Putative male parent of banana cultivar ‘Pakchong KU 46’ using SNP analysis

Identifying parents is crucial in banana breeding programs as it helps breeders understand genetic inheritance patterns, predict trait combinations in hybrids, and select parents to develop cultivars with desirable traits. Banana genome structure is quite complex based on their polyploidy and some sterility, thus bringing challenges for banana breeders. The banana cultivar ‘Pakchong KU 46’ was a natural hybrid derived from seed of the cultivar ‘Namwa Pakchong 50’ with an unknown male parent. This study aimed to identify the unknown male parent of ‘Pakchong KU 46’ using both nuclear and mitochondrial single nucleotide polymorphism (SNP) markers from Diversity Arrays Technology sequencing (DArTseq) and whole-genome re-sequencing. Genetic relationships between the ‘Pakchong KU 46’, ‘Namwa Pakchong 50’ and 179 banana accessions in the banana planting field at the Pakchong Research Station were investigated using cluster analysis. Nuclear SNPs identified ‘Leb Changkut’ as a putative male parent with the most genetically similarity to the ‘Pakchong KU 46’. Further mitochondrial SNP analysis confirmed that ‘Leb Changkut’ was the closest genetic match, with 99% similarity in mitochondrial DNA. These findings provided strong evidence that ‘Leb Changkut’ was most likely the male parent of ‘Pakchong KU 46’, thereby offering valuable insights into its genetic lineage and assisting the future breeding programs to develop banana cultivars.