Genetic Regulatory Networks for Salt-Alkali Stress in Gossypium hirsutum With Differing Morphological Characteristics

Xu, Yanchao; Magwanga, Richard Odongo; Yang, Xiaomin; Jin, Dingsha; Cai, Xiaoyan; Hou, Yuqing; Wei, Yangyang; Zhou, Zhongli; Wang, Kunbo; Liu, Fang

doi:10.21203/rs.2.12440/v3

Cited by 9 publications

(12 citation statements)

References 45 publications

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“…We perform the virus induced gene silencing (VIGS) of candidate genes, RALF and FLA, in G. hirsutum race Marie-Galante 85 according to the strategy of our previous published study [45,46]. Firstly, we construct the VIGS vector of TRV:: RALF, TRV:: FLA and TRV:: PDS and introduced into Agrobacterium tumefaciens strain GV4104.…”

Section: Gene Clustering and Visualizationmentioning

confidence: 99%

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Jin

Cai

et al. 2020

Preprint

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Background Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. Results A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thu rberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180- 55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5% - 17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What’s more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. Conclusion Our study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction processes. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.

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Section: Gene Clustering and Visualizationmentioning

confidence: 99%

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Jin

Cai

et al. 2020

Preprint

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“…The WGCNA [19] package was employed to identify gene co-expression networks and investigate traitrelated modules. The WGCNA Was used as described by Xu et al [45]. The parameter denotes the soft threshold for the correlation matrix, which emphasize denotes a correlations between genes [43].…”

Section: Snp Callingmentioning

confidence: 99%

“…A value of 5 was selected as the determinant of the soft-thresholding power and the evaluation scale for free topology analysis. The dynamic tree-cutting algorithm and the association of modules with the traits were evaluated as described by Xu et al [45].…”

Section: Snp Callingmentioning

confidence: 99%

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Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Magwanga²,

Jin

et al. 2020

Preprint

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BackgroundWild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. ResultsA total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180- 55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5% - 17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What’s more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. ConclusionOur study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.

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“…For example, ion channels and transporters can mitigate Na + toxicity and K + /Na + ratio homeostasis, and overexpression of NHX1 or SOS1 in cotton can improve salt tolerance [19]. GhSOS3 and GhCBL10 are involved in regulating the responses to saline stress and alkaline stress, and the GhSOS3/GhCBL10-SOS2 network also plays a central role in G. hirsutum responses to saline stress and alkaline stress [20]. Besides, overexpression of the OSCU/Zn-SOD gene can improve the detoxi cation capacity of reactive oxygen species and improve the salt tolerance [21].…”

Section: Introductionmentioning

confidence: 99%

Application of compound material alleviates saline and alkaline stress in cotton leaves through regulation of the transcriptome

Wang

Chang

et al. 2020

Preprint

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Background: Soil salinization and alkalinization are the main factors that affect the agricultural productivity. Evaluating the persistence of the compound material applied in field soils is an important part of the regulation of the responses of cotton to saline and alkaline stresses. Result: To determine the molecular effects of compound material on the cotton’s responses to saline stress and alkaline stress, cotton was planted in the salinized soil (NaCl 8g kg -1 ) and alkalized soil (Na 2 CO 3 8g kg -1 ) after application of the compound material, and ion content, physiological characteristics, and transcription of new cotton leaves at flowering and boll-forming stage were analyzed. The results showed that compared with saline stress, alkaline stress increased the contents of Na + , K + , SOD, and MDA in leaves. The application of the compound material reduced the content of Na + but increased the K + /Na + ratio , the activities of SOD, POD, and CAT, and REC. Transcriptome analysis revealed that after the application of the compound material, the Na + /H + exchanger gene in cotton leaves was down-regulated, while the K + transporter, K + channel, and POD genes were up-regulated. Besides, the down-regulation of genes related to lignin synthesis in phenylalanine biosynthesis pathway had a close relationship with the ion content and physiological characteristics in leaves. The quantitative analysis with PCR proved the reliability of the results of RNA sequencing. Conclusion: These findings suggest that the compound material alleviated saline stress and alkaline stress on cotton leaves by regulating candidate genes in key biological pathways, which improves our understanding of the molecular mechanism of the compound material regulating the responses of cotton to saline stress and alkaline stress.

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Genetic Regulatory Networks for Salt-Alkali Stress in Gossypium hirsutum With Differing Morphological Characteristics

Cited by 9 publications

References 45 publications

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

Application of compound material alleviates saline and alkaline stress in cotton leaves through regulation of the transcriptome

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