QTGW12a, a naturally varying QTL, regulates grain weight in rice

Zhixuan Du,Zheng Wu,Changlan Zhu,Junru Fu,Hang Tu,Haohua He,Jie Xu,Jianbin Li,Dahu Zhou,Haihui Fu,Chuihai Zeng,Jianzhong Bao,Zhou Huang

doi:10.1007/s00122-021-03857-4

Zhixuan Du, Zheng Wu + Show 11 more

Open Access

https://doi.org/10.1007/s00122-021-03857-4

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Abstract

Key messageA stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation.Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality. Therefore, the discovery and identification of rice grain size genes can provide pathways for the cultivation of high-yielding varieties. In the present work, 45,607 SNP markers were used to construct a high-density genetic map of rice recombinant inbred lines, and hence a total of 14 quantitative trait loci (QTLs) were detected based on the phenotypic data of grain weight, grain length and grain width under four different environments. qTGW12a and qGL12 are newly detected QTLs related to grain weight, and are located between 22.43 Mb and 22.45 Mb on chromosome 12. Gene annotation shows that the QTL region contains the LOC_Os12g36660 annotated gene, which encodes the multidrug and toxic compound extrusion (MATE) transporter. Mutations in exons and the splice site were responsible for the changes in grain type and weight. Gene knockout experiments were used to verify these results. Hence, these results provide a basis for the cloning of qTGW12a. This discovery provides new insights for studying the genetic mechanism of rice grain morphology, and reveals a promising gene to ultimately increase rice yield.

Highlights

As an important agronomic trait of rice, rice grain type is a principal index to measure the appearance quality of rice; it is the key factor to affect rice yield
Grain size is mostly measured by thousand-grain weight, which is a quantitative trait and is controlled by different genetic factors, such as the embryos, endosperm, and maternal plants
From the perspective of heritability, the heritability of grain length and grain width is moderately high, and these traits are relatively stable under different environments, the heritability of grain thickness is low, with it being affected by the environment (Shi et al 1999)

Summary

Introduction

As an important agronomic trait of rice, rice grain type is a principal index to measure the appearance quality of rice; it is the key factor to affect rice yield. The main attributes reflecting grain type traits include grain length (GL), grain width (GW), grain thickness (GT) and grain aspect ratio (Ertao et al 2008). Grain size is mostly measured by thousand-grain weight, which is a quantitative trait and is controlled by different genetic factors, such as the embryos, endosperm, and maternal plants. From the perspective of heritability, the heritability of grain length and grain width is moderately high, and these traits are relatively stable under different environments, the heritability of grain thickness is low, with it being affected by the environment (Shi et al 1999). With the development and application of molecular marker technology along with rice functional genomics and resequencing methods, using different genetic populations, more than 500

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