A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum
Abstract Background Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high d...
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doaj-d45759947dd844c7b0a858885d1a4f652020-11-24T21:57:28ZengBMCBMC Genomics1471-21642018-12-0119111810.1186/s12864-018-5294-5A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutumIftikhar Ali0Zhonghua Teng1Yuting Bai2Qing Yang3Yongshui Hao4Juan Hou5Yongbin Jia6Lixia Tian7Xueying Liu8Zhaoyun Tan9Wenwen Wang10Kiirya Kenneth11Abdalla Yousef Ahmed Sharkh12Dexin Liu13Kai Guo14Jian Zhang15Dajun Liu16Zhengsheng Zhang17College of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityCollege of Agronomy and Biotechnology, Southwest UniversityAbstract Background Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping. Results In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL. Conclusion A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of ‘stable QTL’ found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs.http://link.springer.com/article/10.1186/s12864-018-5294-5Upland cotton (Gossypium hirsutum L.)Genetic mapFiber quality traitsQuantitative trait loci mappingSpecific locus amplified fragment sequencing (SLAF-seq)Single nucleotide polymorphism marker |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Iftikhar Ali Zhonghua Teng Yuting Bai Qing Yang Yongshui Hao Juan Hou Yongbin Jia Lixia Tian Xueying Liu Zhaoyun Tan Wenwen Wang Kiirya Kenneth Abdalla Yousef Ahmed Sharkh Dexin Liu Kai Guo Jian Zhang Dajun Liu Zhengsheng Zhang |
spellingShingle |
Iftikhar Ali Zhonghua Teng Yuting Bai Qing Yang Yongshui Hao Juan Hou Yongbin Jia Lixia Tian Xueying Liu Zhaoyun Tan Wenwen Wang Kiirya Kenneth Abdalla Yousef Ahmed Sharkh Dexin Liu Kai Guo Jian Zhang Dajun Liu Zhengsheng Zhang A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum BMC Genomics Upland cotton (Gossypium hirsutum L.) Genetic map Fiber quality traits Quantitative trait loci mapping Specific locus amplified fragment sequencing (SLAF-seq) Single nucleotide polymorphism marker |
author_facet |
Iftikhar Ali Zhonghua Teng Yuting Bai Qing Yang Yongshui Hao Juan Hou Yongbin Jia Lixia Tian Xueying Liu Zhaoyun Tan Wenwen Wang Kiirya Kenneth Abdalla Yousef Ahmed Sharkh Dexin Liu Kai Guo Jian Zhang Dajun Liu Zhengsheng Zhang |
author_sort |
Iftikhar Ali |
title |
A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum |
title_short |
A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum |
title_full |
A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum |
title_fullStr |
A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum |
title_full_unstemmed |
A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum |
title_sort |
high density slaf-snp genetic map and qtl detection for fibre quality traits in gossypium hirsutum |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-12-01 |
description |
Abstract Background Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping. Results In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL. Conclusion A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of ‘stable QTL’ found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs. |
topic |
Upland cotton (Gossypium hirsutum L.) Genetic map Fiber quality traits Quantitative trait loci mapping Specific locus amplified fragment sequencing (SLAF-seq) Single nucleotide polymorphism marker |
url |
http://link.springer.com/article/10.1186/s12864-018-5294-5 |
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