Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers
Résumé
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
Modern Cultivars). Parentage analyses established already
known and yet unknown relationships, notably between old
cultivars, with the frequent occurrence of cultivars such as
BKing of Pippin^ and BCalville 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 subcore collection of 48 cultivars contained 71 % of
diversity. For cider apples, a 48-cultivar core collection
contained 83 % of the total cider allelic diversity.