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Animal Genetic Resources Conservation: From Optimal to Feasible

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 39002

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Special Issue Editors

Prof. Dr. Gustavo Gandini

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Guest Editor

Department of Veterinary Medicine, University of Milan, Milan, Italy
Interests: farm animal genetic resources; biodiversity conservation; animal genetics; animal ethics; urban wildlife

Dr. Jesús Fernández

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Guest Editor

Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain

Special Issue Information

Dear Colleagues

Major advances have been achieved in the conservation of farm animal genetic resources (FAnGR) in the last two decades, with contributions coming from geneticists, ecologists, economists, and policy makers. There has been fruitful work on topics like models to manage genetic variation in small selected and unselected populations, frameworks to identify values associated with local breeds (including ecosystem services), economic models to assign market values to non-market benefits, strategies for genetic material storage and use, and policies for the transboundary management of endangered breeds. However, we feel that, with a few exceptions such as characterization studies, the work has been too often confined to a theoretical level, with limited efforts to adapt theory to the real word of conservation. The conservation of FAnGR requires urgent solutions and therefore applicable models that consider the restrictions or limitations found in real life. There is currently a need to fill the gap between theoretical studies and the practical implementation that FAO in situ and ex situ guidelines require. In this Special Issue, we therefore welcome studies in the different areas of conservation of FAnGR that contribute to “make ends meet” and to promote a growing attention for research on models and strategies that can actually be implemented. In this direction, multidisciplinary approaches and the interaction between domains are highly desirable.

Prof. Gustavo Gandini
Dr. Jesús Fernández
Guest Editors

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Keywords

farm animal genetic resources conservation
local breeds
total economic value
selection
rural culture
genetic diversity
ecosystem services,

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Published Papers (9 papers)

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Research

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15 pages, 677 KiB

Open AccessArticle

The Conservation of Native Domestic Animal Breeds in Nordic Countries: From Genetic Resources to Cultural Heritage and Good Governance

by Ulla Ovaska, Auli Bläuer, Charlotte Kroløkke, Maria Kjetså, Juha Kantanen and Mervi Honkatukia

Animals 2021, 11(9), 2730; https://doi.org/10.3390/ani11092730 - 18 Sep 2021

Cited by 12 | Viewed by 4860

Abstract

Native breeds are domestic animal populations that have adapted to their habitats. The genetic value of breeds has been known for a long time, and recently more attention has been paid to their cultural value. Due to both ecological and cultural significance, it is important that native breeds continue to be bred in their native environments. This is supported by various financial support schemes. Support schemes rarely cover the financial gap in output compared to commercial breeds. A solution to this has been sought in special products, such as cheese or wool, and other businesses, such as animal-assisted care and tourism. Less attention has been paid to the role of administration and good governance in the maintenance of native breeds. In this study, a questionnaire was sent to all registered keepers of native breeds in Finland. This survey clarified their reasons for keeping native breeds and their ideas for improving governance structures and practices. The results were discussed in stakeholder workshops, and in a Nordic context. The results show that genetic and cultural values are recognised in several documents and programmes, but farmers need to be engaged more in the design of support schemes and practices. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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15 pages, 3169 KiB

Open AccessArticle

Estimation of Population-Specific Genetic Parameters Important for Long-Term Optimum Contribution Selection—Case Study on a Dairy Istrian Sheep Breed

by Ante Kasap, Jelena Ramljak and Marija Špehar

Animals 2021, 11(8), 2356; https://doi.org/10.3390/ani11082356 - 9 Aug 2021

Cited by 6 | Viewed by 3033

Abstract

The Istrian sheep breed has been subjected to selection for dairy traits for more than two decades. However, a detailed study of some important population-specific parameters such as effective population size (

N_{e}

) and connectedness between flocks has never been carried [...] Read more.

N_{e}

) and connectedness between flocks has never been carried out. The aim of the study was to examine the above parameters in dairy Istrian sheep subjected to a national selection program. The

N_{e}

was estimated as the mean rate of increase in coancestry, and connectedness was determined using four different statistics. The

N_{e}

was estimated at 73 animals with pedigree constraints imposed on 4 equivalent generations and 3 full generations. Analysis of

Δ N_{e}

(“sliding window approach”) revealed a negative

Δ N_{e}

indicating a progressive loss of genetic variability (

Δ N_{e}_{NEG \geq 4}

= −6.6, p < 0.01;

Δ N_{e}_{NFG \geq 3}

= −4.9, p > 0.05). The overall connectedness (

\bar{r}

~ 0.0001) was below the acceptable level for unbiased ranking of the animals belonging to different flocks (

r_{i, j}

= 0.05). OCS appears to be the best option for the long-term survival (self-sufficiency) of the breed, but genetic links between flocks need to be strengthened to allow unbiased ranking of the animals based on the estimated breeding values. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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14 pages, 1938 KiB

Open AccessArticle

Breeding Strategies to Optimize Effective Population Size in Low Census Captive Populations: The Case of Gazella cuvieri

by Candela Ojeda-Marín, Isabel Cervantes, Eulalia Moreno, Félix Goyache and Juan Pablo Gutiérrez

Animals 2021, 11(6), 1559; https://doi.org/10.3390/ani11061559 - 27 May 2021

Cited by 2 | Viewed by 4528

Abstract

Small-sized animal populations can undergo significant loss of genetic variability that can lead to their extinction. Therefore, studies on animal breeding have focused on mating systems for minimizing the disappearance of genetic variability. The main objective of this study was to compare, using computer simulations, the performance of different breeding schemes to limit the loss of genetic diversity in small-sized populations. This objective was achieved by monitoring the evolution of the effective population size obtained by 23 strategies throughout 20 generations in two populations of Gazella cuvieri. The scenarios were designed with different assumptions, in both reference subpopulations, regarding: the use of parents coancestry or offspring coancestry, the use of their increases or the coefficients themselves, and the number of males and females involved. Computations were performed using an experimental module of Endog v4.9 developed for this purpose. The results of the study showed that strategies for minimizing the coancestry of the parents were better in the short term; however, these strategies were worse in the long term. Minimizing the average coancestry of the offspring was a better approach in the long term. Nevertheless, in both populations, the best results were obtained when both the coancestry of the parents and the coancestry of the offspring were weighted at 5% each and neither males nor females were assumed to contribute to the next generation. In any case, not all strategies had the same evolutionary pattern throughout generations in both populations. The current results show that neither traditional nor new strategies have any general use. Therefore, it is important to carefully test these strategies before applying them to different populations with different breeding needs under different conditions, such as different generation intervals, and different natural breeding systems such as monogamy or polygyny. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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18 pages, 4316 KiB

Open AccessArticle

Retriever and Pointer: Software to Evaluate Inbreeding and Genetic Management in Captive Populations

by Jack J. Windig and Ina Hulsegge

Animals 2021, 11(5), 1332; https://doi.org/10.3390/ani11051332 - 7 May 2021

Cited by 5 | Viewed by 3452

Abstract

The Retriever and Pointer software has been developed for genetic management of (small) captive populations The Retriever program uses as input pedigree data and extracts data on population structure that determine inbreeding rates such as skewness of sire contributions. Levels and rates of inbreeding and kinship and effective population sizes are determined as well. Data on population structure can be used as input for the Pointer program. This program uses stochastic simulation to evaluate a population and provides expected levels and rates of inbreeding and kinship, and optionally allelic diversity. The user can simulate different options for genetic management such as sire restrictions, restrictions on inbreeding levels, mean kinships and breeding circles. Both Retriever and Pointer can analyze populations with subpopulations and different rates of exchange between them. Although originally devised for dogs, the software can be, and has been, used for any captive population including livestock and zoo populations, and a number of examples are provide The pointer software is also suitable in education where students may generate their own populations and evaluate effects of different population structures and genetic management on genetic diversity. Input is provided via a graphical user interface. The software can be downloaded for free. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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13 pages, 1857 KiB

Open AccessArticle

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

by Giulietta Minozzi, Barbara Lazzari, Maria Grazia De Iorio, Cecilia Costa, Emanuele Carpana, Paola Crepaldi, Rita Rizzi, Elena Facchini, Gustavo Gandini, Alessandra Stella and Giulio Pagnacco

Animals 2021, 11(5), 1311; https://doi.org/10.3390/ani11051311 - 2 May 2021

Cited by 5 | Viewed by 3903

Abstract

At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee’s population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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16 pages, 1547 KiB

Open AccessArticle

Payments for Conservation of Animal Genetic Resources in Agriculture: One Size Fits All?

by Luka Juvančič, Renata Slabe-Erker, Marko Ogorevc, Adam G. Drucker, Emil Erjavec and Danijela Bojkovski

Animals 2021, 11(3), 846; https://doi.org/10.3390/ani11030846 - 17 Mar 2021

Cited by 6 | Viewed by 3125

Abstract

Local livestock breeds in Slovenia have been eligible for financial incentives in the form of a fixed payment per livestock unit (LU) since 2002. The scheme has however not been successful in reversing the erosion of animal genetic resources (AnGR). This paper investigates an alternative, whereby incentive payments would better reflect breeders’ actual opportunity costs. The paper contributes to the limited existing body of knowledge related to the use of tender mechanisms in the design of the payments for agrobiodiversity conservation schemes (PACS), particularly for AnGR. Empirical findings draw on the results of a stated preference survey involving 301 farmers in Slovenia, engaging, or being potentially able to engage, in the rearing of local pig, sheep and goat breeds. Interval and logistic regression model results suggest that willingness to accept (WTA) conservation support significantly differs from actual payment levels. The estimated WTA was found to be 27% lower for the local sheep and goat breeds and 5% higher for the local pig breed, suggesting that differentiated incentive payments would provide a more cost-effective alternative. Additional analysis of breeders’ preferences and motives for engaging in local livestock breed production further informs understanding regarding AnGR conservation policy and the importance of accompanying actions to reverse negative population trends. These include reducing administrative barriers and enhancing the market valorisation of local breeds. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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Review

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25 pages, 918 KiB

Open AccessReview

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

by Matilde Maria Passamonti, Elisa Somenzi, Mario Barbato, Giovanni Chillemi, Licia Colli, Stéphane Joost, Marco Milanesi, Riccardo Negrini, Monia Santini, Elia Vajana, John Lewis Williams and Paolo Ajmone-Marsan

Animals 2021, 11(10), 2833; https://doi.org/10.3390/ani11102833 - 28 Sep 2021

Cited by 24 | Viewed by 7752

Abstract

Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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Other

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10 pages, 700 KiB

Open AccessCommentary

Disentangling the Multidimensional Relationship between Livestock Breeds and Ecosystem Services

by Elena Velado-Alonso, Antonio Gómez-Sal, Alberto Bernués and Daniel Martín-Collado

Animals 2021, 11(9), 2548; https://doi.org/10.3390/ani11092548 - 30 Aug 2021

Cited by 8 | Viewed by 3094

Abstract

There is an increasing interest in assessing livestock breed contributions to ecosystem services (ES) and including this knowledge in decision making. However, this task has been limited due to the complexity of the multidimensional relationship between livestock diversity and ecosystem services. In this work, we elaborate on the livestock breed characteristics central to developing a comprehensive approach to livestock breed inclusion in the ecosystem services framework. Thus, we explore the multidimensional nature of livestock breeds, i.e., as eco-cultural entities, biodiversity components, and drivers of livestock system heterogeneity and functioning. First, anthropogenic and natural factors have acted jointly to develop breeds as eco-cultural entities. This fact represents an opportunity to move toward farming system sustainability by Nature-Based Solutions and Nature’s Contribution to People paradigms. Second, livestock breeds are components of biodiversity, and as such, can be framed as goods, as final ecosystem services, and as regulators of ecosystem processes. Third, livestock breeds contribute to livestock system heterogeneity and resilience. By integrating these aspects, we might better understand how livestock breeds provide and modulate ecosystem service provision and, therefore, how to improve breed conservation and livestock policies toward farming system sustainability. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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17 pages, 2784 KiB

Open AccessPerspective

Implementation of the Nagoya Protocol in Livestock Sector: What Have We Learnt So Far?

by Elzbieta Martyniuk and Aleksandra Haska

Animals 2021, 11(8), 2354; https://doi.org/10.3390/ani11082354 - 9 Aug 2021

Cited by 2 | Viewed by 2799

Abstract

The aim of the paper was to analyze impacts of seven years of implementation of the Nagoya Protocol on the livestock sector based on available sources of information and literature. Interim National Reports on implementation of the Nagoya Protocol provided by countries and other information available at the ABS Clearing House managed by the Secretariat of the Convention on Biological Diversity, especially Internationally Recognized Certificates of Compliance (IRCC), were analyzed. Moreover, trends in geneflow of breeding products in selected countries, based on the national reports provided to the UN COMATRADE database, have been compared. Analysis from these sources showed limited impact of the implementation of the Nagoya Protocol for livestock breeding and conservation, as out of 2370 IRCC issued by 31 May 2021, only 573 were granted for animal genetic/biological resources including 90 with livestock as the subject matter. Only one IRCC was granted to a foreign user; all other IRCC were issued for domestic users. The intent was to use livestock genetic/biological resources as bioresources for innovation, which should lead to establishment of the Intellectual Property Rights (IPR) with benefits to be shared through the National Competent Authority or for research purposes. Full article

(This article belongs to the Special Issue Animal Genetic Resources Conservation: From Optimal to Feasible)

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