J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (12): 2541-2551.DOI: 10.1111/jipb.13568

• Abiotic Stress Responses • Previous Articles     Next Articles

Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome

Yarong Lin1†, Yiwang Zhu1,2†, Yuchao Cui3†, Hongge Qian2,4†, Qiaoling Yuan2†, Rui Chen1, Yan Lin1, Jianmin Chen1, Xishi Zhou2, Chuanlin Shi2, Huiying He2, Taijiao Hu1, Chenbo Gu1, Xiaoman Yu2, Xiying Zhu2, Yuexing Wang5, Qian Qian2,5,6, Cuijun Zhang2*, Feng Wang1* and Lianguang Shang2,6*   

  1. 1. Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou 350003, China;
    2. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
    3. Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen 361102, China;
    4. College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China;
    5. State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311401, China;
    6. Yazhouwan National Laboratory, Sanya City 572024, China
    These authors contributed equally to this work.
    *Correspondence:Cuijun Zhang(zhangcuijun@caas.cn);Feng Wang(wf@fjage.org);Lianguang Shang(shanglianguang@caas.cn, Dr. Shang is fully responsible for the distributions of plant materials in this article)
  • Received:2023-07-21 Accepted:2023-09-14 Online:2023-09-20

Abstract: Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for the development of high-yield and thermotolerant rice varieties.

Key words: domestication, grain size, heat tolerance, pan-genome, natural variation

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