Linkage disequilibrium in synthetic varieties of perennial ryegrass.
Synthetic varieties obtained after three to four panmictic generations are variable, not structured and so can be used for association studies. The pattern of linkage disequilibrium (LD) decay determines whether a genome scan or a candidate gene approach can be used for an association study between genotype and phenotype. Our goal was to evaluate the effect of the number of parents used to build the synthetic varieties on the pattern of LD decay. LD was investigated in the gibberelic acid insensitive gene (GAI) region in three synthetic varieties of perennial ryegrass (Lolium perenne L.) chosen for their contrasted number of parents in the initial polycrosses. Results were compared with those obtained from a core collection. STS and SSR markers were used to evaluate variation, structuration and LD in each variety. As expected, the varieties variability increased with the number of parents almost up to the core collection variability. No structuration was observed in the varieties. Significant LDs were observed up to 1.6 Mb in a variety originated from six related parents and not above 174 kb in a variety originated from 336 parents. These results suggest that a candidate gene approach can be used when varieties have a large number of parents and a genome scan approach can be envisaged in specific regions when varieties have a low number of parents. Nevertheless, we strongly recommend to estimate the pattern of LD decay in the population and in the genomic region studied before performing an association study.
Auzanneau
J
J
INRA, Unité de Génétique et d'Amélioration des Plantes Fourragères, BP6, 86600, Lusignan, France.
Huyghe
C
C
Julier
B
B
Barre
P
P
D001947:Breeding; D002874:Chromosome Mapping; D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D005838:Genotype; D015810:Linkage Disequilibrium; D008129:Lolium / Q000033:anatomy & histology / Q000235:genetics* / Q000502:physiology; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics / Q000502:physiology
D005819:Genetic Markers
Genetics. 1978 Jul;89(3):583-90
17248844
Annu Rev Plant Biol. 2003;54:357-74
14502995
Theor Appl Genet. 2004 Aug;109(4):681-9
15300382
Nat Rev Genet. 2002 Apr;3(4):299-309
11967554
Plant Mol Biol. 2005 Mar;57(4):461-85
15821975
Bioinformatics. 2003 Dec 12;19(18):2496-7
14668244
Trends Plant Sci. 2007 Feb;12(2):57-63
17224302
Plant Cell. 2003 Jul;15(7):1502-6
12837942
Theor Appl Genet. 2005 Feb;110(3):527-36
15619078
Anim Genet. 2006 Jun;37(3):225-31
16734681
Nat Genet. 2006 Aug;38(8):904-9
16862161
Curr Opin Plant Biol. 2002 Apr;5(2):94-100
11856602
Biotechniques. 2001 Jul;31(1):24-6, 28
11464515
Theor Appl Genet. 2003 Dec;108(1):25-40
12923626
Genes Dev. 1997 Dec 1;11(23):3194-205
9389651
Gene. 2000 Mar 7;245(1):21-9
10713441
Genetics. 2006 May;173(1):321-30
16322511
Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014-8
6096873
Genetics. 2004 Dec;168(4):2169-85
15611184
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11479-84
11562485
Theor Appl Genet. 1968 Jun;38(6):226-31
24442307
Nature. 1999 Jul 15;400(6741):256-61
10421366
Electrophoresis. 1991 Feb-Mar;12(2-3):159-69
2040264
Am J Hum Genet. 2000 Jul;67(1):170-81
10827107
Genetics. 2000 Jun;155(2):945-59
10835412
Evolution. 1984 Nov;38(6):1358-1370
28563791
Ann Bot. 2005 Jan;95(1):45-90
15596457
PCR Methods Appl. 1993 Aug;3(1):69-70
8220189
Nat Genet. 2006 Feb;38(2):203-8
16380716
Genetics. 2002 Nov;162(3):1401-13
12454083