Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana

Abstract

Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminatabased cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the 'Pisang Madu' cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expectedinvolving multiple hybridization stepsand also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant.

Chromosome painting in cultivated banana and their wild relatives (Musaspp.) reveals differences in chromosome structure

“…These observations confirm close genetic relationship between both groups of edible bananas as noted previously (Raboin et al, 2005. According to Martin et al (2017Martin et al ( , 2020, 2n gamete donor, which contributed to the origin of dessert banana clones with AAA genomes, including 'Cavendish' and 'Gros Michel', belongs to the Mchare (Mlali) sub-group. The genome of this ancient sub-group, which probably originated somewhere around Java, Borneo and New Guinea, but today is only found in East Africa, is based on zebrina / microcarpa and banksii subspecies (Perrier et al, 2009).…”

“…This agrees with the results obtained by genotyping using molecular markers(Christelová et al, 2017). Most recently, complex hybridization scheme of Mchare bananas was supported also by application of transcriptomic data for identification of specific SNPs in 23 Musa species and edible cultivars(Martin et al, 2020).Genome structure and origin of cultivated triploid Musa clonesPlantains are an important group of triploid starchy bananas with AAB genome constitution, which originated after hybridization between M. acuminata and M. balbisiana.As expected, chromosome painting in '3 Hands Planty', 'Amou' and 'Obino l'Ewai' cultivars revealed B-genome specific translocation of 8 Mb segment from the long arm of chromosome 3 to the long arm of chromosome 1. Unlike the B-genome chromosome set, the two Agenome chromosome sets of plantains lacked any detectable translocation.…”

“…We observed reciprocal translocation between chromosomes 3 and 8, which is typical for (Carreel et al, 2002, Li et al, 2013, Kitavi et al, 2016, Němečková et al, 2018, Martin et al, 2020. origin.…”

“…Fusion of unreduced gametes produced by diploid edible and partially sterile cultivars with normal haploid gametes from fertile diploid (Simmonds, 1962, Carreel et al, 1994, Raboin et al, 2005 would give rise to triploids. The number one export dessert banana type Cavendish as well as other important dessert bananas, such as Gros Michel and Pome types, originated according to this scenario by hybridization of a diploid representative of subgroup 'Mchare' (originally named 'Mlali') (AA genome; zebrina / microcarpa and banksii ascendance) which served as a donor of an unreduced diploid gamete with haploid gamete of 'Khai' (malaccensis ascendance) (Perrier et al, 2009, Perrier et al, 2019, Martin et al, 2020.…”

Safeguarding and using global banana diversity: a holistic approach

“…In cultivated bananas, the chromosome structures of allopolyploid hybrids were explored allowing to clarify the path that led to their creation (Baurens et al 2019;Cenci et al 2019Cenci et al , 2020. Current efforts focus on resolving the mosaic structure of cultivated banana by looking at the ancestral contribution of the different M. acuminata subspecies along chromosomes (Martin et al 2020). This information will be of particular importance for breeders requesting material.…”