Abstract
BackgroundUpland 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.ResultsIn 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.ConclusionA 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.
Highlights
Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber
Correlations among all five fiber quality traits were significant except fiber uniformity (FU)-fiber micronaire (FM) and FM-fiber elongation (FE) (Table 3)
Quantitative trait locus/loci (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 explained more than 10% of the phenotypic variance
Summary
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. Cotton fiber yield is of primary importance for cotton growers, whereas the textile industry demands high fiber quality. Simple sequence repeats (SSR), a type of DNA marker, have been used for genetic mapping and QTL detection for about two decades. SNP markers are effective for creating high density genetic maps, mapping QTL and use in MAS [5,6,7,8], understanding population structure and studying genetic diversity [9]
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