Combined bulked segregant analysis and Kompetitive Allele-Specific PCR genotyping identifies candidate genes related to the node of the first fruiting branch in upland cotton (Gossypium hirsutum L.)

The node of the first fruiting branch (NFFB) is a credible morphological indicator for the identification of early maturity in upland cotton (Gossypium hirsutum L.). In this study, a large F₂ population resulting from a cross between genotypes ‘XSK28’ (early-maturity) and ‘TM-1’ (late-maturity) was constructed to identify candidate genes for the NFFB in upland cotton by bulked segregant analysis (BSA) and Kompetitive Allele-Specific PCR (KASP) genotyping. A total of 2,120,783 high-quality single-nucleotide polymorphisms were detected between two parents and between two DNA pools. By BSA technology, a candidate region of 7.2-Mb on chromosome A09 was identified as the target QTL region for the NFFB. Subsequently, QTL mapping and t-test based on KASP genotyping narrowed the QTL region to 260 kb, containing 20 functionally annotated genes. The quantitative reverse transcription PCR results showed the expression levels of two candidate genes, namely Gh_A09G087700 and Gh_A09G087800, in the early-maturity parent ‘XSK28’ were significantly lower than in the late-maturity parent ‘TM-1’ at all three stages of flower bud growth. These two genes may be involved in regulating the formation of the NFFB and can be regarded as promising candidate genes. The study provids valuable information for further revealing the molecular mechanism of the NFFB and marker-assisted selection breeding of cotton early maturity.