African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12227

Full Length Research Paper

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

Ude, George N*
  • Ude, George N*
  • Department of Natural Sciences, Bowie State University, Bowie, Maryland, United States.
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Acquaah, George
  • Acquaah, George
  • Department of Natural Sciences, Bowie State University, Bowie, Maryland, United States.
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Irish, Brian M
  • Irish, Brian M
  • USDA-ARS, Tropical Agriculture Research Station, Mayaguez, Puerto Rico.
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Das, Aditi
  • Das, Aditi
  • Department of Natural Sciences, Bowie State University, Bowie, Maryland, United States.
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  •  Received: 30 September 2014
  •  Accepted: 03 October 2014
  •  Published: 08 October 2014

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 (NGS) technologies has opened up new avenues for answering biological questions in moderate to large genomes of complex polyploid species like banana. Most edible cultivated 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 Musa balbisiana (B-genome). In this study, 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. The study confirms 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, for characterizing associations between genotypic and phenotypic variation in Musa by using sequence variants as molecular markers.

 

Key words: Sequence capture, in-solution hybridization, nucleotide variants, polyploidy, bananas (Musa spp.)

Abbreviation

NGS, Next generation sequencing, MNPs, multi-nucleotide polymorphisms; INDELs, insertions and deletions; MQ, mapping quality; CDS, coding sequence; SNPs, single nucleotide polymorphisms; AFLP, amplified fragment length polymorphism.