棉花FLA基因家族的全基因组鉴定及GhFLA05在棉纤维发育中的功能分析

doi:10.3864/j.issn.0578-1752.2023.23.004

Abstract

Abstract:

【Background】It is of great importance to improve the quality of cotton fiber to meet the improvement of cotton textile production and the pursue of people for high quality cotton. Fasciclin-like arabinogalactan proteins (FLAs) play an important role in the initial development of cotton fibers and secondary wall synthesis. 【Objective】Comprehensive identification and analysis of cotton FLA gene family members to reveal their common characteristics and specific expression patterns, provided a reference for the function study of FLAs in cotton fiber development.【Method】According to the whole genome data of cotton, members of FLA gene family were identified by HMMER3.0 and further verified by online softwares of Pfam and Smart. Physical and chemical properties and transmembrane domains of these proteins were analyzed by ExPASy and TMHMM. Phylogenetic tree construction, chromosome localization, collinearity analysis and protein conserved domain sequence alignment were conducted and displayed using GSDS, MCScanX, MEGA, MEME, TBtools and Jalview. Expression of FLA genes in different tissues were analyzed by cotton transcriptome data. Expression differences of GhFLAs in different developmental stages of ovules and fibers between different fiber quality materials was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Function of GhFLA05 was verified by virus induced gene silencing (VIGS). 【Result】A total of 41, 40, 20 and 21 FLA family members were identified in G.hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. The phylogenetic tree showed that cotton FLA proteins could be divided into four groups. Gene structure and motif composition were relatively conserved in each group. Further analysis of FLA proteins in Gossypium hirsutum showed that all 41 FLA members had 1-2 AGP-like glycosylation regions and 1-2 fasciclin-like domains (FAS), 37 of which contained signal peptide (SP) and 25 contained glycosylphosphatidylinositol anchored protein (GPI) anchoring signals. Subcellular localization showed that GhFLA05_D showing aggregated granules in the cytoplasm was probably localized in endoplasmic reticulum, and GhFLA18_A and GhFLA22 were expressed in cell membrane/wall, cytoplasm and nucleus. Transcriptome sequencing results showed that FLA proteins in Group A and B were mainly highly expressed in fibers, which may be involved in the process of cotton fiber elongation development and secondary wall thickening. In general, group A and B members had a similar expression pattern in two materials with significant differences in fiber quality and expressed mainly in the secondary wall development stage, especially in 20-25 DPA period. GhFLA05 exhibited specific expression at the secondary wall thickening stage with significant differences between two materials, which expressed with a high maximum value in earlier stage of secondary wall thickening stage in high specific strength material RIL229, suggesting GhFLA05 may take a part in the regulation of cotton fiber strength difference formation. The fiber strength and micronaire value decreased in GhFLA05 gene-silenced cotton plants by VIGS.【Conclusion】A sum of 122 FLA family members were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii, which could be divided into four groups. Members of different groups had high structural and functional similarities, and the genes related to cotton fiber development were identified. It was clarified that GhFLA05 specifically expressed in the secondary wall synthesis stage, and closely related to the difference in fiber strength of different upland cotton materials.

Key words: cotton, FLA, fiber development, gene family, expression analysis

TANG LiYuan, CAI Xiao, WANG HaiTao, LI XingHe, ZHANG SuJun, LIU CunJing, ZHANG JianHong. Genome-Wide Identification of Cotton FLA Gene Family and Functional Analysis of GhFLA05 in Cotton Fiber Development[J].Scientia Agricultura Sinica, 2023, 56(23): 4602-4620.

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棉种类型 Type of Gossypium	氨基酸数量 No. of amino acid (aa)	分子量 Mw (kDa)	等电点 pI	不稳定系数 Instability index	亲水性平均系数 Grand average of hydropathicity (GRAVY)	跨膜结构域数量No. of predicted TMHs
陆地棉G. hirsutum	241－499	25.61－53.52	5.11－9.27	27.90－54.92	-0.24－0.28	0－3
海岛棉G. barbadense	241－460	25.58－50.83	5.11－9.27	27.90－55.73	-0.24－0.28	0－1
亚洲棉G. arboreum	239－459	25.42－50.71	5.25－9.04	26.95－57.71	-0.25－0.28	0－3
雷蒙德氏棉G. ramondii	239－515	25.50－57.29	5.11－9.41	24.91－54.76	-0.25－0.26	0－2

Genome-Wide Identification of Cotton FLA Gene Family and Functional Analysis of GhFLA05 in Cotton Fiber Development

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