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Otto PI, Guimarães SEF, Verardo LL, Azevedo ALS, Vandenplas J, Sevillano CA, Marques DBD, Pires MDFA, de Freitas C, Verneque RS, Martins MF, Panetto JCC, Carvalho WA, Gobo DOR, da Silva MVGB, Machado MA. Genome-wide association studies for heat stress response in Bos taurus × Bos indicus crossbred cattle. J Dairy Sci 2019; 102:8148-8158. [PMID: 31279558 DOI: 10.3168/jds.2018-15305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 05/05/2019] [Indexed: 12/13/2022]
Abstract
Heat stress is an important issue in the global dairy industry. In tropical areas, an alternative to overcome heat stress is the use of crossbred animals or synthetic breeds, such as the Girolando. In this study, we performed a genome-wide association study (GWAS) and post-GWAS analyses for heat stress in an experimental Gir × Holstein F2 population. Rectal temperature (RT) was measured in heat-stressed F2 animals, and the variation between 2 consecutive RT measurements (ΔRT) was used as the dependent variable. Illumina BovineSNP50v1 BeadChip (Illumina Inc., San Diego, CA) and single-SNP approach were used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene-transcription factor (TF) networks, generated from enriched TF. The breed origin of marker alleles in the F2 population was assigned using the breed of origin of alleles (BOA) approach. Heritability and repeatability estimates (± standard error) for ΔRT were 0.13 ± 0.08 and 0.29 ± 0.06, respectively. Association analysis revealed 6 SNP significantly associated with ΔRT. Genes involved with biological processes in response to heat stress effects (LIF, OSM, TXNRD2, and DGCR8) were identified as putative candidate genes. After performing the BOA approach, the 10% of F2 animals with the lowest breeding values for ΔRT were classified as low-ΔRT, and the 10% with the highest breeding values for ΔRT were classified as high-ΔRT. On average, 49.4% of low-ΔRT animals had 2 alleles from the Holstein breed (HH), and 39% had both alleles from the Gir breed (GG). In high-ΔRT animals, the average proportion of animals for HH and GG were 1.4 and 50.2%, respectively. This study allowed the identification of candidate genes for ΔRT in Gir × Holstein crossbred animals. According to the BOA approach, Holstein breed alleles could be associated with better response to heat stress effects, which could be explained by the fact that Holstein animals are more affected by heat stress than Gir animals and thus require a genetic architecture to defend the body from the deleterious effects of heat stress. Future studies can provide further knowledge to uncover the genetic architecture underlying heat stress in crossbred cattle.
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Affiliation(s)
- Pamela I Otto
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Simone E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Lucas L Verardo
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | | | - Jeremie Vandenplas
- Wageningen University and Research Animal Breeding and Genomics, Wageningen 6700, the Netherlands
| | - Claudia A Sevillano
- Wageningen University and Research Animal Breeding and Genomics, Wageningen 6700, the Netherlands; Topigs Norsvin Research Center, Beuningen 6640, the Netherlands
| | - Daniele B D Marques
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | | | - Célio de Freitas
- Embrapa Dairy Cattle Research Center, Juiz de Fora 36038-330, Brazil
| | - Rui S Verneque
- Embrapa Dairy Cattle Research Center, Juiz de Fora 36038-330, Brazil
| | | | | | | | - Diego O R Gobo
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | | | - Marco A Machado
- Embrapa Dairy Cattle Research Center, Juiz de Fora 36038-330, Brazil.
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Otto PI, Guimarães SEF, Verardo LL, Azevedo ALS, Vandenplas J, Soares ACC, Sevillano CA, Veroneze R, de Fatima A Pires M, de Freitas C, Prata MCA, Furlong J, Verneque RS, Martins MF, Panetto JCC, Carvalho WA, Gobo DOR, da Silva MVGB, Machado MA. Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle: A deeper look into this intricate mechanism. J Dairy Sci 2018; 101:11020-11032. [PMID: 30243625 DOI: 10.3168/jds.2017-14223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/29/2018] [Indexed: 01/12/2023]
Abstract
Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in the dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.
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Affiliation(s)
- Pamela I Otto
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | - Simone E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | - Lucas L Verardo
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | | | - Jeremie Vandenplas
- Wageningen University & Research Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - Aline C C Soares
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | - Claudia A Sevillano
- Wageningen University & Research Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands; Topigs Norsvin Research Center, 6640 AA Beuningen, the Netherlands
| | - Renata Veroneze
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | | | - Célio de Freitas
- EMBRAPA, Dairy Cattle Research Center, Juiz de Fora, MG, 36038-330 Brazil
| | | | - John Furlong
- EMBRAPA, Dairy Cattle Research Center, Juiz de Fora, MG, 36038-330 Brazil
| | - Rui S Verneque
- EMBRAPA, Dairy Cattle Research Center, Juiz de Fora, MG, 36038-330 Brazil
| | | | | | - Wanessa A Carvalho
- EMBRAPA, Dairy Cattle Research Center, Juiz de Fora, MG, 36038-330 Brazil
| | - Diego O R Gobo
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-977 Brazil
| | | | - Marco A Machado
- EMBRAPA, Dairy Cattle Research Center, Juiz de Fora, MG, 36038-330 Brazil.
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Machado MA, S Azevedo AL, Teodoro RL, Pires MA, CD Peixoto MG, de Freitas C, Prata MCA, Furlong J, da Silva MVGB, Guimarães SEF, Regitano LCA, Coutinho LL, Gasparin G, Verneque RS. Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus x Bos indicus). BMC Genomics 2010; 11:280. [PMID: 20433753 PMCID: PMC2880304 DOI: 10.1186/1471-2164-11-280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 04/30/2010] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) x Holstein (Bos taurus) cross. RESULTS Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. CONCLUSIONS The experimental F2 population derived from Gyr x Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Simone EF Guimarães
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | - Luiz L Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Gustavo Gasparin
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luiz km 235, São Carlos/SP 13565-905, Brazil
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