Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites

Kantartzi, Stella K.; Ulloa, Mauricio; Sacks, Erik J.; Stewart, James Mc D.

doi:10.1007/s10709-008-9327-x

Cited by 51 publications

(46 citation statements)

References 28 publications

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“…Another reason is that the high portion of trinucleotide repeats in coding regions may be due to the exertion of selection pressure for selecting particular single amino acid stretches (Morgante et al 2002). Also the most informative SSRs contained C10 repeats which are in agreement with the previous studies (Vigouroux et al 2002;Qureshi et al 2004;Kantartzi et al 2009). It was also observed that position of the SSR loci on the chromosome has no effect on the corresponding PIC values (Lacape et al 2003(Lacape et al , 2007.…”

Section: Genetic Characterizationsupporting

confidence: 85%

“…In this study, we proposed 22 (11 BNLs and 11 MGHES) out of the 75 SSRs-based on their high PIC values (PIC C 5.0) and potential to amplify distinct DNA fragments for calculating the extent of genetic diversity among the 36 Gossypium species. Such findings were reported in multiple investigations including 39 SSRs for cotton genetics studies (Lacape et al 2007) and 25 SSRs for G. arboreum accessions (Kantartzi et al 2009). Large number of informative gSSRs had di-nucleotide repeats while larger portion of informative EST-SSRs had tri-nucleotide motif.…”

Section: Genetic Characterizationsupporting

confidence: 68%

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Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

2013

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The genus Gossypium is comprised of 50 diverse cotton species representing eight different genomes (A through G and K), however, phylogenetic relationship using various DNA marker types such as RAPD and SSRs was determined on limited number of cotton species. In this report, we have demonstrated the application of genomic SSRs (gSSRs) and EST-SSRs, and after combining both the data sets, for resolving the phylogenies of 36 cotton species including seven races. Out of the 100 primer pairs surveyed (50 for gSSRs and 50 for ESTSSRs), 75 produced scorable amplification products in all species. Out of these, 73 were found to be polymorphic and amplified 135 alleles ranging from 1 to 5 alleles per SSR marker (average 2.87 alleles per marker). The gSSRs amplified higher number of alleles (72) compared to the EST-SSRs (63). In total 22 highly informative SSRs with PIC values C0.5 were identified. Genomic SSRs containing di-while EST-SSRs containing tri-nucleotide repeats exhibited high polymorphism compared to the other nucleotide repeats containing gSSRs/EST-SSRs. Number of tandem repeats and polymorphism were positively correlated. Neither the type of chromosome nor the location of the SSRs showed association with the polymorphism. Gossypium herbaceum var. africanum (Watt) Hutch. ex and Ghose and Gossypium robinsonii F. Muell. were found the most genetically diverse, while among races of Gossypium hirsutum L. ''yucatanense'' and G. hirsutum ''punctatum'' were found genetically diverse. Of the three data sets, clustering analysis based on EST-SSRs and combined data sets, revealed parallel results reported in earlier studies. This study further confirmed that Gossypium darwinii Watt has close relationship with Gossypium barbadense L. Moreover, Gossypium raimondii Ulbr. and G. herbaceum/Gossypium arboreum L. are close living relatives of the ancestor allotetraploid species. Our studies suggest that for resolving phylogenetic relationship among the various plant species EST-SSRs could be a better choice. This information can be instrumental in transferring novel alleles or loci from the wild species into the cultivated cotton species which would set a stage for cultivating genetically diverse cultivars-a way to achieve sustainable cotton production in changing climate.

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Section: Genetic Characterizationsupporting

confidence: 85%

Section: Genetic Characterizationsupporting

confidence: 68%

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

2013

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“…The PIC values ranged from 0.021 to 0.80 (average 0.206) ( Table 2). The average PIC obtained during the present study was less to that obtained by Kantartzi et al (2009) (average PIC 0.42), while analyzing genetic diversity in G. arboreum cultivars using microsatellites, though the range obtained by them was also different (0.00 to 0.68). Liu et al (2006) also reported high average PIC (0.31), compared to that obtained in present study, and the average PIC value obtained by Lacape et al (2007) was also higher (average 0.55) than our value.…”

Section: Microsatellite Diversitycontrasting

confidence: 83%

“…Efforts have also been made for genetic diversity analysis of selected G. arboreum germplasm using different markers like RAPD (Rana and Bhat 2004;Mahmood et al 2009;Mandaliya et al 2010;Deosarkar et al 2010;Dongre et al 2011), ISSR Khandagale et al 2007;Bardak and Bolek 2012) and microsatellites or simple sequence repeats (SSRs) Liu et al 2006;Dongre et al 2007;Kantartzi et al 2009;Deosarkar et al 2010;Dongre et al 2011;Noormohammadi et al 2013), though no study explored the polymorphism among the six races of G. arboreum. So, the present work was designed to study genetic diversity among elite genotypes of six different races of G. arboreum using microsatellite markers, since microsatellites markers have edge over other marker system in cultivar fingerprinting and diversity studies,…”

Section: Introductionmentioning

confidence: 99%

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers

Sethi

Siwach

Verma

2015

Physiol Mol Biol Plants

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Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it has not been explored fully. During the present study, 100 polymorphic SSR loci were used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.

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“…Several molecular markers such as AFLP (Rana et al, 2005;Westengen et al, 2005), RAPD (Vafai-Tabar et al, 2004), SSR (Lacape et al, 2007;Kantartzi et al, 2009;Luo et al, 2010) and ISSR (Dongre et al, 2004) have been used in upland cotton germplasm analysis, which is helpful to reveal the genetic diversity of these varieties in future breeding. Molecular markers such as SSR Chen et al, 2005;Li et al, 2009;Wu et al, 2010), ISSR (Jiang et al, 2008) and SRAP (Li et al, 2008) have also been applied in determining the genetic diversity of sea-island cotton.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of sea-island cotton (Gossypium barbadense) revealed by mapped SSRs

Wang

Feng²,

Lin³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. In order to evaluate the genetic diversity of seaisland cotton (Gossypium barbadense), 237 commonly mapped SSR markers covering the cotton genome were used to genotype 56 seaisland cotton accessions. A total of 218 polymorphic primer pairs (91.98%) amplified 361 loci, with a mean of 1.66 loci. Polymorphism information content values of the SSR primers ranged from 0.035 to 0.862, with a mean of 0.320. The highest mean polymorphism information content value for the SSR motifs was from a compound motif (0.402), and for the chromosomes it was Chr10 (0.589); the highest ratio of polymorphic primers in Xinjiang accessions was from Chr21 (83.33%). Genetic diversity was high in Xinjiang accessions. AMOVA showed that variation was 8 and 92% among populations and within populations, respectively. The 56 sea-island accessions were divided into three groups in the UPGMA dendrogram: Xinhai5 was in the first group; accessions from Xinjiang, except the five main ones, were in the second group, and the other 34 accessions ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 10 (4): 3620-3631 (2011) Genetic diversity of sea-island cotton by mapped SSRs 3621were in the third group. Accessions from the former Soviet Union and Xinjiang main accessions were closely related. Both PCA and UPGMA confirmed that Xinhai5 was distinct from the other accessions, and accessions from Xinjiang were in an independent group. Given the differences between principal components analysis and UPGMA results, it is necessary to combine molecular markers and pedigree information so that genetic diversity can be objectively analyzed.

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Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites

Cited by 51 publications

References 28 publications

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers

Genetic diversity of sea-island cotton (Gossypium barbadense) revealed by mapped SSRs

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