Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle
The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study...
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| Format: | Article |
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MDPI AG
2021-05-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/11/5/1386 |
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| author | Ana Paula Sbardella Rafael Nakamura Watanabe Rebeka Magalhães da Costa Priscila Arrigucci Bernardes Larissa Graciano Braga Fernando Sebastián Baldi Rey Raysildo Barbosa Lôbo Danísio Prado Munari |
| author_facet | Ana Paula Sbardella Rafael Nakamura Watanabe Rebeka Magalhães da Costa Priscila Arrigucci Bernardes Larissa Graciano Braga Fernando Sebastián Baldi Rey Raysildo Barbosa Lôbo Danísio Prado Munari |
| author_sort | Ana Paula Sbardella |
| collection | DOAJ |
| description | The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them <i>CAMK1D</i>, <i>TASP1</i>, <i>ACOXL</i>, <i>RAB11FIP5</i>, and <i>SFXN5</i>. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs. |
| first_indexed | 2024-03-10T11:27:01Z |
| format | Article |
| id | doaj.art-9c60c18ceb724985aef245579f35d120 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T11:27:01Z |
| publishDate | 2021-05-01 |
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| record_format | Article |
| series | Animals |
| spelling | doaj.art-9c60c18ceb724985aef245579f35d1202023-11-21T19:33:13ZengMDPI AGAnimals2076-26152021-05-01115138610.3390/ani11051386Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore CattleAna Paula Sbardella0Rafael Nakamura Watanabe1Rebeka Magalhães da Costa2Priscila Arrigucci Bernardes3Larissa Graciano Braga4Fernando Sebastián Baldi Rey5Raysildo Barbosa Lôbo6Danísio Prado Munari 7Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilDepartamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilDepartamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilDepartamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis 88034-000, Santa Catarina, BrazilDepartamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilDepartamento de Zootecnia, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilDepartamento de Genética, Universidade de São Paulo, Ribeirão Preto 14040-030, São Paulo, BrazilDepartamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal 14884-900, São Paulo, BrazilThe identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them <i>CAMK1D</i>, <i>TASP1</i>, <i>ACOXL</i>, <i>RAB11FIP5</i>, and <i>SFXN5</i>. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.https://www.mdpi.com/2076-2615/11/5/1386beef cattleWssGWASreproductioncandidate genes |
| spellingShingle | Ana Paula Sbardella Rafael Nakamura Watanabe Rebeka Magalhães da Costa Priscila Arrigucci Bernardes Larissa Graciano Braga Fernando Sebastián Baldi Rey Raysildo Barbosa Lôbo Danísio Prado Munari Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle Animals beef cattle WssGWAS reproduction candidate genes |
| title | Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle |
| title_full | Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle |
| title_fullStr | Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle |
| title_full_unstemmed | Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle |
| title_short | Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle |
| title_sort | genome wide association study provides insights into important genes for reproductive traits in nelore cattle |
| topic | beef cattle WssGWAS reproduction candidate genes |
| url | https://www.mdpi.com/2076-2615/11/5/1386 |
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