SAN DIEGO (GenomeWeb) – Work presented at the annual Plant and Animal Genomes meeting here yesterday suggests genome-wide association studies are feasible in the banana — a herbaceous crop plant with a complex domestication history that is often represented by diverse clonal plants.
Because GWAS are most often applied to diploid organisms from large, randomly breeding populations, the existence of both diploid and triploid banana plants in a largely non-random breeding system have made it difficult to search for associations in banana, explained Julie Sardos, from Bioversity International in France, during a workshop on banana genomics.
"In banana, the most popular cultivars are triploids, often hybrids between different species," she and her co-authors noted in the talk's abstract. "[A]nd due to the absence of seeds in the fruit, a wide amount of the diversity observed ensues from the clonal diversification of a few initial genotypes."
With that in mind, the team focused its GWAS efforts on 106 diploid banana accessions from the Musa acuminata species, using genotyping-by-sequencing to track down SNP markers with potential ties to domestication-related banana features such as seedlessness and sterility.
The effort was helped along by the availability of a banana reference genome, French researchers described in Nature in 2012.
Though features such as population structure, relatively small population sizes, and non-random mating may confound GWAS analyses, Sardos noted, the team was able to circumvent some potential GWAS challenges by focusing on a combination of cultivated and wild M. acuminata accessions with diploid genomes.
With their initial genotyping-by-sequencing analyses, the researchers uncovered roughly 148,000 banana SNPs. From those, they subsequently narrowed in on more than 5,500 SNP markers — a set that was used to identify four genetic clusters in banana and to search for associations with the seedless phenotype and sterility.
Along with analyses on the full set of bananas, the team also double-checked some of their potential associations in wild and cultivated accessions from a single genetic cluster of banana accessions found in Papua New Guinea.
Their preliminary search led to nine regions of the banana genome — spanning more than 100 genes — that showed potential associations with the seedless phenotype, Sardos noted.
These included signals stemming from parts of the genome containing several hormone-related genes with plausible ties to parthenocarpy, or fertilization-free fruit production.
While "it's not easy" to perform GWAS in banana, Sardos said results suggest it is possible. She noted that the existing set of banana SNPs will be made available once the current findings are published, though the researchers are also are keen to uncover more SNP markers to increase coverage of the banana genome.
Along with targeted re-sequencing on parts of the genome showing promising associations, the researchers plan to use a similar GWAS strategy to delve into the genetics of drought tolerance and disease resistance in banana.
Speaking during the same session, the International Institute of Tropical Agriculture's Allan Brown described ongoing efforts to characterize banana genetics in East Africa in the hopes of developing more efficient and effective banana breeding schemes.
Though that work also relied on a genotyping-by-sequencing method for identifying genetic markers — in that case in more than 300 banana genotypes — Brown urged his fellow banana investigators to consider developing custom SNP arrays for genotyping bananas in a more standardized manner in the future.
Still other investigators presenting at the workshop touched on genomic efforts to understand and thwart the Panama disease-causing fungus Fusarium oxysporum f. sp. cubense; metabolomic profiling of bananas from different wild and domestic banana accessions in vitro; and transcriptome sequencing in the roots of banana plants exposed to osmotic stress.