Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.)

Liu, Wei; Song, Chengxiang; Ren, Zhongying; Zhang, Zhiqiang; Pei, Xinwu; Liu, Yangai; He, Kunlun; Zhang, Fei; Zhao, Junjie; Zhang, Jie; Wang, Xingxing; Yang, Daigang; Li, Wei

doi:10.1186/s12870-020-02611-0

Cited by 26 publications

(19 citation statements)

References 63 publications

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“…In the current study, we observed large phenotypic variations for FL, FS, and Mic in natural populations of 242 genotypes for multiple years. Compared to yield and components (Su et al, 2016 ; Nie et al, 2020 ), fiber quality traits had a higher heritability of more than 80%, consistent with previous reports (Zhang et al, 2019 ; Liu et al, 2020 ). Correlation analysis showed that each trait had high correlations in different environments, indicating the genetic stability of fiber quality traits.…”

Section: Discussionsupporting

confidence: 87%

“…GWAS has been widely applied in other crops, such as wheat (Juliana et al, 2019 ), rice (Chen et al, 2014 ), soybean (Lu et al, 2020 ), and maize (Wang et al, 2020 ). In cotton, a large number of associated loci for fiber quality have also been reported via GWAS analysis (Zhang et al, 2019 ; Liu et al, 2020 ). Nevertheless, multi-year and -environment phenotype investigation is more effective to mine stable QTLs and genes related to fiber quality due to the complex genetic nature of quantitative traits.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum)

et al. 2021

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Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum)

et al. 2021

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“…TFs play regulatory roles in growth and development, morphogenesis, secondary metabolism, and stress resistance in higher plants ( Shan et al, 2020 ). Furthermore, the development of cotton fiber is a complex and dynamic process, involving the initiation, elongation, SCW synthesis, and maturation stages, and there are a large number of genes taking part in the transcriptional regulation at different developmental periods, especially TFs ( Liu et al, 2020 ). A total of 3,412 expressed TFs, including all the known TF families in cotton, were identified in our study, which indicates a tanglesome regulation network in cotton fiber development ( Supplementary Table 4 ), whereas how these factors form intricate and delicate regulatory networks has not been well-elucidated.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development

Zhang

Mei

et al. 2022

Front. Plant Sci.

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Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton.

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“…More than 7.3 thousand SNPs were associated with fiber quality traits and covered 4,820 genes; more fiber-related genes were determined in D subgenome than in the A subgenome. Liu et al (2020) have identified 42 SNPs and 31 QTLs significantly associated with five fiber quality traits ( Liu et al, 2020 ). Twenty-five QTLs are the same as QTLs identified in previous studies, and six novel QTLs were firstly identified in their work.…”

Section: Genetic Mapping and Qtl Analysis For Agronomically And Economically Valuable Traits In Cottonmentioning

confidence: 99%

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

et al. 2021

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Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.

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Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.)

Cited by 26 publications

References 63 publications

Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum)

Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum)

Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

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