Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies
BMC Plant Biology. 2016-03-22; 16(1):
DOI: 10.1186/s12870-016-0754-z
1. BMC Plant Biol. 2016 Mar 22;16:74. doi: 10.1186/s12870-016-0754-z.
Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis
vinifera L) diversity panel newly designed for association studies.
Nicolas SD(1)(2), Péros JP(1), Lacombe T(1), Launay A(1), Le Paslier MC(3),
Bérard A(3), Mangin B(4), Valière S(5), Martins F(5)(6), Le Cunff L(7), Laucou
V(1), Bacilieri R(1), Dereeper A(1)(8), Chatelet P(1), This P(1), Doligez A(9).
Author information:
(1)INRA, UMR AGAP, F-34060, Montpellier, France.
(2)GQE-Le Moulon, INRA – Univ. Paris-Sud – CNRS – AgroParisTech – Université
Paris-Saclay, Ferme du Moulon, F-91190, Gif-sur-Yvette, France.
(3)INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
(4)INRA, UR MIAT, F-31326, Castanet-Tolosan, France.
(5)INRA, Plateforme Génomique, F-31326, Castanet-Tolosan, France.
(6)INSERM, UMR1048, F-31432, Toulouse, France.
(7)IFV, UMT Genovigne, F-34060, Montpellier, France.
(8)IRD, UMR IPME, F-34394, Montpellier 5, France.
(9)INRA, UMR AGAP, F-34060, Montpellier, France. .
BACKGROUND: As for many crops, new high-quality grapevine varieties requiring
less pesticide and adapted to climate change are needed. In perennial species,
breeding is a long process which can be speeded up by gaining knowledge about
quantitative trait loci linked to agronomic traits variation. However, due to
the long juvenile period of these species, establishing numerous highly
recombinant populations for high resolution mapping is both costly and
time-consuming. Genome wide association studies in germplasm panels is an
alternative method of choice, since it allows identifying the main quantitative
trait loci with high resolution by exploiting past recombination events between
cultivars. Such studies require adequate panel design to represent most of the
available genetic and phenotypic diversity. Assessing linkage disequilibrium
extent and panel power is also needed to determine the marker density required
for association studies.
RESULTS: Starting from the largest grapevine collection worldwide maintained in
Vassal (France), we designed a diversity panel of 279 cultivars with limited
relatedness, reflecting the low structuration in three genetic pools resulting
from different uses (table vs wine) and geographical origin (East vs West), and
including the major founders of modern cultivars. With 20 simple sequence repeat
markers and five quantitative traits, we showed that our panel adequately
captured most of the genetic and phenotypic diversity existing within the entire
Vassal collection. To assess linkage disequilibrium extent and panel power, we
genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129
distributed over the whole genome. Linkage disequilibrium, measured by
correlation corrected for kinship, reached 0.2 for a physical distance between 9
and 458 Kb depending on genetic pool and genomic region, with varying size of
linkage disequilibrium blocks. This panel achieved reasonable power to detect
associations between traits with high broad-sense heritability (> 0.7) and
causal loci with intermediate allelic frequency and strong effect
(explaining > 10 % of total variance).
CONCLUSIONS: Our association panel constitutes a new, highly valuable resource
for genetic association studies in grapevine, and deserves dissemination to
diverse field and greenhouse trials to gain more insight into the genetic
control of many agronomic traits and their interaction with the environment.
DOI: 10.1186/s12870-016-0754-z
PMCID: PMC4802926
PMID: 27005772 [Indexed for MEDLINE]