Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling.

TitleDiscovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling.
Publication TypeJournal Article
Year of Publication2010
AuthorsTill BJ, Jankowicz-Cieslak J, Sági L, Huynh OA, Utsushi H, Swennen R, Terauchi R, Mba C
JournalTheor Appl Genet
Volume121
Issue7
Pagination1381-9
Date Published2010 Nov
ISSN1432-2242
KeywordsAlleles, Breeding, Diploidy, Gene Pool, Genome, Plant, Genomics, Humans, Musa, Phototropism, Polymorphism, Single Nucleotide, Polyploidy
Abstract

<p>Musa (banana and plantain) is an important genus for the global export market and in local markets where it provides staple food for approximately 400 million people. Hybridization and polyploidization of several (sub)species, combined with vegetative propagation and human selection have produced a complex genetic history. We describe the application of the Ecotilling method for the discovery and characterization of nucleotide polymorphisms in diploid and polyploid accessions of Musa. We discovered over 800 novel alleles in 80 accessions. Sequencing and band evaluation shows Ecotilling to be a robust and accurate platform for the discovery of polymorphisms in homologous and homeologous gene targets. In the process of validating the method, we identified two single nucleotide polymorphisms that may be deleterious for the function of a gene putatively important for phototropism. Evaluation of heterozygous polymorphism and haplotype blocks revealed a high level of nucleotide diversity in Musa accessions. We further applied a strategy for the simultaneous discovery of heterozygous and homozygous polymorphisms in diploid accessions to rapidly evaluate nucleotide diversity in accessions of the same genome type. This strategy can be used to develop hypotheses for inheritance patterns of nucleotide polymorphisms within and between genome types. We conclude that Ecotilling is suitable for diversity studies in Musa, that it can be considered for functional genomics studies and as tool in selecting germplasm for traditional and mutation breeding approaches.</p>

DOI10.1007/s00122-010-1395-5
Alternate JournalTheor. Appl. Genet.
PubMed ID20589365
PubMed Central IDPMC2955235
Showing 34 of 74 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Musa acuminata ssp. banksii ITC0896 acuminata subsp. banksii Papua New Guinea ITC
Long Tavoy ITC0283 acuminata subsp. burmannica Unknown ITC
Mbwazirume ITC1356 AAA subgr. Mutika/Lujugira Unknown ITC
Mbwazirume ITC0084 AAA subgr. Mutika/Lujugira Burundi ITC
Obino l'Ewai ITC0109 AAB subgr. Plantain Unknown ITC
Truncata ITC0393 acuminata subsp. truncata Unknown ITC
Pisang Lilin ITC1400 AA Unknown Unknown ITC
Pisang Glintong ITC0683 AAA Unknown Indonesia ITC
Honduras ITC0247 balbisiana Unknown Unknown ITC
Bluggoe ITC1404 ABB subgr. Bluggoe Unknown ITC
Yangambi KM5 ITC1123 AAA subgr. Ibota Unknown ITC
Ihitisim ITC0121 AAB subgr. Plantain Unknown ITC
Schizocarpa ITC0599 schizocarpa Unknown Papua New Guinea ITC
Niyarma Yik
ITC0269 AA Unknown Unknown ITC
Mai'a maoli koa'e
ITC1167 AAB Unknown Unknown ITC
Yawa 2
ITC1238 ABBT Unknown Papua New Guinea ITC
Wompa
ITC1152 AS Unknown Papua New Guinea ITC
Basjoo
ITC0061 basjoo subsp. basjoo Unknown ITC
Gran Enano
ITC1256 AAA subgr. Cavendish Unknown ITC
Gros Michel
ITC1481 AAA subgr. Gros Michel Unknown ITC
Laknau
ITC0332 AAB subgr. Laknao Unknown ITC
Musa laterita
ITC0627 laterita subsp. laterita Unknown ITC
Popoulou
ITC0335 AAB subgr. Maia Maoli/Popoulu Unknown ITC
Madang
ITC0254 acuminata subsp. malaccensis Unknown ITC
Kunnan
ITC1034 AB subgr. Ney Poovan Unknown ITC
Pisang Kayu
ITC0420 AAA subgr. Orotava Indonesia ITC
Pisang Awak
ITC0339 ABB subgr. Pisang Awak Unknown ITC
Pome
ITC0125 AAB subgr. Pome Unknown ITC
Lady Finger (Nelson)
ITC0582 AAB subgr. Pome Unknown ITC
Red
ITC0486 AAA subgr. Red Unknown ITC
Saba
ITC1138 ABB subgr. Saba Unknown ITC
Red Yade
ITC1140 AAB subgr. Plantain Unknown ITC
Musa textilis
ITC0539 textilis subsp. textilis Unknown ITC
Ensete ventricosum
ITC1387 ventricosum subsp. ventricosum Unknown ITC

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