Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton

Early-maturity varieties of upland cotton are becoming increasingly important for farmers to improve their economic benefits through double cropping practices and mechanical harvesting production in China. However, fiber qualities of early-maturing varieties are relatively poor compared with those o...

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Autores principales: Su, Junji, Ma, Qi, Li, Mei, Hao, Fushun, Wang, Caixiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107031/
https://www.ncbi.nlm.nih.gov/pubmed/30166989
http://dx.doi.org/10.3389/fpls.2018.01169
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author Su, Junji
Ma, Qi
Li, Mei
Hao, Fushun
Wang, Caixiang
author_facet Su, Junji
Ma, Qi
Li, Mei
Hao, Fushun
Wang, Caixiang
author_sort Su, Junji
collection PubMed
description Early-maturity varieties of upland cotton are becoming increasingly important for farmers to improve their economic benefits through double cropping practices and mechanical harvesting production in China. However, fiber qualities of early-maturing varieties are relatively poor compared with those of middle- and late- maturing ones. Therefore, it is crucial for researchers to elucidate the genetic bases controlling fiber-quality related traits in early-maturity cultivars, and to improve synergistically cotton earliness and fiber quality. Here, multi-locus genome-wide association studies (ML-GWAS) were conducted in a panel consisting of 160 early-maturing cotton accessions. Each accession was genotyped by 72,792 high-quality single nucleotide polymorphisms (SNPs) using specific-locus amplified fragment sequencing (SLAF-seq) approach, and fiber quality-related traits under four environmental conditions were measured. Applying at least three ML-GWAS methods, a total of 70 significant quantitative trait nucleotides (QTNs) were identified to be associated with five objective traits, including fiber length (FL), fiber strength (FS), fiber micronaire (FM), fiber uniformity (FU) and fiber elongation (FE). Among these QTNs, D11_21619830, A05_28352019 and D03_34920546 were found to be significantly associated with FL, FS, and FM, respectively, across at least two environments. Among 96 genes located in the three target genomic regions (A05: 27.95 28.75, D03: 34.52 35.32, and D11: 21.22 22.02 Mbp), six genes (Gh_A05G2325, Gh_A05G2329, Gh_A05G2334, Gh_D11G1853, Gh_D11G1876, and Gh_D11G1879) were detected to be highly expressed in fibers relative to other eight tissues by transcriptome sequencing method in 12 cotton tissues. Together, multiple favorable QTN alleles and six candidate key genes were characterized to regulate fiber development in early-maturity cotton. This will lay a solid foundation for breeding novel cotton varieties with earliness and excellent fiber-quality in the future.
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spelling pubmed-61070312018-08-30 Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton Su, Junji Ma, Qi Li, Mei Hao, Fushun Wang, Caixiang Front Plant Sci Plant Science Early-maturity varieties of upland cotton are becoming increasingly important for farmers to improve their economic benefits through double cropping practices and mechanical harvesting production in China. However, fiber qualities of early-maturing varieties are relatively poor compared with those of middle- and late- maturing ones. Therefore, it is crucial for researchers to elucidate the genetic bases controlling fiber-quality related traits in early-maturity cultivars, and to improve synergistically cotton earliness and fiber quality. Here, multi-locus genome-wide association studies (ML-GWAS) were conducted in a panel consisting of 160 early-maturing cotton accessions. Each accession was genotyped by 72,792 high-quality single nucleotide polymorphisms (SNPs) using specific-locus amplified fragment sequencing (SLAF-seq) approach, and fiber quality-related traits under four environmental conditions were measured. Applying at least three ML-GWAS methods, a total of 70 significant quantitative trait nucleotides (QTNs) were identified to be associated with five objective traits, including fiber length (FL), fiber strength (FS), fiber micronaire (FM), fiber uniformity (FU) and fiber elongation (FE). Among these QTNs, D11_21619830, A05_28352019 and D03_34920546 were found to be significantly associated with FL, FS, and FM, respectively, across at least two environments. Among 96 genes located in the three target genomic regions (A05: 27.95 28.75, D03: 34.52 35.32, and D11: 21.22 22.02 Mbp), six genes (Gh_A05G2325, Gh_A05G2329, Gh_A05G2334, Gh_D11G1853, Gh_D11G1876, and Gh_D11G1879) were detected to be highly expressed in fibers relative to other eight tissues by transcriptome sequencing method in 12 cotton tissues. Together, multiple favorable QTN alleles and six candidate key genes were characterized to regulate fiber development in early-maturity cotton. This will lay a solid foundation for breeding novel cotton varieties with earliness and excellent fiber-quality in the future. Frontiers Media S.A. 2018-08-16 /pmc/articles/PMC6107031/ /pubmed/30166989 http://dx.doi.org/10.3389/fpls.2018.01169 Text en Copyright © 2018 Su, Ma, Li, Hao and Wang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Su, Junji
Ma, Qi
Li, Mei
Hao, Fushun
Wang, Caixiang
Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title_full Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title_fullStr Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title_full_unstemmed Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title_short Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
title_sort multi-locus genome-wide association studies of fiber-quality related traits in chinese early-maturity upland cotton
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107031/
https://www.ncbi.nlm.nih.gov/pubmed/30166989
http://dx.doi.org/10.3389/fpls.2018.01169
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