title: Pedigree- and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle.
abstract: Genetic diversity is often evaluated using pedigree information. Currently, diversity can be evaluated in more detail over the genome based on large numbers of SNP markers. Pedigree- and SNP-based diversity were compared for two small related groups of Holstein animals genotyped with the 50 k SNP chip, genome-wide, per chromosome and for part of the genome examined. Diversity was estimated with coefficient of kinship (pedigree) and expected heterozygosity (SNP). SNP-based diversity at chromosome regions was determined using 5-Mb sliding windows, and significance of difference between groups was determined by bootstrapping. Both pedigree- and SNP-based diversity indicated more diversity in one of the groups; 26 of the 30 chromosomes showed significantly more diversity for the same group, as did 25.9% of the chromosome regions. Even in small populations that are genetically close, differences in diversity can be detected. Pedigree- and SNP-based diversity give comparable differences, but SNP-based diversity shows on which chromosome regions these differences are based. For maintaining diversity in a gene bank, SNP-based diversity gives a more detailed picture than pedigree-based diversity.
authors.affiliation: Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, Lelystad, The Netherlands. krista.engelsma@wur.nl
authors.forename: K A
authors.initials: KA
authors.lastname: Engelsma
authors.forename: R F
authors.initials: RF
authors.lastname: Veerkamp
authors.forename: M P L
authors.initials: MP
authors.lastname: Calus
authors.forename: P
authors.initials: P
authors.lastname: Bijma
authors.forename: J J
authors.initials: JJ
authors.lastname: Windig
mesh_terms: D000818:Animals; D002417:Cattle / Q000145:classification / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics; D005838:Genotype; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers