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Álvarez Cecco P, Balbi M, Bonamy M, Rogberg Muñoz A, Olivera H, Giovambattista G, Fernández ME. Skin transcriptome analysis in Brangus cattle under heat stress. J Therm Biol 2024; 121:103852. [PMID: 38615495 DOI: 10.1016/j.jtherbio.2024.103852] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/04/2023] [Revised: 02/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N = 5) and non-stressed (N = 5) groups. Skin transcriptomics was performed and correlations between breed composition, phenotypic and skin histological traits were evaluated. Results showed 4309 differentially expressed genes (P < 0.01), 2113 downregulated and 2196 upregulated. Enrichment and ontology analyses revealed 132 GO terms and 67 pathways (P < 0.01), including thermogenesis, glycolysis, gluconeogenesis, mitochondrial activity, antioxidant and immune response, and apoptosis. The identity of the terms and pathways indicated the diversity of mechanisms directed to relieve the animals' suffering, acting from simple passive mechanisms (conduction, convection and radiation) to more complex active ones (behavioural changes, evaporation, vasodilation and wheezing). Furthermore, significant differences between phenotypic and skin histological traits and correlations between pairs of traits suggested a direction towards heat dissipation processes. In this sense, number of vessels was positively correlated with number of sweat glands (P < 0.001) and both were positively correlated with zebuine genetic content (P < 0.05 and P < 0.01, respectively), gland size was positively correlated with epidermal thickness and negatively with hair length (P < 0.05), and epidermal thickness was negatively correlated with gland-epidermis distance (P < 0.0005). These results support the notion that response to heat stress is physiologically complex, producing significant changes in the expression of genes involved in several biological pathways, while the animal's ability to face it depends greatly on their skin features.
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Affiliation(s)
- Paulo Álvarez Cecco
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Marianela Balbi
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Martín Bonamy
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ, Buenos Aires, Argentina
| | - Hernán Olivera
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - Guillermo Giovambattista
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina
| | - María Elena Fernández
- Instituto de Genética Veterinaria (IGEVET), Facultad de Ciencias Veterinarias, UNLP-CONICET, B100, La Plata, Argentina.
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Toro-Ospina AM, Herrera Rios AC, Pimenta Schettini G, Vallejo Aristizabal VH, Bizarria dos Santos W, Zapata CA, Ortiz Morea EG. Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia). Genes (Basel) 2022; 13:genes13071232. [PMID: 35886015 PMCID: PMC9318017 DOI: 10.3390/genes13071232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.
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Affiliation(s)
- Alejandra M. Toro-Ospina
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Correspondence:
| | - Ana C. Herrera Rios
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia
| | - Gustavo Pimenta Schettini
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA;
| | - Viviana H. Vallejo Aristizabal
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil;
| | - Cesar A. Zapata
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Edna Gicela Ortiz Morea
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
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Balbi M, Bonamy M, Fernandez ME, Cecco P, Vaca RJA, Rogberg Muñoz A, Peral Gacía P, Prando AJ, Giovambattista G. Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001-48,100,000 bp. Anim Biotechnol 2022:1-7. [PMID: 35130466 DOI: 10.1080/10495398.2022.2029464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (n = 108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446-48,030,219 bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.
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Affiliation(s)
- Marianela Balbi
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martín Bonamy
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Elena Fernandez
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Paulo Cecco
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Roberto J A Vaca
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Facultad de Agronomía, INPA-Instituto de Producción Animal UBA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pilar Peral Gacía
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Alberto J Prando
- Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang FH, Zhang L, Gong G, Yan XC, Zhang LT, Zhang FT, Liu HF, Lv Q, Wang ZY, Wang RJ, Zhang YJ, Wang ZX, Liu ZH, He LB, Su R, Zhao YH, Li JQ. Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats. Anim Genet 2021; 52:375-379. [PMID: 33778967 PMCID: PMC8251931 DOI: 10.1111/age.13053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
Inner Mongolia Cashmere goat is a well-known local cashmere goat breed in China. It is famous for excellent fleece quality and a significant advantage in cashmere yield compared to other cashmere goat breeds. In this study, a genome-wide association study was used to investigate fiber length, fiber diameter, and cashmere yield of 192 Inner Mongolia Cashmere goats using the Illumina GoatSNP52K Beadchip panel. We discovered that four single nucleotide polymorphisms (SNPs) reached genome-wide significance levels. These SNPs were located in some genes, e.g. FGF12, SEMA3D, EVPL, and SOX5, possibly related to fleece traits in Inner Mongolia Cashmere goat. Gene ontology enrichment analysis revealed that these genes were enriched in several biological pathways that were involved in hair follicle development in cashmere goats. In summary, the identified significant SNPs and genes provide useful information to explore genetic mechanisms underlying the variation in fleece traits and genomic selection of Chinese cashmere goat.
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Affiliation(s)
- F. H. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - G. Gong
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - X. C. Yan
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - L. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - F. T. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - H. F. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Q. Lv
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. Y. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - R. J. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. J. Zhang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Z. X. Wang
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Animal Genetics, Breeding and ReproductionHohhotInner Mongolia Autonomous Region010018China
| | - Z. H. Liu
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - L. B. He
- Key Laboratory of Mutton Sheep Genetics and BreedingMinistry of Agriculture and Rural AffairsHohhot010018China
| | - R. Su
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - Y. H. Zhao
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
| | - J. Q. Li
- College of Animal ScienceInner Mongolia Agricultural UniversityHohhotInner Mongolia010018China
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Rodríguez-Valera Y, Rocha D, Naves M, Renand G, Pérez-Pineda E, Ramayo-Caldas Y, Ramos-Onsins SE. The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle. Animals (Basel) 2020; 10:ani10122233. [PMID: 33261195 PMCID: PMC7760288 DOI: 10.3390/ani10122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Charolais de Cuba cattle is a tropical adapted breed founded in Cuba around 120 years ago from Charolais French specimens. Nowadays, it is still a closed breed and remains as a small population. In this work, we analyzed the inbreeding and diversity patterns, as well as the population size, of this recent adapted breed via a run of homozygosity (ROH) analysis. We found that the genomic inbreeding levels are higher in the Charolais de Cuba breed compared to French and British Charolais populations. Nevertheless, we detected that the effective population size experienced a very similar decline during the last century in the three Charolais populations studied. Finally, a number of regions with exceptional patterns of long homozygosity were identified in this breed, and these could be related to processes of adaptation to tropical conditions. Abstract Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
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Affiliation(s)
- Yoel Rodríguez-Valera
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Dominique Rocha
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Michel Naves
- INRAE, URZ, 97170 Petit Bourg, Guadeloupe, France;
| | - Gilles Renand
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Eliecer Pérez-Pineda
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Yuliaxis Ramayo-Caldas
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre of Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
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