Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes.
Within the Dutch genomics initiative the "Centre for Biosystems Genomics" (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies.
van Berloo
Ralph
R
Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands. ralph.van-berloo@keygene.com
Zhu
Aiguo
A
Ursem
Remco
R
Verbakel
Henk
H
Gort
Gerrit
G
van Eeuwijk
Fred Antonis
FA
D054458:Amplified Fragment Length Polymorphism Analysis; D001499:Bayes Theorem; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D018551:Solanum lycopersicum / Q000235:genetics*; D010641:Phenotype
D005819:Genetic Markers