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

doi:10.11983/CBB23004

Abstract

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

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[J]. Chinese Bulletin of Botany, 2024, 59(1): 34-53.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB23004

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

Figures/Tables 11

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

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

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

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).

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.

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

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

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.

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

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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