Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example

Abstract Background Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the p...

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Autores principales:	Rostam Abdollahi-Arpanahi, Daniela Lourenco, Andres Legarra, Ignacy Misztal
Formato:	article
Lenguaje:	DE EN FR
Publicado:	BMC 2021
Materias:	Animal culture SF1-1100 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/da68384a2e31422ebd4498c347b7f173
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spelling	oai:doaj.org-article:da68384a2e31422ebd4498c347b7f1732021-11-28T12:24:45ZDissecting genetic trends to understand breeding practices in livestock: a maternal pig line example10.1186/s12711-021-00683-61297-9686https://doaj.org/article/da68384a2e31422ebd4498c347b7f1732021-11-01T00:00:00Zhttps://doi.org/10.1186/s12711-021-00683-6https://doaj.org/toc/1297-9686Abstract Background Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females. Methods We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control. Phenotypic data included 228,427, 101,225, and 11,444 records for birth weight, average daily gain in the nursery, and feed intake, respectively. Breeding values were predicted in a multiple-trait framework using BLUP and ssGBLUP. Results The points of divergence of the genetic and RMS trends estimated by BLUP and ssGBLUP indicated that genomic selection effectively started in 2019. Partitioning the overall genetic trends into that for genotyped and non-genotyped individuals revealed that the contribution of genotyped animals to the overall genetic trend increased rapidly from ~ 74% in 2016 to 90% in 2019. The contribution of the female pathway to the genetic trend also increased since genomic selection was implemented in this pig population, which reflects the changes in the genotyping strategy in recent years. Conclusions Our results show that an assessment of breeding program practices can be done based on the point of divergence of genetic and RMS trends between BLUP and ssGBLUP and based on the partitioning of the genetic trend into contributions from different selection pathways. However, it should be noted that genetic trends can diverge before the onset of genomic selection if superior animals are genotyped retroactively. For the pig population example, the results showed that genomic selection was effective in this population.Rostam Abdollahi-ArpanahiDaniela LourencoAndres LegarraIgnacy MisztalBMCarticleAnimal cultureSF1-1100GeneticsQH426-470DEENFRGenetics Selection Evolution, Vol 53, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	DE EN FR
topic	Animal culture SF1-1100 Genetics QH426-470
spellingShingle	Animal culture SF1-1100 Genetics QH426-470 Rostam Abdollahi-Arpanahi Daniela Lourenco Andres Legarra Ignacy Misztal Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
description	Abstract Background Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females. Methods We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control. Phenotypic data included 228,427, 101,225, and 11,444 records for birth weight, average daily gain in the nursery, and feed intake, respectively. Breeding values were predicted in a multiple-trait framework using BLUP and ssGBLUP. Results The points of divergence of the genetic and RMS trends estimated by BLUP and ssGBLUP indicated that genomic selection effectively started in 2019. Partitioning the overall genetic trends into that for genotyped and non-genotyped individuals revealed that the contribution of genotyped animals to the overall genetic trend increased rapidly from ~ 74% in 2016 to 90% in 2019. The contribution of the female pathway to the genetic trend also increased since genomic selection was implemented in this pig population, which reflects the changes in the genotyping strategy in recent years. Conclusions Our results show that an assessment of breeding program practices can be done based on the point of divergence of genetic and RMS trends between BLUP and ssGBLUP and based on the partitioning of the genetic trend into contributions from different selection pathways. However, it should be noted that genetic trends can diverge before the onset of genomic selection if superior animals are genotyped retroactively. For the pig population example, the results showed that genomic selection was effective in this population.
format	article
author	Rostam Abdollahi-Arpanahi Daniela Lourenco Andres Legarra Ignacy Misztal
author_facet	Rostam Abdollahi-Arpanahi Daniela Lourenco Andres Legarra Ignacy Misztal
author_sort	Rostam Abdollahi-Arpanahi
title	Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
title_short	Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
title_full	Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
title_fullStr	Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
title_full_unstemmed	Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
title_sort	dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example
publisher	BMC
publishDate	2021
url	https://doaj.org/article/da68384a2e31422ebd4498c347b7f173
work_keys_str_mv	AT rostamabdollahiarpanahi dissectinggenetictrendstounderstandbreedingpracticesinlivestockamaternalpiglineexample AT danielalourenco dissectinggenetictrendstounderstandbreedingpracticesinlivestockamaternalpiglineexample AT andreslegarra dissectinggenetictrendstounderstandbreedingpracticesinlivestockamaternalpiglineexample AT ignacymisztal dissectinggenetictrendstounderstandbreedingpracticesinlivestockamaternalpiglineexample
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Dissecting genetic trends to understand breeding practices in livestock: a maternal pig line example

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