Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Yan Zheng; Khin Mar Thi; Lihui Lin; Xiaofang Xie; Ei Ei Khine; Ei Ei Nyein; Min Htay Wai Lin; Win Win New; San San Aye; Weiren Wu

doi:10.3389/fpls.2023.1250854

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Front Plant Sci. 2023 Aug 30:14:1250854. doi: 10.3389/fpls.2023.1250854. eCollection 2023.

Authors

Yan Zheng^{1

2

3}, Khin Mar Thi^{2

3}, Lihui Lin^{2

3}, Xiaofang Xie^{1

2

3}, Ei Ei Khine^{2

3}, Ei Ei Nyein^{2

3}, Min Htay Wai Lin⁴, Win Win New⁴, San San Aye⁴, Weiren Wu^{2

3}

Affiliations

¹ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
² Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
³ Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
⁴ Department of Botany, Mawlamyine University, Mawlamyine, Myanmar.

Abstract

Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.

Keywords: Genome-wide association study (GWAS); grain breadth expansion index (GBEI); grain length expansion index (GLEI); grain length-breadth relative expansion index (GREI); rice.

Grants and funding

This work was supported by Natural Science Foundation of Fujian Province (CN) (2020I0009, 2022J01596), Cooperation Project on University Industry-Education-Research of Fujian Provincial Science and Technology Plan (CN) (2022N5011), Lancang-Mekong Cooperation Special Fund (2017-2018), International Sci-Tech Cooperation and Communication Program of Fujian Agriculture and Forestry University (KXGH17014).