice [1]. Compared with traditional transplanted rice, dry direct-seeded rice has been proposed as a water-efficient and labor-saving approach, which can reduce the cost of water and labor at about. Dry direct-seeded rice could efficiently utilize early-season rainfall in drought-prone. Direct seeding has been adopted by more than 25% of the worldwide rice cultivation area [1]. Dry direct-seeded rice is becoming a popular option in Philippines, India, Thailand, Cambodia, Laos and Indonesia in tropical Asia as well as the US, Australia and Latin America [5,6]

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