Article (Scientific journals)
Genetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers
Lassois, Ludivine; Denancé, Caroline; Ravon, Elisa et al.
2016In Plant Molecular Biology Reporter, 34 (4), p. 827-844
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Keywords :
Malus domestica; SSR; diversity; genetic structure; parentage analysis; core collection
Abstract :
[en] In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P(ID) over the 21 retained SSR loci close to 10-28. Pairwise comparisons revealed 34% redundancy and 18.5% putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity He of 0.82 and observed heterozygosity Ho of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider and Moderncultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as ‘King of Pippin’ and ‘Calville Rouge d’Hiver’ as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90% of the total dessert allelic diversity, whereas a dessert sub-core collection of 48 cultivars contained 71% of diversity. For cider apples, a 48-cultivars core collection contained 83% of the total cider allelic diversity.
Disciplines :
Genetics & genetic processes
Author, co-author :
Lassois, Ludivine  ;  Université de Liège > Ingénierie des biosystèmes (Biose) > Gestion des ressources forestières et des milieux naturels
Denancé, Caroline
Ravon, Elisa
Guyader, Arnaud
Guisnel, Rémi
Hibrand-Saint-Oyan, Laurence
Poncet, Charles
Lasserre-Zuber, Pauline
Feugey, Laurence
Durel, Charles-Eric
Language :
English
Title :
Genetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers
Publication date :
2016
Journal title :
Plant Molecular Biology Reporter
ISSN :
0735-9640
Publisher :
International Society of Plant Molecular Biology
Volume :
34
Issue :
4
Pages :
827-844
Peer reviewed :
Peer Reviewed verified by ORBi
European Projects :
FP7 - 265582 - FRUIT BREEDOMICS - Integrated approach for increasing breeding efficiency in fruit tree crops
Funders :
CE - Commission Européenne [BE]
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since 18 January 2016

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