Development, characterization, and variability analysis of microsatellites from a commercial cultivar of Musa acuminata

Wang, J. Y.; Zheng, Lu; Huang, Bin; Liu, W. L.; Wu, Yan

doi:10.1007/s10722-009-9493-4

Cited by 20 publications

(15 citation statements)

References 22 publications

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“…Thirty-six of these sequences were selected, and 36 pairs of primers flanking the SSR loci were designed, one for each, and 24 of them generated clear and reproducible bands of expected size, and 13 of them showed polymorphism when amplifying selected samples. 86.9% of all sequenced clones were positive, and frequency of SSR marker showing polymorphism was 13.1%, which is lower than [22] results for rubber trees (24.6%) and Wang et al [23] for banana (19.5%). This may be due to variations between different materials; although SSRs are widely distributed in eukaryotic genomes, their content, type, and copy number vary between different materials.…”

Section: Discussionmentioning

confidence: 55%

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Feng

Tong

You

et al. 2013

BioMed Research International

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Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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Section: Discussionmentioning

confidence: 55%

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Feng

Tong

You

et al. 2013

BioMed Research International

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“…Despite this profusion of markers, it was considerable that they still be far behind available genetic analyses in other important crop plants. Most of the SSR markers sets in bananas were mainly developed in M. acuminata (Crouch et al 1997;Kaemmer et al 1997;Lagoda et al 1998;Creste et al 2006;Miller et al 2010;Wang et al 2010), a few were done in M. balbisiana (Buhariwalla et al 2005;Ravishankar et al 2013), possibly due to the abundance of germplasms in the former species, whereas limited in the later.…”

Section: Introductionmentioning

confidence: 99%

Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas

et al. 2016

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Bananas in Thailand have been surveyed by our team to be at least 140 cultivars in the plantations, 10 wild species and, 4 introduced species. To characterize the genetic relationship of species and cultivars, a set of novel SSR markers was developed. Totaling 53 clones containing SSR motifs were isolated from SSR-enriched library of wild Musa balbisiana Colla 'Tani' (BB). Selected positive clones were used to design 28 primer pairs for amplification of 12 wild and 82 cultivar accessions with genome designations AA, AB, AAA, AAB, ABB, and BBB. These SSR markers loci were homology searched to the banana genomes to map their locations. The seven-sets multiplex PCR approach using four fluorescent-labeled universal primers were utilized for cost effectiveness. Capillary fragment analysis yielded the accurate size of amplicons for evaluation of particular patterns for each cultivar. Phylogram and Structure analysis presented the specific genotype of genome groups (A and B genotypes, polyploid hybrid genomes) and cultivar groups. By A:B specific alleles ratio, accurate genome designations of hybrids can be determined. Additionally, a marker, characterized to be partial plastid ycf2 gene, indicated the maternal identification of hybrid cultivars. One SSR marker was also preliminary tested with some wild species and advised to be the candidate fingerprinting marker for species identification. In conclusion, SSR marker sets developed here proved their exploitation in detailed identity and relationship of cultivated bananas, which would be useful for genetic conservation and ongoing breeding programs in Thailand and other areas.

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“…Ning (2007), para genotipar 50 genótipos de bananeira de diferentes origens, utilizou 10 pares de primers SSR, encontrando 92 alelos, média de 9,2 alelos por primer. Estudo recente publicado por Wang et al (2010) detectaram uma média de 3,76 alelos ao avaliar a variabilidade dentro de 26 cultivares de banana por meio do uso de 21 primers SSR.…”

Section: Resultsunclassified

“…Em contraste com os marcadores morfológicos, os marcadores moleculares podem revelar diferenças entre os genótipos em nível de DNA, permitindo uma caracterização direta e eficiente, suficiente para discriminar a variação genética existente entre indivíduos e dentro de populações (WANG et al, 2010). Dentre os marcadores existentes, os microssatélites (SSR) têm sido considerados os ideais para a caracterização e a avaliação da variabilidade genética, são abundantes, dispersos ao acaso no genoma, lócus específico, codominantes e multialélicos.…”

Section: Introductionunclassified

Diversidade genética de clones de bananeira 'Prata-Anã' (AAB) por meio de marcadores SSR

Librelon¹,

Costa

Nietsche

et al. 2013

Rev. Bras. Frutic.

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Diversidade genética de 20 clones de 'Prata-Anã Gorutuba', quatro clones de 'Prata-Rio', quatro clones de 'Prata-Catarina' e as cultivares Caipira, Thap Maeo, Tropical, Maçã e Prata-Anã Comum foi avaliada por meio de marcadores moleculares Simple Sequence Repeats. De um total de 19 pares de primers SSRs utilizados, 57,8% deles amplificaram bandas polimórficas e distintas, 26,3% não produziram produtos específicos e 15,7% apresentaram falhas na amplificação de alguns indivíduos. O dendrograma indicou a formação de dois grupos. O primeiro grupo com a cultivar triploide Caipira, genoma exclusivamente A; enquanto o segundo (formado por sete subgrupos) agrupou todas as cultivares resultantes da hibridação natural ou artificial entre Musa acuminata e M. balbisiana, o subgrupo II, Tropical (AAAB) e o subgrupo III, Maçã (AAB). Os subgrupos IV, V, VI e VII foram formados, respectivamente, por: 'Prata-Catarina' clones 1 e 2; 'Prata-Rio' clones 1 e 2; 'Prata-Catarina' clone 3; 'Prata-Gorutuba' clones 12 e 17, 'Prata-Catarina' clone 4, 'Prata-Rio' clone 4, 'Thap Maeo' e 'Prata-Anã'. O subgrupo VIII foi formado exclusivamente pelos clones de' Prata-Anã Gorutuba'. Os resultados indicam a eficiência dos marcadores microssatélites na discriminação e na caracterização dos clones da 'Prata-Anã Gorutuba' da cultivar Prata-Anã.

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Development, characterization, and variability analysis of microsatellites from a commercial cultivar of Musa acuminata

Cited by 20 publications

References 22 publications

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas

Diversidade genética de clones de bananeira 'Prata-Anã' (AAB) por meio de marcadores SSR

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