title: High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination.
abstract: BACKGROUND
  The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies.
  
  
  RESULTS
  In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set. The offspring of three-generation outbred and inbred mapping pedigrees were then genotyped. The inbred pedigree consisted of a classical F2 population resulting from the selfing of a single inter-provenance (Landes x Corsica) hybrid tree, whereas the outbred pedigree (G2) resulted from a controlled cross of two intra-provenance (Landes x Landes) hybrid trees. This resulted in the generation of three linkage maps based on SNP markers: one from the parental genotype of the F2 population (1,131 markers in 1,708 centimorgan (cM)), and one for each parent of the G2 population (1,015 and 1,110 markers in 1,447 and 1,425 cM for the female and male parents, respectively). A comparison of segregation patterns in the progeny obtained from the two types of mating (inbreeding and outbreeding) led to the identification of a chromosomal region carrying an embryo viability locus with a semi-lethal allele. Following selfing and segregation, zygote mortality resulted in a deficit of Corsican homozygous genotypes in the F2 population. This dataset was also used to study the extent and distribution of meiotic recombination along the length of the chromosomes and the effect of sex and/or genetic background on recombination. The genetic background of trees in which meiotic recombination occurred was found to have a significant effect on the frequency of recombination. Furthermore, only a small proportion of the recombination hot- and cold-spots were common to all three genotypes, suggesting that the spatial pattern of recombination was genetically variable.
  
  
  CONCLUSIONS
  This study led to the development of classical genomic tools for this ecologically and economically important species. It also identified a chromosomal region bearing a semi-lethal recessive allele and demonstrated the genetic variability of recombination rate over the genome.
authors.affiliation: INRA, UMR1202 BIOGECO, F-33610 Cestas, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Chancerel
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Lamy
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lesur
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: François
authors.initials: F
authors.lastname: Ehrenmann
authors.forename: Christophe
authors.initials: C
authors.lastname: Boury
authors.forename: Grégoire Le
authors.initials: GL
authors.lastname: Provost
authors.forename: Philippe
authors.initials: P
authors.lastname: Label
authors.forename: Céline
authors.initials: C
authors.lastname: Lalanne
authors.forename: Valérie
authors.initials: V
authors.lastname: Léger
authors.forename: Franck
authors.initials: F
authors.lastname: Salin
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Gion
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D020090:Chromosome Segregation / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D017343:Genes, Plant / Q000235:genetics; D008040:Genetic Linkage; D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D060005:Genotyping Techniques; D007178:Inbreeding; D008540:Meiosis / Q000235:genetics*; D028223:Pinus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers