The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton ( Gossypium hirsutum L.) fibres

Abstract

HighlightThe brown fibre cotton Lc1 locus is linked to a 1.4Mb genomic inversion that activates GhTT2_A07. This mutation upregulates flavonoid biosynthesis and confers natural flame retardancy.

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

“…In the linkage map of the Lc 1 region (Figure c), a long cosegregating region was identified on chromosome A07, which reduced the fine‐mapping resolution of the target gene. A genomic inversion event around Lc 1 has been reported previously (Hinchliffe et al ., ), which might cause the lower recombination rate. Such a long cosegregating region could easily cause linkage drag, which is disadvantageous in the modification of a target trait because of the unfavourable QTLs linked with the favourable gene (Voss‐Fels et al ., ).…”

“…The QTL of qBF-A07-1 was fine-mapped to Gh_A07G2341, which encodes an R2R3-MYB transcription factor that was previously reported to be up-regulated in brown fibre (Hinchliffe et al, 2016). MYB transcription factors are the main regulatory factors in the flavonoid pathway, and they can combine proteins of the WD40 and bHLH families to regulate expression levels in the flavonoid pathway (Koes et al, 2005;Xu et al, 2015).…”

“…MYB transcription factors are the main regulatory factors in the flavonoid pathway, and they can combine proteins of the WD40 and bHLH families to regulate expression levels in the flavonoid pathway (Koes et al, 2005;Xu et al, 2015). A number of studies have shown that the transcripts of the structural genes C4H, CHS, F3 0 H and F3 0 5 0 H are highly expressed in the brown fibre of cotton (Feng et al, 2013;Hinchliffe et al, 2016;Tan et al, 2013). Abundant polymorphisms have been identified in Gh_A07G2341; in the future, we can conduct experiments to locate the natural functional variation in this gene.…”

“…Natural brown fibre represents an excellent model for the cultivation of elite coloured cotton. The genetic loci of brown fibre have been demonstrated to be Lc 1 , Lc 2 , Lc 3 , Lc 4 , Lc 5 and Lc 6 (Kohel, 1985); among them, Lc 1 is the best studied one (Hinchliffe et al, 2016;Li et al, 2012;Wang et al, 2014). Lc 1 is located on chromosome A07 near the telomere (Hinchliffe et al, 2016).…”

“…The genetic loci of brown fibre have been demonstrated to be Lc 1 , Lc 2 , Lc 3 , Lc 4 , Lc 5 and Lc 6 (Kohel, 1985); among them, Lc 1 is the best studied one (Hinchliffe et al, 2016;Li et al, 2012;Wang et al, 2014). Lc 1 is located on chromosome A07 near the telomere (Hinchliffe et al, 2016). It has been reported that the metabolites of proanthocyanidins occur as pigments in the seed coats of plants and are the main product related to the pigmentation of brown fibre (Feng et al, 2014;Lepiniec et al, 2006).…”