Fine-mapping and genetic analysis of a fibre strength QTL introgressed from Gossypium barbadense into Gossypium hirsutum

Cotton fibre is an important industrial raw material, the quality determines its market value. However, breeding cotton with improved fibre quality constitutes a major challenge due to the limited genetic diversity and close genetic linkage among modern cotton varieties. In this study, we anchored three quality-related QTLs, qFS-D06–1 , qFM-D03–1 , and qFM-D06–2 , using a secondary F 2 population constructed from the chromosome segment substitution line (CSSL) HY2654, which has significantly superior fibre micronaire (FM) and fibre strength (FS) value. The QTLs demonstrated definitive overlap with two major introgression segments identified on chromosome D03 and D06. The qFS-D06–1 locus, which accounts for 8.88 % of FS variation, was further fine-mapped to a 1.75 Mb interval on chromosome D06. Twelve genes located in this QTL region exhibit significantly differential expression in both HY2654 and its donor parent Gossypium barbadense acc. 3–79. Four of these genes, which have their orthologues generally known to be involved in cell growth and in physiological and biochemical processes relevant to fibre development, are expressed in fibres of all sampling periods and could be focused upon in further research. The current research could provide a strategy for accelerating the acquisition of the map-based identification of genetic features that underlie complex qualities. Further development of this foundation will put novel insights into important agronomic traits of plants. • Three fibre quality-related QTLs were anchored based on the chromosome segment substitution line strategy. • Two major introgression segments were identified, which were definetly overlapped with these QTLs. • The cis- differential expression of introgressed genes driven the trans- differential expression of key pathway genes. • The qFS-D06–1 was fine-mapped furtherly with four candidate genes that may make contribution to the fibre strength.