Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

Richard Odongo Magwanga,Hejun Lu,Xingxing Wang,Xiaoyan Cai,Zhongli Zhou,Zhenmei Zhang,Joy Nyangasi Kirungu,Haron Salih,Pu Lu,Kunbo Wang,Fang Liu

doi:10.1186/s12863-017-0596-1

Abstract

BackgroundLate embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Increased cotton production in the face of declining precipitation and availability of fresh water for agriculture use is the focus for breeders, cotton being the backbone of textile industries and a cash crop for many countries globally.ResultsIn this work, a total of 242, 136 and 142 LEA genes were identified in G. hirsutum, G. arboreum and G. raimondii respectively. The identified genes were classified into eight groups based on their conserved domain and phylogenetic tree analysis. LEA 2 were the most abundant, this could be attributed to their hydrophobic character. Upland cotton LEA genes have fewer introns and are distributed in all chromosomes. Majority of the duplicated LEA genes were segmental. Syntenic analysis showed that greater percentages of LEA genes are conserved. Segmental gene duplication played a key role in the expansion of LEA genes. Sixty three miRNAs were found to target 89 genes, such as miR164, ghr-miR394 among others. Gene ontology analysis revealed that LEA genes are involved in desiccation and defense responses. Almost all the LEA genes in their promoters contained ABRE, MBS, W-Box and TAC-elements, functionally known to be involved in drought stress and other stress responses. Majority of the LEA genes were involved in secretory pathways. Expression profile analysis indicated that most of the LEA genes were highly expressed in drought tolerant cultivars Gossypium tomentosum as opposed to drought susceptible, G. hirsutum. The tolerant genotypes have a greater ability to modulate genes under drought stress than the more susceptible upland cotton cultivars.ConclusionThe finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress.

Highlights

Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants
In order to identify the late embryogenesis abundant (LEA) proteins in cotton, the HHM profile of LEA protein was subsequently employed as a query to perform a HMMER search [23] against the G. hirsutum and G. arboreum, which were obtained from cotton genome project and G. raimondii genome downloaded from Phytozome, with E-value
Two hundred and eighty LEA genes were identified in upland cotton, Gossypium hirsutum, one hundred-seventy LEA genes in G. raimondii and one hundred-fifty LEA genes in G. arboreum

Summary

Introduction

Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton. Water deficit stress do led to a series of changes including biochemical alterations like accumulation of osmolytes and specific proteins involved in stress tolerance [3]. Drought is the main abiotic stress responsible for plant growth compromise and severe yield loss. Water is an essential element for biotic component of the biosphere, such that various responses have evolved to withstand water deficit in all plants and animals, to enable them withstand long periods of water deprivation by adopting a type of life condition known as anhydrobiosis [6]

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Conclusion