Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress

Abstract

Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of <i>TLP</i> gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in <i>Gossypium</i> species has not been reported till date. Here, we systematically identified 105 <i>TLP</i> gene family members in cotton (<i>Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum</i>, and <i>Gossypium barbadense</i>) genomes and classified them into eight phylogenetic groups. Cotton <i>TLP12</i> gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton <i>TLP</i> gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton <i>TLPs</i> paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of <i>GhTLPs</i> indicated that <i>GhTLP11A</i> and <i>GhTLP12A.1</i> genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and <i>cis</i>-regulatory elements of <i>GhTLP11A</i> and <i>GhTLP12A.1</i> genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of <i>GhTLP11A</i> and <i>GhTLP12A.1</i> genes in exerting control over salt and drought stress responses in <i>G. hirsutum</i> and also provides a reference for future research, elaborating the biological roles of <i>G. hirsutum TLPs</i> in both stress responses.