Cuilian Xu1, Muhammad Kashif Ilyas2,3, Richard Odongo Magwanga2,4, Hejun Lu2, M Kashif Riaz Khan2,5, Zhongli Zhou2, Yujun Li6, Zhengcheng Kuang6, Asif Javaid3, Danish Ibrar3, Abdul Ghafoor7, Kunbo Wang2, Fang Liu2, Haodong Chen8,9. 1. Research Base of Tarium, University of State Key Laboratory of Cotton Biology, Tarium University, Alar, 843300, Xinjiang, China. xclzky@163.com. 2. State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. 3. National Agricultural Research Centre, Park Road, Islamabad, Pakistan. 4. School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya. 5. Nuclear Institute for Agriculture & Biology (NIAB), Faisalabad, Pakistan. 6. Cotton Sciences Research Institute of Hunan/National Hybrid Cotton Research Promotion Center, Changde, 415101, Hunan, China. 7. National Agricultural Research Centre, Park Road, Islamabad, Pakistan. ghafoor59pk@yahoo.com. 8. Cotton Sciences Research Institute of Hunan/National Hybrid Cotton Research Promotion Center, Changde, 415101, Hunan, China. chdmks@163.com. 9. State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. chdmks@163.com.
Abstract
BACKGROUND: Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. MATERIALS AND METHODS: In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. RESULTS: A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. CONCLUSION: The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.
BACKGROUND: Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. MATERIALS AND METHODS: In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. RESULTS: A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. CONCLUSION: The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.
Authors: Yibing Yuan; Jill E Cairns; Raman Babu; Manje Gowda; Dan Makumbi; Cosmos Magorokosho; Ao Zhang; Yubo Liu; Nan Wang; Zhuanfang Hao; Felix San Vicente; Michael S Olsen; Boddupalli M Prasanna; Yanli Lu; Xuecai Zhang Journal: Front Plant Sci Date: 2019-01-30 Impact factor: 5.753
Authors: Richard O Magwanga; Joy N Kirungu; Pu Lu; Xiu Yang; Qi Dong; Xiaoyan Cai; Yanchao Xu; Xingxing Wang; Zhongli Zhou; Yuqing Hou; Regina Nyunja; Stephen G Agong; Jinping Hua; Baohong Zhang; Kunbo Wang; Fang Liu Journal: Physiol Plant Date: 2019-02-13 Impact factor: 4.500