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 40 of 74 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Kluai Tiparot ITC0652 ABB Unknown Unknown ITC
Safet Velchi ITC0245 AB subgr. Ney Poovan India ITC
Figue Pomme Géante ITC0769 AAB subgr. Silk Unknown ITC
Novaria ITC1329 AAA subgr. Cavendish Unknown ITC
Musa ornata ITC0370 ornata subsp. ornata Unknown ITC
Namwa Khom ITC0659 ABB subgr. Pisang Awak Thailand ITC
Foconah ITC0649 AAB subgr. Pome Unknown ITC
Tuu Gia ITC0610 AA Unknown Unknown ITC
Agutay ITC1028 acuminata Unknown Unknown ITC
Butuhan, intermediate apex ITC0565 balbisiana Unknown Philippines ITC
Calcutta 4 ITC0249 acuminata subsp. burmannicoides India ITC
Pahang ITC0609 acuminata subsp. malaccensis Unknown ITC
Zebrina ITC1177 acuminata subsp. zebrina Indonesia ITC
Paka ITC1254 AA Unknown Unknown ITC
FHIA-01 ITC0504 AAAB Unknown Honduras ITC
Pelipita ITC0472 ABB Unknown Philippines ITC
Pisang Jari Buaya ITC0312 AA subgr. Pisang Jari Buaya Malaysia ITC
Musa beccarii ITC1070 beccarii subsp. beccarii Unknown ITC
Khae (Phrae) ITC0660 acuminata subsp. siamea Thailand ITC
Mun ITC0463 AAA Unknown Papua New Guinea ITC
Dwarf Parfitt ITC0548 AAA subgr. Cavendish Unknown ITC
Petite Naine ITC0654 AAA subgr. Cavendish Unknown ITC
Pisang Ceylan ITC1441 AAB subgr. Mysore Unknown ITC
Silk ITC0348 AAB subgr. Silk Unknown ITC
Prata ana ITC0962 AAB subgr. Pome Unknown ITC
Leite ITC0277 AAA subgr. Rio Unknown ITC
Tomolo ITC1187 AA Unknown Papua New Guinea ITC
Kamaramasenge ITC0127 AAB subgr. Kamaramasenge Unknown ITC
Pisang Mas ITC0653 AA subgr. Sucrier Malaysia ITC
Tani ITC1120 balbisiana Unknown Unknown ITC
Ice cream ITC0020 ABB subgr. Ney Mannan Gabon ITC
Dole ITC0767 ABB subgr. Bluggoe Unknown ITC
Grande Naine ITC0180 AAA subgr. Cavendish Unknown ITC
Igitsiri (Intuntu) ITC0081 AAA subgr. Mutika/Lujugira Burundi ITC
Fougamou 1 ITC0101 ABB subgr. Pisang Awak Gabon ITC
Orishele ITC0517 AAB subgr. Plantain Unknown ITC
Borneo ITC0253 acuminata subsp. microcarpa Malaysia ITC
Pisang Rojo Uter ITC1158 AA Unknown Indonesia ITC
Bie Yeng ITC0279 AA Unknown Unknown ITC
Akondro Mainty ITC0281 AA Unknown Unknown ITC

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