Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling |
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Authors: | Bradley J Till Joanna Jankowicz-Cieslak László Sági Owen A Huynh Hiroe Utsushi Rony Swennen Ryohei Terauchi Chikelu Mba |
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Institution: | (1) Plant Breeding Unit, FAO/IAEA Agricultural and Biotechnology Laboratory, International Atomic Energy Agency, P.O. Box 100, Vienna International Centre, 1400 Vienna, Austria;(2) Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven (K.U.Leuven), Kasteelpark Arenberg 13 bus 2455, 3001 Leuven, Belgium;(3) Iwate Biotechnology Research Center, 174-4 22 Chiwari, Narita, Kitakami Iwate, 024-0003, Japan;(4) Bioversity International, Kasteelpark Arenberg 13 bus 2455, 3001 Leuven, Belgium |
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Abstract: | 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. |
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