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Brereton JE. What is the role of the studbook in zoo and aquarium research? Zoo Biol 2024; 43:22-31. [PMID: 37548418 DOI: 10.1002/zoo.21797] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
In zoos and aquariums globally, studbooks provide a format by which threatened or important species populations can be carefully managed. These documents can be used to answer complex questions about animal population demographics, animal husbandry, breeding success and mortality. Given the time-intensive nature of studbook collation, only a subset of all animal species held in zoological facilities are managed using these programs. The purpose of this project was to identify how studbooks are being used by researchers, the topics being investigated, and the taxa being covered. To achieve this, data were collected on the types of research paper being produced using studbook information. A literature search, covering several zoo and aquarium journals, was utilized. Data on the types of studbook available were additionally collected for three international zoo organizations. A Poisson regression was run to determine the predictive power of taxonomic class, animal threat status and studbook type on a studbook featuring in published research. Overall, the study identified that taxonomic class and threat status were significant predictors of the number of published studbook papers, with threatened species being more likely to appear in papers. Additionally, population demography was the most common use of studbook data, followed by genetics and reproduction. Not all taxonomic groups were featured in the literature, with mammals featuring much more frequently than would be expected based on the types of studbook available.
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de Toledo RB, de Faria OAC, Leme LO, Magnabosco CU, Guimarães R, Eifert EDC, Dos Santos IR, Oliveira RV, Dode MAN, Malaquias JV, Pivato I, Martins CF. Effect of food supplementation on in vitro embryo production and growth performance in prepubertal Nelore heifers. Anim Biotechnol 2023; 34:5087-5096. [PMID: 37975200 DOI: 10.1080/10495398.2023.2279612] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
In vitro embryos production from prepubertal heifers can help contribute to breeding programs; however, strategies are necessary to increase their embryo production. The aim of this study was to investigate the effects of two nutritional plans on oocyte recovery, embryo production and growth performance of prepubertal Nelore heifers. Thirty-four Nelore heifers with age of 6.5 months were divided into two feeding treatments (NP1 and NP2). The NP1 diets served as the control and NP2 diets were formulated to contain an average of 1.22-fold more energy than NP1. After 3 months of supplementation, the animals underwent follicular aspiration (ovum pick-up, OPU) every 21 d for 3 months and embryos were produced in vitro. Wither height, chest depth, body weight and subcutaneous fat of animals were measured. The number of retrieved and viable oocytes per OPU were 1.49-fold and 1.42-fold greater in NP2 heifers (p = 0.018 and p = 0.049, respectively) than those in NP1 heifers. Heifers administered NP2 produced 29.7% blastocysts, a percentage higher than NP1 animals that produced 24.40% embryos (p < 0.05). Consequently, females in the NP2 treatment showed improved body development. These results indicate a positive effect of a higher energy diet on assisted reproduction and body development in prepubertal heifers.
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Affiliation(s)
- Ricardo Braz de Toledo
- Brazilian Agricultural Research Corporation (Embrapa Cerrados), Planaltina, Brazil
- University of Brasília, Brasília, Brazil
| | - Otávio Augusto Costa de Faria
- University of Brasília, Brasília, Brazil
- Brazilian Agricultural Research Corporation (Embrapa Recursos Genéticos e Biotecnologia), Brasília, Brazil
| | - Ligiane Oliveira Leme
- Brazilian Agricultural Research Corporation (Embrapa Recursos Genéticos e Biotecnologia), Brasília, Brazil
| | | | - Roberto Guimarães
- Brazilian Agricultural Research Corporation (Embrapa Cerrados), Planaltina, Brazil
| | | | | | | | - Margot Alves Nunes Dode
- Brazilian Agricultural Research Corporation (Embrapa Recursos Genéticos e Biotecnologia), Brasília, Brazil
| | | | - Ivo Pivato
- University of Brasília, Brasília, Brazil
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Hobbs RJ, Upton R, Calatayud NE, Silla AJ, Daly J, McFadden MS, O’Brien JK. Cryopreservation Cooling Rate Impacts Post-Thaw Sperm Motility and Survival in Litoria booroolongensis. Animals (Basel) 2023; 13:3014. [PMID: 37835620 PMCID: PMC10571529 DOI: 10.3390/ani13193014] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The cryopreservation and storage of gametes (biobanking) can provide a long-term, low-cost option for the preservation of population genetic diversity and is particularly impactful when applied to manage selective breeding within conservation breeding programs (CBPs). This study aimed to develop a sperm cryopreservation protocol for the critically endangered Booroolong frog (Litoria booroolongensis) to capture founder genetics within the recently established (est. 2019) CBP for this species. Hormone-induced sperm release was achieved using established protocols, and spermic urine samples were collected over a 6-h period. Pooled spermic urine samples (n = 3 males) were divided equally between two cryoprotectant (CPA) treatments and diluted by 1:5 (sperm:CPA) with either 15% (v/v) dimethyl sulfoxide + 1% (w/v) sucrose in simplified amphibian Ringer's (SAR; CPAA) or 10% (v/v) dimethylformamide + 10% (w/v) trehalose dihydrate in SAR (CPAB). The samples were cryopreserved in 0.25 mL straws using either a programmable freezer (FrA) or an adapted dry shipper method (FrB). The thawed samples were activated via dilution in water and assessed for viability and motility using both manual assessment and computer-assisted sperm analysis (CASA; 0 h, 0.5 h post-thaw). Upon activation, the survival and recovery of motility (total motility, forward progression and velocity) of cryopreserved sperm suspensions were higher for sperm preserved using FrB than FrA, regardless of CPA composition. This work supports our long-term goal to pioneer the integration of biobanked cryopreserved sperm with population genetic management to maximize restoration program outcomes for Australian amphibian species.
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Affiliation(s)
- Rebecca J. Hobbs
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia (J.K.O.)
| | - Rose Upton
- Conservation Biology Research Group, School of Environmental and Life Sciences, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Natalie E. Calatayud
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, 15600 San Pasqual Valley Road, Escondido, CA 92025, USA
| | - Aimee J. Silla
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Jonathan Daly
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia (J.K.O.)
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael S. McFadden
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia (J.K.O.)
| | - Justine K. O’Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia (J.K.O.)
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Bianchi EM, Ferrari C, Aguirre NC, Filippi CV, Vera PA, Puebla AF, Gennari GP, Rodríguez GA, Scannapieco AC, Acuña CV, Lanzavecchia SB. Phenotypic and genetic characterization of Africanized Apis mellifera colonies with natural tolerance to Varroa destructor and contrasting defensive behavior. Front Insect Sci 2023; 3:1175760. [PMID: 38469487 PMCID: PMC10926445 DOI: 10.3389/finsc.2023.1175760] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/27/2023] [Indexed: 03/13/2024]
Abstract
Africanized Apis mellifera colonies with promising characteristics for beekeeping have been detected in northern Argentina (subtropical climate) and are considered of interest for breeding programs. Integral evaluation of this feral material revealed high colony strength and resistance/tolerance to brood diseases. However, these Africanized honeybees (AHB) also showed variable negative behavioral traits for beekeeping, such as defensiveness, tendency to swarm and avoidance behavior. We developed a protocol for the selection of AHB stocks based on defensive behavior and characterized contrasting colonies for this trait using NGS technologies. For this purpose, population and behavioral parameters were surveyed throughout a beekeeping season in nine daughter colonies obtained from a mother colony (A1 mitochondrial haplotype) with valuable characteristics (tolerance to the mite Varroa destructor, high colony strength and low defensiveness). A Defensive Behavior Index was developed and tested in the colonies under study. Mother and two daughter colonies displaying contrasting defensive behavior were analyzed by ddRADseq. High-quality DNA samples were obtained from 16 workers of each colony. Six pooled samples, including two replicates of each of the three colonies, were processed. A total of 12,971 SNPs were detected against the reference genome of A. mellifera, 142 of which showed significant differences between colonies. We detected SNPs in coding regions, lncRNA, miRNA, rRNA, tRNA, among others. From the original data set, we also identified 647 SNPs located in protein-coding regions, 128 of which are related to 21 genes previously associated with defensive behavior, such as dop3 and dopR2, CaMKII and ADAR, obp9 and obp10, and members of the 5-HT family. We discuss the obtained results by considering the influence of polyandry and paternal lineages on the defensive behavior in AHB and provide baseline information to use this innovative molecular approach, ddRADseq, to assist in the selection and evaluation of honey bee stocks showing low defensive behavior for commercial uses.
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Affiliation(s)
- Eliana Mariel Bianchi
- Área Animal, Instituto de Investigación Animal del Chaco-Semiárido (IIACS) - Instituto Nacional de Tecnología Agropecuaria (INTA), Santa Rosa de Leales, Tucumán, Argentina
| | - Carolina Ferrari
- Escuela de Ciencias Agrarias, Naturales y Ambientales (ECANA), Universidad Nacional del Noroeste de Buenos Aires (UNNOBA), Pergamino, Buenos Aires, Argentina
| | - Natalia C. Aguirre
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Carla V. Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Pablo A. Vera
- Unidad de Genómica, Instituto de Biotecnología-Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Unidad de Genómica, Instituto de Biotecnología-Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Gerardo P. Gennari
- Estación Experimental Agropecuaria (EEA) Famaillá, Instituto Nacional de Tecnología Agropecuaria (INTA), Famaillá, Tucumán, Argentina
| | - Graciela A. Rodríguez
- Estación Experimental Agropecuaria (EEA) Ascasubi, Instituto Nacional de Tecnología Agropecuaria (INTA), Hilario Ascasubi, Buenos Aires, Argentina
| | - Alejandra Carla Scannapieco
- Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Cintia V. Acuña
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Silvia B. Lanzavecchia
- Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
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Moreno-Olivares JD, Paladines-Quezada DF, Giménez-Bañón MJ, Bleda-Sánchez JA, Cebrián-Pérez A, Gómez-Martínez JC, Gil-Muñoz R. Proanthocyanidins composition in new varieties descended from Monastrell. J Sci Food Agric 2023; 103:5039-5049. [PMID: 36977630 DOI: 10.1002/jsfa.12578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The wine sector is constantly evolving, in order to adapt to consumer tastes. The organoleptic characteristics in wines are the main factors to obtain quality wines. Proanthocyanidins (PAs) are responsible in an important way for positive aspects in quality wines, such as body and color stability in red wines, but they are also responsible for sensory characteristics that can be negative for their quality when found in excessive concentrations. One strategy to improve grapevines and wines is to obtain new varieties, so our research institute has been selecting some of them from direct crosses between Monastrell and other considered premium varieties such as Cabernet Sauvignon and Syrah. RESULTS A quantitative analysis in grapes, seeds and wines was carried out during three consecutive seasons (2018, 2019 and 2020) in order to characterize PAs composition and concentration in the following new varieties: MC80 (Monastrell × Cabernet Sauvignon), MC98, MC4, MC18 and MS10 (Monastrell × Syrah). Other aspect to study was the extraction capacity of the different new varieties of PAs during maceration process into must/wine. CONCLUSION In general, the results showed higher concentrations in PAs in most crosses for the three seasons studied compared to Monastrell variety. It was remarkable that a higher concentration of epigallocatechin was found in most of the wines elaborated with the crosses, being a positive aspect from an organoleptic point of view, since this compound provides softness to the wines. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Juan Daniel Moreno-Olivares
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - Diego Fernando Paladines-Quezada
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - María José Giménez-Bañón
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - Juan Antonio Bleda-Sánchez
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - Ana Cebrián-Pérez
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - José Cayetano Gómez-Martínez
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
| | - Rocío Gil-Muñoz
- Murcian Institute of Agricultural and Environmental Research and Development, Department of Viticulture and Oenology, Murcia, Spain
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Wang Y, Wang J, Chen D, Hui Z, Hu X. Shade Increased Seed Yield and Quality of Incarvillea sinensis var. przewalskii. Plants (Basel) 2023; 12:2934. [PMID: 37631146 PMCID: PMC10459102 DOI: 10.3390/plants12162934] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
Incarvillea sinensis var. przewalskii has attracted great attention because of the anticancer value of its alkaloids and the potential use of the species for ecological restoration. However, the scarcity of high-quality seeds has significantly hindered the cultivation and efficient utilization of this species. Understanding how seeds respond to maternal environmental conditions is crucial for developing high-yield and top-notch seed accessions, but the available knowledge in this area is limited. Here, we determined the effect of shading treatments on seed development, seed quality, and yield. Compared to the control, shade significantly increased the seed germination rate and 1000-seed weight by 29.2% and 25.6%, respectively. Regardless of light conditions, the seed germination rate and 1000-seed weight decreased by 7.13% and 37.5%, respectively, as the fruit positioned from base to apical. The seed yield per plant was 27.9% higher under shade than under the control treatment. The structural equation model showed that shade promoted seed yield through increasing flowers per reproductive branch and seed numbers per capsule. These findings suggest that adjusting shading conditions and optimizing inflorescence development can lead to high-yield and high-quality seeds. Additionally, prioritizing the number of flowers per reproductive branch and seeds per capsule in breeding programs can further enhance the seed yield of I. sinensis var. przewalskii.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou 730000, China; (Y.W.); (D.C.); (Z.H.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jingjing Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou 730000, China; (Y.W.); (D.C.); (Z.H.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Dali Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou 730000, China; (Y.W.); (D.C.); (Z.H.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Zhenning Hui
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou 730000, China; (Y.W.); (D.C.); (Z.H.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xiaowen Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou 730000, China; (Y.W.); (D.C.); (Z.H.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
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Palma-Granados P, García-Casco JM, Caraballo C, Vázquez-Ortego P, Gómez-Carballar F, Sánchez-Esquiliche F, Óvilo C, Muñoz M. Design of a low-density SNP panel for intramuscular fat content and fatty acid composition of backfat in free-range Iberian pigs. J Anim Sci 2023; 101:7079844. [PMID: 36930061 PMCID: PMC10118394 DOI: 10.1093/jas/skad079] [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: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 03/18/2023] Open
Abstract
Intramuscular fat (IMF) content and fatty acids (FA) profile determine important sensory and technological characteristics of the meat, being interesting traits to be included in breeding programs for Iberian pig. In a previous study, we analyzed the longissimus dorsi transcriptome of Iberian pigs with divergent breeding values for IMF identifying 63 and 12 functional candidate genes and long non-coding RNA being differentially expressed. The first objective of this work was to use the RNA-seq data generated in that study in order to design a low-density panel with 50 single nucleotide polymorphisms (SNP). The second aim was to evaluate the effects of this SNP panel on IMF content and backfat FA profile in a closed commercial population of Iberian pigs. The IMF content and backfat FA composition were determined in 940 Iberian pigs. A total of 837 SNP were identified in the selection of genes and lncRNA. Out of the 50 selected SNP, 11 were monomorphic in the population and 2 failed in their genotyping. Association analyses were carried out for the 37 SNP segregating in the population (minor allele frequency, MAF > 0.05). Regarding IMF content, a significant additive effect (q - value < 0.05) was observed for ADIPOQ:g.124646194T>G SNP, in which the G allele was linked to an increase of 7.59% (additive effect expressed as a percentage of the mean of the trait). For the backfat FA composition, we observed 24 SNP with significant associations. The strongest effects were detected for the ELOVL6:g.112186423A>G and FASN_rs331694510G>A SNP. The A allele of both SNP were associated to a lower percentage of palmitic (C16:0) and palmitoleic (C16:1) acids and an increase in oleic acid (C18:1). In addition, the AMPD3:g.49043886C>G SNP had significant effects on C16:0, stearic (C18:0), C18:1 and on the sum of saturated and monounsaturated fatty acids. Finally, significant effects of the EGR2:66286345G>T SNP on C18:0 and C18:1 and other minor FA were observed. Our findings reveal ADIPOQ:g.124646194T>G, ELOVL6:g.112186423A>G and FASN_rs331694510G>A may be useful in breeding programs for Iberian pigs including FA profile and IMF content as selection goals, provided that their potential effects on other traits of interest are controlled.
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Affiliation(s)
- Patricia Palma-Granados
- Centro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.,Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Juan María García-Casco
- Centro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.,Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Carmen Caraballo
- Centro de I+D en Cerdo Ibérico, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra. EX101 km 4,7, 06300 Zafra, Spain.,Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Pedro Vázquez-Ortego
- Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | | | | | - Cristina Óvilo
- Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - María Muñoz
- Dpto. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Ctra La Coruña km 7,5, 28040 Madrid, Spain
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Song Y, Bouteiller XP, Larter M, Plomion C, Sin F, Delzon S. A safe breeding ground: genetically improved maritime pine for growth and stem form has more efficient but not more vulnerable xylem. Tree Physiol 2023; 43:366-378. [PMID: 36263989 DOI: 10.1093/treephys/tpac125] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 05/03/2023]
Abstract
Through repeated cycles of selection and recombination, tree breeding programs deliver genetically improved varieties for a range of target characteristics such as biomass production, stem form, resistance to biotic stresses, wood properties, etc. However, in the context of increased drought and heat waves, it is not yet known whether growth performance will impede drought resistance. To address this question, we compared the hydraulic properties, such as hydraulic efficiency and hydraulic safety, in four varieties over successive varieties of genetically improved maritime pines (i.e., Pinus pinaster Aït.) for growth and stem form. We measured 22 functional traits related to hydraulic efficiency, hydraulic safety, xylem anatomy and wood density. We found that improved varieties presented higher hydraulic conductivity with larger tracheid lumen size and tracheid lumen fraction, and smaller wall thickness reinforcement and tracheid density, but not at the cost of reduced embolism resistance. The reported absence of trade-off between hydraulic conductivity and embolism resistance is a strong asset to improve biomass productivity, through increased hydraulic efficiency, without impacting drought resistance, and should enable new maritime pine varieties to cope with a drier climate. Our study is one of the first to reveal the hydraulic mechanisms over successive varieties of genetic improvement for tree growth. It provides guidelines for sustainable forest management through breeding for other forest tree species.
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Affiliation(s)
- Yanjun Song
- UMR BIOGECO, INRAE, Univ. Bordeaux, 33615 Pessac, France
| | | | | | | | - Fabrice Sin
- National Forest Office, Bordeaux, 33524 Bruges, France
| | - Sylvain Delzon
- UMR BIOGECO, INRAE, Univ. Bordeaux, 33615 Pessac, France
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Ranjan A, Jain A, Verma A, Sinha R, Joshi P, Gowane GR, Alex R. Optimization of test day for milk yield recording and sire evaluation in Murrah buffaloes. J Anim Breed Genet 2023. [PMID: 36883272 DOI: 10.1111/jbg.12767] [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: 03/23/2022] [Accepted: 02/18/2023] [Indexed: 03/09/2023]
Abstract
In the present study, random regression models (RRM) were used to estimate genetic parameters for test-day milk yield in Murrah buffaloes using Legendre polynomial function (LP), with the objective to find the best combination of "minimum test-day model," which would be essential and sufficient to evaluate the trait successfully. Data included for analysis were 10,615 first lactation monthly test-day milk yield records (5th, 35th, 65th, …, 305th) from 965 Murrah buffaloes for the period 1975-2018. Cubic to octic-order orthogonal polynomials with homogeneous residual variances were used for the estimation of genetic parameters. Random regression models with sixth-order were selected based on goodness of fit criteria like lower AIC, BIC and residual variance. Heritability estimates ranged from 0.079 (TD6) to 0.21(TD10). For both ends of lactation, the additive genetic and environmental variances were higher and ranged from 0.21 ± 0.12 (TD6) to 0.85 ± 0.35 kg2 (TD1) and 3.74 ± 0.36 (TD11) to 1.36 ± 0.14 kg2 (TD9), respectively. Between adjacent test-day records, genetic correlation estimates ranged from 0.09 ± 0.31 (TD1 and TD2) to 0.97 ± 0.03 (TD3 and TD4; TD4 and TD5), but values gradually declined as the distance between test days increased. Negative genetic correlations were also obtained between TD1 with TD3 to TD9, TD2 with TD9 and TD10, and TD3 with TD10. On the basis of genetic correlations, models with 5 and/or 6 test-days combination were able to account for 86.1%-98.7% of variation along the lactation. Models with fourth and fifth-order LP functions were considered to account for variance with combinations of 5 and/or 6 test-day milk yields. The model with 6 test-day combinations had a higher rank correlation (0.93) with model using 11 monthly test-day milk yield records. On the basis of relative efficiency, the model with 6 monthly test day combinations with fifth-order was more efficient (maximum 99%) than the model using 11 monthly test-day milk yield records. Looking into the similar accuracy with the 11TD model, and the low resources requirement, we recommend the use of the "6 test-day combination model" for sire evaluation. These models may help in reducing the cost and time for data recording of milk yield.
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Affiliation(s)
| | | | | | - Ranjana Sinha
- Animal and Fish Resources Department, Government of Bihar, Patna, India
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10
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Valverde P, Barranco D, López-Escudero FJ, Díez CM, Trapero C. Efficiency of breeding olives for resistance to Verticillium wilt. Front Plant Sci 2023; 14:1149570. [PMID: 36909426 PMCID: PMC9994353 DOI: 10.3389/fpls.2023.1149570] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Olive trees are the most cultivated evergreen trees in the Mediterranean Basin, where they have deep historical and socioeconomic roots. The fungus Verticillium dahliae develops inside the vascular bundles of the host, and there are no effective applicable treatments, making it difficult to control the disease. In this sense, the use of integrated disease management, specifically the use of resistant cultivars, is the most effective means to alleviate the serious damage that these diseases are causing and reduce the expansion of this pathogen. In 2008, the University of Cordoba started a project under the UCO Olive Breeding Program whose main objective has been to develop new olive cultivars with high resistance to Verticillium wilt. Since 2008, more than 18,000 genotypes from 154 progenies have been evaluated. Only 19.9% have shown some resistance to the disease in controlled conditions and only 28 have been preselected due to their resistance in field condition and remarkable agronomic characteristics. The results of this study represent an important advancement in the generation of resistant olive genotypes that will become commercial cultivars currently demanded by the olive growing sector. Our breeding program has proven successful, allowing the selection of several new genotypes with high resistance to the disease and agronomical performance. It also highlights the need for long-term field evaluations for the evaluation of resistance and characterization of olive genotypes.
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11
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Shterzer N, Sbehat Y, Poudel B, Rothschild N, Oloko OE, Headrick J, Petersen E, Druyan S, Mills E. Differences in gut bacterial community composition between modern and slower-growing broiler breeder lines: Implications of growth selection on microbiome composition. Front Physiol 2023; 14:1151151. [PMID: 37025381 PMCID: PMC10070808 DOI: 10.3389/fphys.2023.1151151] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
In the last century broiler chicken lines have undergone an extensive breeding regime aimed primarily at growth and high meat yield. It is not known if breeding has also resulted in a change to the broiler breeder's associated gut microbiota. Here we compared the gut microbiota of 37-week-old commercial Cobb breeding dams with dams from a broiler Legacy line which has not undergone selection since 1986. The dams from both lines were kept together in the same shed under the same management protocol from day of hatch to avoid additional confounders. We chose this age to allow significant bacterial exchange, thus avoiding exposure dependent artifacts and so that we could compare dams at the same developmental state of adulthood and peak laying performance. Significant differences in the composition of the cecum bacterial communities were found. Bacteria of the genus Akkermansia, implicated in mucin degradation and associated with host metabolic health, accounted for 4.98% ± 5.04% of the Cobb cecum community, but were mostly absent from the ceca of the Legacy line dams. Inversely, Legacy dams had higher levels of Clostridiales, Lactobacillales and Aeromonadales. These results show that breeding has resulted in a change in the gut microbiota composition, likely by changing the physiological conditions in the mucosa. It remains unclear if changes in gut microbiota composition are a part of the mechanism affecting growth or are a secondary result of other physiological changes accelerating growth. Therefore, the identification of these changes opens the door to further targeted research.
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Affiliation(s)
- Naama Shterzer
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yara Sbehat
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Binita Poudel
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nir Rothschild
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Olanrewaju Eunice Oloko
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Agricultural Research Organization, Volcani Center, Department of Poultry and Aquaculture Science, Rishon LeTsiyon, Israel
| | - Joseph Headrick
- Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, TN, United States
| | - Erik Petersen
- Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, TN, United States
| | - Shelly Druyan
- Agricultural Research Organization, Volcani Center, Department of Poultry and Aquaculture Science, Rishon LeTsiyon, Israel
| | - Erez Mills
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Erez Mills,
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Qadri QR, Zhao Q, Lai X, Zhang Z, Zhao W, Pan Y, Wang Q. Estimation of Complex-Trait Prediction Accuracy from the Different Holo-Omics Interaction Models. Genes (Basel) 2022; 13:genes13091580. [PMID: 36140748 PMCID: PMC9498715 DOI: 10.3390/genes13091580] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
Statistical models play a significant role in designing competent breeding programs related to complex traits. Recently; the holo-omics framework has been productively utilized in trait prediction; but it contains many complexities. Therefore; it is desirable to establish prediction accuracy while combining the host’s genome and microbiome data. Several methods can be used to combine the two data in the model and study their effectiveness by estimating the prediction accuracy. We validate our holo-omics interaction models with analysis from two publicly available datasets and compare them with genomic and microbiome prediction models. We illustrate that the holo-omics interactive models achieved the highest prediction accuracy in ten out of eleven traits. In particular; the holo-omics interaction matrix estimated using the Hadamard product displayed the highest accuracy in nine out of eleven traits, with the direct holo-omics model and microbiome model showing the highest prediction accuracy in the remaining two traits. We conclude that comparing prediction accuracy in different traits using real data showed important intuitions into the holo-omics architecture of complex traits.
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Affiliation(s)
- Qamar Raza Qadri
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingbo Zhao
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xueshuang Lai
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenyang Zhang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou 310030, China
| | - Wei Zhao
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou 310030, China
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou 310030, China
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
- Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research, Hangzhou 310030, China
- Correspondence:
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13
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Bilodeau L. Genetic Diversity and Structure in a Closed Breeding System of Russian Honey Bees. J Econ Entomol 2022; 115:682-687. [PMID: 35078218 DOI: 10.1093/jee/toab266] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 06/14/2023]
Abstract
High levels of genetic diversity are critical to the success of breeding programs. Russian honey bees are a selected stock that undergoes breeding in a closed block-based mating system. Given its established history, Russian stock has longitudinal measures of genetic integrity (i.e., genetically based stock identity) and diversity. Assessments using genetic stock identification (GSI) have shown that genetic diversity parameters were assessed across breeding blocks for three generations, spanning 6 yr (2014, 2017, and 2020), showing levels comparable to those when the stock was initially released in 2008. Allelic richness (mean number of alleles) and gene diversity levels were consistent over time and among blocks. Blocks were generally not differentiated from one another within each year. However, the 2020 population was distinct when compared with bees sampled in both 2014 and 2017. Genetic distance relationships supported differentiation of the 2020 population by distinct clustering. The patterns observed here are consistent with historical changes made to the breeding program to increase stringency of the selection criteria.
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Affiliation(s)
- Lelania Bilodeau
- USDA-ARS Honey Bee Breeding, Genetics, and Physiology Laboratory, Baton Rouge, LA, USA
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Martínez JF, Galina CS, Ortiz P, Corro MD, Rubio I, Romero-Zuñiga JJ. Backfat Thickness Does Affect the Restoration of Ovarian Activity Postpartum in Different Breeding Programs in Zebu Cattle. Front Vet Sci 2021; 8:794632. [PMID: 34957287 PMCID: PMC8695602 DOI: 10.3389/fvets.2021.794632] [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: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
The backfat thickness (BFT) was used to forecast the onset of ovarian activity and predict the calf growth. Eighty Brahman cows with their calves were allocated in two groups of 40 distributed in 4 months according to the month of calving, starting in March and finishing in June. One was synchronized and inseminated at fixed time following by natural mating (TAI+NM); whilst the other only by natural mating (NM). The programs started at 60 ± 5 days postpartum and ended 60 days later. From day 30 postpartum, serial ultrasound examinations and progesterone samples were used to monitor the onset of ovarian activity. The BFT in the rump area was measured by ultrasound from 30 days postpartum and every 15 days thereafter. The weight of the calves was recorded at birth and at weaning on 160 days. The adjusted effect of BFT on ovarian activity and the calves' development was assessed by binomial logistic regression at 30, 60, 75, and 120 days postpartum. The cycling cows averaged higher BFT irrespective of breeding program (P < 0.001). Also, slower changes in BFT were recorded during the follow-up at each time for all cows. However, the former had the higher BFT values from calving to the end of the study (P < 0.001). At 60, 75, and 120 days, the BFT measured, at the preceding time, was the only factor predicting the commencement of cyclicity (P < 0.001). The accumulative pregnancy through time was higher in TAI+NM (P = 0.003). Daily weight gain and weaning weight of the calves born in March was significantly heavier (P < 0.001) than peers born in April, May, or June. The most critical element to forecast the onset of ovarian activity is the monitoring of BFT around calving regardless of the breeding program. BFT to estimate the development of the calves until weaning was unpredictable.
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Affiliation(s)
- José F Martínez
- Faculty of Veterinary Medicine and Zootechnics, Department of Reproduction, National Autonomous University of Mexico, Mexico City, Mexico
| | - Carlos S Galina
- Faculty of Veterinary Medicine and Zootechnics, Department of Reproduction, National Autonomous University of Mexico, Mexico City, Mexico
| | - Pablo Ortiz
- Faculty of Veterinary Medicine and Zootechnics, Department of Reproduction, National Autonomous University of Mexico, Mexico City, Mexico
| | - Manuel D Corro
- Centre for Teaching, Research and Extension in Tropical Animal Husbandry, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Tlapacoyan, Mexico
| | - Ivette Rubio
- Centre for Teaching, Research and Extension in Tropical Animal Husbandry, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Tlapacoyan, Mexico
| | - Juan J Romero-Zuñiga
- Research Program in Population Medicine, Veterinary Medicine School, National University, Heredia, Costa Rica
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Slagboom M, Sørensen AC, Thomasen JR, Liu H, Kargo M, Hjortø L. Ignoring genotype by environment interaction in the genetic evaluation of dairy cattle reduces accuracy but may increase selection intensity. J Dairy Sci 2021; 104:12756-12764. [PMID: 34600706 DOI: 10.3168/jds.2021-20876] [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: 06/15/2021] [Accepted: 07/27/2021] [Indexed: 11/19/2022]
Abstract
Genotype by environment interaction (G×E) may exist for traits that are expressed in different environments. The G×E is often ignored in the genetic evaluation of selection candidates. We hypothesized that genetic gain in 2 environments is always higher when the true value of the genetic correlation (rg) between traits expressed in different environments is considered in the genetic evaluation. We tested this hypothesis by stochastic simulation of dairy cattle breeding programs in a mainstream and a niche environment. The rg was varied from 0 to 1 in steps of 0.1. We simulated the following 3 scenarios: 1Trait_1Index, 2Traits_1Index, and 2Traits_2Indices. The G×E was ignored in the genetic evaluation in the scenario with 1Trait and included in scenarios with 2Traits. Selection was based on the mainstream selection index in both environments in scenarios with 1Index. Selection in the mainstream environment was based on the mainstream selection index and selection in the niche environment was based on the niche selection index in the scenario with 2Indices. With moderate G×E (rg between 0.6 and 0.9), the highest genetic gain was achieved in the niche environment by selecting for the mainstream selection index and ignoring G×E. At lower rg, the highest genetic gain was achieved when considering G×E and selecting for the niche selection index. For the mainstream environment, it was never an advantage to ignore G×E. Therefore, although our hypothesis was confirmed in most cases, there were cases where ignoring G×E was the better option, and using the correct evaluation led to inferior genetic gain. The results of the current study can be used in animal breeding programs that encompass multiple environments.
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Affiliation(s)
- Margot Slagboom
- Centre for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé, 8830 Tjele, Denmark.
| | | | | | - Huiming Liu
- Centre for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé, 8830 Tjele, Denmark
| | - Morten Kargo
- Centre for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé, 8830 Tjele, Denmark
| | - Line Hjortø
- SEGES, Agro Food Park 15, 8200 Aarhus N, Denmark
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Fugeray-Scarbel A, Bastien C, Dupont-Nivet M, Lemarié S. Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience. Front Genet 2021; 12:629737. [PMID: 34305998 PMCID: PMC8301370 DOI: 10.3389/fgene.2021.629737] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.
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Affiliation(s)
| | | | | | | | - Stéphane Lemarié
- Université Grenoble Alpes, INRAE, CNRS, Grenoble INP, GAEL, Grenoble, France
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17
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Wurzinger M, Gutiérrez GA, Sölkner J, Probst L. Community-Based Livestock Breeding: Coordinated Action or Relational Process? Front Vet Sci 2021; 8:613505. [PMID: 34109229 PMCID: PMC8180570 DOI: 10.3389/fvets.2021.613505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/02/2020] [Accepted: 04/09/2021] [Indexed: 11/22/2022] Open
Abstract
Over the past decade, community-based breeding programs (CBBPs) have been promoted as a viable approach to improving smallholder livelihoods through a systematic livestock breeding. CBBPs aim to initiate systematic breeding at the community level, including an organized animal identification and recording of performance and pedigree data. To ensure the breeding programs' continuity, building capacities, and ownership among participants are essential to the approach. This study's purpose was to understand how CBBPs have evolved in specific institutional settings and which dynamics occur in the course of implementation. We addressed these questions in reflective conversations with six coordinators of a diverse sample of CBBPs: goats (Malawi, Uganda, and Mexico), sheep (Ethiopia), alpaca (Peru), and cattle (Burkina Faso). The interviews and analysis were guided by categories of the multi-level perspective. The respondents considered lack of funding and weak institutionalization as the main constraints on the CBBPs. While the idea of participation and localized ownership was at the center of the programs, linear paradigms of knowledge transfer prevailed. In all cases, the impulse to start a CBBP came from individual researchers, who relied on intermediaries, such as extension agents, for implementation. Personal relations and trust were seen as both a factor in the success and a positive outcome of CBBPs. We conclude that these findings have different implications depending on how rural development is conceptualized: proponents of the innovation systems perspective would call for stakeholders to further align their interests and coordinate their actions. Proponents of process-relational concepts, in contrast, would not consider the CBBP a product but a starting-point for initiators and participants to continuously discover new ways of collaboration and engagement.
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Affiliation(s)
- Maria Wurzinger
- Faculty of Animal Sciences, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Gustavo A Gutiérrez
- Faculty of Animal Sciences, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lorenz Probst
- Department of Sustainable Agricultural Systems, Institute for Development Research, University of Natural Resources and Life Sciences, Vienna, Austria
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Maucourt S, Fortin F, Robert C, Giovenazzo P. Genetic Parameters of Honey Bee Colonies Traits in a Canadian Selection Program. Insects 2020; 11:insects11090587. [PMID: 32882855 PMCID: PMC7564374 DOI: 10.3390/insects11090587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 11/16/2022]
Abstract
Genetic selection has led to spectacular advances in animal production in many domestic species. However, it is still little applied to honey bees (Apis mellifera), whose complex genetic and reproductive characteristics are a challenge to model statistically. Advances in informatics now enable creation of a statistical model consistent with honey bee genetics, and, consequently, genetic selection for this species. The aim of this project was to determine the genetic parameters of several traits important for Canadian beekeepers with a view to establishing a breeding program in a northern context. Our results show that the five traits measured (Varroa destructor infestation, spring development, honey production, winter consumption, and hygienic behavior) are heritable. Thus, the rate of V. destructor infestation has a high heritability (h2 = 0.44 ± 0.56), spring development and honey production have a medium heritability (respectively, h2 = 0.30 ± 0.14 and h2 = 0.20 ± 0.13), and winter consumption and hygienic behavior have a low heritability (respectively, h2 = 0.11 ± 0.09 and h2 = 0.18 ± 0.13). Furthermore, the genetic correlations between these traits are all positive or null, except between hygienic behavior and V. destructor infestation level. These genetic parameters will be instrumental to the development of a selection index that will be used to improve the capacity of honey bees to thrive in northern conditions.
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Affiliation(s)
- Ségolène Maucourt
- Department of Biology, Vachon Pavillon, Université Laval, Québec, QC G1V 0A6, Canada;
- Correspondence:
| | - Frédéric Fortin
- Centre de Développement du porc du Québec, 450-2590 Boulevard Laurier, Québec, QC G1V 4M6, Canada;
| | - Claude Robert
- Department of Animal Science, Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Pierre Giovenazzo
- Department of Biology, Vachon Pavillon, Université Laval, Québec, QC G1V 0A6, Canada;
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Hazzouri KM, Flowers JM, Nelson D, Lemansour A, Masmoudi K, Amiri KMA. Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era. Front Plant Sci 2020; 11:293. [PMID: 32256513 PMCID: PMC7090123 DOI: 10.3389/fpls.2020.00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 05/05/2023]
Abstract
Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.
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Affiliation(s)
- Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University, New York, NY, United States
| | - David Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Khaled Masmoudi
- College of Food and Agriculture, Department of Integrative Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- College of Science, Department of Biology, United Arab Emirates University, Al Ain, United Arab Emirates
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de Castro AI, Rallo P, Suárez MP, Torres-Sánchez J, Casanova L, Jiménez-Brenes FM, Morales-Sillero A, Jiménez MR, López-Granados F. High-Throughput System for the Early Quantification of Major Architectural Traits in Olive Breeding Trials Using UAV Images and OBIA Techniques. Front Plant Sci 2019; 10:1472. [PMID: 31803210 PMCID: PMC6876562 DOI: 10.3389/fpls.2019.01472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 10/22/2019] [Indexed: 05/28/2023]
Abstract
The need for the olive farm modernization have encouraged the research of more efficient crop management strategies through cross-breeding programs to release new olive cultivars more suitable for mechanization and use in intensive orchards, with high quality production and resistance to biotic and abiotic stresses. The advancement of breeding programs are hampered by the lack of efficient phenotyping methods to quickly and accurately acquire crop traits such as morphological attributes (tree vigor and vegetative growth habits), which are key to identify desirable genotypes as early as possible. In this context, an UAV-based high-throughput system for olive breeding program applications was developed to extract tree traits in large-scale phenotyping studies under field conditions. The system consisted of UAV-flight configurations, in terms of flight altitude and image overlaps, and a novel, automatic, and accurate object-based image analysis (OBIA) algorithm based on point clouds, which was evaluated in two experimental trials in the framework of a table olive breeding program, with the aim to determine the earliest date for suitable quantifying of tree architectural traits. Two training systems (intensive and hedgerow) were evaluated at two very early stages of tree growth: 15 and 27 months after planting. Digital Terrain Models (DTMs) were automatically and accurately generated by the algorithm as well as every olive tree identified, independently of the training system and tree age. The architectural traits, specially tree height and crown area, were estimated with high accuracy in the second flight campaign, i.e. 27 months after planting. Differences in the quality of 3D crown reconstruction were found for the growth patterns derived from each training system. These key phenotyping traits could be used in several olive breeding programs, as well as to address some agronomical goals. In addition, this system is cost and time optimized, so that requested architectural traits could be provided in the same day as UAV flights. This high-throughput system may solve the actual bottleneck of plant phenotyping of "linking genotype and phenotype," considered a major challenge for crop research in the 21st century, and bring forward the crucial time of decision making for breeders.
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Affiliation(s)
- Ana I. de Castro
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
| | - Pilar Rallo
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | - María Paz Suárez
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | - Jorge Torres-Sánchez
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
| | - Laura Casanova
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | - Francisco M. Jiménez-Brenes
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
| | - Ana Morales-Sillero
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | - María Rocío Jiménez
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, Spain
| | - Francisca López-Granados
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
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21
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Godinho RM, Bergsma R, Silva FF, Sevillano CA, Knol EF, Komen H, Guimarães SEF, Lopes MS, Bastiaansen JWM. Genetic correlations between growth performance and carcass traits of purebred and crossbred pigs raised in tropical and temperate climates1. J Anim Sci 2019; 97:3648-3657. [PMID: 31278865 PMCID: PMC6735805 DOI: 10.1093/jas/skz229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/03/2019] [Indexed: 11/14/2022] Open
Abstract
In pig breeding, selection commonly takes place in purebred (PB) pigs raised mainly in temperate climates (TEMP) under optimal environmental conditions in nucleus farms. However, pork production typically makes use of crossbred (CB) animals raised in nonstandardized commercial farms, which are located not only in TEMP regions but also in tropical and subtropical regions (TROP). Besides the differences in the genetic background of PB and CB, differences in climate conditions, and differences between nucleus and commercial farms can lower the genetic correlation between the performance of PB in the TEMP (PBTEMP) and CB in the TROP (CBTROP). Genetic correlations (rg) between the performance of PB and CB growing-finishing pigs in TROP and TEMP environments have not been reported yet, due to the scarcity of data in both CB and TROP. Therefore, the present study aimed 1) to verify the presence of genotype × environment interaction (G × E) and 2) to estimate the rg for carcass and growth performance traits when PB and 3-way CB pigs are raised in 2 different climatic environments (TROP and TEMP). Phenotypic records of 217,332 PB and 195,978 CB, representing 2 climatic environments: TROP (Brazil) and TEMP (Canada, France, and the Netherlands) were available for this study. The PB population consisted of 2 sire lines, and the CB population consisted of terminal 3-way cross progeny generated by crossing sires from one of the PB sire lines with commercially available 2-way maternal sow crosses. G × E appears to be present for average daily gain, protein deposition, and muscle depth given the rg estimates between PB in both environments (0.64 to 0.79). With the presence of G × E, phenotypes should be collected in TROP when the objective is to improve the performance of CB in the TROP. Also, based on the rg estimates between PBTEMP and CBTROP (0.22 to 0.25), and on the expected responses to selection, selecting based only on the performance of PBTEMP would give limited genetic progress in the CBTROP. The rg estimates between PBTROP and CBTROP are high (0.80 to 0.99), suggesting that combined crossbred-purebred selection schemes would probably not be necessary to increase genetic progress in CBTROP. However, the calculated responses to selection show that when the objective is the improvement of CBTROP, direct selection based on the performance of CBTROP has the potential to lead to the higher genetic progress compared with indirect selection on the performance of PBTROP.
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Affiliation(s)
- Rodrigo M Godinho
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, The Netherlands
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Rob Bergsma
- Topigs Norsvin Research Center, Beuningen, The Netherlands
| | - Fabyano F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Claudia A Sevillano
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, The Netherlands
- Topigs Norsvin Research Center, Beuningen, The Netherlands
| | - Egbert F Knol
- Topigs Norsvin Research Center, Beuningen, The Netherlands
| | - Hans Komen
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, The Netherlands
| | | | - Marcos S Lopes
- Topigs Norsvin Research Center, Beuningen, The Netherlands
- Topigs Norsvin, Curitiba, Paraná, Brazil
| | - John W M Bastiaansen
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, The Netherlands
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Schodl K, Revermann R, Winckler C, Fuerst-Waltl B, Leeb C, Willam A, Knapp P, Pfeiffer C. Assessment of Piglet Vitality by Farmers-Validation of A Scoring Scheme and Estimation of Associated Genetic Parameters. Animals (Basel) 2019; 9:ani9060317. [PMID: 31167450 PMCID: PMC6616928 DOI: 10.3390/ani9060317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/24/2019] [Accepted: 06/01/2019] [Indexed: 11/24/2022] Open
Abstract
Simple Summary The aim of animal breeding is to improve desirable traits in animals over generations by selecting those animals with the best performance for producing offspring. Sows have been bred for bearing and raising large litters. However, piglets in large litters are often underweight at birth and have a higher risk of dying before weaning. Therefore, breeding for large litters presents an animal welfare issue and focus should be put on new traits, such as piglet vitality. To select the best performing sows, breeders need a scheme to assess piglet vitality on a routine basis. In this study, 23 farmers used a four-point scoring scheme for piglet vitality (1 = low vitality to 4 = high vitality) to assess 3171 litters. To validate the new scoring scheme, i.e., to see if it assesses what it is supposed to assess, the vitality scores were compared to the piglet mortality rate of the respective litters. The results show that litters assessed with low vitality scores had the highest mortality rate and vice versa. Furthermore, genetic analysis showed that the trait is hereditary. Therefore, including piglet vitality into breeding programs may contribute to animal welfare improvement. Abstract Maternal breeds for sows have been bred for high prolificacy during recent decades. Although large litters may be beneficial for economic efficiency, pre-weaning mortality is increased. Thus, focus should instead be put on new traits such as piglet vitality (PV). Until now, no validated scoring scheme for piglet vitality exists, which is feasible to be applied for routine on-farm trait recording. The objective of this study was to validate a four-point vitality scoring scheme (1 = low vitality to 4 = high vitality) applied by farmers based on pre-weaning mortality and to estimate genetic parameters. A linear mixed model was fitted for piglet vitality for 3172 litters from Large White and Landrace sows on 23 farms and correlations were calculated for vitality score and piglet mortality. A subsample of 2900 records was used for genetic analysis. Pre-weaning mortality differed significantly between all vitality score categories except for 1 and 2, ranging between 7.98% (category 4) and 29.1% (category 1). PV was genetically negatively correlated to litter size (−0.68) and mortality rate (−0.65), whereas litter size was positively correlated with mortality rate (0.59). Including PV into breeding programs may, thus, improve animal welfare.
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Affiliation(s)
- Katharina Schodl
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Regine Revermann
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Christoph Winckler
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Birgit Fuerst-Waltl
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Christine Leeb
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Alfons Willam
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
| | - Peter Knapp
- Schweinezuchtverband & Besamung OOE, 4641 Waldstraße 4, Austria.
| | - Christina Pfeiffer
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences (BOKU), Vienna, Gregor-Mendel Strasse 33, 1180 Vienna, Austria.
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Marshall K, Gibson JP, Mwai O, Mwacharo JM, Haile A, Getachew T, Mrode R, Kemp SJ. Livestock Genomics for Developing Countries - African Examples in Practice. Front Genet 2019; 10:297. [PMID: 31105735 PMCID: PMC6491883 DOI: 10.3389/fgene.2019.00297] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/19/2019] [Indexed: 01/17/2023] Open
Abstract
African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small- and medium-scale systems transforming, to varying degrees, to become more profitable. In these systems the women and men livestock keepers are often seeking new livestock breeds or genotypes - typically those that increase household income through having enhanced productivity in comparison to traditional breeds while maintaining adaptedness. In recent years genomic approaches have started to be utilized in the identification and development of such breeds, and in this article we describe a number of examples to this end from sub-Saharan Africa. These comprise case studies on: (a) dairy cattle in Kenya and Senegal, as well as sheep in Ethiopia, where genomic approaches aided the identification of the most appropriate breed-type for the local productions systems; (b) a cross-breeding program for dairy cattle in East Africa incorporating genomic selection as well as other applications of genomics; (c) ongoing work toward creating a new cattle breed for East Africa that is both productive and resistant to trypanosomiasis; and (d) the use of African cattle as resource populations to identify genomic variants of economic or ecological significance, including a specific case where the discovery data was from a community based breeding program for small ruminants in Ethiopia. Lessons learnt from the various case studies are highlighted, and the concluding section of the paper gives recommendations for African livestock systems to increasingly capitalize on genomic technologies.
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Affiliation(s)
- Karen Marshall
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - John P. Gibson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Okeyo Mwai
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Tesfaye Getachew
- Small Ruminant Breeding and Genomics Group, International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Raphael Mrode
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Scotland’s Rural College, Edinburgh, United Kingdom
| | - Stephen J. Kemp
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
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Abstract
Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to the state pertained before exposure to a disturbance. However, indicators for general resilience to environmental disturbances have not yet been defined, and perhaps therefore resilience is not yet included in breeding goals. The current developments on big data collection give opportunities to determine new resilience indicators based on longitudinal data, which can aid to incorporate resilience in animal breeding goals. The objectives of this paper were: (1) to define resilience indicator traits based on big data, (2) to define economic values for resilience, and (3) to show the potential to improve resilience of livestock through inclusion of resilience in breeding goals. Resilience might be measured based on deviations from expected production levels over a period of time. Suitable resilience indicators could be the variance of deviations, the autocorrelation of deviations, the skewness of deviations, and the slope of a reaction norm. These (new) resilience indicators provide opportunity to include resilience in breeding programs. Economic values of resilience indicators in the selection index can be calculated based on reduced costs due to labor and treatments. For example, when labor time is restricted, the economic value of resilience increases with an increasing number of animals per farm, and can become as large as the economic value of production. This shows the importance of including resilience in breeding goals. Two scenarios were described to show the additional benefit of including resilience in breeding programs. These examples showed that it is hard to improve resilience with only production traits in the selection index, but that it is possible to greatly improve resilience by including resilience indicators in the selection index. However, when health-related traits are already present in the selection index, the effect is smaller. Nevertheless, inclusion of resilience indicators in the selection index increases the response in the breeding goal and resilience, which results in less labor-demanding, and thus easier-to-manage livestock. Current developments on massive collection of data, and new phenotypes based on these data, offer exciting opportunities to breed for improved resilience of livestock.
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Affiliation(s)
- Tom V. L. Berghof
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Netherlands
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25
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Powell DM, Dorsey CL, Faust LJ. Advancing the science behind animal program sustainability: An overview of the special issue. Zoo Biol 2019; 38:5-11. [PMID: 30629303 DOI: 10.1002/zoo.21474] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 07/16/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 11/05/2022]
Abstract
Over the last ten years, zoos and aquariums around the world have been coming to grips with the "sustainability crisis" - the realization that most of our collaboratively managed animal populations are not viable for the long-term. Many initiatives have been launched at the regional, zoological association, program, and institutional levels to improve the long-term trajectories of these populations. This Special Issue of Zoo Biology highlights some of the scientific approaches that are aimed at addressing population viability and sustainability challenges. The approaches range from development of new analytical tools, to analysis of large datasets, and re-examination of population management principles and philosophies. While much progress has been made in the last ten years, it is clear that continued work on population viability and sustainability is critical and difficult management decisions must be made. In this paper, we identify some of the actions that the zoological community can take to fortify our animal programs and prevent the outright extinction of species.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri
| | - Candice L Dorsey
- Conservation, Management & Welfare Sciences, Association of Zoos & Aquariums, Silver Spring, Maryland
| | - Lisa J Faust
- Alexander Center for Applied Population Biology, Lincoln Park Zoo, Chicago, Illinois
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Ostos-Garrido FJ, de Castro AI, Torres-Sánchez J, Pistón F, Peña JM. High-Throughput Phenotyping of Bioethanol Potential in Cereals Using UAV-Based Multi-Spectral Imagery. Front Plant Sci 2019; 10:948. [PMID: 31396251 PMCID: PMC6664021 DOI: 10.3389/fpls.2019.00948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 07/08/2019] [Indexed: 05/09/2023]
Abstract
Bioethanol production obtained from cereal straw has aroused great interest in recent years, which has led to the development of breeding programs to improve the quality of lignocellulosic material in terms of the biomass and sugar content. This process requires the analysis of genotype-phenotype relationships, and although genotyping tools are very advanced, phenotypic tools are not usually capable of satisfying the massive evaluation that is required to identify potential characters for bioethanol production in field trials. However, unmanned aerial vehicle (UAV) platforms have demonstrated their capacity for efficient and non-destructive acquisition of crop data with an application in high-throughput phenotyping. This work shows the first evaluation of UAV-based multi-spectral images for estimating bioethanol-related variables (total biomass dry weight, sugar release, and theoretical ethanol yield) of several accessions of wheat, barley, and triticale (234 cereal plots). The full procedure involved several stages: (1) the acquisition of multi-temporal UAV images by a six-band camera along different crop phenology stages (94, 104, 119, 130, 143, 161, and 175 days after sowing), (2) the generation of ortho-mosaicked images of the full field experiment, (3) the image analysis with an object-based (OBIA) algorithm and the calculation of vegetation indices (VIs), (4) the statistical analysis of spectral data and bioethanol-related variables to predict a UAV-based ranking of cereal accessions in terms of theoretical ethanol yield. The UAV-based system captured the high variability observed in the field trials over time. Three VIs created with visible wavebands and four VIs that incorporated the near-infrared (NIR) waveband were studied, obtaining that the NIR-based VIs were the best at estimating the crop biomass, while the visible-based VIs were suitable for estimating crop sugar release. The temporal factor was very helpful in achieving better estimations. The results that were obtained from single dates [i.e., temporal scenario 1 (TS-1)] were always less accurate for estimating the sugar release than those obtained in TS-2 (i.e., averaging the values of each VI obtained during plant anthesis) and less accurate for estimating the crop biomass and theoretical ethanol yield than those obtained in TS-3 (i.e., averaging the values of each VI obtained during full crop development). The highest correlation to theoretical ethanol yield was obtained with the normalized difference vegetation index (R 2 = 0.66), which allowed to rank the cereal accessions in terms of potential for bioethanol production.
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Affiliation(s)
| | - Ana I. de Castro
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Jorge Torres-Sánchez
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Fernando Pistón
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - José M. Peña
- Institute of Agricultural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
- *Correspondence: José M. Peña,
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Godinho RM, Bastiaansen JWM, Sevillano CA, Silva FF, Guimarães SEF, Bergsma R. Genotype by feed interaction for feed efficiency and growth performance traits in pigs. J Anim Sci 2018; 96:4125-4135. [PMID: 30272227 PMCID: PMC6162583 DOI: 10.1093/jas/sky304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
A major objective of pork producers is to reduce production cost. Feeding may account for over 75% of pork production costs. Thus, selecting pigs for feed efficiency (FE) traits is a priority in pig breeding programs. While in the Americas, pigs are typically fed high-input diets, based on corn and soybean meal (CS); in Western Europe, pigs are commonly fed diets based on wheat and barley with high amounts of added protein-rich coproducts (WB), e.g., from milling and seed-oil industries. These two feeding scenarios provided a realistic setting for investigating a specific type of genotype by environment interaction; thus, we investigated the genotype by feed interaction (GxF). In the presence of a GxF, different feed compositions should be considered when selecting for FE. This study aimed to 1) verify the presence of a GxF for FE and growth performance traits in different growth phases (starter, grower, and finisher) of 3-way crossbred growing-finishing pigs fed either a CS (547 boars and 558 gilts) or WB (567 boars and 558 gilts) diet; and 2) to assess and compare the expected responses to direct selection under the 2 diets and the expected correlated responses for one diet to indirect selection under the other diet. We found that GxF did not interfere in the ranking of genotypes under both diets for growth, protein deposition, feed intake, energy intake, or feed conversion rate. Therefore, for these traits, we recommend changing the diet of growing-finishing pigs from high-input feed (i.e., CS) to feed with less valuable ingredients, as WB, to reduce production costs and the environmental impact, regardless of which diet is used in selection. We found that GxF interfered in the ranking of genotypes and caused heterogeneity of genetic variance under both diets for lipid deposition (LD), residual energy intake (REI), and residual feed intake (RFI). Thus, selecting pigs under a diet different from the diet used for growing-finishing performance could compromise the LD in all growth phases, compromise the REI and RFI during the starter phase, and severely compromise the REI during the grower phase. In particular, when pigs are required to consume a WB diet for growing-finishing performance, pigs should be selected for FE under the same diet. Breeding pigs for FE under lower-input diets should be considered, because FE traits will become more important and lower-input diets will become more widespread in the near future.
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Affiliation(s)
- R M Godinho
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Gelderland, the Netherlands
| | - J W M Bastiaansen
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Gelderland, the Netherlands
| | - C A Sevillano
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Gelderland, the Netherlands
- Topigs Norsvin Research Center, Beuningen, Gelderland, the Netherlands
| | - F F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - S E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R Bergsma
- Topigs Norsvin Research Center, Beuningen, Gelderland, the Netherlands
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28
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Godinho RM, Bergsma R, Silva FF, Sevillano CA, Knol EF, Lopes MS, Lopes PS, Bastiaansen JWM, Guimarães SEF. Genetic correlations between feed efficiency traits, and growth performance and carcass traits in purebred and crossbred pigs. J Anim Sci 2018; 96:817-829. [PMID: 29378008 PMCID: PMC6093586 DOI: 10.1093/jas/skx011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/23/2017] [Indexed: 11/14/2022] Open
Abstract
Selection for feed efficiency (FE) is a strategy to reduce the production costs per unit of animal product, which is one of the major objectives of current animal breeding programs. In pig breeding, selection for FE and other traits traditionally takes place based on purebred pig (PB) performance at the nucleus level, while pork production typically makes use of crossbred animals (CB). The success of this selection, therefore, depends on the genetic correlation between the performance of PB and CB (rpc) and on the genetic correlation (rg) between FE and the other traits that are currently under selection. Different traits are being used to account for FE, but the rpc has been reported only for feed conversion rate. Therefore, this study aimed 1) to estimate the rpc for growth performance, carcass, and FE traits; 2) to estimate rg between traits within PB and CB populations; and 3) to compare three different traits representing FE: feed conversion rate, residual energy intake (REI), and residual feed intake (RFI). Phenotypes of 194,445 PB animals from 23 nucleus farms, and 46,328 CB animals from three farms where research is conducted under near commercial production conditions were available for this study. From these, 22,984 PB and 8,657 CB presented records for feed intake. The PB population consisted of five sire and four dam lines, and the CB population consisted of terminal cross-progeny generated by crossing sires from one of the five PB sire lines with commercially available two-way maternal sow crosses. Estimates of rpc ranged from 0.61 to 0.71 for growth performance traits, from 0.75 to 0.82 for carcass traits, and from 0.62 to 0.67 for FE traits. Estimates of rg between growth performance, carcass, and FE traits differed within PB and CB. REI and RFI showed substantial positive rg estimates in PB (0.84) and CB (0.90) populations. The magnitudes of rpc estimates indicate that genetic progress is being realized in CB at the production level from selection on PB performance at nucleus level. However, including CB phenotypes recorded on production farms, when predicting breeding values, has the potential to increase genetic progress for these traits in CB. Given the genetic correlations with growth performance traits and the genetic correlation between the performance of PB and CB, REI is an attractive FE parameter for a breeding program.
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Affiliation(s)
- R M Godinho
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, the Netherlands
| | - R Bergsma
- Topigs Norsvin Research Center, Beuningen, the Netherlands
| | - F F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - C A Sevillano
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, the Netherlands
- Topigs Norsvin Research Center, Beuningen, the Netherlands
| | - E F Knol
- Topigs Norsvin Research Center, Beuningen, the Netherlands
| | - M S Lopes
- Topigs Norsvin Research Center, Beuningen, the Netherlands
- Topigs Norsvin, Curitiba, Brazil
| | - P S Lopes
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - J W M Bastiaansen
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, the Netherlands
| | - S E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
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Liu H, Tessema BB, Jensen J, Cericola F, Andersen JR, Sørensen AC. ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs. Front Plant Sci 2018; 9:1926. [PMID: 30687343 PMCID: PMC6333911 DOI: 10.3389/fpls.2018.01926] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/11/2018] [Indexed: 05/11/2023]
Abstract
Making decisions on plant breeding programs require plant breeders to be able to test different breeding strategies by taking into account all the crucial factors affecting crop genetic improvement. Due to the complexity of the decisions, computer simulation serves as an important tool for researchers and plant breeders. This paper describes ADAM-plant, which is a computer software that models breeding schemes for self-pollinated and cross-pollinated crop plants using stochastic simulation. The program simulates a population of plants and traces the genetic changes in the population under different breeding scenarios. It takes into account different population structures, genomic models, selection (strategies and units) and crossing strategies. It also covers important features e.g., allowing users to perform genomic selection (GS) and speed breeding, simulate genotype-by-environment interactions using multiple trait approach, simulate parallel breeding cycles and consider plot sizes. In addition, the software can be used to simulate datasets produced from very complex breeding program in order to test new statistical methodology to analyze such data. As an example, three wheat-breeding strategies were simulated in the current study: (1) phenotypic selection, (2) GS, and (3) speed breeding with genomic information. The results indicate that the genetic gain can be doubled by GS compared to phenotypic selection and genetic gain can be further increased considerably by speed breeding. In conclusion, ADAM-plant is an important tool for comparing strategies for plant breeding and for estimating the effects of allocation of different resources to the breeding program. In the current study, it was used to compare different methodologies for utilizing genomic information in cereal breeding programs for selection of best-fit breeding strategy as per available resources.
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Affiliation(s)
- Huiming Liu
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- *Correspondence: Huiming Liu, Jeppe Reitan Andersen,
| | - Biructawit Bekele Tessema
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Anders Christian Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Eriksson S, Jonas E, Rydhmer L, Röcklinsberg H. Invited review: Breeding and ethical perspectives on genetically modified and genome edited cattle. J Dairy Sci 2017; 101:1-17. [PMID: 29102147 DOI: 10.3168/jds.2017-12962] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 03/31/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022]
Abstract
The hot topic of genetic modification and genome editing is sometimes presented as a rapid solution to various problems in the field of animal breeding and genetics. These technologies hold potential for future use in agriculture but we need to be aware of difficulties in large-scale application and integration in breeding schemes. In this review, we discuss applications of both classical genetic modifications (GM) using vectors and genome editing in dairy cattle breeding. We use an interdisciplinary approach considering both ethical and animal breeding perspectives. Decisions on how to make use of these techniques need to be made based not only on what is possible, but on what is reasonable to do. Principles of animal integrity, naturalness, risk perception, and animal welfare issues are examples of ethically relevant factors to consider. These factors also influence public perception and decisions about regulations by authorities. We need to acknowledge that we lack complete understanding of the genetic background of complex traits. It may be difficult, therefore, to predict the full effect of certain modifications in large-scale breeding programs. We present 2 potential applications: genome editing to dispense with dehorning, and insertion of human genes in bovine genomes to improve udder health as an example of classical GM. Both of these cases could be seen as beneficial for animal welfare but they differ in other aspects. In the former case, a genetic variant already present within the species is introduced, whereas in the latter case, transgenic animals are generated-this difference may influence how society regards the applications. We underline that the use of GM, as well as genome editing, of farm animals such as cattle is not independent of the context, and should be considered as part of an entire process, including, for example, the assisted reproduction technology that needs to be used. We propose that breeding organizations and breeding companies should take an active role in ethical discussions about the use of these techniques and thereby signal to society that these questions are being responsibly addressed.
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Affiliation(s)
- S Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
| | - E Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - L Rydhmer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - H Röcklinsberg
- Department of Animal Environment and Health, 75007 Uppsala, Sweden
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Abstract
Some mutations (or 'major genes') have a desirable effect in heterozygous carriers but an undesirable effect in homozygous carriers. When these mutations affect a trait of significant economic importance, their eradication, depending on their effect and frequency, may be counterproductive. This is especially the case of major genes affecting the ovulation rate and thus the prolificacy in meat sheep populations. To manage such situations, a mating design based on the major genotypes of reproducers has to be optimized. Both the effect of the major gene and the cost of genotyping candidates at this locus influence the expected genetic progress and profitability of the breeding plan. The aim of this study was to determine the optimal combination of matings that maximizes profitability at the level of the whole population (nucleus + commercial flocks). A deterministic model was developed and, using sequential quadratic programming methodology, the optimal strategy (optimal combination of matings) that maximized the economic gain achieved by the population across a range of genotype effects and genotyping costs was determined. The optimal strategy was compared with simpler and more practical strategies based on a limited number of parental genotype mating types. Depending on the genotype effect and genotyping costs, the optimal strategy varied, such that either the heterozygous frequency and/or polygenic gain was maximized with a large number of animals genotyped, or when genotyping costs were higher, the optimization led to lower heterozygous frequency and/or polygenic gain with fewer animals genotyped. Comparisons showed that some simpler strategies were close to the optimal strategy. An overlapping model was then derived as an application of the real case of the French Lacaune meat sheep OVI-TEST breeding program. Results showed that a practical strategy based on mating non-carriers to heterozygous carriers was only slightly less effective than the optimal strategy, with a reduction in efficiency from 3% to 8%, depending on the genotyping costs. Based on only two different parental genotype mating types, this strategy would be easy to implement.
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Godbout J, Tremblay L, Levasseur C, Lavigne P, Rainville A, Mackay J, Bousquet J, Isabel N. Development of a Traceability System Based on a SNP Array for Large-Scale Production of High-Value White Spruce ( Picea glauca). Front Plant Sci 2017; 8:1264. [PMID: 28791035 PMCID: PMC5524734 DOI: 10.3389/fpls.2017.01264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Biological material is at the forefront of research programs, as well as application fields such as breeding, aquaculture, and reforestation. While sophisticated techniques are used to produce this material, all too often, there is no strict monitoring during the "production" process to ensure that the specific varieties are the expected ones. Confidence rather than evidence is often applied when the time comes to start a new experiment or to deploy selected varieties in the field. During the last decade, genomics research has led to the development of important resources, which have created opportunities for easily developing tools to assess the conformity of the material along the production chains. In this study, we present a simple methodology that enables the development of a traceability system which, is in fact a by-product of previous genomic projects. The plant production system in white spruce (Picea glauca) is used to illustrate our purpose. In Quebec, one of the favored strategies to produce elite varieties is to use somatic embryogenesis (SE). In order to detect human errors both upstream and downstream of the white spruce production process, this project had two main objectives: (i) to develop methods that make it possible to trace the origin of plants produced, and (ii) to generate a unique genetic fingerprint that could be used to differentiate each embryogenic cell line and ensure its genetic monitoring. Such a system had to rely on a minimum number of low-cost DNA markers and be easy to use by non-specialists. An efficient marker selection process was operationalized by testing different classification methods on simulated datasets. These datasets were generated using in-house bioinformatics tools that simulated crosses involved in the breeding program for which genotypes from hundreds of SNP markers were already available. The rate of misidentification was estimated and various sources of mishandling or contamination were identified. The method can easily be applied to other production systems for which genomic resources are already available.
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Affiliation(s)
- Julie Godbout
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, QC, Canada
| | - Laurence Tremblay
- Direction Générale de la Production de Semences et des Plants Forestiers, Ministère des Forêts, de la Faune et des Parcs du QuébecQuébec, QC, Canada
| | - Caroline Levasseur
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, QC, Canada
| | - Patricia Lavigne
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, QC, Canada
| | - André Rainville
- Direction de la Recherche Forestière (Forest Research Branch), Ministère des Forêts, de la Faune et des Parcs du QuébecQuébec, QC, Canada
| | - John Mackay
- Department of Plant Sciences, University of OxfordOxford, United Kingdom
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université LavalQuébec, QC, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, QC, Canada
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université LavalQuébec, QC, Canada
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Timm LL, Carter JE, Frey J, Prappas J, Wells RJD. Birth of common shovelnose rays (Glaucostegus typus) under captive conditions. Zoo Biol 2014; 33:357-9. [PMID: 25043106 DOI: 10.1002/zoo.21145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/24/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 11/06/2022]
Abstract
The common shovelnose ray (Glaucostegus typus) is a poorly studied species of the Rhinobatidae family that occurs throughout the Indo-West Pacific. Although common in aquariums throughout the United States, there are currently no records of captive birth events. In 2013, a female common shovelnose ray housed at the Downtown Aquarium in Houston, Texas, USA gave birth to eleven pups. Although all pups were stillborn, this event demonstrates that it is possible to breed common shovelnose rays in a controlled environment. The single female and two male common shovelnose rays at the aquarium are of sexually mature size (between 206 and 240 cm total length, TL), demonstrate mating behaviors, and provide an excellent opportunity to investigate the reproductive biology of this species. Captive environmental conditions of the birth enclosure may be useful in replicating the birthing event in order to develop a breeding program that could potentially relieve collection pressures on wild populations of guitarfish given their vulnerable status.
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Affiliation(s)
- Lori L Timm
- Downtown Aquarium Houston, Houston, Texas; Texas A&M University, Department of Marine Biology, Galveston, Texas
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