@article{fdi:010066693,
  title = {{G}enetic diversity, linkage disequilibrium and power of a large grapevine ({V}itis vinifera {L}.) diversity panel newly designed for association studies},
  author = {{N}icolas, {S}. {D}. and {P}eros, {J}. {P}. and {L}acombe, {T}. and {L}aunay, {A}. and {L}e {P}aslier, {M}. {C}. and {B}erard, {A}. and {M}angin, {B}. and {V}aliere, {S}. and {M}artins, {F}. and {L}e {C}unff, {L}. and {L}aucou, {V}. and {B}acilieri, {R}. and {D}ereeper, {A}lexis and {C}hatelet, {P}. and {T}his, {P}. and {D}oligez, {A}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {A}s for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. {I}n perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. {H}owever, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. {G}enome 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. {S}uch studies require adequate panel design to represent most of the available genetic and phenotypic diversity. {A}ssessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies. {R}esults: {S}tarting from the largest grapevine collection worldwide maintained in {V}assal ({F}rance), 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 ({E}ast vs {W}est), and including the major founders of modern cultivars. {W}ith 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 {V}assal collection. {T}o assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. {L}inkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 {K}b depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. {T}his 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). {C}onclusions: {O}ur 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.},
  keywords = {{V}itis ; {A}ssociation panel ; {L}inkage disequilibrium ; {P}ower ; {G}enome-wide association studies ; {SSR} ; {SNP} ; sylvestris ; {V}assal collection ; {H}aplotype ; {K}inship ; {FRANCE}},
  booktitle = {},
  journal = {{BMC} {P}lant {B}iology},
  volume = {16},
  numero = {},
  pages = {art. 74 [19 p.]},
  ISSN = {1471-2229},
  year = {2016},
  DOI = {10.1186/s12870-016-0754-z},
  URL = {https://www.documentation.ird.fr/hor/fdi:010066693},
}