Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Andrea Talenti; Isabelle Palhière; Flavie Tortereau; Giulio Pagnacco; Alessandra Stella; Ezequiel L Nicolazzi; Paola Crepaldi; Gwenola Tosser-Klopp; AdaptMap consortium

doi:10.1186/s12711-018-0423-9

Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Andrea Talenti
, Isabelle Palhière
, Flavie Tortereau
, Giulio Pagnacco
, Alessandra Stella
, Ezequiel L Nicolazzi
, Paola Crepaldi
, Gwenola Tosser-Klopp
, AdaptMap consortium

Research output: Contribution to journal › Article › peer-review

17 Citations (Scopus)

Abstract

BACKGROUND: International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs.

RESULTS: Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires.

CONCLUSIONS: In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.

Original language	English
Article number	55
Journal	Genetics Selection Evolution
Volume	50
Issue number	1
DOIs	https://doi.org/10.1186/s12711-018-0423-9
Publication status	Print publication - 19 Nov 2018
Externally published	Yes

Keywords

Animals
Breeding/methods
Female
Gene Frequency
Goats/genetics
Linkage Disequilibrium
Male
Polymorphism, Single Nucleotide
Sex Determination Processes

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10.1186/s12711-018-0423-9

Cite this

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title = "Functional SNP panel for parentage assessment and assignment in worldwide goat breeds",

abstract = "BACKGROUND: International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs.RESULTS: Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100\% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires.CONCLUSIONS: In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.",

keywords = "Animals, Breeding/methods, Female, Gene Frequency, Goats/genetics, Linkage Disequilibrium, Male, Polymorphism, Single Nucleotide, Sex Determination Processes",

author = "Andrea Talenti and Isabelle Palhi{\`e}re and Flavie Tortereau and Giulio Pagnacco and Alessandra Stella and Nicolazzi, \{Ezequiel L\} and Paola Crepaldi and Gwenola Tosser-Klopp and \{AdaptMap consortium\} and JM Mwacharo",

year = "2018",

month = nov,

day = "19",

doi = "10.1186/s12711-018-0423-9",

language = "English",

volume = "50",

journal = "Genetics Selection Evolution",

issn = "0999-193X",

publisher = "BioMed Central",

number = "1",

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T1 - Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

AU - Talenti, Andrea

AU - Palhière, Isabelle

AU - Tortereau, Flavie

AU - Pagnacco, Giulio

AU - Stella, Alessandra

AU - Nicolazzi, Ezequiel L

AU - Crepaldi, Paola

AU - Tosser-Klopp, Gwenola

AU - AdaptMap consortium

AU - Mwacharo, JM

PY - 2018/11/19

Y1 - 2018/11/19

N2 - BACKGROUND: International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs.RESULTS: Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires.CONCLUSIONS: In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.

AB - BACKGROUND: International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs.RESULTS: Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires.CONCLUSIONS: In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.

KW - Animals

KW - Breeding/methods

KW - Female

KW - Gene Frequency

KW - Goats/genetics

KW - Linkage Disequilibrium

KW - Male

KW - Polymorphism, Single Nucleotide

KW - Sex Determination Processes

U2 - 10.1186/s12711-018-0423-9

DO - 10.1186/s12711-018-0423-9

M3 - Article

C2 - 30449282

SN - 0999-193X

VL - 50

JO - Genetics Selection Evolution

JF - Genetics Selection Evolution

IS - 1

M1 - 55

ER -

Functional SNP panel for parentage assessment and assignment in worldwide goat breeds

Abstract

Keywords

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