Genome-wide association study for reproduction traits in a Brazilian Holstein population
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Tipo de documento: | Dissertação |
Idioma: | eng |
Título da fonte: | Biblioteca Digital de Teses e Dissertações da USP |
Texto Completo: | https://www.teses.usp.br/teses/disponiveis/11/11139/tde-03012023-165533/ |
Resumo: | Brazil is in an important position in the world of the dairy productive chain, and the efficiency of the production has been discussed in different fields in this chain, among those, reproductive efficiency. Studies on improvement for better comprehension of the management, dietary intake, sanity, and genetic terms, have been applied to comprehend ways to optimize dairy production and turn it more and more profitable for the producer. Reproductive phenotypic characteristics such as age at first calving (AFC), calving interval (CI), and quantity of inseminations needed to impregnate the cow are parameters for understanding and monitoring the reproductive activity of a herd. The ideal is that the cow is as precocious and has the smaller calving interval as possible. It is known that reproductive characteristics have low heritability, undergoing great environmental influence. In this line, it is necessary to know the genes that are involved in this process to have more and more clarity. With genomic association studies and advances in molecular biology, it is possible to explain the genetic background of these characteristics and with the use of molecular markers, we find regions responsible for the origins of the biological variation that show us these characteristics. Thus, this study aimed to identify genomic regions associated with age at first calving (AFC), to calving interval (CI), in a population of Holstein cattle. To identify regions that possibly alter the phenotype, GWAS was applied to the database of phenotypic data of AFC, IC of 39,336 daughters, and genotype of 555 bulls, in 187 different herds, contemporary groups were formed and analyzed in GWAS. Data underwent quality control and by the end, there were 75,925 SNPs. BLUPF90 family software was used for statistical analysis and known pedigree animal model, with 10 SNPs fixed windows, and explained variance over 1.5%. A total of 34 genes were identified: 24 genes linked to AFC and 10 genes linked to CI. The main genes were APP, PRSS16 e BTN1A1, once linked to the animal immune response to the postpartum intemperance and to the reproductive system recovery. The genes CYYR1, PRSS16 e WEE2 are known to be related to embryogenesis, linking them to the reproductive traits of the animals. Some of the identified genes, in the present study, were associated with reproductive and immunological characteristics of the animals, corroborating the hypothesis of a different genetic expression among the investigated animals, and indicating the need for the development of new studies in this field. |
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Genome-wide association study for reproduction traits in a Brazilian Holstein populationEstudo de associação genômica de características reprodutivas em uma população de raça holandesaBovinocultura de leiteCaracterísticas reprodutivasDairy cattleGene interactionGWASGWASHolstein breedInteração gênicaRaça holandesaReproductive traitsBrazil is in an important position in the world of the dairy productive chain, and the efficiency of the production has been discussed in different fields in this chain, among those, reproductive efficiency. Studies on improvement for better comprehension of the management, dietary intake, sanity, and genetic terms, have been applied to comprehend ways to optimize dairy production and turn it more and more profitable for the producer. Reproductive phenotypic characteristics such as age at first calving (AFC), calving interval (CI), and quantity of inseminations needed to impregnate the cow are parameters for understanding and monitoring the reproductive activity of a herd. The ideal is that the cow is as precocious and has the smaller calving interval as possible. It is known that reproductive characteristics have low heritability, undergoing great environmental influence. In this line, it is necessary to know the genes that are involved in this process to have more and more clarity. With genomic association studies and advances in molecular biology, it is possible to explain the genetic background of these characteristics and with the use of molecular markers, we find regions responsible for the origins of the biological variation that show us these characteristics. Thus, this study aimed to identify genomic regions associated with age at first calving (AFC), to calving interval (CI), in a population of Holstein cattle. To identify regions that possibly alter the phenotype, GWAS was applied to the database of phenotypic data of AFC, IC of 39,336 daughters, and genotype of 555 bulls, in 187 different herds, contemporary groups were formed and analyzed in GWAS. Data underwent quality control and by the end, there were 75,925 SNPs. BLUPF90 family software was used for statistical analysis and known pedigree animal model, with 10 SNPs fixed windows, and explained variance over 1.5%. A total of 34 genes were identified: 24 genes linked to AFC and 10 genes linked to CI. The main genes were APP, PRSS16 e BTN1A1, once linked to the animal immune response to the postpartum intemperance and to the reproductive system recovery. The genes CYYR1, PRSS16 e WEE2 are known to be related to embryogenesis, linking them to the reproductive traits of the animals. Some of the identified genes, in the present study, were associated with reproductive and immunological characteristics of the animals, corroborating the hypothesis of a different genetic expression among the investigated animals, and indicating the need for the development of new studies in this field.O Brasil ocupa uma posição importante dentro da cadeia produtiva do leite no mundo, e a eficiência na produção vem sendo discutida em diversas áreas dentro dessa cadeia, entre elas a eficiência reprodutiva. Estudo de melhoria e para o melhor entendimento do manejo, da alimentação, da sanidade e em termos genéticos tem sido aplicados para compreender como otimizar a produção leiteira e torná-la cada vez mais rentável para o produtor. Características reprodutivas fenotípica como idade ao primeiro parto, intervalo entre partos e a quantidade de inseminações necessárias para vaca ficar prenha são parâmetros para entender e monitorar a atividade reprodutiva de um rebanho. O ideal é que a vaca seja precoce e que ela tenha o menor intervalo entre partos possível. Já se sabe que características reprodutivas tem baixa herdabilidade, sofrendo grande influência do ambiente. Nessa linha se vê necessário conhecer os genes que estão envolvidos nesse processo para se ter cada vez mais clareza. Com os estudos de associação genômica e os avanços da biologia molecular é possível explicar o fundo genético dessas características e com o uso de marcadores moleculares encontramos regiões responsáveis pelas origens da variação biológica que nos mostram essas características. Dessa forma, o objetivo desse estudo foi identificar regiões genômicas associadas à idade ao primeiro parto (IPP) e ao intervalo entre partos (IP) em uma população de bovinos da raça Holandesa. Para identificar as regiões que possivelmente alteram o fenótipo, o GWAS foi aplicado no banco de dados de dados fenotípicos de (IPP) e intervalo entre partos (IP) de 39.336 filhas e genótipos de 555 touros em 187 rebanhos diferentes. Os dados passaram por um controle de qualidade e ao final restaram 75.925 SNPs. Os softwares da família BLUPF90 foram utilizados para análise estatística e o modelo animal para pedigree conhecido, com as janelas fixas de 10 SNPs e a variância explicada maior que 1,5 %. Os genes encontrados totalizaram 34 genes, sendo eles: 24 genes relacionados à IPP e 10 genes para IP. Os principais genes encontrados foram APP, PRSS16 e BTN1A1. Esses genes são ligados à resposta imune e podem interferir na resposta do animal à intemperança pós-parto e na recuperação do sistema reprodutivo. Os genes CYYR1, PRSS16 e WEE2 são conhecidos por estarem relacionados à embriogênese, relacionando-os às características reprodutivas dos animais. Alguns dos genes identificados no presente estudo foram associados as características reprodutivas e respostas imunológicas dos animais, corroborando com a hipótese de uma expressão genética diferente nos animais estudados e indicando a necessidade o desenvolvimento de novos estudos nesta área.Biblioteca Digitais de Teses e Dissertações da USPCoutinho, Luiz LehmannPaulin, Graciela Vieira2022-10-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttps://www.teses.usp.br/teses/disponiveis/11/11139/tde-03012023-165533/reponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USPLiberar o conteúdo para acesso público.info:eu-repo/semantics/openAccesseng2023-01-04T17:12:36Zoai:teses.usp.br:tde-03012023-165533Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212023-01-04T17:12:36Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false |
dc.title.none.fl_str_mv |
Genome-wide association study for reproduction traits in a Brazilian Holstein population Estudo de associação genômica de características reprodutivas em uma população de raça holandesa |
title |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
spellingShingle |
Genome-wide association study for reproduction traits in a Brazilian Holstein population Paulin, Graciela Vieira Bovinocultura de leite Características reprodutivas Dairy cattle Gene interaction GWAS GWAS Holstein breed Interação gênica Raça holandesa Reproductive traits |
title_short |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
title_full |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
title_fullStr |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
title_full_unstemmed |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
title_sort |
Genome-wide association study for reproduction traits in a Brazilian Holstein population |
author |
Paulin, Graciela Vieira |
author_facet |
Paulin, Graciela Vieira |
author_role |
author |
dc.contributor.none.fl_str_mv |
Coutinho, Luiz Lehmann |
dc.contributor.author.fl_str_mv |
Paulin, Graciela Vieira |
dc.subject.por.fl_str_mv |
Bovinocultura de leite Características reprodutivas Dairy cattle Gene interaction GWAS GWAS Holstein breed Interação gênica Raça holandesa Reproductive traits |
topic |
Bovinocultura de leite Características reprodutivas Dairy cattle Gene interaction GWAS GWAS Holstein breed Interação gênica Raça holandesa Reproductive traits |
description |
Brazil is in an important position in the world of the dairy productive chain, and the efficiency of the production has been discussed in different fields in this chain, among those, reproductive efficiency. Studies on improvement for better comprehension of the management, dietary intake, sanity, and genetic terms, have been applied to comprehend ways to optimize dairy production and turn it more and more profitable for the producer. Reproductive phenotypic characteristics such as age at first calving (AFC), calving interval (CI), and quantity of inseminations needed to impregnate the cow are parameters for understanding and monitoring the reproductive activity of a herd. The ideal is that the cow is as precocious and has the smaller calving interval as possible. It is known that reproductive characteristics have low heritability, undergoing great environmental influence. In this line, it is necessary to know the genes that are involved in this process to have more and more clarity. With genomic association studies and advances in molecular biology, it is possible to explain the genetic background of these characteristics and with the use of molecular markers, we find regions responsible for the origins of the biological variation that show us these characteristics. Thus, this study aimed to identify genomic regions associated with age at first calving (AFC), to calving interval (CI), in a population of Holstein cattle. To identify regions that possibly alter the phenotype, GWAS was applied to the database of phenotypic data of AFC, IC of 39,336 daughters, and genotype of 555 bulls, in 187 different herds, contemporary groups were formed and analyzed in GWAS. Data underwent quality control and by the end, there were 75,925 SNPs. BLUPF90 family software was used for statistical analysis and known pedigree animal model, with 10 SNPs fixed windows, and explained variance over 1.5%. A total of 34 genes were identified: 24 genes linked to AFC and 10 genes linked to CI. The main genes were APP, PRSS16 e BTN1A1, once linked to the animal immune response to the postpartum intemperance and to the reproductive system recovery. The genes CYYR1, PRSS16 e WEE2 are known to be related to embryogenesis, linking them to the reproductive traits of the animals. Some of the identified genes, in the present study, were associated with reproductive and immunological characteristics of the animals, corroborating the hypothesis of a different genetic expression among the investigated animals, and indicating the need for the development of new studies in this field. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-10-03 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://www.teses.usp.br/teses/disponiveis/11/11139/tde-03012023-165533/ |
url |
https://www.teses.usp.br/teses/disponiveis/11/11139/tde-03012023-165533/ |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
|
dc.rights.driver.fl_str_mv |
Liberar o conteúdo para acesso público. info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Liberar o conteúdo para acesso público. |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.coverage.none.fl_str_mv |
|
dc.publisher.none.fl_str_mv |
Biblioteca Digitais de Teses e Dissertações da USP |
publisher.none.fl_str_mv |
Biblioteca Digitais de Teses e Dissertações da USP |
dc.source.none.fl_str_mv |
reponame:Biblioteca Digital de Teses e Dissertações da USP instname:Universidade de São Paulo (USP) instacron:USP |
instname_str |
Universidade de São Paulo (USP) |
instacron_str |
USP |
institution |
USP |
reponame_str |
Biblioteca Digital de Teses e Dissertações da USP |
collection |
Biblioteca Digital de Teses e Dissertações da USP |
repository.name.fl_str_mv |
Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP) |
repository.mail.fl_str_mv |
virginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.br |
_version_ |
1809090325731344384 |