title: Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers.
abstract: BACKGROUND
  Lentil is a self-pollinated annual diploid (2n = 2× = 14) crop with a restricted history of genetic improvement through breeding, particularly when compared to cereal crops. This limited breeding has probably contributed to the narrow genetic base of local cultivars, and a corresponding potential to continue yield increases and stability. Therefore, knowledge of genetic variation and relationships between populations is important for understanding of available genetic variability and its potential for use in breeding programs. Single nucleotide polymorphism (SNP) markers provide a method for rapid automated genotyping and subsequent data analysis over large numbers of samples, allowing assessment of genetic relationships between genotypes.
  
  
  RESULTS
  In order to investigate levels of genetic diversity within lentil germplasm, 505 cultivars and landraces were genotyped with 384 genome-wide distributed SNP markers, of which 266 (69.2%) obtained successful amplification and detected polymorphisms. Gene diversity and PIC values varied between 0.108-0.5 and 0.102-0.375, with averages of 0.419 and 0.328, respectively. On the basis of clarity and interest to lentil breeders, the genetic structure of the germplasm collection was analysed separately for cultivars and landraces. A neighbour-joining (NJ) dendrogram was constructed for commercial cultivars, in which lentil cultivars were sorted into three major groups (G-I, G-II and G-III). These results were further supported by principal coordinate analysis (PCoA) and STRUCTURE, from which three clear clusters were defined based on differences in geographical location. In the case of landraces, a weak correlation between geographical origin and genetic relationships was observed. The landraces from the Mediterranean region, predominantly Greece and Turkey, revealed very high levels of genetic diversity.
  
  
  CONCLUSIONS
  Lentil cultivars revealed clear clustering based on geographical origin, but much more limited correlation between geographic origin and genetic diversity was observed for landraces. These results suggest that selection of divergent parental genotypes for breeding should be made actively on the basis of systematic assessment of genetic distance between genotypes, rather than passively based on geographical distance.
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. maria.lombardi@depi.vic.gov.au.
authors.forename: Maria
authors.initials: M
authors.lastname: Lombardi
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, 3401, Victoria, Australia. michael.materne@depi.vic.gov.au.
authors.forename: Michael
authors.initials: M
authors.lastname: Materne
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. noel.cogan@depi.vic.gov.au.
authors.forename: Noel O I
authors.initials: NO
authors.lastname: Cogan
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, 3401, Victoria, Australia. matthew.rodda@depi.vic.gov.au.
authors.forename: Matthew
authors.initials: M
authors.lastname: Rodda
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. hans.daetwyler@depi.vic.gov.au.
authors.forename: Hans D
authors.initials: HD
authors.lastname: Daetwyler
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. tony.slater@depi.vic.gov.au.
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Slater
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. john.forster@depi.vic.gov.au.|La Trobe University, Bundoora, Melbourne, 3086, Victoria, Australia. john.forster@depi.vic.gov.au.
authors.forename: John W
authors.initials: JW
authors.lastname: Forster
authors.affiliation: Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, 3083, Victoria, Australia. sukhjiwan.kaur@depi.vic.gov.au.
authors.forename: Sukhjiwan
authors.initials: S
authors.lastname: Kaur
mesh_terms: D016000:Cluster Analysis; D017343:Genes, Plant; D005819:Genetic Markers; D027806:Lens Plant / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers