Identification and validation of single-nucleotide polymorphism markers linked to first flower node in kenaf by using combined specific-locus amplified fragment sequencing and bulked segregant analysis

Abstract It is important to develop DNA markers closely linked to the first flower node for molecular marker-assisted selection in kenaf breeding. Kenaf ( Hibiscus cannabinus L.) is an annual, multipurpose industrial crop with a worldwide distribution. The higher the node of the first flower, the greater is the fiber yield. In this study, a population of 130 F 2 individuals was constructed through the cross of K215(♀)×K89(♂). Twenty-five individuals with higher first flower node and twenty-five individuals with lower first flower node were chosen and their DNA were pooled to construct two bulked DNA pools according to the phenotype. Specific-locus amplified fragment sequencing (SLAF-seq) combined with bulked segregant analysis (BSA) was used to identify candidate DNA markers closely linked to the first flower node. Sixteen single-nucleotide polymorphism (SNP) loci were obtained from 11 related SLAF markers associated with the first flower node. SNP locus validation was performed using Sanger sequencing method. The SNP locus S961-2 in Sanger sequencing by using the primer M41961 was consistent with the SNP locus in the related SLAF-seq. The accuracy rate of the genotypes consistent with the first flower node was 91.2% (31/34). To our knowledge, S961-2 is the first SNP locus to be identified that is closely linked to the first flower node. This SNP locus may be useful for marker-assisted selection in breeding of high fiber yielding varieties of kenaf.