Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Inghelandt, Delphine Van; Melchinger, Albrecht E.; Lebreton, Claude; Stich, Benjamin

doi:10.1007/s00122-009-1256-2

Cited by 240 publications

(222 citation statements)

References 27 publications

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“…Although increasing numbers of SNP (single nucleotide polymorphism) markers are available for common bean, SSRs continue to be the most informative class of markers in genetic diversity studies (Yang et al, 2011). Studies comparing these markers have shown that at least 10 times more SNPs are necessary to generate the same informative estimates of genetic parameters obtained using SSRs (Yu et al, 2009;Van Inghelandt et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Discrimination of common bean cultivars using multiplexed microsatellite markers

Cardoso¹,

Brondani²,

Menezes³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Analysis of DNA polymorphisms allows for the genetic identification and precise discrimination of species with a narrow genetic base such as common bean. The primary objectives of the present study were to molecularly characterize commercial common bean varieties developed at various research institutions using microsatellite markers and to determine the degree of genetic diversity among the bean varieties analyzed. Fifty cultivars representing 12 grain classes and 64 genitors, i.e., accessions used to develop these cultivars, were characterized. Based on an analysis of 24 simple sequence repeats, the estimates for the average number of alleles and genetic diversity were 8.29 and 0.646, respectively. The combined probability of identity was estimated at 7.05 x 10 -17 , indicating a high individual discriminatory power. Thirtytwo percent of the cultivars exhibited heterogeneity for multiple loci that reflected either homozygosity for different alleles of a given locus in different individuals or heterozygosity for the locus. The average 1964-1978 (2014) Molecular characterization of cultivated common bean genetic diversity for the groups of cultivars and genitors was 0.605 and 0.660, respectively, with no genetic differentiation (F ST ) between these groups. Although similar estimates of expected heterozygosity were observed when the cultivars were grouped by release date, a greater number of private alleles was observed in the most recent cultivars. The genetic differentiation among cultivars originating from different institutions was not different from zero (F ST = 0.01). The molecular profile database derived from these analyses may increase the statistical power of genetic estimates and may be incorporated into breeding programs for common bean. Furthermore, the profiles obtained for the different cultivars may be used as molecular descriptors to complement traditional descriptors used in distinctiveness, uniformity and stability tests, thereby improving the traceability of samples and their derivatives and helping to protect the intellectual property rights of breeders.

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Section: Discussionmentioning

confidence: 99%

Discrimination of common bean cultivars using multiplexed microsatellite markers

Cardoso¹,

Brondani²,

Menezes³

et al. 2014

Genet. Mol. Res.

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“…When comparing SNP markers with microsatellite markers in corn, Yang et al (2011) reported low estimates for H E and PIC using SNPs. Moreover, Van Inghelandt et al (2010) showed that although similar inferences could be made regarding the structure and diversity of the heterotic groups in corn using either SNPs or microsatellites, the number of markers needed to obtain similar estimates of genetic diversity was 7 times greater for SNPs than for microsatellites, and the modified Roger's distance was 11 times greater for SNPs than for microsatellites.…”

Section: Selection Of Core Collections and Comparison With The Entirementioning

confidence: 96%

Development of a cassava core collection based on single nucleotide polymorphism markers

et al. 2014

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ABSTRACT. Single nucleotide polymorphism (SNP) markers were used in the largest cassava (Manihot esculenta Crantz) germplasm collection from Brazil to develop core collections based on the maximization strategy. Subsets with 61, 64, 84, 128, 256, and 384 cassava accessions were selected and named PoHEU, MST64, PoRAN, MST128, MST256, and MST384, respectively. All the 798 alleles identified by 402 SNP markers in the entire collection were captured in all core collections. Only small alterations in the diversity parameters were observed for the different core collections compared with the complete collection. Because of the optimal adjustment of the validation parameters representative of the complete collection, the absence of genotypes with high genetic similarity and the maximization of the genetic distances between accessions of the PoHEU core collection, which contained 4.7% of the accessions of the complete collection, maximized the genetic conservation of this important cassava collection. Furthermore, the development of this core collection will allow concentrated efforts toward future characterization and agronomic evaluation of accessions to maximize the diversity and genetic gains in

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“…Genetic diversity analysis using molecular markers has been used in plant breeding and in studies involving germplasm conservation (Belaj et al, 2012), association mapping (Li et al, 2011), population structure (Van Inghelandt et al, 2010), genetic relationships among populations (Bracco et al, 2009), association between genetic distance and heterosis or specific combining ability, geographic adaptation and pedigree information (Legesse et al, 2007(Legesse et al, , 2008, linkage disequilibrium (Stich et al, 2006), and heterotic group identification (Xia et al, 2004(Xia et al, , 2005. Most studies with maize (Zea mays L. subsp mays) have used inbred lines.…”

Section: Introductionmentioning

confidence: 99%

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

Lanes¹,

Viana²,

Paes³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. The objectives of this study were to identify the population structure and to assess the genetic diversity of maize inbreds. We genotyped 81 microsatellite loci of 90 maize inbreds that were derived from tropical hybrids and populations. The population structure analysis was based on a Bayesian approach. Each subpopulation was characterized for the effective number of alleles, gene diversity, and number of private alleles. We also performed an analysis of molecular variance and computed a measure of population differentiation (F ST ). The genetic distances were computed from the similarity index of Lynch and the dissimilarity measures proposed by Smouse and Peakall. The cluster analyses were based on the unweighted pair-group method using arithmetic averages and Tocher method. The clustering efficiency was assessed by the error rate of the discriminant analysis. We also performed a principal coordinates analysis. The population structure analysis revealed three tropical heterotic pools, which have been used by worldwide and Brazilian maize seed companies. The degree of genetic differentiation and of intra-and inter-population genetic diversity for these tropical heterotic pools are comparable to that observed for temperate and subtropical heterotic pools. The higher allelic frequency variation within each tropical heterotic pool and the high genetic diversity between the inbreds were evidence of heterotic groups within the main tropical heterotic pools.

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Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Cited by 240 publications

References 27 publications

Discrimination of common bean cultivars using multiplexed microsatellite markers

Discrimination of common bean cultivars using multiplexed microsatellite markers

Development of a cassava core collection based on single nucleotide polymorphism markers

Population structure and genetic diversity of maize inbreds derived from tropical hybrids

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