Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis.

Sun Sun,Ma Ma,Liu Liu,Wang Wang,Li Li

doi:10.3390/genes10100730

Abstract

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

Highlights

Upland cotton (Gossypium hirsutum) is an important economic crop, produces large amounts of natural fibers as raw material for the textile industry, and is used to extract nutrient-rich edible oil from cottonseed [1,2]
To identify the gene family members, the hidden Markov models (HMMs) of auxin response factor (ARF) (PF06507), Auxin/Indole-3-Acetic Acid (Aux/indoleacetic acid (IAA)) (PF02309), Gretchen Hagen3 (GH3) (PF03321), and small auxin upregulated RNA (SAUR) (PF02519) were downloaded from the Pfam database [30], which served as queries for the homologues search (E-value < 1) against the proteome of G. hirsutum conducted by HMMER v.3.1b2 software [31]
A total of 71 ARF, 86 Aux/IAA, 63 GH3, and 194 SAUR genes were identified in upland cotton

Summary

Introduction

Upland cotton (Gossypium hirsutum) is an important economic crop, produces large amounts of natural fibers as raw material for the textile industry, and is used to extract nutrient-rich edible oil from cottonseed [1,2]. Given its substantial economic worth, the improvement of yield, fiber quality, stress tolerance, disease resistance, and other desired traits of cotton are important. Agrobacterium-mediated genetic transformation has been the most widely used approach to incorporate exogenous genes into explants [4,5]. This transformation method is genotype-dependent, and upland cotton with different genotypes has a variable somatic embryogenesis ability during regeneration. The inability of regeneration via somatic embryogenesis severely constrains cotton genetic engineering

Methods

Results

Discussion

Conclusion