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Malosetti, Marcos; Abadie, T.

doi:10.1023/a:1012003611371

Cited by 41 publications

(22 citation statements)

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“…The principal component analysis validated LDSS method and Seuclid distance combining Single cluster method in core subset construction. The Seuclid distance was also validated in maize core subset construction (Crossa et al, 1995;Malosetti and Abadie, 2001). Core subsets constructed by Cosine and Correlation showed bad representativeness compared to those constructed by Euclid, Seuclid, Mahal and Cityblock.…”

Section: Discussionmentioning

confidence: 99%

Assessment of different genetic distances in constructing cotton core subset by genotypic values

Wang

Huang

et al. 2008

J. Zhejiang Univ. Sci. B

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Abstract:One hundred and sixty-eight genotypes of cotton from the same growing region were used as a germplasm group to study the validity of different genetic distances in constructing cotton core subset. Mixed linear model approach was employed to unbiasedly predict genotypic values of 20 traits for eliminating the environmental effect. Six commonly used genetic distances (Euclidean, standardized Euclidean, Mahalanobis, city block, cosine and correlation distances) combining four commonly used hierarchical cluster methods (single distance, complete distance, unweighted pair-group average and Ward's methods) were used in the least distance stepwise sampling (LDSS) method for constructing different core subsets. The analyses of variance (ANOVA) of different evaluating parameters showed that the validities of cosine and correlation distances were inferior to those of Euclidean, standardized Euclidean, Mahalanobis and city block distances. Standardized Euclidean distance was slightly more effective than Euclidean, Mahalanobis and city block distances. The principal analysis validated standardized Euclidean distance in the course of constructing practical core subsets. The covariance matrix of accessions might be ill-conditioned when Mahalanobis distance was used to calculate genetic distance at low sampling percentages, which led to bias in small-sized core subset construction. The standardized Euclidean distance is recommended in core subset construction with LDSS method.

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Section: Discussionmentioning

confidence: 99%

Assessment of different genetic distances in constructing cotton core subset by genotypic values

Wang

Huang

et al. 2008

J. Zhejiang Univ. Sci. B

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“…Core collections have been assembled based on several algorithms [5-8] in several crops, including durum and bread wheats [5,6], barley [7], potato [8], maize [9], peanut [10], and rice [11]. The usage of molecular markers as descriptors of population structure provides the most reliable criteria when assembling core collections [12].…”

Section: Introductionmentioning

confidence: 99%

Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

et al. 2012

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BackgroundThe goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD) in seven genomic regions using simple sequence repeat (SSR) markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome.ResultsA genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA) and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2). The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure.ConclusionsA global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

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“…The majority of the proposed strategies vary in their methods by either the stratification of the reference collection in groups that are genetically closer when examined according to some criteria, or by taking a straight sample of the accessions that will make up the core collection according to a specific methodology. Stratification can be based on criteria which include morpho-physiological and agronomical traits [3], geographical parameters [4], biochemical traits [5], or molecular data [6]. Stratified random sampling methodologies include random sampling with no regard to group origin, sampling proportionate to the size of the groups, or proportionate to the natural logarithms of the size of the groups that are composed after the first stage of stratification [7], or may even be based on more concrete data on allelic composition of the reference population [8] or based on genetic distance estimated by biochemical or molecular markers [9-13].…”

Section: Introductionmentioning

confidence: 99%

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

2010

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BackgroundBreeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size.ResultsThe thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed.ConclusionsBuilding of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum allele richness with the smallest sample size from a larger thematic collection. As an example, we used the development of a thematic core collection for drought tolerance in rice. It is expected that such thematic collections increase the use of germplasm by breeding programs and facilitate the study of the traits under consideration. The definition of a core collection to study drought resistance is a valuable contribution towards the understanding of the genetic control and the physiological mechanisms involved in water use efficiency in plants.

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Cited by 41 publications

References 14 publications

Assessment of different genetic distances in constructing cotton core subset by genotypic values

Assessment of different genetic distances in constructing cotton core subset by genotypic values

Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

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