Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

Chunping, Guo; Pan, Zhenyuan; You, Chunyuan; Zhou, Xianghai; Huang, Cong; Shen, Chao; Zhao, Ruihai; Yang, Qingyong; Zhu, Lu; Lin, Zhenhua; Nie, Xiaoqin

doi:10.1186/s42397-021-00087-3

Cited by 6 publications

(3 citation statements)

References 54 publications

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“…The variance, normality statistical analyses, and basic statistics, including extreme values, mean value, standard deviation, coefficient of variation, and statistics for the correlation between traits were performed using SPSS v22.0 software (IBM Corp., Armonk, NY, USA). Correlation analyses and boxplots between environments were drawn using R software (Guo et al, 2021).…”

Section: Phenotype Investigation and Statistical Analysismentioning

confidence: 99%

Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Shui,

Lin,

et al. 2024

J Cotton Res

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Background Cotton is an economically important crop. It is crucial to find an effective method to improve cotton yield, and one approach is to decrease the abscission of cotton bolls and buds. However, the lack of knowledge of the genetic and molecular mechanisms underlying cotton boll abscission traits has hindered genetic improvements. Results Pearson’s correlation analysis revealed a significant positive correlation between boll abscission rates 1 (AR1) and boll abscission rates 2 (AR2). A genome-wide association study was conducted on 145 loci that exhibited high polymorphism and were uniformly distributed across 26 chromosomes (pair). The study revealed 18, 46, and 62 markers that were significantly associated with boll abscission, fiber quality, and yield traits (P < 0.05), explaining 1.75%–7.13%, 1.16%–9.58%, and 1.40%–5.44% of the phenotypic variation, respectively. Notably, the marker MON_SHIN-1584b was associated with the cotton boll abscission trait, whereas MON_CGR5732a was associated with cotton boll abscission and fiber quality traits. Thirteen of the marker loci identified in this study had been previously reported. Based on phenotypic effects, six typical cultivars with elite alleles related to cotton boll abscission, fiber quality, and yield traits were identified. These cultivars hold great promise for widespread utilization in breeding programs. Conclusions These results lay the foundation for understanding the molecular regulatory mechanism of cotton boll abscission and provide data for the future improvement of cotton breeding.

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Section: Phenotype Investigation and Statistical Analysismentioning

confidence: 99%

Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Shui,

Lin,

et al. 2024

J Cotton Res

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“…The variance, normality statistical analyses and basic statistics including extreme values, mean value, standard deviation, variable coe cient, and the statistics for the correlation between traits were performed by using SPSS software 22.0. Correlation analysis and boxplot between environments were drawn using R software (Guo et al 2021).…”

Section: Phenotype Analysismentioning

confidence: 99%

Identification of SSR markers linked to the abscission of cotton bolls traits and mining germplasm in Cotton

Guangling,

Hairong,

Xiaomei

et al. 2023

Preprint

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Background: Cotton is one of the most important economic crops. To effectively improve yield of cotton, an urgent way is decreasing the abscission of cotton bolls and buds. However, unclear genetic and molecular mechanism underlying cotton bolls abscission traits hindered the genetic improvement of cotton. Methods: In this study, the correlation analysis between abscission traits and other agronomically important traits were carried out by Pearson correlation analysis. Then, a genome-wide association study for these traits were performed based on 145 alleles locus with highly polymorphism and uniformly distributed on 26 chromosomes by TASSEL V2.1 software. The loci of elite allelic variation and typical materials carrying elite alleles were determined by association study. Results: The Pearson correlation analysis showed a significant positive correlation among AR1 (boll abscission rate 1) and AR2 (boll abscission rate 2). There were 18, 46 and 62 markers significantly associated with abscission traits, fiber quality traits and yield traits (P < 0.05), and explaining 1.75% ~ 7.13%, 1.16% ~ 9.58% and 1.40% ~ 5.44% of the phenotypic variation respectively. Among these markers, MON_CGR5732aand MON_CGR5732b markers were associated with cotton abscission traits, fiber quality traits and yield traits loci, and 13 marker loci have been reported by previous studies. In addition, based on phenotypic effects six typical materials with elite allele loci related to fiber quality traits were identified and they will be widely used in practical breeding. Conclusions: Phenotypic analysis of 238 accessions showed that the traits were relatively stable under four environmental conditions, and AR2 was an important indicator of abscission. Association analysis based on SSR markers provides two excellent allelic variants associated with low abscission rate and the six typical materials with excellent alleles.

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“…The first association mapping study in cotton focusing on fiber quality was reported in G. arboretum ( Kantartzi and Stewart, 2008 ). Subsequently, association mapping has been extensively applied in upland cotton to investigate crucial economic traits, including fiber quality ( Abdurakhmonov et al., 2008 ; Nie et al., 2016 ; Liu et al., 2020 ; Song et al., 2021 ), seed oil content ( Liu G. et al., 2015 ; Yuan et al., 2018 ; Zhao et al., 2019 ), fiber yield ( Ademe et al., 2017 ; Sun et al., 2018 ; GUO et al., 2021 ; Niu et al., 2023 ), and biotic and abiotic stresses ( Fang et al., 2010 ; Bardak et al., 2021 ; Xu et al., 2021 ; Zhang et al., 2021 ; Zhao et al., 2021 ), as well as those associated with epistasis and environmental interactions ( Jia et al., 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.)

Joshi,

Singh,

Tiwari

et al. 2023

Front. Plant Sci.

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Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

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Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

Cited by 6 publications

References 54 publications

Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Identification of SSR markers linked to the abscission of cotton bolls traits and mining germplasm in Cotton

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.)

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