A method for single nucleotide polymorphism selection for parentage assessment in goats

Abstract

Accurate pedigrees are essential to optimize genetic improvement and conservation of animal genetic resources. In goats, the use of mating groups and kidding management procedures hamper the identification of parentage. Small panels of single nucleotide polymorphisms (SNP) have been proposed in other species to substitute microsatellites for parentage assessment. Using data from the current GoatSNP50 chip, we developed a new 3-step procedure to identify a low-density SNP panel for highly accurate parentage assessment. Methodologies for SNP selection used in other species are less suitable in the goat because of uncertainties in the genome assembly. The procedure developed in this study is based on parent-offspring identification and on estimation of Mendelian errors, followed by canonical discriminant analysis identification and stepwise regression reduction. Starting from a reference sample of 109 Alpine goats with known pedigree relationships, we first identified a panel of 200 SNP that was further reduced to 2 final panels of 130 and 114 SNP with random coincidental match inclusion of 1.51×10(-57) and 2.94×10(-34), respectively. In our reference data set, all panels correctly identified all parent-offspring combinations, revealing a 40% pedigree error rate in the information provided by breeders. All reference trios were confirmed by official tests based on microsatellites. Panels were also tested on Saanen and Teramana breeds. Although the testing on a larger set of breeds in the reference population is still needed to validate these results, our findings suggest that our procedure could identify SNP panels for accurate parentage assessment in goats or in other species with unreliable marker positioning.

The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions

“…The first goat genome of a Yunnan black female goat was completely assembled and officially released about one year before in 2013 (Du et al 2012;Tosser-Klopp et al 2012;Dong et al 2013). Since the Caprine 52 K SNP chip was recently developed, only a limited number of studies have been reported but they encompass a wide variety of aspects including (i) linkage disequilibrium, population distribution, and structure analyses in several goat breeds (Kijas et al 2013;Nicoloso et al 2015;Lashmar et al 2015); (ii) implementation and development of marker-assisted breeding scheme strategies (Brito et al 2015;Lashmar et al 2015); (iii) development of SNP chipbased caprine parentage tests (Talenti et al 2016); and (iv) signatures of selection and GWAS analyses for phenotypic traits and adaptation (Becker et al 2015;Kim et al 2015;Reber et al 2015). Italy is a country that can be considered an important reservoir of genetic resources for goat species in Europe.…”

Genetic diversity and patterns of population structure in Creole goats from the Americas

“…In goats, SNP arrays have been used for parentage testing (Talenti et al . ), to investigate genetic diversity and population structure (Nicoloso et al . ; Visser et al .…”

Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

“…To identify individuals with high relatedness (e.g., parent–offspring pairs), we used an in-house script to calculate the number of Mendelian errors (ME) in pairwise comparisons between all individuals [ 37 ]. Pairs of animals with less than 100 ME were considered as related [ 38 ].…”