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Gutiérrez JP, Cruz A, Morante R, Burgos A, Formoso-Rafferty N, Cervantes I. Genetic parameters for fleece uniformity in alpacas. J Anim Sci 2023; 101:skad140. [PMID: 37144830 PMCID: PMC10195205 DOI: 10.1093/jas/skad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/03/2023] [Indexed: 05/06/2023] Open
Abstract
Fiber diameter is the main selection objective and criterion in alpaca breeding programs, but it can vary across anatomic regions of the animal. As fiber diameter is usually registered from a unique sample from the mid side of the body, fiber diameter variability within fleece is never addressed and phenotypic and genetic differences may exist for fleece uniformity in alpaca populations. The objective of this work was to estimate the genetic parameters of fleece uniformity in an alpaca population. Fiber diameters measured in three different locations were used as repeated records of the same animal and studied for fitting a model that considers heterogeneous the residual variance of the model. Also, the logarithm of the standard deviation of the three measures was used as a measure of the fleece variability. Estimate of the additive genetic variance of the environmental variability was 0.43±0.14, enough high to suggest the existence of wide room to select for fleece uniformity. Genetic correlation of the trait with its environmental variability was 0.76±0.13 showing that fleece uniformity will be indirectly selected when aiming to reduce the fiber diameter. In the light of these parameters, and due to the cost of registering and the cost of opportunity, it looks no worthy to include uniformity as a selection criterion in alpaca breeding programs.
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Affiliation(s)
- Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Alan Cruz
- Universidad Nacional Agraria La Molina, Avda. La Molina s/n, 15024 Lima, Peru
- Estación Científica Pacomarca, Inca Tops SA., Avda, Miguel Forga 348, 04007 Arequipa, Peru
| | - Renzo Morante
- Estación Científica Pacomarca, Inca Tops SA., Avda, Miguel Forga 348, 04007 Arequipa, Peru
| | - Alonso Burgos
- Estación Científica Pacomarca, Inca Tops SA., Avda, Miguel Forga 348, 04007 Arequipa, Peru
| | - Nora Formoso-Rafferty
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2, 28040 Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
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A milk-sharing economy allows placental mammals to overcome their metabolic limits. Proc Natl Acad Sci U S A 2022; 119:e2114674119. [PMID: 35238685 PMCID: PMC8915790 DOI: 10.1073/pnas.2114674119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we demonstrate that a naturally evolving behavior (allonursing) has greater effect on reproductive power (mass per unit of time) and output (litter mass at birth) than does artificial selection (domestication). Additionally, we demonstrate the importance of resource optimization afforded by sociality (rather than resource abundance per se) in shaping a species’ life history profile and its ability to overcome its own physiological constraints. Maternal resource availability and metabolism have a strong limiting effect on reproductive output. Allomaternal care and domestication increase the energy available to the mother and should correlate with an increase in reproductive output. Here, we take a comparative approach to understand how this increase is accomplished (e.g., litter mass, reproductive frequency, etc.) and the strength of the effect among different forms of external energetic supplementation. We find that domestication and all forms of allocare correlate with increased fertility. All forms of provisioning correlate with larger litters without compromising offspring size. The greatest increase we observe in reproductive power is in species that practice allonursing. Our results suggest that the ultimate factor limiting reproductive output in placental mammals is maternal metabolic power rather than resource availability.
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Cytogenetic Mapping of 35 New Markers in the Alpaca ( Vicugna pacos). Genes (Basel) 2020; 11:genes11050522. [PMID: 32397072 PMCID: PMC7288448 DOI: 10.3390/genes11050522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022] Open
Abstract
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (BMP4, COL1A2, GLI1, SFRP4), coat color (TYR) and development (CHD7, PAX7). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human–camelid conserved synteny data, except for mapping BMP4 to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly VicPac3.1 by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics.
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Cruz A, Menéndez-Buxadera A, Gutiérrez G, Morante R, Burgos A, Gutiérrez JP. Genetic (co)variance across age of fiber diameter and standard deviation in Huacaya alpacas, estimated by repeatability, multi-trait and random regression models. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Richardson MF, Munyard K, Croft LJ, Allnutt TR, Jackling F, Alshanbari F, Jevit M, Wright GA, Cransberg R, Tibary A, Perelman P, Appleton B, Raudsepp T. Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. Front Genet 2019; 10:586. [PMID: 31293619 PMCID: PMC6598621 DOI: 10.3389/fgene.2019.00586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.
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Affiliation(s)
- Mark F Richardson
- Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Kylie Munyard
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Larry J Croft
- Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Theodore R Allnutt
- Bioinformatics Core Research Group, Deakin University, Geelong, VIC, Australia
| | - Felicity Jackling
- Department of Genetics, The University of Melbourne, Melbourne, VIC, Australia
| | - Fahad Alshanbari
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Matthew Jevit
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Gus A Wright
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Rhys Cransberg
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Ahmed Tibary
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Polina Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Belinda Appleton
- Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia
| | - Terje Raudsepp
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
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Mendoza MN, Raudsepp T, Alshanbari F, Gutiérrez G, Ponce de León FA. Chromosomal Localization of Candidate Genes for Fiber Growth and Color in Alpaca ( Vicugna pacos). Front Genet 2019; 10:583. [PMID: 31275359 PMCID: PMC6593342 DOI: 10.3389/fgene.2019.00583] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/04/2019] [Indexed: 12/20/2022] Open
Abstract
The alpaca (Vicugna pacos) is an economically important and cultural signature species in Peru. Thus, molecular genomic information about the genes underlying the traits of interest, such as fiber properties and color, is critical for improved breeding and management schemes. Current knowledge about the alpaca genome, particularly the chromosomal location of such genes of interest is limited and lags far behind other livestock species. The main objective of this work was to localize alpaca candidate genes for fiber growth and color using fluorescence in situ hybridization (FISH). We report the mapping of candidate genes for fiber growth COL1A1, CTNNB1, DAB2IP, KRT15, KRTAP13-1, and TNFSF12 to chromosomes 16, 17, 4, 16, 1, and 16, respectively. Likewise, we report the mapping of candidate genes for fiber color ALX3, NCOA6, SOX9, ZIC1, and ZIC5 to chromosomes 9, 19, 16, 1, and 14, respectively. In addition, since KRT15 clusters with five other keratin genes (KRT31, KRT13, KRT9, KRT14, and KRT16) in scaffold 450 (Vic.Pac 2.0.2), the entire gene cluster was assigned to chromosome 16. Similarly, mapping NCOA6 to chromosome 19, anchored scaffold 34 with 8 genes, viz., RALY, EIF2S2, XPOTP1, ASIP, AHCY, ITCH, PIGU, and GGT7 to chromosome 19. These results are concordant with known conserved synteny blocks between camelids and humans, cattle and pigs.
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Affiliation(s)
- Mayra N. Mendoza
- Programa de Mejoramiento Animal, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Terje Raudsepp
- Molecular Cytogenetics and Genomics Laboratory, Texas A&M University, College Station, TX, United States
| | - Fahad Alshanbari
- Molecular Cytogenetics and Genomics Laboratory, Texas A&M University, College Station, TX, United States
| | - Gustavo Gutiérrez
- Programa de Mejoramiento Animal, Universidad Nacional Agraria La Molina, Lima, Peru
| | - F. Abel Ponce de León
- Department of Animal Science, University of Minnesota, Minneapolis, MN, United States
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Cruz A, Morante R, Gutiérrez JP, Torres R, Burgos A, Cervantes I. Genetic parameters for medullated fiber and its relationship with other productive traits in alpacas. Animal 2018; 13:1358-1364. [PMID: 30567623 DOI: 10.1017/s1751731118003282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The alpaca fiber diameter (FD) varies from 18 to 36 μm, being the finer fiber categories highly appreciated. However, the alpaca fiber presents some limitations in the textile industry due to the high incidence of fiber medullation and diameter variability, both reduces the comfort feeling of the garments. Decreasing or even removing medullation could be a possible selection objective in alpaca breeding programs for increasing economic value of the alpaca fiber. Therefore, the present work aimed to estimate genetic parameters regarding medullation traits, as well as the genetic correlations with other economical important traits, to be able to select the appropriate criteria to reduce or remove medullation on alpaca fiber and help to reduce the prickle factor in the garments. The data was collected from 2000 to 2017 and belonged to the Pacomarca experimental farm. There were 3698 medullation records corresponding to 1869 Huacaya and 414 Suri genetic types. The fiber samples were taken from the mid side, and were analyzed in an OFDA 100® device. The traits analyzed were percentage of medullation (PM), medullated fiber diameter (MFD), FD, standard deviation of FD, greasy fleece weight as fiber traits; density, crimp in Huacaya and lock structure in Suri, head conformation, leg coverage as morphological traits; weaning weight and age at first calving as secondary and functional traits. Genetic parameters were estimated via a multitrait restricted maximum likelihood. The heritabilities for PM and MFD were 0.225 and 0.237 in Huacaya genetic type and 0.664 and 0.237 in Suri genetic type, respectively; heritabilities for other traits were moderate for productive and morphological traits, and low to moderate for secondary and functional traits. The genetic correlations PM-FD and MFD-FD were high and favorable in both genetic types, between 0.531 and 0.975; the genetic correlation PM-MFD was 0.121 in Huacaya and 0.427 in Suri. The rest of genetic correlations with other traits were in general moderate and favorable. The repeatabilities were 0.556 and 0.668 for PM, and 0.322 and 0.293 for MFD in Huacaya and Suri genetic types, respectively. As a conclusion, PM was identified to be a good selection criterion, probably combined in an index with FD to reduce prickling factor.
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Affiliation(s)
- A Cruz
- 1Fundo Pacomarca - INCA TOPS S.A.,Avda. Miguel Forga 348,P.O. BOX 94,Arequipa,Peru
| | - R Morante
- 1Fundo Pacomarca - INCA TOPS S.A.,Avda. Miguel Forga 348,P.O. BOX 94,Arequipa,Peru
| | - J P Gutiérrez
- 2Departamento de Producción Animal,Universidad Complutense de Madrid,Avda. Puerta de Hierro s-n,E-28040 Madrid,Spain
| | - R Torres
- 1Fundo Pacomarca - INCA TOPS S.A.,Avda. Miguel Forga 348,P.O. BOX 94,Arequipa,Peru
| | - A Burgos
- 1Fundo Pacomarca - INCA TOPS S.A.,Avda. Miguel Forga 348,P.O. BOX 94,Arequipa,Peru
| | - I Cervantes
- 2Departamento de Producción Animal,Universidad Complutense de Madrid,Avda. Puerta de Hierro s-n,E-28040 Madrid,Spain
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Abreu LRA, Ribeiro VMP, Gouveia GC, Cardoso EP, Toral FLB. Genetic trends and trade-offs between growth and reproductive traits in a Nellore herd. PLoS One 2018; 13:e0201392. [PMID: 30114191 PMCID: PMC6095503 DOI: 10.1371/journal.pone.0201392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/13/2018] [Indexed: 11/19/2022] Open
Abstract
The knowledge of genetic trends and trade-offs between growth and reproductive traits might be useful to understand the evolution of these traits in livestock and natural populations of animals. We estimated the genetic trends and trade-offs between pre-weaning growth and calving intervals of Nellore animals from a commercial farm. Two-trait animal models were used to estimate covariance components and breeding values (EBV) for direct and maternal genetic effects of pre-weaning growth and direct genetic effects of calving intervals. Regression analyses were performed to examine the relationship between direct and maternal EBV of pre-weaning growth and direct EBV of calving intervals (dependent variables) and the coefficient of generation of each animal (independent variable). We also performed regression analyses to examine the relationship between direct EBV of calving intervals (dependent variables) and direct and maternal EBV of pre-weaning growth (independent variables). The genetic trends for direct and maternal genetic effect for pre-weaning growth were significant and presented genetic evolution in the studied Nellore herd. The genetic trends for the reproductive traits were also significant but indicated genetic changes in an unfavorable way. The genetic correlations between direct effects of pre-weaning growth and calving intervals traits and the genetic correlations between maternal effects of pre-weaning growth traits and direct effects of calving interval traits were not different from zero. The presence of trade-offs between the direct effects of growth and reproductive traits were confirmed through regression from direct EBV of calving intervals over EBV of pre-weaning growth traits. In addition, regression analyses showed that selection to increase pre-weaning growth also increased calving intervals. Our results showed that pre-weaning growth and calving intervals are increasing over generations and that trade-offs occurred between those traits in the studied Nellore herd.
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Affiliation(s)
- Luiza Rodrigues Alves Abreu
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Gabriela Canabrava Gouveia
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Fabio Luiz Buranelo Toral
- Departamento de Zootecnia, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
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