Ruifeng Cui1,2,3, Xiaoge Wang2, Waqar Afzal Malik2, Xuke Lu2, Xiugui Chen2, Delong Wang2, Junjuan Wang2, Shuai Wang2, Chao Chen2, Lixue Guo2, Quanjia Chen4, Wuwei Ye5,6. 1. College of Agriculture / Xinjiang Agricultural University / Xinjiang Research Base, State Key Laboratory of Cotton Biology, Urumqi, 830052, Xinjiang, China. 2. State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. 3. College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China. 4. College of Agriculture / Xinjiang Agricultural University / Xinjiang Research Base, State Key Laboratory of Cotton Biology, Urumqi, 830052, Xinjiang, China. chqjia@126.com. 5. College of Agriculture / Xinjiang Agricultural University / Xinjiang Research Base, State Key Laboratory of Cotton Biology, Urumqi, 830052, Xinjiang, China. yew158@163.com. 6. State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. yew158@163.com.
Abstract
BACKGROUND: The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. RESULTS: In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. CONCLUSION: The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.
BACKGROUND: The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. RESULTS: In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. CONCLUSION: The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.
Authors: Congli Wang; Mauricio Ulloa; Xinyi Shi; Xiaohui Yuan; Christopher Saski; John Z Yu; Philip A Roberts Journal: Front Plant Sci Date: 2015-10-02 Impact factor: 5.753