Biodiv Sci ›› 2022, Vol. 30 ›› Issue (2): 21258.  DOI: 10.17520/biods.2021258

• Original Papers: Genetic Diversity • Previous Articles     Next Articles

Nucleotide diversity and adaptation of CTB4a gene related to cold tolerance in rice

Jia Song1, Mingyang Zhi1, Qiang Chen2, Yueying Li1, Longkun Wu3, Baoxuan Nong4, Danting Li4, Hongbo Pang1,*(), Xiaoming Zheng5,*()   

  1. 1 College of Life Sciences, Shenyang Normal University, Shenyang 110034
    2 Experimental Center, Shenyang Normal University, Shenyang 110034
    3 College of Grain, Shenyang Normal University, Shenyang 110034
    4 Rice Research Institute, Guangxi Academy of Agricultural Sciences/Key Laboratory of Rice Genetics and Breeding, Nanning 530007
    5 Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2021-06-29 Accepted:2021-10-14 Online:2022-02-20 Published:2022-02-28
  • Contact: Hongbo Pang,Xiaoming Zheng


Aims: To explore whether the natural variation of CTB4a gene is related to low-temperature tolerance in cultivated rice seedlings.

Methods: A total of 133 representative samples of cultivated rice (Oryza sativa L.) and 35 samples of wild rice (O. rufipogon Griff.) from all over the world were used as experimental materials to analyze the nucleotide diversity, the relationship between haplotypes and geographical distribution in gene coding region of CTB4a gene.

Results: There were 14 nucleotide variations and 33 haplotypes in the coding region of CTB4a gene. According to single nucleotide polymorphism variation, the network of these haplotypes was divided into two groups (A and B) in variation at 286 bp (+2,035,097 bp, G > C; +96 aa, Ala→Pro). There were 56 samples in Group A, 43 samples (76.79%) were japonica rice mainly distributed in middle and high latitudes, while Group B contains 77 samples, and 63 indica rice (83.12%) mainly distributed in tropical or subtropical countries. The low-temperature tolerance of Group A is significantly lower than that of Group B by 30% at the seedling stage on average. The variation at 286 bp only exists in Group A, but not in Group B.

Conclusion: As the rice planting area moved northward, CTB4ajap appeared and was fixed during the breeding process. This research provides a theoretical basis for understanding the molecular genetic mechanism of rice adapting to low temperature and breeding cold-tolerant rice varieties.

Key words: cultivated rice, CTB4a, nucleotide diversity, haplotype, adaptability