Division of Crop Improvement, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India.
Division of Crop Protection, ICAR - Central Institute for Cotton Research (CICR), Nagpur, Maharashtra, India.
Sci Rep. 2021 Apr 28;11(1):9177. doi: 10.1038/s41598-021-87934-0.
Asiatic cotton (Gossypium arboreum) cultivated as 'desi cotton' in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X-C-X-H-X-C)-X-(C-X-C-X-C-X-H)] and [(C-X-C-X-H-X-C)-X-(C-X-C-X-C-X-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.
亚洲棉（Gossypium arboreum）作为印度的“土棉”种植，以其对气候的适应能力和对生物及非生物胁迫的抵抗力而闻名。因此，G. arboreum 的基因组被认为是一个宝贵的信息储备库，可用于发现新的基因或基因功能，以改善目前全球棉花种植中的性状。在本研究中，我们对土棉中的 LIM 基因家族进行了全基因组分析，鉴定了 20 个 LIM 结构域蛋白（GaLIMs），其中包括 16 个动物 CRP 样 GaLIMs 和 4 个具有 UIM（泛素相互作用基序）存在（GaDA1）或不存在（GaDAR）的植物特异性 GaLIMs。在这 16 个 CRP 样 GaLIMs 中，有 11 个具有两个常规 LIM 结构域，而 5 个具有单个 LIM 结构域，除了在拟南芥、鹰嘴豆和杨树的 LIM 基因家族中，在研究的植物物种中没有报道过这种结构域。将这 20 个 GaLIM 蛋白与拟南芥、鹰嘴豆和杨树的 LIMs 进行系统发育分析，将它们分为不同的 CRP-like LIMs 的 αLIM1、βLIM1、γLIM2、δLIM2 组，以及植物特异性 LIMs 的 GaDA1 和 GaDAR 组。结构域分析表明，动物 CRP 样 GaLIMs 的第一个和/或第二个 LIM 结构域分别保守的 [(C-X-C-X-H-X-C)-X-(C-X-C-X-C-X-H)] 和 [(C-X-C-X-H-X-C)-X-(C-X-C-X-C-X-H)] 基序。有趣的是，含有单个 LIM 结构域的 GaLIM15 被发现含有独特的基序，具有更长的锌指间隔区，但第二锌指基序更短。这 20 个 GaLIMs 均表现出不同的时空表达模式，因此进一步分为不同的 αLIM1、βLIM1、γLIM2、δLIM2 和植物特异性 LIM（DA1/DAR）组。这是首次在棉花中研究生物和非生物胁迫下 GaDA1/DAR 的响应，包括用植物激素（茉莉酸和脱落酸）、盐（NaCl）和引起萎蔫的病原体（尖孢镰刀菌）处理。GaDA1/DAR 的表达模式表现出不同的响应，并鉴定出 GaDA2 可能是 G. arboreum 中抗胁迫的候选基因。
