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

Magwanga et al. BMC Genetics (2018) 19:6 DOI 10.1186/s12863-017-0596-1 RESEARCH ARTICLE Open Access Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton Richard Odongo Magwanga1,2, Pu Lu1, Joy Nyangasi Kirungu1, Hejun Lu1, Xingxing Wang1, Xiaoyan Cai1, Zhongli Zhou1, Zhenmei Zhang1, Haron Salih1, Kunbo Wang1* and Fang Liu1* Abstract Background: 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. 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. Results: In 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. Conclusion: The finding provides comprehensive information on LEA genes in upland cotton, G. hirsutum and possible function in plants under drought stress. Keywords: Cotton (Gossypium spp), Identification, LEA proteins, miRNAs, Gene ontology, Gene expression, Genome, Drought * Correspondence: ; 1 Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang 455000, China Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Magwanga et al. BMC Genetics (2018) 19:6 Background Drought stress has resulted in to massive losses in crop production and also has altered the natural equilibrium of the environment [1]. To save the ecosystem and enhance production, advanced molecular breeding is the recipe for activation and regulation of specific stressrelated genes [2]. 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]. One of the proteins that play a role in the mechanism of drought resistance is the LEA types of protein known as dehydrin [4]. In cotton production, drought is the main abiotic stress responsible for plant growth compromise and severe yield loss. Even though cotton is considered to be relatively tolerant to water deficit, its optimal growth and yield negatively affected when water supply is limited or interrupted [5]. 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]. There is great agronomic significance to understand cotton plant responses to water deficit due to the huge economic losses that results from drought [7]. Cotton metabolism and yield are negatively affected under water deficit conditions, especially at flowering stage [8]. Plants have acquired an evolutionary response to withstand the effect of low water availability, a condition that can disadvantage their growth and development. As immobile organisms, plants possess diverse strategies of responses to drought. Among the molecules highly associated with plant responses to water limitation are the late embryogenesis abundant (LEA) proteins [9]. These proteins are widespread in the plant kingdom and highly enriched during the late stages of embryogenesis and in vegetative tissues in response to water deficit [10]. LEA proteins were first discovered more than 30 years ago and were observed to accumulate at late stages of plant seed development [11]. The LEA proteins have been found in various tissues of abiotic stressed plants and non-plant organisms known to be tolerant to desiccation, such as bacteria and some invertebrates [12]. LEA proteins are members of a large group of hydrophilic, glycine-rich proteins present in a wide range of plant species [13]. This class of proteins are known to be intrinsically disordered in their structures and are mainly expressed under water deprivation condition [14]. The LEA genes are highly diverse, with wide distribution in the plant kingdom and has pivotal role in various stress tolerance responses [15]. Scientific investigations on LEA protein families have been on-going for more than two decades [16]. Although there has been a strong association of LEA protein Page 2 of 31 families with environmental stress tolerance of significance drought and cold stress [17], LEA protein families for most of that time, their function has been entirely obscure [18]. Considerable evidence gives an indication that LEA genes are involved in desiccation, though their precise function is unknown [19]. The bacterial group 1 LEA pro (...truncated)