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. 2018 Dec 6;19(1):879.
doi: 10.1186/s12864-018-5294-5.

A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum

Iftikhar Ali  1 , Zhonghua Teng  1 , Yuting Bai  1 , Qing Yang  1 , Yongshui Hao  1 , Juan Hou  1 , Yongbin Jia  1 , Lixia Tian  1 , Xueying Liu  1 , Zhaoyun Tan  1 , Wenwen Wang  1 , Kiirya Kenneth  1 , Abdalla Yousef Ahmed Sharkh  1 , Dexin Liu  1 , Kai Guo  1 , Jian Zhang  1 , Dajun Liu  1 , Zhengsheng Zhang  2
Affiliations

A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum

Iftikhar Ali et al. BMC Genomics. .

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.

Keywords: Fiber quality traits; Genetic map; Quantitative trait loci mapping; Single nucleotide polymorphism marker; Specific locus amplified fragment sequencing (SLAF-seq); Upland cotton (Gossypium hirsutum L.).

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Conflict of interest statement

Ethics approval and consent to participate

We have all relevant rights to the materials used in this study. All materials were grown in the field in accordance with local legislation.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Genetic maps of Chr01/Chr15 and Chr02/Chr14 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. Map distances were given in centiMorgans (cM). Markers favoring Yumian 1 alleles were followed by asterisks with the level of ** P < 0.05, *** P < 0.01, **** P < 0.005, ***** P < 0.001, ****** P < 0.0005, ******* P < 0.0001 according the standard of Joinmap 4.0. The replaced sign (#) indicated markers favoring CA3084 alleles. Bars along the genetic map indicated the QTL likelihood interval. QTL were shown as FL for fiber length, FU for fiber uniformity, FS for fiber strength, FE for fiber elongation, and FM for fiber micronaire
Fig. 2
Fig. 2
Genetic maps of Chr03/Chr17 and Chr04/Chr22 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 3
Fig. 3
Genetic maps of Chr05/Chr19 and Chr06/Chr25 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 4
Fig. 4
Genetic maps of Chr07/Chr16 and Chr08/Chr24 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 5
Fig. 5
Genetic maps of Chr09/Chr23 and Chr10/Chr20 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 6
Fig. 6
Genetic maps of Chr11/Chr21 and Chr12/Chr26 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 7
Fig. 7
Genetic maps of Chr13/Chr18 homoeologous chromosomes and QTL for fiber quality in the Yumian 1 × CA3084 RIL population. All notes are the same as Fig. 1
Fig. 8
Fig. 8
Colinearity between the Yumian 1 × CA3084 genetic map and physical map. a Colinearity for the At 581 subgenome. b Colinearity for the Dt subgenome
See this image and copyright information in PMC

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