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ARS Home » Southeast Area » Mayaguez, Puerto Rico » Tropical Crops and Germplasm Research » Research » Publications at this Location » Publication #311834

Research Project: Management of Tropical/Subtropical Plant Genetic Resources and Associated Information

Location: Tropical Crops and Germplasm Research

Title: Targeted parallel sequencing of the Musa species: searching for an alternative model system for polyploidy studies

Author
item Ude, George - Bowie State University
item Acquaah, George - Bowie State University
item Irish, Brian
item Das, Aditi - Bowie State University

Submitted to: African Journal of Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2014
Publication Date: 10/8/2014
Citation: Ude, G.N., Acquaah, G., Irish, B.M., Das, A. 2014. Targeted parallel sequencing of the Musa species: searching for an alternative model system for polyploidy studies. African Journal of Biotechnology. 13(41):4052-4060.

Interpretive Summary: Consumed as a dessert and as a staple, bananas (Musa spp.) are one of the most important agricultural fruit products in the world. The number and frequency of emerging pests and diseases continues to increase and limit banana’s productivity. In this research, a technique using modern biotechnology (e.g., next generation sequencing and bioinformatics’) is described for the development of a large number of genetic markers in banana. The markers were identified in a subset of bananas representing ancestral and contemporary cultivars. The markers developed can be used to better understand the origin and the history of cultivated bananas, to study their genetic diversity and possibly aid in the complicated process of banana-breeding.

Technical Abstract: Modern day genomics holds the promise of solving the complexities of basic plant sciences, and of catalyzing practical advances in plant breeding. While contiguous, "base perfect" deep sequencing is a key module of any genome project, recent advances in parallel next generation sequencing technologies has opened up new avenues for answering biological questions in moderate to large genomes of complex polyploid species like banana. Most edible bananas belong to the Eumusa section of the Musaceae, and are diploid or triploid hybrids from their wild diploid ancestors: Musa acuminata (A-genome) alone or from hybridization with M. balbisiana (B-genome). In this manuscript, a second-generation parallel sequencing method was implemented to identify nucleotide variants in Musa spp. This strategy reduced genome complexity by enrichment with a hybridization capture library, targeting primarily exons of coding genes. The resulting marker dataset was successful in sampling broadly within the A and B genome groups and their derived hybrids. This study confirmed the sequence diversity of Musa on a genome-wide scale even in a modest subset of Musa cultivars. Importantly, the experimental approach undertaken here is an efficient means of producing data for the design of high and low-density nucleotide polymorphism (single-base substitutions, small insertions and deletions or INDELs) genotyping assays applicable to a wide range of Musa cultivars. Thus, an excellent alternative method is reported in this paper, for characterizing associations between genotypic and phenotypic variation in Musa by using sequence variants as molecular markers.