Development of InDel Markers for Identification of a Single Mendelian Locus Controlling Leaf Shape in Kenaf (Hibiscus cannabinus)

Kenaf is one of the most important natural fiber crops. The lack of molecular markers has resulted in a large gap in the improvement of kenaf. Previously, de novo 90,175 unigenes in kenaf were assembled. In this study, 7453 small InDels were called from these uingenes. The indel size 10 bp have frequencies of 71.50%, 23.05%, and 5.45%. 337 InDels locating in genes encoding transcription factors were used to survey polymorphisms with 24 kenaf accessions. Of 337 InDels, 305 (90.5%) successfully amplified at least one fragment and detected polymorphism among the 24 diverse genotypes. Furthermore, one InDel marker, HcID266, was co-segregated with leaf shape, which was inherited as a single Mendelian locus, in the F2 population with 390 individuals. To our knowledge, this is the first large-scale InDels development for kenaf. These InDel markers will be helpful for genetic researches in kenaf.