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de Andrade Pantoja MH, Poleti MD, de Novais FJ, Duarte KKS, Mateescu RG, Mourão GB, Coutinho LL, Fukumasu H, Titto CG. Skin transcriptomic analysis reveals candidate genes and pathways associated with thermotolerance in hair sheep. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:435-444. [PMID: 38147121 DOI: 10.1007/s00484-023-02602-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/10/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023]
Abstract
The skin plays an important role in thermoregulation. Identification of genes on the skin that contribute to increased heat tolerance can be used to select animals with the best performance in warm environments. Our objective was to identify candidate genes associated with the heat stress response in the skin of Santa Ines sheep. A group of 80 sheep assessed for thermotolerance was kept in a climatic chamber for 8 days at a stress level temperature of 36 °C (10 am to 04 pm) and a maintenance temperature of 28 °C (04 pm to 10 am). Two divergent groups, with seven animals each, were formed after ranking them by thermotolerance using rectal temperature. From skin biopsy samples, total RNA was extracted, quantified, and used for RNA-seq analysis. 15,989 genes were expressed in sheep skin samples, of which 4 genes were differentially expressed (DE; FDR < 0.05) and 11 DE (FDR 0.05-0.177) between the two divergent groups. These genes are involved in cellular protection against stress (HSPA1A and HSPA6), ribosome assembly (28S, 18S, and 5S ribosomal RNA), and immune response (IGHG4, GNLY, CXCL1, CAPN14, and SAA-4). The candidate genes and main pathways related to heat tolerance in Santa Ines sheep require further investigation to understand their response to heat stress in different climatic conditions and under solar radiation. It is essential to verify whether these genes and pathways are present in different breeds and to understand the relationship between heat stress and other genes identified in this study.
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Affiliation(s)
- Messy Hannear de Andrade Pantoja
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Mirele Daiana Poleti
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Francisco José de Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Kelly Kéffny Souza Duarte
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Gerson Barreto Mourão
- Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Cristiane Gonçalves Titto
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil.
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Pantoja MHDA, Novais FJD, Mourão GB, Mateescu RG, Poleti MD, Beline M, Monteiro CP, Fukumasu H, Titto CG. Exploring candidate genes for heat tolerance in ovine through liver gene expression. Heliyon 2024; 10:e25692. [PMID: 38370230 PMCID: PMC10869868 DOI: 10.1016/j.heliyon.2024.e25692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
Thermotolerance has become an essential factor in the prevention of the adverse effects of heat stress, but it varies among animals. Identifying genes related to heat adaptability traits is important for improving thermotolerance and for selecting more productive animals in hot environments. The primary objective of this research was to find candidate genes in the liver that play a crucial role in the heat stress response of Santa Ines sheep, which exhibit varying levels of heat tolerance. To achieve this goal, 80 sheep were selected based on their thermotolerance and placed in a climate chamber for 10 days, during which the average temperature was maintained at 36 °C from 10 a.m. to 4 p.m. and 28 °C from 4 p.m. to 10 a.m. A subset of 14 extreme animals, with seven thermotolerant and seven non-thermotolerant animals based on heat loss (rectal temperature), were selected for liver sampling. RNA sequencing and differential gene expression analysis were performed. Thermotolerant sheep showed higher expression of genes GPx3, RGS6, GPAT3, VLDLR, LOC101108817, and EVC. These genes were mainly related to the Hedgehog signaling pathway, glutathione metabolism, glycerolipid metabolism, and thyroid hormone synthesis. These enhanced pathways in thermotolerant animals could potentially mitigate the negative effects of heat stress, conferring greater heat resistance.
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Affiliation(s)
- Messy Hannear de Andrade Pantoja
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Francisco José de Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Gerson Barreto Mourão
- Escola Superior de Agricultura Luiz de Queiroz, Universidade São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Raluca G. Mateescu
- Department of Animal Science, University of Florida, Gainesville, FL, United States
| | - Mirele Daiana Poleti
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Mariane Beline
- Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061-0002, United States
| | - Camylla Pedrosa Monteiro
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Cristiane Gonçalves Titto
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
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Contreras-Méndez LA, Medrano JF, Thomas MG, Enns RM, Speidel SE, Luna-Nevárez G, López-Castro PA, Rivera-Acuña F, Luna-Nevárez P. The Anti-Müllerian Hormone as Endocrine and Molecular Marker Associated with Reproductive Performance in Holstein Dairy Cows Exposed to Heat Stress. Animals (Basel) 2024; 14:213. [PMID: 38254382 PMCID: PMC10812537 DOI: 10.3390/ani14020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Anti-Müllerian hormone (AMH) is proposed as a biomarker for fertility in cattle, yet this associative relationship appears to be influenced by heat stress (HS). The objective was to test serum AMH and AMH-related single nucleotide polymorphisms (SNPs) as markers potentially predictive of reproductive traits in dairy cows experiencing HS. The study included 300 Holstein cows that were genotyped using BovineSNP50 (54,000 SNP). A genome-wide association study was then executed. Nine intragenic SNPs within the pathways that influence the AMH gene were found important with multiple comparisons adjustment tests (p < 1.09 × 10-6). A further validation study was performed in an independent Holstein cattle population, which was divided into moderate (MH; n = 152) and severe heat-stressed (SH; n = 128) groups and then subjected to a summer reproductive management program. Serum AMH was confirmed as a predictor of fertility measures (p < 0.05) in MH but not in the SH group. Cows were genotyped, which revealed four SNPs as predictive markers for serum AMH (p < 0.01), reproductive traits (p < 0.01), and additional physiological variables (p < 0.05). These SNPs were in the genes AMH, IGFBP1, LGR5, and TLR4. In conclusion, serum AMH concentrations and AMH polymorphisms are proposed as predictive markers that can be used in conjunction with genomic breeding value approaches to improve reproductive performance in Holstein cows exposed to summer HS conditions.
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Affiliation(s)
- Luis A. Contreras-Méndez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Juan F. Medrano
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | | | - R. Mark Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Scott E. Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pedro A. López-Castro
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Fernando Rivera-Acuña
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
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Luna-Ramirez RI, Limesand SW, Goyal R, Pendleton AL, Rincón G, Zeng X, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress. Genes (Basel) 2023; 14:1590. [PMID: 37628641 PMCID: PMC10454332 DOI: 10.3390/genes14081590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.
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Affiliation(s)
- Rosa I. Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sean W. Limesand
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Ravi Goyal
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander L. Pendleton
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Xi Zeng
- Zoetis Inc., VMRD Genetics R&D, Kalamazoo, MI 49007, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Javier R. Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
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Castillo-Salas CA, Luna-Nevárez G, Reyna-Granados JR, Luna-Ramirez RI, Limesand SW, Luna-Nevárez P. Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment. J Therm Biol 2023; 112:103475. [PMID: 36796920 DOI: 10.1016/j.jtherbio.2023.103475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st.- March 31st.; n = 101) or warm (April 1st.- August 31st.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.
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Affiliation(s)
- Candelario A Castillo-Salas
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
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Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. Sci Rep 2022; 12:12264. [PMID: 35851076 PMCID: PMC9293982 DOI: 10.1038/s41598-022-15986-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.
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Luna-Nevárez G, Pendleton AL, Luna-Ramirez RI, Limesand SW, Reyna-Granados JR, Luna-Nevárez P. Genome-wide association study of a thermo-tolerance indicator in pregnant ewes exposed to an artificial heat-stressed environment. J Therm Biol 2021; 101:103095. [PMID: 34879913 DOI: 10.1016/j.jtherbio.2021.103095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Environmental heat stress negatively influences sheep production in warm semi-arid regions. An animal's ability to tolerate warm weather is difficult to measure naturally due to environmental variability and genetic variation between animals. In this study we developed a thermo-tolerance indicator (TTI) to define heat stress tolerance in pregnant sheep in a controlled environment. Next, we performed a genome-wide association study (GWAS) to identify genomic regions and target genes associated with thermo-tolerance in sheep. Pregnant Columbia-Rambouillet crossbred ewes (n = 127) were heat-stressed inside a climate-controlled chamber for 57 days by increasing the temperature-humidity index to ≥30. Rectal temperature (RT) and feed intake (FI) data were collected daily and used for the predictive TTI analysis. After the tenth day of heat stress, the regression analyses revealed that FI was stable; however, when the ewe's RT exceeded 39.8 °C their FI was less than thermo-tolerant ewes. This average predicted temperature was used to classify each ewe as heat stress tolerant (≤39.8 °C) and non-heat stress tolerant (>39.8 °C). A GWAS analysis was performed and genomic regions were compared between heat stress tolerant and non-tolerant ewes. The single-marker genomic analysis detected 16 single nucleotide polymorphisms (SNP) associated with heat stress tolerance (P < 0.0001), whereas the multi-marker Bayesian analysis identified 8 overlapped 1-Mb chromosomal regions accounting for 11.39% of the genetic variation associated with tolerance to heat stress. Four intragenic SNP showed a remarkable contribution to thermo-tolerance, and these markers were within the genes FBXO11 (rs407804467), PHC3 (rs414179061), TSHR (rs418575898) and STAT1 (rs417581105). In conclusion, genomic regions harboring four intragenic SNP were associated with heat stress tolerance, and these candidate genes are proposed to influence heat tolerance in pregnant ewes subjected to an artificially induced warm climate. Moreover, these genetic markers could be suitable for use in further genetic selection programs in sheep managed in semi-arid regions.
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Affiliation(s)
- Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Alexander L Pendleton
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
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