title: Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions.
abstract: Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after <6 cM on all chromosomes in both pools. In the wild beet accessions, there was a strong LD decay: on average LD disappeared after 1 cM when LD was calculated with a correction for genetic relatedness. Persistence of LD was not only observed between distant SNPs on the same chromosome, but also between SNPs on different chromosomes. Regions on chromosomes 3 and 4 that harbor disease resistance and monogermy loci showed strong genetic differentiation between the pollen and seed parent pools. Other regions, on chromosomes 8 and 9, for which no a priori information was available with respect to their contribution to the phenotype, still contributed to clustering of lines in the elite breeding material.
authors.affiliation: SESVanderHave, Soldatenplein 15, 3300, Tienen, Belgium.
authors.forename: Ibraheem
authors.initials: I
authors.lastname: Adetunji
authors.forename: Glenda
authors.initials: G
authors.lastname: Willems
authors.forename: Hendrik
authors.initials: H
authors.lastname: Tschoep
authors.forename: Alexandra
authors.initials: A
authors.lastname: Bürkholz
authors.forename: Steve
authors.initials: S
authors.lastname: Barnes
authors.forename: Martin
authors.initials: M
authors.lastname: Boer
authors.forename: Marcos
authors.initials: M
authors.lastname: Malosetti
authors.forename: Stefaan
authors.initials: S
authors.lastname: Horemans
authors.forename: Fred
authors.initials: F
authors.lastname: van Eeuwijk
mesh_terms: D027461:Beta vulgaris / Q000235:genetics*; D001947:Breeding; D018744:DNA, Plant / Q000235:genetics; D056426:Genetic Loci; D005819:Genetic Markers; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers