Genomic analysis of marker-associated fiber development genes in upland cotton (Gossypium hirsutum L)

Yu, John Z.; Gervers, Kyle A.

doi:10.1007/s10681-019-2388-3

Cited by 5 publications

(5 citation statements)

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“…In recent decades, large numbers of QTLs or GWAS signals associated with fiber quality traits in cotton have been identified using different genetic populations or different mapping methods [ 18 , 34 ]. Among the 31 QTLs associated with these five fiber quality traits detected in the present study, 25 QTLs fell within or adjacent to QTL intervals or GWAS signals identified in previous studies (Additional file 1 : Table S3).…”

Section: Discussionmentioning

confidence: 99%

“…Compared with traditional linkage mapping, association mapping can reveal the associations between genotypes and phenotypes using natural populations and simultaneously detect many natural allelic variations in a study [ 17 ]. Using this mapping method, many QTLs and candidate genes associated with fiber quality have been identified [ 18 ]. For example, Sun et al (2017) performed a genome-wide association study (GWAS) of fiber quality traits using 719 diverse accessions of upland cotton and 10,511 polymorphic SNPs identified using the CottonSNP63K array.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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Background Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. To better understand the genetic mechanisms responsible for fiber quality traits, we conducted a genome-wide association study to identify and mine fiber-quality-related quantitative trait loci (QTLs) and genes. Results In total, 42 single nucleotide polymorphisms (SNPs) and 31 QTLs were identified as being significantly associated with five fiber quality traits. Twenty-five QTLs were identified in previous studies, and six novel QTLs were firstly identified in this study. In the QTL regions, 822 genes were identified and divided into four clusters based on their expression profiles. We also identified two pleiotropic SNPs. The SNP locus i52359Gb was associated with fiber elongation, strength, length and uniformity, while i11316Gh was associated with fiber strength and length. Moreover, these two SNPs were nonsynonymous and located in genes Gh_D09G2376 and Gh_D06G1908 , respectively. RT-qPCR analysis revealed that these two genes were preferentially expressed at one or more stages of cotton fiber development, which was consistent with the RNA-seq data. Thus, Gh_D09G2376 and Gh_D06G1908 may be involved in fiber developmental processes. Conclusions The findings of this study provide insights into the genetic bases of fiber quality traits, and the identified QTLs or genes may be applicable in cotton breeding to improve fiber quality.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…As mentioned above, PH1.1 was probably a domesticated QTL, consistent with the roles of the AP2 gene family involved in the domestication of broomcorn millet. Another candidate gene, longmi011482 , encodes a trichome birefringence-like protein related to cell wall polysaccharide O -acetylation in Arabidopsis ( Schultink et al., 2015 ) and fiber development in upland cotton ( Yu and Gervers, 2019 ). Thus, it may participate in the development of the cell wall to affect the elongation of the broomcorn millet internode and then regulate plant height.…”

Section: Discussionmentioning

confidence: 99%

Identification and fine-mapping of a major QTL (PH1.1) conferring plant height in broomcorn millet (Panicum miliaceum)

Liu

et al. 2022

Front. Plant Sci.

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The plant height of broomcorn millet (Panicum miliaceum) is a significant agronomic trait that is closely related to its plant architecture, lodging resistance, and final yield. However, the genes underlying the regulation of plant height in broomcorn millet are rarely reported. Here, an F2 population derived from a cross between a normal variety, “Longmi12,” and a dwarf mutant, “Zhang778,” was constructed. Genetic analysis for the F2 and F2:3 populations revealed that the plant height was controlled by more than one locus. A major quantitative trait locus (QTL), PH1.1, was preliminarily identified in chromosome 1 using bulked segregant analysis sequencing (BSA-seq). PH1.1 was fine-mapped to a 109-kb genomic region with 15 genes using a high-density map. Among them, longmi011482 and longmi011489, containing nonsynonymous variations in their coding regions, and longmi011496, covering multiple insertion/deletion sequences in the promoter regions, may be possible candidate genes for PH1.1. Three diagnostic markers closely linked to PH1.1 were developed to validate the PH1.1 region in broomcorn millet germplasm. These findings laid the foundation for further understanding of the molecular mechanism of plant height regulation in broomcorn millet and are also beneficial to the breeding program for developing new varieties with optimal height.

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“…The cotton cultivars currently used in production are mostly annuals. Four different Gossypium species are cultivated: Gossypium herbaceum and Gossypium arboreum, which are diploids (2n = 2x = 26) that originate from African-Asian stocks, and Gossypium hirsutum and Gossypium barbadense, which are tetraploids (2n = 4x = 52) that originate from the Americas; G. hirsutum currently contributes more than 90% of the world's textile fiber (John and Gervers, 2019;Teodoro et al, 2019).…”

Section: Ratoon Cotton Culturementioning

confidence: 99%

Ratooning Annual Cotton (Gossypium spp.) for Perennial Utilization of Heterosis

Zhang

Zhou

et al. 2020

Front. Plant Sci.

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This paper reviews an important topic within the broader framework of the use of ratoon cotton for the development of a cost-saving and efficient method for the perennial production of hybrid cotton seeds. Cotton has a botanically indeterminate perennial growth habit and originated in the tropics. However, cotton has been domesticated as an annual crop in temperate areas worldwide. Ratoon cultivation has an important application value and is important for cotton production, breeding, and basic research. In particular, ratooned male-sterile lines have four advantages: an established root system, an indeterminate flowering habit, ratooning ability, and perennial maintenance of sterility in the absence of a matched maintainer. These advantages can help reduce the costs of producing F1 hybrid cotton seeds and can help breed high-yielding hybrid combinations because ratooning is a type of asexual reproduction that allows genotypes to remain unchanged. However, ratooning of cotton is highly complex and leads to problems, such as the accumulation of pests and diseases, decreased boll size, stand loss during severe winters, and harmful regrowth during mild winters, which need to be resolved. In summary, ratoon cotton has advantages and disadvantages for the production of hybrid cotton seeds, and future prospects of ratooning annual cotton for the perennial utilization of heterosis are promising if the mechanization of seed production can be widely applied in practice.

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Genomic analysis of marker-associated fiber development genes in upland cotton (Gossypium hirsutum L)

Cited by 5 publications

References 31 publications

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

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

Identification and fine-mapping of a major QTL (PH1.1) conferring plant height in broomcorn millet (Panicum miliaceum)

Ratooning Annual Cotton (Gossypium spp.) for Perennial Utilization of Heterosis

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