棉属光敏色素PHY基因家族的全基因组鉴定与驯化选择分析

doi:10.11983/CBB23004

植物学报 ›› 2024, Vol. 59 ›› Issue (1): 34-53.DOI: 10.11983/CBB23004

棉属光敏色素PHY基因家族的全基因组鉴定与驯化选择分析

顾家琦¹^,²^,^†, 朱福慧¹^,²^,^†, 谢沛豪¹^,², 孟庆营¹^,², 郑颖², 张献龙¹^,², 袁道军¹^,²^,³^,^*()

¹华中农业大学作物遗传改良全国重点实验室, 武汉 430070
²华中农业大学植物科学技术学院, 武汉 430070
³新疆农业大学农学院, 乌鲁木齐 830052

收稿日期:2023-01-02 接受日期:2023-07-08 出版日期:2024-01-01 发布日期:2023-07-21
通讯作者: *E-mail: robert@mail.hzau.edu.cn
作者简介:
†共同第一作者
基金资助:
国家重点研发计划(2021YFF1000102);华中农业大学中央高校基本科研项目(2021ZKPY013)

Genome-wide Identification and Domestication Analysis of the Phytochrome PHY Gene Family in Gossypium

Jiaqi Gu¹^,²^,^†, Fuhui Zhu¹^,²^,^†, Peihao Xie¹^,², Qingying Meng¹^,², Ying Zheng², Xianlong Zhang¹^,², Daojun Yuan¹^,²^,³^,^*()

¹National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
²College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
³College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China

Received:2023-01-02 Accepted:2023-07-08 Online:2024-01-01 Published:2023-07-21
Contact: *E-mail: robert@mail.hzau.edu.cn
About author:
†These authors contributed equally to this paper

1. 附录.pdf(4675KB)

摘要/Abstract

摘要： 光敏色素(PHY)作为植物体内重要的红光(R)和远红光(FR)受体, 在调节植物花期、提高作物产量以及调控植物抗逆性方面均具有重要作用。鉴定棉花PHY基因, 探究其驯化和改良的遗传调控网络, 发掘棉花光敏色素关键基因, 为早熟棉花品种的从头驯化和育种提供新见解。以5个拟南芥(Arabidopsis thaliana)光敏色素基因作为种子序列, 利用生物信息学方法, 对不同棉种中的PHY基因进行全基因组系统鉴定。系统发育分析表明, 锦葵科植物中的PHY基因包括PHYA、PHYB、PHYC与PHYE四个亚家族。PHY基因在陆地棉(Gossypium hirsutum)不同群体间的驯化选择分析结果表明, PHY基因的驯化过程可分为早期驯化和后期遗传改良2个阶段。对陆地棉野生种和栽培品种在长、短日照下的转录组分析显示, GhPHYA1Dt和GhPHYB1Dt在长、短日照下的表达差异显著; 在长日照处理14小时后, 栽培品种GhPHYC1At和GHPHYE1At的表达量显著低于野生种。研究结果为进一步揭示棉花PHY基因的驯化选择和功能机制奠定了基础, 为棉花早熟新品种选育和从头驯化提供了理论依据。

关键词: 棉花, 驯化, 光敏色素, 基因家族

Abstract: Phytochrome is an important receptor for red and far-red light sensing in plants, and it plays a vital role in regulating the plant flowering period, improving crop yield potential and regulating plant stress resistance. Identification of PHY family genes in Gossypium, exploration of the patterns of inheritance and regulatory network of domestication and improvement, and identification of the key phytochrome genes in Gossypium, provides insights into the de novo domestication and breeding of early maturing Gossypium species. To identify the phytochrome genes of Gossypium, we used bioinformatics methods to analyze 5 phytochrome genes in Arabidopsis thaliana. Phylogenetic analysis showed that the PHY genes in Malvaceae species consisted of 4 subfamilies (PHYA, PHYB, PHYC and PHYE). Moreover, the domestication selection analysis of PHY genes among different populations of G. hirsutum showed that the domestication process of PHY genes could be divided into two stages: domestication and improvement. Furthermore, the gene expression of the PHY gene family was analyzed using leaf RNA-sequencing data obtained from wild and cultivar genotypes of G. hirsutum under short-day (SD) and long-day (LD) conditions. The results showed that the expression of GhPHYA1Dt and GhPHYB1Dt were significantly different between SD and LD conditions. After 14 hours of long-day treatment, the expression of GhPHYC1At and GHPHYE1At in the cultivar was significantly lower than that in wild species. These results lay a foundation for further study on domestication selection and functional mechanisms of Gossypium PHY genes and provide a theoretical basis for breeding new early maturing Gossypium varieties and de novo domestication.

Key words: cotton, domestication, phytochrome, gene family

顾家琦, 朱福慧, 谢沛豪, 孟庆营, 郑颖, 张献龙, 袁道军. 棉属光敏色素PHY基因家族的全基因组鉴定与驯化选择分析. 植物学报, 2024, 59(1): 34-53.

Jiaqi Gu, Fuhui Zhu, Peihao Xie, Qingying Meng, Ying Zheng, Xianlong Zhang, Daojun Yuan. Genome-wide Identification and Domestication Analysis of the Phytochrome PHY Gene Family in Gossypium. Chinese Bulletin of Botany, 2024, 59(1): 34-53.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB23004

https://www.chinbullbotany.com/CN/Y2024/V59/I1/34

图/表 11

图1 棉属及其它植物中PHY家族成员的系统发育分析 At: 拟南芥; Cc: 圆果种黄麻; Co: 长果种黄麻; Ga: 亚洲棉; Garm: 辣根棉; Gau: 澳洲棉; Gb: 海岛棉; Gdav: 戴维逊棉; Gh: 陆地棉; Ghe: 草棉; Gk: 克劳茨基棉; Gl: 长萼棉; Gm: 黄褐棉; Gr: 雷蒙德氏棉; Gth: 瑟伯氏棉; Gto: 毛棉; Gtr: 三裂棉; Gtu: 特纳氏棉; Gkir: 叉柱棉; Hs: 木槿; Hu: 哥伦比亚锦葵; Tc: 可可

Figure 1 Phylogenetic analysis of PHY family members of Gossypium and other plants At: Arabidopsis thaliana; Cc: Corchorus capsularis; Co: C. olitorius; Ga: G. arboreum; Garm: G. armourianum; Gau: G. australe; Gb: G. barbadense; Gdav: G. davidsonii; Gh: G. hirsutum; Ghe: G. herbaceum; Gk: G. klotzschianum; Gl: G. longicalyx; Gm: G. mustelinum; Gr: G. raimondii; Gth: G. thurberi; Gto: G. tomentosum; Gtr: G. trilobum; Gtu: G. turneri; Gkir: Gossypioides kirkii; Hs: Hibiscus syriacus; Hu: Herrania umbratica; Tc: Theobroma cacao

图2 棉花PHY基因结构和蛋白保守基序分析 (A) 系统进化树; (B) 蛋白保守基序; (C) 基因结构

Figure 2 Analysis of the PHY gene structure and protein conserved motifs of Gossypium (A) Phylogenetic tree; (B) Protein conserved motif; (C) Gene structure

图3 棉花PHY基因光响应顺式作用元件分布

Figure 3 Distribution of light response cis-acting elements in the Gossypium PHY genes

图4 陆地棉PHY基因在不同器官和组织中的表达聚类分析不同颜色的矩形代表陆地棉不同PHY基因的表达水平, 即log2 (1+FPKM)。

Figure 4 Clustering analysis of the expression of Gossypium hirsutum PHY genes in different organs and tissues The rectangles with different colors represent the expression levels of different PHY genes in upland cotton, namely log2(1+ FPKM).

图5 陆地棉PHY基因在不同群体间的核苷酸多样性分析不同颜色的矩形代表陆地棉不同材料中每个基因及其上、下游、外显子和内含子的核苷酸多样性(Pi×10-4)。

Figure 5 Analysis of nucleotide diversity of Gossypium hirsutum PHY genes among different populations Different color rectangles represent the nucleotide diversity (Pi×10-4 value) of each gene and its upstream, downstream, exon and intron in different materials of upland cotton.

表1 陆地棉不同群体间PHY基因的核苷酸多样性(Pi)比值

Table 1 Nucleotide diversity (Pi) ratio of PHY genes in Gossypium hirsutum among different populations

Gene name	Gene ID	Pi_Wild/ Pi_Landrace	Pi_Landrace/ Pi_Cultivar
GhPHYA1At	Gohir.A11G261900	0.7891	5.1234
GhPHYA2At	Gohir.A13G172900	1.8274	1.4509
GhPHYA1Dt	Gohir.D11G271900	1.4826	99.2593
GhPHYA2Dt	Gohir.D13G178700	3.5917	2.3415
GhPHYB1At	Gohir.A10G172500	3.4313	16.8376
GhPHYB1Dt	Gohir.D10G179000	0.6808	38.3027
GhPHYC1At	Gohir.A11G149100	0.7955	1.5879
GhPHYC1Dt	Gohir.D11G156200	1.0780	15.8177
GhPHYE1At	Gohir.A10G037800	1.3580	3.4484
GhPHYE1Dt	Gohir.D10G038800	1.4530	1.0696

表2 陆地棉PHY基因在不同群体间的遗传分化系数(Fst)分析

Table 2 Analysis of genetic differentiation coefficients (Fst) of PHY genes of Gossypium hirsutum among different populations

Gene name	Gene ID	Fst_Wild/ Fst_Landrace	Fst_Landrace/ Fst_Cultivar
GhPHYA1At	Gohir.A11G261900	0.5843	0.2320
GhPHYA2At	Gohir.A13G172900	0.4386	0.1680
GhPHYA1Dt	Gohir.D11G271900	0.0569	0.2137
GhPHYA2Dt	Gohir.D13G178700	0.6049	0.0374
GhPHYB1At	Gohir.A10G172500	0.7068	0.5372
GhPHYB1Dt	Gohir.D10G179000	0.5158	0.7092
GhPHYC1At	Gohir.A11G149100	0.2304	0.4461
GhPHYC1Dt	Gohir.D11G156200	0.5470	0.8466
GhPHYE1At	Gohir.A10G037800	0.4756	0.4709
GhPHYE1Dt	Gohir.D10G038800	0.4096	0.1872

图6 PHY基因在野生种、半野生种及栽培品种中的单倍型分析左图代表不同材料的聚类, 右图代表不同单倍型在野生种、半野生种及栽培品种中所占的比例。

Figure 6 Haplotype analysis of PHY genes in wild, landrace and cultivar The left figure represents the clustering of different materials, and the right figure represents the proportion of different haplotypes in wild, landrace and cultivar.

图7 陆地棉GhPHYE1基因在不同亚基因组中的表达 LD: 长日照; SD: 短日照; *P<0.05; **P<0.01

Figure 7 Expression of GhPHYE1 genes in different subgenomes of Gossypium hirsutum LD: Long-day; SD: Short-day; *P<0.05; **P<0.01

图8 陆地棉PHY基因在不同光照处理条件下的表达 (A) PHYA1基因的表达; (B) PHYB1基因的表达; (C) PHYE1基因的表达。*P<0.05; **P<0.01

Figure 8 Expression of PHY genes in Gossypium hirsutum under different light treatment conditions (A) Expression of PHYA1 genes; (B) Expression of PHYB1 genes; (C) Expression of PHYE1 genes. *P<0.05; **P<0.01

图9 陆地棉PHY基因在栽培品种与野生种中的表达 (A) PHYA1基因的表达; (B) PHYB1基因的表达; (C) PHYC1基因的表达。*P<0.05; **P<0.01

Figure 9 Expression of PHY genes in cultivated and wild Gossypium hirsutum (A) Expression of PHYA1 gene; (B) Expression of PHYB1 gene; (C) Expression of PHYC1 gene. *P<0.05; **P<0.01

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棉属光敏色素PHY基因家族的全基因组鉴定与驯化选择分析

Genome-wide Identification and Domestication Analysis of the Phytochrome PHY Gene Family in Gossypium

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