Dataset Information

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality.

ABSTRACT: Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (Gossypium hirsutum L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of 30 and 23 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits were identified across the 408 cotton accessions in six environments and the best linear unbiased predictions, respectively. Among these SNPs, seven loci were the same, and 128 candidate genes were predicted in a 1-Mb region (±500 kb of the peak SNP). Furthermore, two major genome regions (GR1 and GR2) associated with multiple fiber qualities in multiple environments on chromosomes A07 and A13 were identified, and within them, 22 candidate genes were annotated. Of these, 11 genes were expressed [log2(1 + FPKM)>1] in the fiber development stages (5, 10, 20, and 25 dpa) using RNA-Seq. This study provides fundamental insight relevant to identification of genes associated with fiber quality and will accelerate future efforts toward improving fiber quality of upland cotton.

SUBMITTER: Dong C

PROVIDER: S-EPMC6334163 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Identifying Functional Genes Influencing <i>Gossypium hirsutum</i> Fiber Quality.

Dong Chengguang C Wang Juan J Yu Yu Y Ju Longzhen L Zhou Xiaofeng X Ma Xiaomei X Mei Gaofu G Han Zegang Z Si Zhanfeng Z Li Baocheng B Chen Hong H Zhang Tianzhen T

Frontiers in plant science 20190109

Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (<i>Gossypium hirsutum</i> L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of ...[more]

PMID: 30687363

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Project description:Transient waterlogging occurs frequently in the Yangtze River and adversely affects cotton fiber quality. However, the carbohydrate metabolic mechanism that affects fiber quality after waterlogging remains undescribed. Here, the effects of five waterlogging levels (0, 3, 6, 9, and 12 days) were assessed during flowering and boll formation to characterize the carbohydrates, enzymes and genes that affect the fiber quality of cotton after waterlogging. The cellulose and sucrose contents of cotton fibers were significantly decreased after waterlogging for 6 (WL6), 9 (WL9), and 12 d (WL12), although these properties were unaffected after 3 (WL3) and 6 days at the fruiting branch 14-15 (FB14-15). Sucrose phosphate synthase (SPS) was the most sensitive to waterlogging among the enzymes tested. SPS activity was decreased by waterlogging at FB6-7, whereas it was significantly enhanced under WL3-6 at FB10-15. Waterlogging down-regulated the expression of fiber invertase at 10 days post anthesis (DPA), whereas that of expansin, β-1,4-glucanase and endoxyloglucan transferase (XET) was up-regulated with increasing waterlogging time. Increased mRNA levels and activities of fiber SuSy at each fruiting branch indicated that SuSy was the main enzyme responsible for sucrose degradation because it was markedly induced by waterlogging and was active even when waterlogging was discontinued. We therefore concluded that the reduction in fiber sucrose and down-regulation of invertase at 10 DPA led to a markedly shorter fiber length under conditions WL6-12. Significantly decreased fiber strength at FB6-11 for WL6-12 was the result of the inhibition of cellulose synthesis and the up-regulation of expansin, β-1,4-glucanase and XET, whereas fiber strength increased under WL3-6 at FB14-15 due to the increased cellulose content of the fibers. Most of the indictors tested revealed that WL6 resulted in the best compensatory performance, whereas exposure to waterlogged conditions for more than 6 days led to an irreversible limitation in fiber development.

Project description:Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

Dataset Information

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality.

Publications

Identifying Functional Genes Influencing <i>Gossypium hirsutum</i> Fiber Quality.

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