A gap-free and haplotype-resolved genome of an early-season <i>indica</i> variety provides insights into rice thermotolerance and grain quality

Wenjing Tao; Leilei Qiu; Jingsheng Zheng; Liangrong Jiang; Qiwen Xu; Shaowei Xu; Shiting Song; Zhibiao Fan; Qixin Zheng; Qinqin Wu; Jiupan Han; Rui Li; Jingxian Wang; Yuchao Cui; Xi Huang; Changlin Zheng; Hai Zhang; Rongyu Huang; Xinhao Ouyang

doi:10.1016/j.jgg.2025.04.020

Volume 52 Issue 11

Nov. 2025

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Article Navigation > Journal of Genetics and Genomics > 2025 > 52(11): 1417-1420

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A gap-free and haplotype-resolved genome of an early-season indica variety provides insights into rice thermotolerance and grain quality

doi: 10.1016/j.jgg.2025.04.020

1. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China;
2. Rice Research Institute of Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350018, China;
3. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China

Funds:

This work was supported by the National Natural Science Foundation of China (32270250 and 32400202), National Science Foundation of Fujian Province of China (2022J02004), Fujian Provincial Science and Technology Key Project (2024NZ029027), and China Postdoctoral Science Foundation (2022M712665).

Received Date: 2025-01-13
Accepted Date: 2025-04-29
Rev Recd Date: 2025-04-28
Publish Date: 2025-05-06

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Chen, Z., Lu, Y., Feng, L., Hao, W., Li, C., Yang, Y., Fan, X., Li, Q., Zhang, C., Liu, Q., 2020. Genetic dissection and functional differentiation of ALKa and ALKb, two natural alleles of the ALK/SSIIa gene, responding to low gelatinization temperature in rice. Rice (N Y) 13, 39.

Dong, F., Miller, J.T., Jackson, S.A., Wang, G.L., Ronald, P.C., Jiang, J., 1998. Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc. Natl. Acad. Sci. U. S. A. 95, 8135-8140.

Fan, C., Xing, Y., Mao, H., Lu, T., Han, B., Xu, C., Li, X., Zhang, Q., 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164-1171.

Gao, Z., Zeng, D., Cheng, F., Tian, Z., Guo, L., Su, Y., Yan, M., Jiang, H., Dong, G., Huang, Y., et al., 2011. ALK, the key gene for gelatinization temperature, is a modifier gene for gel consistency in rice. J. Integr. Plant Biol. 53, 756-765.

He, N., Huang, F., Yang, D., 2023. Fine mapping and cloning of a qRA2 affect the ratooning ability in rice (Oryza sativa L.). Int. J. Mol. Sci. 24, 967.

Jiang, L., Huang, J., Zhang, K., Huang, Y., Wang, H., Song, S., Zhou, K., 2007. Rice genetic map construction based on elite indica rice, Jiafuzhan. Journal of Xiamen University (Natural Science), 262-267.

Kan, Y., Mu, X.R., Zhang, H., Gao, J., Shan, J.X., Ye, W.W., Lin, H.X., 2022. TT2 controls rice thermotolerance through SCT1-dependent alteration of wax biosynthesis. Nat. Plants 8, 53-67.

Li, X.M., Chao, D.Y., Wu, Y., Huang, X., Chen, K., Cui, L.G., Su, L., Ye, W.W., Chen, H., Chen, H.C., et al., 2015. Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice. Nat. Genet. 47, 827-833.

Ou, S., Chen, J., Jiang, N., 2018. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126.

Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al., 2021a. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184, 3542-3558.

Qin, P., Zhang, G., Hu, B., Wu, J., Chen, W., Ren, Z., Liu, Y., Xie, J., Yuan, H., Tu, B., et al., 2021b. Leaf-derived ABA regulates rice seed development via a transporter-mediated and temperature-sensitive mechanism. Sci. Adv. 7, eabc8873.

Song, J.M., Xie, W.Z., Wang, S., Guo, Y.X., Koo, D.H., Kudrna, D., Gong, C., Huang, Y., Feng, J.W., Zhang, W., et al., 2021. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol. Plant 14, 1757-1767.

Tabassum, R., Dosaka, T., Ichida, H., Morita, R., Ding, Y., Abe, T., Katsube-Tanaka, T., 2020. FLOURY ENDOSPERM11-2 encodes plastid HSP70-2 involved with the temperature-dependent chalkiness of rice (Oryza sativa L.) grains. Plant J. 103, 604-616.

Wada, H., Hatakeyama, Y., Onda, Y., Nonami, H., Nakashima, T., Erra-Balsells, R., Morita, S., Hiraoka, K., Tanaka, F., Nakano, H., 2019. Multiple strategies for heat adaptation to prevent chalkiness in the rice endosperm. J. Exp. Bot. 70, 1299-1311.

Wang, H., Huang, H., Qiu, S., Zhang, S., Fang, Y., Cai, J., Zheng, X., Huang, Y., Chen, R., Sun, C., et al., 2006. Breeding and applicantion of Jiafuzhan——a new breed of early indica rice of high quality. Journal of Xiamen University (Natural Science), 114-119.

Wei, X., Qiu, J., Yong, K., Fan, J., Zhang, Q., Hua, H., Liu, J., Wang, Q., Olsen, K.M., Han, B., et al., 2021. A quantitative genomics map of rice provides genetic insights and guides breeding. Nat. Genet. 53, 243-253.

Xu, H., Li, X., Zhang, H., Wang, L., Zhu, Z., Gao, J., Li, C., Zhu, Y., 2020. High temperature inhibits the accumulation of storage materials by inducing alternative splicing of OsbZIP58 during filling stage in rice. Plant Cell Environ. 43, 1879-1896.

Zhang, A., Kong, T., Sun, B., Qiu, S., Guo, J., Ruan, S., Guo, Y., Guo, J., Zhang, Z., Liu, Y., et al., 2024. A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max. Crop J. 12, 142-153.

Zhang, C., Zhu, J., Chen, S., Fan, X., Li, Q., Lu, Y., Wang, M., Yu, H., Yi, C., Tang, S., et al., 2019. Wxlv, the ancestral allele of rice Waxy gene. Mol. Plant 12, 1157-1166.

Zhao, D., Zhang, C., Li, Q., Liu, Q., 2022. Genetic control of grain appearance quality in rice. Biotechnol. Adv. 60, 108014.

Zhao, D.S., Li, Q.F., Zhang, C.Q., Zhang, C., Yang, Q.Q., Pan, L.X., Ren, X.Y., Lu, J., Gu, M.H., Liu, Q.Q., 2018. GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nat. Commun. 9, 1240.

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