Literature DB >> 17180377

Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce.

J Jansen1, Th van Hintum.   

Abstract

This paper introduces a novel sampling method for obtaining core collections, entitled genetic distance sampling. The method incorporates information about distances between individual accessions into a random sampling procedure. A basic feature of the method is that automatically larger samples are obtained if accessions are further apart and smaller samples if accessions are closer together. Genetic distance sampling can be used in conjunction with predefined stratifications of the accessions. Sample sizes are determined automatically; they depend on the distances between accessions within strata. The method is applied to the collection of cultivated lettuce of the Centre for Genetic Resources, the Netherlands. In this paper, genetic distances between accessions are obtained using AFLP marker data. However, genetic distance sampling can be applied using any measure of genetic distance between accessions. Some properties of genetic distance sampling are discussed.

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Year:  2006        PMID： 17180377     DOI： 10.1007/s00122-006-0433-9

Source DB:  PubMed          Journal:  Theor Appl Genet        ISSN： 0040-5752            Impact factor:   5.699


  5 in total

1.  MSTRAT: an algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness.

Authors:  B Gouesnard; T M Bataillon; G Decoux; C Rozale; D J Schoen; J L David
Journal:  J Hered       Date:  2001 Jan-Feb       Impact factor: 2.645

2.  Molecular markers: tools to improve genebank efficiency.

Authors:  Theo J L Van Hintum; Rob Van Treuren
Journal:  Cell Mol Biol Lett       Date:  2002       Impact factor: 5.787

3.  AFLP: a new technique for DNA fingerprinting.

Authors:  P Vos; R Hogers; M Bleeker; M Reijans; T van de Lee; M Hornes; A Frijters; J Pot; J Peleman; M Kuiper
Journal:  Nucleic Acids Res       Date:  1995-11-11       Impact factor: 16.971

4.  Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers.

Authors:  D J Schoen; A H Brown
Journal:  Proc Natl Acad Sci U S A       Date:  1993-11-15       Impact factor: 11.205

5.  A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers.

Authors:  J Jansen; H Verbakel; J Peleman; Th J L van Hintum
Journal:  Theor Appl Genet       Date:  2005-12-03       Impact factor: 5.699
  5 in total
  20 in total

1.  Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions.

Authors:  Brigitte Uwimana; Marinus J M Smulders; Danny A P Hooftman; Yorike Hartman; Peter H van Tienderen; Johannes Jansen; Leah K McHale; Richard W Michelmore; Clemens C M van de Wiel; Richard G F Visser
Journal:  Theor Appl Genet       Date:  2012-06-04       Impact factor: 5.699

2.  Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data.

Authors:  Joost van Heerwaarden; T L Odong; F A van Eeuwijk
Journal:  Theor Appl Genet       Date:  2012-11-21       Impact factor: 5.699

3.  Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses.

Authors:  Umezuruike Linus Opara; Dan Jacobson; Nadiya Abubakar Al-Saady
Journal:  J Zhejiang Univ Sci B       Date:  2010-05       Impact factor: 3.066

4.  Retention of agronomically important variation in germplasm core collections: implications for allele mining.

Authors:  Patrick A Reeves; Lee W Panella; Christopher M Richards
Journal:  Theor Appl Genet       Date:  2012-01-07       Impact factor: 5.699

5.  Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Authors:  T L Odong; J van Heerwaarden; J Jansen; T J L van Hintum; F A van Eeuwijk
Journal:  Theor Appl Genet       Date:  2011-04-07       Impact factor: 5.699

6.  Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures.

Authors:  Chris Thachuk; José Crossa; Jorge Franco; Susanne Dreisigacker; Marilyn Warburton; Guy F Davenport
Journal:  BMC Bioinformatics       Date:  2009-08-06       Impact factor: 3.169

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

Authors:  Marco Pessoa-Filho; Paulo H N Rangel; Marcio E Ferreira
Journal:  BMC Plant Biol       Date:  2010-06-24       Impact factor: 4.215

Review 8.  Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation.

Authors:  T L Odong; J Jansen; F A van Eeuwijk; T J L van Hintum
Journal:  Theor Appl Genet       Date:  2012-09-15       Impact factor: 5.699

9.  Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation.

Authors:  Gerrit Gort; Theo van Hintum; Fred van Eeuwijk
Journal:  Theor Appl Genet       Date:  2009-05-13       Impact factor: 5.699

10.  Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search.

Authors:  Herman De Beukelaer; Petr Smýkal; Guy F Davenport; Veerle Fack
Journal:  BMC Bioinformatics       Date:  2012-11-23       Impact factor: 3.169
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