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

doi:10.17520/biods.2021258

Abstract

Abstract:

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, CTB4a^japappeared 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

Jia Song, Mingyang Zhi, Qiang Chen, Yueying Li, Longkun Wu, Baoxuan Nong, Danting Li, Hongbo Pang, Xiaoming Zheng. Nucleotide diversity and adaptation of CTB4a gene related to cold tolerance in rice[J]. Biodiv Sci, 2022, 30(2): 21258.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2021258

https://www.biodiversity-science.net/EN/Y2022/V30/I2/21258

Figures/Tables 3

Fig. 1 Nucleotide diversity in the CTB4a coding region. A, Nucleotide diversity in the coding region of CTB4a gene in 133 cultivated rice samples; B, Amino acid sequence and domains encoded by CTB4a gene, the gray part shows the LRR-RLK domain; C, Nucleotide diversity in the Coding Region of 35 wild rice. Amino acid variation sites in gray. In A and C, Amino acid variation sites (SNP and InDel) and average yellow leaf rate (LYR) values of indica rice population in two groups were shown in gray. And the first column of A and C shows the names of 33 haplotypes of CTB4a gene and 33 wild rice, respectively. cvs, Cultivars; LYR, Yellow leaf rate; I, O. sativa ssp. indica; J, O. sativa ssp. japonica.

Table 1 Cis-acting elements analysis of CTB4a gene promoter

元件名称 Name	元件功能 Function	元件存在类型 Existence type	元件数量 Number
LTR	低温诱导 Low-temperature induction	耐寒/不耐寒 Cold tolerance/intolerance	1
ABRE	脱落酸诱导 Abscisic acid induction		3
AE-box	光诱导 Light induction		10
G-box
Box 4
Box II
GATA-motif
TCCC-motif
TCT-motif
ACA-motif		耐寒 Cold tolerance	1
MBS	干旱诱导 Drought induction	不耐寒 Cold intolerance	1

Fig. 2 Network of haplotypes of CTB4a coding region (A) and geographic distribution map in cultivated rice (B). A, The network of all haplotypes for CTB4a, O. sativa ssp. japonica in red and O. sativa ssp. indica in yellow; B, Geographic distribution map of cultivated rice in group A and group B. Group A in pink and Group B in blue; O. sativa ssp. japonica with triangle and O. sativa ssp. indica with circle; H9 haplotype in square; H3 haplotype in circle.

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