Dominant allele phylogeny and constitutive subgenome haplotype inference in bananas usingmitochondrial and nuclear markers

Abstract

Cultivated bananas (Musa spp.) have undergone domestication patterns involving crosses of wild progenitors followed by long periods of clonal propagation.Majority of cultivated bananas are polyploidswith different constitutive subgenomes and knowledge on phylogenies to their progenitors at the species and subspecies levels is essential. Here, the mitochondrial (NAD1) and nuclear (CENH3) markers were used to phylogenetically position cultivated banana genotypes to diploid progenitors. The CENH3 nuclear marker was used to identify a minimum representative haplotype number in polyploids and diploid bananas based on single nucleotide polymorphisms.ThemitochondrialmarkerNAD1wasobservedtobeideal indifferentiatingbananasofdifferentgenomic constitutions based on size of amplicons as well as sequence. The genotypes phylogenetically segregated based on the dominant genome;AAB genotypes groupedwithAA andAAA, and the ABB togetherwith BB. Bothmarkers differentiated banana sections, but could not differentiate subspecieswithin theAgenomic group.On the basis of CENH3marker, a total of 13 haplotypes (five in both diploid and triploid, three in diploids, and rest unique to triploids) were identified from the genotypes tested. The presence of haplotypes, which were common in diploids and triploids, stipulate possibility of a shared ancestry in the genotypes involved in this study. Furthermore, the presence of multiple haplotypes in some diploid bananas indicates their being heterozygous. The haplotypes identified in this study are of importance because they can be used to check the level of homozygozity in breeding lines as well as to track segregation in progenies.