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High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L
BACKGROUND: Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant inbred line population (RIL) containing 137 lines, and performed linkage map cons...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106845/ https://www.ncbi.nlm.nih.gov/pubmed/27835938 http://dx.doi.org/10.1186/s12864-016-3269-y |
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author | Jia, Xiaoyun Pang, Chaoyou Wei, Hengling Wang, Hantao Ma, Qifeng Yang, Jilong Cheng, Shuaishuai Su, Junji Fan, Shuli Song, Meizhen Wusiman, Nusireti Yu, Shuxun |
author_facet | Jia, Xiaoyun Pang, Chaoyou Wei, Hengling Wang, Hantao Ma, Qifeng Yang, Jilong Cheng, Shuaishuai Su, Junji Fan, Shuli Song, Meizhen Wusiman, Nusireti Yu, Shuxun |
author_sort | Jia, Xiaoyun |
collection | PubMed |
description | BACKGROUND: Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant inbred line population (RIL) containing 137 lines, and performed linkage map construction and quantitative trait locus (QTL) mapping. RESULTS: Using restriction-site associated DNA sequencing, a genetic map composed of 6,434 loci, including 6,295 single nucleotide polymorphisms and 139 simple sequence repeat loci, was developed from RIL population. This map spanned 4,071.98 cM, with an average distance of 0.63 cM between adjacent markers. A total of 247 QTLs for six earliness-related traits were detected in 6 consecutive years. In addition, 55 QTL coincidence regions representing more than 60 % of total QTLs were found on 22 chromosomes, which indicated that several earliness-related traits might be simultaneously improved. Fine-mapping of a 2-Mb region on chromosome D3 associated with five stable QTLs between Marker25958 and Marker25963 revealed that lines containing alleles derived from CCRI36 in this region exhibited smaller phenotypes and earlier maturity. One candidate gene (EMF2) was predicted and validated by quantitative real-time PCR in early-, medium- and late-maturing cultivars from 3- to 6-leaf stages, with highest expression level in early-maturing cultivar, CCRI74, lowest expression level in late-maturing cultivar, Bomian1. CONCLUSIONS: We developed an SNP-based genetic map, and this map is the first high-density genetic map for short-season cotton and has the potential to provide deeper insights into earliness. Cotton earliness-related QTLs and QTL coincidence regions will provide useful materials for QTL fine mapping, gene positional cloning and MAS. And the gene, EMF2, is promising for further study. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3269-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5106845 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-51068452016-11-25 High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L Jia, Xiaoyun Pang, Chaoyou Wei, Hengling Wang, Hantao Ma, Qifeng Yang, Jilong Cheng, Shuaishuai Su, Junji Fan, Shuli Song, Meizhen Wusiman, Nusireti Yu, Shuxun BMC Genomics Research Article BACKGROUND: Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber. To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant inbred line population (RIL) containing 137 lines, and performed linkage map construction and quantitative trait locus (QTL) mapping. RESULTS: Using restriction-site associated DNA sequencing, a genetic map composed of 6,434 loci, including 6,295 single nucleotide polymorphisms and 139 simple sequence repeat loci, was developed from RIL population. This map spanned 4,071.98 cM, with an average distance of 0.63 cM between adjacent markers. A total of 247 QTLs for six earliness-related traits were detected in 6 consecutive years. In addition, 55 QTL coincidence regions representing more than 60 % of total QTLs were found on 22 chromosomes, which indicated that several earliness-related traits might be simultaneously improved. Fine-mapping of a 2-Mb region on chromosome D3 associated with five stable QTLs between Marker25958 and Marker25963 revealed that lines containing alleles derived from CCRI36 in this region exhibited smaller phenotypes and earlier maturity. One candidate gene (EMF2) was predicted and validated by quantitative real-time PCR in early-, medium- and late-maturing cultivars from 3- to 6-leaf stages, with highest expression level in early-maturing cultivar, CCRI74, lowest expression level in late-maturing cultivar, Bomian1. CONCLUSIONS: We developed an SNP-based genetic map, and this map is the first high-density genetic map for short-season cotton and has the potential to provide deeper insights into earliness. Cotton earliness-related QTLs and QTL coincidence regions will provide useful materials for QTL fine mapping, gene positional cloning and MAS. And the gene, EMF2, is promising for further study. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3269-y) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-11 /pmc/articles/PMC5106845/ /pubmed/27835938 http://dx.doi.org/10.1186/s12864-016-3269-y Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Jia, Xiaoyun Pang, Chaoyou Wei, Hengling Wang, Hantao Ma, Qifeng Yang, Jilong Cheng, Shuaishuai Su, Junji Fan, Shuli Song, Meizhen Wusiman, Nusireti Yu, Shuxun High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title | High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title_full | High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title_fullStr | High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title_full_unstemmed | High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title_short | High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L |
title_sort | high-density linkage map construction and qtl analysis for earliness-related traits in gossypium hirsutum l |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106845/ https://www.ncbi.nlm.nih.gov/pubmed/27835938 http://dx.doi.org/10.1186/s12864-016-3269-y |
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