Dominant Allele Phylogeny and Constitutive Subgenome Haplotype Inference in Bananas Using Mitochondrial 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 polyploids with 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. The mitochondrial marker NAD1 was observed to be ideal in differentiating bananas of different genomic constitutions based on size of amplicons as well as sequence. The genotypes phylogenetically segregated based on the dominant genome; AAB genotypes grouped with AA and AAA, and the ABB together with BB. Both markers differentiated banana sections, but could not differentiate subspecies within the A genomic group. On the basis of CENH3 marker, 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.

East African diploid and triploid bananas: a genetic complex transported from South-East Asia

“…Another confirmation is the type Vβ of their cytoplasmic genomes (Carreel et al, 2002), the chloroplastic V type being typical of the subspecies banksii and the mitochondrial β typical of the subspecies zebrina. Muiruri et al (2017) also confirmed the contribution of subspecies zebrina to 'Mbwazirume', a popular Mutika accession, and to Ngombe, an AAA accession from Kenya. Therefore, the region of the basic origin of all these AAAs is likely the contact zone of the banksii and zebrina subspecies in present southern Indonesia.…”

Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages

“…Despite lack of separation between A groups, the majority of AAA seemed to cluster around two AAcv Pisang Jari Buaya (ITC0312) and Pisang Mas (ITC0653), which might suggest those accessions emerged from the same genepool 22 , 49 . A significant difference between the juvenile and pre-flowering stages was the clear separation of AAB and ABB accessions into two cluster, as described by several genotyping studies 18 , 24 , 50 . The wild M. balbisiana Tani (ITC1120) was located between these two genome groups as described for the juvenile data set.…”

“…M. ornata , the only accession of the section Rhodochlamys, clustered on the far side of group B. Genetic studies are in contradiction whether M. ornata is more similar to M. balbisiana 15 , 23 , 24 or M. acuminata 16 , 17 , but the metabolite profile of this accession suggests a chemotype more similar to the B genome. The wild M. acuminata accessions showed a mixed cluster of malaccensis and burmannica subspecies, which were located closer to the banksii accession than the zebrina and microcarpa accessions.…”