Population genomics reveals selection signatures and favorable haplotypes for low chalkiness in <i>indica</i> rice

Risheng Li; Yamei Ma; Shuai Nie; Jingbo Zhou; Yunmeng Cao; Ke Zheng; Hui Wang; Tifeng Yang; Jingfang Dong; Jiansong Chen; Jian Wang; Lian Zhou; Lei Zhao; Shaochuan Zhou; Chongrong Wang; Junliang Zhao; Ziqiang Liu; Haifei Hu

doi:10.1016/j.jgg.2026.04.013

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Population genomics reveals selection signatures and favorable haplotypes for low chalkiness in indica rice

doi: 10.1016/j.jgg.2026.04.013

a. Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Rice Science and Technology, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, Guangdong 510640, China;
b. Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China;
c. College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China;
d. Jingu Meixiang Industry Co., Ltd, Shenzhen, Guangdong 518000, China

Funds:

2024YG01), The Introduction of Young Key Talents of Guangdong Academy of Agricultural Sciences (R2023YJ-QC001), Guangdong Provincial Key Laboratory of New Technology in Rice Breeding (2023B1212060042), National Key R&

This research was supported by Guangdong Provincial Key R&

D Fund (JSGGKQTD20221101115652015) and Guangdong Laboratory for Lingnan Modern Agriculture (NT25002).

D Program Project (2025B0202050001), the National Natural Science Foundation of China (32400512 and 32470347), Guangdong Pearl River Talents Program (2024QN11N336), The GuangDong Basic and Applied Basic Research Foundation (2024A1515011981), Youth S&

D Program of China (2024YFD1200801), Shenzhen Science and Technology R&

T Talent Support Programme of Guangdong Provincial Association for Science and Technology (SKXRC2025531), The “YouGu” Plan of Rice Research Institute of Guangdong Academy of Agricultural Sciences (2023YG04&

Received Date: 2025-11-20
Accepted Date: 2026-04-19
Rev Recd Date: 2026-04-18

Available Online: 2026-04-28

Abstract

Abstract

Grain chalkiness compromises rice appearance quality and market value. The genetic basis of chalkiness reduction in indica rice remains less well understood than that in japonica. Modern Guangdong indica varieties released since the 1980s have long, translucent grains with low chalkiness, making them a suitable system to dissect quality improvement in indica. Here, we analyse whole-genome variation in 154 Guangdong indica varieties and 229 genetically diverse international indica accessions. Integrating population genomics, haplotype association analysis, and endosperm expression profiling, we identify four major chalkiness-associated genes, Wx, Chalk5, OsDER1, and OsATG8b, showing strong genetic differentiation consistent with breeding selection in Guangdong germplasm. Superior haplotypes at all four loci are significantly associated with reduced chalkiness in multi-year phenotyping in Guangzhou and in independent trials from the Philippines. Analysis of HuangHuaZhan pedigree further reveals stepwise pyramiding and fixation of these haplotypes during grain-quality improvement. Across other indica-growing provinces in southern China, favourable haplotypes at Wx and OsDER1 are largely fixed in cultivated varieties, whereas those at Chalk5 and OsATG8b remain less deployed. Variants in these four genes also enable efficient prediction of chalkiness across multiple machine learning models. Together, these results illustrate how breeding enriched favourable haplotypes for low chalkiness in indica rice.
- Haplotype analysis,
- Oryza sativa indica,
- Chalkiness,
- Genetic basis,
- Pedigree

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