SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.

GOLDBERG, V. - MACEDO, F. - CIAPPESONI, G.

Resumen:

ABSTRACT.Pedigree information is required to estimate breeding values accurately and to ensure high rates of genetic gain. DNA markers information can be used as an alternative to traditional recording of pedigree, being SNPs the markers of choice for parentage verification. The aim of the present study was to determine sheep parentage by SNPs using a very low density panel in: 1) a stud Merino flock to know the percentage of parentage error in order to correct pedigree misidentification and; 2) a commercial Highlander flock, to study the possibility to not control lambing anymore because for the breeder it is very laborious, time-consuming and disturb the relationship ewe-lambs during parturition. Genomic DNA was isolated from 200 samples of Merino sheep in 2015 and from 108 and 904 samples of Merino and Highlander sheep in 2016, respectively; and were genotyped with a very low density panel containing 507 SNPs. In 2015, for the 91 lambs genotyped, the error in parentage assignment was 16.5%. Although the assigned sire did not match with the declared sire for 15 lambs, the true sire was assigned for 14 of them. Thus, 99% of the lambs genotyped, had a sire assigned by the SNP panel. For the 80 lambs with their dams genotyped, the error rate was 12.5%. For the 10 lambs with mismatches with the declared dams, the true dam was assigned for five of them. In 2016, Merino samples were genotyped to link only lambs with their sires. For the 101 lambs, the error of parentage assignment was 21.8%. For Highlander, 7.5% of samples failed the genotyping and analyses was conducted without knowledge of the relationships between lambs with sires and dams. The 51% of the lambs genotyped had a sire and a dam assigned, 21% had only the sire assigned and 15% had only assigned a dam. Thus, genotyping by SNPs assigned a sire to the 72% of the lambs and a dam to the 66% of the lambs. The main problem was that only 5 of the 11 rams used as sires were genotyped and the high percentage of samples which failed the genotyping. However, taking into account the lack of information related to pedigree, we consider that a high rate of lambs had a sire and a dam assigned by the SNP panel. In conclusion, the development of a SNP panel for parentage assignment at a low price, would provide breeders with the opportunity of making mating management and control lambing easier and more relaxed while improving the known of pedigree information, ensuring high rates of genetic gain. Keywords: molecular markers, parentage exclusion, parentage verification, sheep.


Detalles Bibliográficos
2018
Molecular markers
Parentage exclusion
Parentage verification
Sheep
OVINOS
MARCADORES MOLECULARES
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61916&biblioteca=vazio&busca=61916&qFacets=61916
Acceso abierto
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author GOLDBERG, V.
author2 MACEDO, F.
CIAPPESONI, G.
author2_role author
author
author_facet GOLDBERG, V.
MACEDO, F.
CIAPPESONI, G.
author_role author
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dc.creator.none.fl_str_mv GOLDBERG, V.
MACEDO, F.
CIAPPESONI, G.
dc.date.accessioned.none.fl_str_mv 2022-10-21T01:48:51Z
dc.date.available.none.fl_str_mv 2022-10-21T01:48:51Z
dc.date.issued.none.fl_str_mv 2018
dc.date.updated.none.fl_str_mv 2022-10-21T01:48:51Z
dc.description.abstract.none.fl_txt_mv ABSTRACT.Pedigree information is required to estimate breeding values accurately and to ensure high rates of genetic gain. DNA markers information can be used as an alternative to traditional recording of pedigree, being SNPs the markers of choice for parentage verification. The aim of the present study was to determine sheep parentage by SNPs using a very low density panel in: 1) a stud Merino flock to know the percentage of parentage error in order to correct pedigree misidentification and; 2) a commercial Highlander flock, to study the possibility to not control lambing anymore because for the breeder it is very laborious, time-consuming and disturb the relationship ewe-lambs during parturition. Genomic DNA was isolated from 200 samples of Merino sheep in 2015 and from 108 and 904 samples of Merino and Highlander sheep in 2016, respectively; and were genotyped with a very low density panel containing 507 SNPs. In 2015, for the 91 lambs genotyped, the error in parentage assignment was 16.5%. Although the assigned sire did not match with the declared sire for 15 lambs, the true sire was assigned for 14 of them. Thus, 99% of the lambs genotyped, had a sire assigned by the SNP panel. For the 80 lambs with their dams genotyped, the error rate was 12.5%. For the 10 lambs with mismatches with the declared dams, the true dam was assigned for five of them. In 2016, Merino samples were genotyped to link only lambs with their sires. For the 101 lambs, the error of parentage assignment was 21.8%. For Highlander, 7.5% of samples failed the genotyping and analyses was conducted without knowledge of the relationships between lambs with sires and dams. The 51% of the lambs genotyped had a sire and a dam assigned, 21% had only the sire assigned and 15% had only assigned a dam. Thus, genotyping by SNPs assigned a sire to the 72% of the lambs and a dam to the 66% of the lambs. The main problem was that only 5 of the 11 rams used as sires were genotyped and the high percentage of samples which failed the genotyping. However, taking into account the lack of information related to pedigree, we consider that a high rate of lambs had a sire and a dam assigned by the SNP panel. In conclusion, the development of a SNP panel for parentage assignment at a low price, would provide breeders with the opportunity of making mating management and control lambing easier and more relaxed while improving the known of pedigree information, ensuring high rates of genetic gain. Keywords: molecular markers, parentage exclusion, parentage verification, sheep.
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dc.language.iso.none.fl_str_mv en
eng
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instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv Molecular markers
Parentage exclusion
Parentage verification
Sheep
OVINOS
MARCADORES MOLECULARES
dc.title.none.fl_str_mv SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
dc.type.none.fl_str_mv ConferenceObject
PublishedVersion
info:eu-repo/semantics/conferenceObject
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description ABSTRACT.Pedigree information is required to estimate breeding values accurately and to ensure high rates of genetic gain. DNA markers information can be used as an alternative to traditional recording of pedigree, being SNPs the markers of choice for parentage verification. The aim of the present study was to determine sheep parentage by SNPs using a very low density panel in: 1) a stud Merino flock to know the percentage of parentage error in order to correct pedigree misidentification and; 2) a commercial Highlander flock, to study the possibility to not control lambing anymore because for the breeder it is very laborious, time-consuming and disturb the relationship ewe-lambs during parturition. Genomic DNA was isolated from 200 samples of Merino sheep in 2015 and from 108 and 904 samples of Merino and Highlander sheep in 2016, respectively; and were genotyped with a very low density panel containing 507 SNPs. In 2015, for the 91 lambs genotyped, the error in parentage assignment was 16.5%. Although the assigned sire did not match with the declared sire for 15 lambs, the true sire was assigned for 14 of them. Thus, 99% of the lambs genotyped, had a sire assigned by the SNP panel. For the 80 lambs with their dams genotyped, the error rate was 12.5%. For the 10 lambs with mismatches with the declared dams, the true dam was assigned for five of them. In 2016, Merino samples were genotyped to link only lambs with their sires. For the 101 lambs, the error of parentage assignment was 21.8%. For Highlander, 7.5% of samples failed the genotyping and analyses was conducted without knowledge of the relationships between lambs with sires and dams. The 51% of the lambs genotyped had a sire and a dam assigned, 21% had only the sire assigned and 15% had only assigned a dam. Thus, genotyping by SNPs assigned a sire to the 72% of the lambs and a dam to the 66% of the lambs. The main problem was that only 5 of the 11 rams used as sires were genotyped and the high percentage of samples which failed the genotyping. However, taking into account the lack of information related to pedigree, we consider that a high rate of lambs had a sire and a dam assigned by the SNP panel. In conclusion, the development of a SNP panel for parentage assignment at a low price, would provide breeders with the opportunity of making mating management and control lambing easier and more relaxed while improving the known of pedigree information, ensuring high rates of genetic gain. Keywords: molecular markers, parentage exclusion, parentage verification, sheep.
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spelling 2022-10-21T01:48:51Z2022-10-21T01:48:51Z20182022-10-21T01:48:51Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=61916&biblioteca=vazio&busca=61916&qFacets=61916ABSTRACT.Pedigree information is required to estimate breeding values accurately and to ensure high rates of genetic gain. DNA markers information can be used as an alternative to traditional recording of pedigree, being SNPs the markers of choice for parentage verification. The aim of the present study was to determine sheep parentage by SNPs using a very low density panel in: 1) a stud Merino flock to know the percentage of parentage error in order to correct pedigree misidentification and; 2) a commercial Highlander flock, to study the possibility to not control lambing anymore because for the breeder it is very laborious, time-consuming and disturb the relationship ewe-lambs during parturition. Genomic DNA was isolated from 200 samples of Merino sheep in 2015 and from 108 and 904 samples of Merino and Highlander sheep in 2016, respectively; and were genotyped with a very low density panel containing 507 SNPs. In 2015, for the 91 lambs genotyped, the error in parentage assignment was 16.5%. Although the assigned sire did not match with the declared sire for 15 lambs, the true sire was assigned for 14 of them. Thus, 99% of the lambs genotyped, had a sire assigned by the SNP panel. For the 80 lambs with their dams genotyped, the error rate was 12.5%. For the 10 lambs with mismatches with the declared dams, the true dam was assigned for five of them. In 2016, Merino samples were genotyped to link only lambs with their sires. For the 101 lambs, the error of parentage assignment was 21.8%. For Highlander, 7.5% of samples failed the genotyping and analyses was conducted without knowledge of the relationships between lambs with sires and dams. The 51% of the lambs genotyped had a sire and a dam assigned, 21% had only the sire assigned and 15% had only assigned a dam. Thus, genotyping by SNPs assigned a sire to the 72% of the lambs and a dam to the 66% of the lambs. The main problem was that only 5 of the 11 rams used as sires were genotyped and the high percentage of samples which failed the genotyping. However, taking into account the lack of information related to pedigree, we consider that a high rate of lambs had a sire and a dam assigned by the SNP panel. In conclusion, the development of a SNP panel for parentage assignment at a low price, would provide breeders with the opportunity of making mating management and control lambing easier and more relaxed while improving the known of pedigree information, ensuring high rates of genetic gain. Keywords: molecular markers, parentage exclusion, parentage verification, sheep.https://hdl.handle.net/20.500.12381/1726enenginfo:eu-repo/semantics/openAccessAcceso abiertoMolecular markersParentage exclusionParentage verificationSheepOVINOSMARCADORES MOLECULARESSNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.ConferenceObjectPublishedVersioninfo:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaGOLDBERG, V.MACEDO, F.CIAPPESONI, G.SWORDsword-2022-10-20T22:48:51.original.xmlOriginal SWORD entry documentapplication/octet-stream3706https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1726/1/sword-2022-10-20T22%3a48%3a51.original.xmle6407b4c5df64fbe3aca718f20c015d8MD5120.500.12381/17262022-10-20 22:48:51.437oai:redi.anii.org.uy:20.500.12381/1726Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:48:51AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
GOLDBERG, V.
Molecular markers
Parentage exclusion
Parentage verification
Sheep
OVINOS
MARCADORES MOLECULARES
status_str publishedVersion
title SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
title_full SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
title_fullStr SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
title_full_unstemmed SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
title_short SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
title_sort SNP genotyping for parentage identification in a Merino nucleus and in a commercial Highlander flock.
topic Molecular markers
Parentage exclusion
Parentage verification
Sheep
OVINOS
MARCADORES MOLECULARES
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=61916&biblioteca=vazio&busca=61916&qFacets=61916