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Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (Gossypium spp.) Species Under Drought Stress.

ABSTRACT: Drought is one of the most important abiotic stresses that seriously affects cotton growth, development, and production worldwide. However, the molecular mechanism, key pathway, and responsible genes for drought tolerance incotton have not been stated clearly. In this research, high-throughput next generation sequencing technique was utilized to investigate gene expression profiles of three cotton species (Gossypium hirsutum, Gossypium arboreum, and Gossypium barbadense L.) under drought stress. A total of 6968 differentially expressed genes (DEGs) were identified, where 2053, 742, and 4173 genes were tested as statistically significant; 648, 320, and 1998 genes were up-regulated, and 1405, 422, and 2175 were down-regulated in TM-1, Zhongmian-16, and Pima4-S, respectively. Total DEGs were annotated and classified into functional groups under gene ontology analysis. The biological process was present only in tolerant species(TM-1), indicating drought tolerance condition. The Kyoto encyclopedia of genes and genomes showed the involvement of plant hormone signal transduction and metabolic pathways enrichment under drought stress. Several transcription factors associated with ethylene-responsive genes (ICE1, MYB44, FAMA, etc.) were identified as playing key roles in acclimatizing to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to abscisic acid (ABA) responses (NCED, PYL, PP2C, and SRK2E), reactive oxygen species (ROS) related in small heat shock protein and 18.1 kDa I heat shock protein, YLS3, and ODORANT1 genes. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in cotton.

SUBMITTER: Hasan MM

PROVIDER: S-EPMC6539811 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (Gossypium spp.) Species Under Drought Stress.

Hasan Md Mosfeq-Ul MM Ma Fanglu F Islam Faisal F Sajid Muhammad M Prodhan Zakaria H ZH Li Feng F Shen Hao H Chen Yadong Y Wang Xuede X

International journal of molecular sciences 20190427 9

Drought is one of the most important abiotic stresses that seriously affects cotton growth, development, and production worldwide. However, the molecular mechanism, key pathway, and responsible genes for drought tolerance incotton have not been stated clearly. In this research, high-throughput next generation sequencing technique was utilized to investigate gene expression profiles of three cotton species (Gossypium hirsutum, Gossypium arboreum, and Gossypium barbadense L.) ...[more]

PMID: 31035558

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Project description:Cotton (Gossypium spp.) is an important crop plant that is widely grown to produce both natural textile fibers and cottonseed oil. Cotton fibers, the economically more important product of the cotton plant, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that large numbers of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across At and Dt subgenomes of tetraploid AD cottons. In the present study, the organization and evolution of the fiber development genes were investigated through the construction of an integrated genetic and physical map of fiber development genes whose functions have been verified and confirmed. A total of 535 cotton fiber development genes, including 103 fiber transcription factors, 259 fiber development genes, and 173 SSR-contained fiber ESTs, were analyzed at the subgenome level. A total of 499 fiber related contigs were selected and assembled. Together these contigs covered about 151 Mb in physical length, or about 6.7% of the tetraploid cotton genome. Among the 499 contigs, 397 were anchored onto individual chromosomes. Results from our studies on the distribution patterns of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more transcription factors were from Dt subgenome than At, whereas more fiber development genes were from At subgenome than Dt. Combining our mapping results with previous reports that more fiber QTLs were mapped in Dt subgenome than At subgenome, the results suggested a new functional hypothesis for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided most of the genes for fiber development, because it continues to function similar to its fiber producing diploid A genome ancestor. On the other hand, the Dt subgenome, with its non-fiber producing D genome ancestor, provides more transcription factors that regulate the expression of the fiber genes in the At subgenome. This hypothesis would explain previously published mapping results. At the same time, this integrated map of fiber development genes would provide a framework to clone individual full-length fiber genes, to elucidate the physiological mechanisms of the fiber differentiation, elongation, and maturation, and to systematically study the functional network of these genes that interact during the process of fiber development in the tetraploid cottons.

Dataset Information

Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (Gossypium spp.) Species Under Drought Stress.

Publications

Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (<i>Gossypium</i> spp.) Species Under Drought Stress.

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