Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions

KEY MESSAGE : 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 investiga...

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Bibliographic Details
Published in:Theoretical and applied genetics 2014-03, Vol.127 (3), p.559-571
Main Authors: Adetunji, Ibraheem, Willems, Glenda, Tschoep, Hendrik, Bürkholz, Alexandra, Barnes, Steve, Boer, Martin, Malosetti, Marcos, Horemans, Stefaan, van Eeuwijk, Fred
Format: Article
Language:English
Subjects:
Agricultural production
Agriculture
beets
Beta vulgaris - genetics
beta-vulgaris l
Biochemistry
Biological diversity
Biomedical and Life Sciences
Biotechnology
Breeding
breeding lines
Chromosomes
disease resistance
dna
DNA, Plant - genetics
Genetic aspects
Genetic diversity
Genetic Loci
Genetic Markers
genetic relationships
genetic variation
Genome, Plant
genome-wide association
Genomes
Germplasm
Life Sciences
Linkage (Genetics)
Linkage Disequilibrium
loci
markers
Original Paper
phenotype
Physiological aspects
Plant Biochemistry
Plant Breeding/Biotechnology
Plant Genetics and Genomics
pollen
Polymorphism, Single Nucleotide
population-structure
restorer gene
rhizomania resistance
Seeds
Seeds - genetics
single nucleotide polymorphism
ssp maritima
Sugar beet
yellow-vein-virus
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Summary:KEY MESSAGE : 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
ISSN:0040-5752
1432-2242
DOI:10.1007/s00122-013-2239-x