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Animals
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Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock
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Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock

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 January 2024) | Viewed by 9733

Special Issue Editor

Prof. Dr. Shanyuan Chen

E-Mail Website
Guest Editor
School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
Interests: animal domestication; livestock genomics; population genomics; admixture; selection; metagenomics

Special Issue Information

Dear Colleagues,

Despite extensive efforts that have been made to protect indigenous breeds of livestock species worldwide, the loss of indigenous livestock breeds around the world remains ongoing, as demonstrated by the UN’s Food and Agriculture Organization. For the sustainable use of these local livestock genetic resources, it is urgently needed to explore and identify their genetic characteristics using cutting-edge methods including high-throughput phenotyping and genotyping technologies.

Unsurprisingly, there are a few successful examples of the sustainable use of indigenous livestock breeds. One way out of such awkward situations is to use indigenous livestock breeds as one parent for developing composite new breeds. This is the case for Yunnan native cattle and goats, which were used to crossbreed with other commercial breeds, and final, new composite breeds were developed: Yunling cattle and Yunshang Black goats. Although further studies are needed to identify and quantify the advantageous combinations of mosaic genomes in such composite breeds, this method highlights one of the most important ways to protect and maintain indigenous livestock breeds.

The aim of this Special Issue is to present recent research and reviews on the sustainable use of indigenous livestock breeds from multi-layered perspectives, with the aim of stimulating interest, understanding, and the exploration of this important subject.

Prof. Dr. Shanyuan Chen
Guest Editor

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Keywords

  • indigenous breeds
  • native breeds
  • livestock
  • phenotyping
  • genotyping
  • breeding
  • whole genome sequencing
  • RNA-sequencing
  • proteomics
  • genomic diversity
  • genomic architecture

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Published Papers (5 papers)

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Research

18 pages, 4404 KiB  
Article
Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose (Anser cygnoides) Breeds Based on Mitochondrial CYTB
by Shangzong Qi, Suyu Fan, Haoyu Li, Yufan He, Yang Zhang, Wenming Zhao, Qi Xu and Guohong Chen
Animals 2024, 14(10), 1480; https://doi.org/10.3390/ani14101480 - 16 May 2024
Cited by 2 | Viewed by 1358
Abstract
The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese [...] Read more.
The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese goose breeds. In this study, we collected blood samples from Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ) geese (Anser cygnoides) and used Sanger sequencing to determine the partial sequence of the cytochrome b (CYTB) gene in a total of 180 geese. A total of 117 polymorphic sites were detected in the 707 bp sequence of the mtDNA CYTB gene after shearing and correction, accounting for approximately 16.55% of the entire sequence. The AT content (51.03%) of the processed sequence was slightly higher than the GC content (48.97%), indicating a preference for purine bases. The YJ, YE, and WZ breeds had the highest population genetic diversity, with a haplotype diversity greater than 0.9 (Hd > 0.9) and average population nucleotide difference of 8.01 (K > 8.01). A total of 81 haplotypes were detected and divided into six major branches. Among the six goose breeds, there were frequent genetic exchanges among LX, YJ, YE, and WZ geese (Nm > 15.00). We analyzed the distribution of base-mismatch differences in goose breeds and tested their historical dynamics for neutrality in Tajima’s D and Fu’s Fs. For YJ and WZ geese, Tajima’s D > 0, but the difference was not significant (p > 0.05). The actual values for the two breeds exhibited multimodal Poisson distributions. The population patterns of the WZ and YJ geese are purportedly relatively stable, and the breeds have not experienced population expansions or bottleneck effects, which is consistent with the neutrality test results. This study provides new insights into the diverse genetic origins and historical dynamics that sustain endemic endangered goose breeds. Full article
(This article belongs to the Special Issue Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock)
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11 pages, 1574 KiB  
Article
Single-Nucleotide Polymorphisms of Growth Hormone Gene and Its Relationship with Growth Traits in Black Bengal Goats
by Chollada Buranakarl, Sumonwan Chamsuwan, Sumpun Thammacharoen, Panupat Ratchakom and Natthaya Chuaypen
Animals 2024, 14(6), 834; https://doi.org/10.3390/ani14060834 - 8 Mar 2024
Cited by 3 | Viewed by 2092
Abstract
The single-nucleotide polymorphisms (SNPs) of the growth hormone (GH) gene could be related to growth traits, particularly in farm animals. This study aimed to identify the SNPs of the GH gene (A781G and A1575G) in Black Bengal (BB) goats in Thailand. Seventy-seven BB [...] Read more.
The single-nucleotide polymorphisms (SNPs) of the growth hormone (GH) gene could be related to growth traits, particularly in farm animals. This study aimed to identify the SNPs of the GH gene (A781G and A1575G) in Black Bengal (BB) goats in Thailand. Seventy-seven BB goats of both sexes were recruited, and their genotypes were identified. Preweaning growth at birth (weight, W0; height, H0; length, L0; and chest girth, C0) and at 10 weeks postpartum (W10, H10, L10, and C10), including average daily gain (ADG) at 0–4 weeks (ADG0–4W), 4–8 weeks (ADG4–8W), and 8–12 weeks (ADG8–12W), was compared among the different genotypes in goats born from twin litter-size dams. The results showed one genotype, CC, for A1575G and three genotypes, AA, AB, and BB, for A781G. The AA gene had significantly higher W10 than AB (p < 0.05) and BB (p < 0.05). The AA had significantly higher L10 than AB (p < 0.05), while C10 was only higher in male goats (p < 0.01). The ADG4–8W of the AA genotype was significantly higher than the BB genotype (p < 0.01). We came to the conclusion that A781G is associated with growth traits during the preweaning period, while the AA genotype showed better performance than the other genotypes. Full article
(This article belongs to the Special Issue Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock)
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15 pages, 1098 KiB  
Article
The Crucial Role of Breeder and Dog Owners Associations in Safeguarding Genetic Heritage of Endangered Balearic Dog Breeds: Gender Preference and Registry Adscription
by José Manuel Alanzor Puente, Águeda Laura Pons Barro, Antonio González Ariza, Carmen Marín Navas, Juan Vicente Delgado Bermejo and Francisco Javier Navas González
Animals 2024, 14(4), 639; https://doi.org/10.3390/ani14040639 - 16 Feb 2024
Viewed by 1539
Abstract
This study delves into the complex relationships between indigenous dog breeds in the Balearic Isles and their human counterparts, specifically breeders and owners. Using Canonical Correlation Analysis, the research examines variables such as breed registries and the number of breeders/owners, uncovering significant correlations [...] Read more.
This study delves into the complex relationships between indigenous dog breeds in the Balearic Isles and their human counterparts, specifically breeders and owners. Using Canonical Correlation Analysis, the research examines variables such as breed registries and the number of breeders/owners, uncovering significant correlations within registries. For example, an increase in female auxiliary registrations corresponds to a decline in foundational registrations, indicating shifts in breed documentation dynamics. Similarly, a rise in definitive female registrations coincides with a decrease in foundational female registrations, suggesting increased pedigree awareness across generations. Beyond registries, the study explores the correlation between breeders/owners and various initial records, highlighting that a notable increase in breeders positively influences initial registrations, definitive totals, and overall counts, underscoring their crucial role in early breed stages. Gender preferences in registrations are noted, with a historical bias towards female entries during foundational stages gradually shifting in favor of males in definitive registrations. In conclusion, the research underscores the interconnected roles of breeders, owners, and comprehensive registries in preserving genetic diversity among Balearic dog breeds, emphasizing the need for ongoing efforts to address gaps in genealogical data for a more accurate understanding of breed dynamics. Full article
(This article belongs to the Special Issue Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock)
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11 pages, 1910 KiB  
Article
Expression and Variations in EPO Associated with Oxygen Metabolism in Tibetan Sheep
by Yue Ren, Qiming Xi, Zhaohua He, Hongxian Sun and Shaobin Li
Animals 2024, 14(4), 535; https://doi.org/10.3390/ani14040535 - 6 Feb 2024
Cited by 1 | Viewed by 1579
Abstract
After a long period of adaptive evolution, Tibetan sheep have adapted to the plateau environment in terms of genetics, physiology and biochemistry, but the mechanism of hypoxia adaptation has not been fully elucidated, and the functional genes and molecular mechanisms regulating the hypoxia [...] Read more.
After a long period of adaptive evolution, Tibetan sheep have adapted to the plateau environment in terms of genetics, physiology and biochemistry, but the mechanism of hypoxia adaptation has not been fully elucidated, and the functional genes and molecular mechanisms regulating the hypoxia adaptation of Tibetan sheep need to be further studied. In this study, Tibetan sheep were selected as the research object, and the mRNA expression levels of the hypoxa-related gene EPO in heart, lung, kidney, liver, spleen and longissimus dorsi muscle of Hu sheep (100 m) and Tibetan sheep at different altitudes (2500 m, 3500 m, 4500 m) were assessed by RT-qPCR. The SNPs loci were detected by sequencing and Kompetitive Allele-Specific PCR (KASP) technology, then the correlation between genetic polymorphism and blood gas was analyzed. The results show that the expression of the EPO gene was the highest in the kidney, indicating that the expression of EPO gene had tissue differences. The expression levels of the EPO gene in the heart, lung and liver of Tibetan sheep at a 4500 m altitude were significantly higher than those in Hu sheep (p < 0.05), and the levels in the hearts of Tibetan sheep increased with the increase in altitude. Three mutations were identified in the EPO gene, the SNPs (g.855 A > C) in exon 1 and the SNPs (g.1985 T > G and g.2115 G > C) in exon 4, which were named EPO-SNP1, EPO-SNP2 and EPO-SNP3, respectively, and all three SNPs showed three genotypes. Correlation analysis showed that g.2115 G > C sites were significantly correlated with pO2 (p < 0.05), and haplotype combinations were significantly correlated with pO2 (p < 0.05). Thesee results suggest that the expression of the EPO gene is altitude-differentiated and organ-differentiated, and the EPO gene variants have significant effects on pO2, which may be beneficial to the adaptation of Tibetan sheep to hypoxia stress. Full article
(This article belongs to the Special Issue Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock)
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18 pages, 2256 KiB  
Article
Comparative Proteomics Analysis of Pig Muscle Exudate through Label-Free Liquid Chromatography-Mass Spectrometry
by Alessio Di Luca, Andrea Ianni, Francesca Bennato, Camillo Martino, Michael Henry, Paula Meleady and Giuseppe Martino
Animals 2023, 13(9), 1460; https://doi.org/10.3390/ani13091460 - 25 Apr 2023
Cited by 1 | Viewed by 2103
Abstract
Capital-driven animal husbandry systems undertaken in the last century led to the abandoning of many pig breeds that were not profitable. These local pig breeds and their respective production systems have great potential as they are able to respond to the high criteria [...] Read more.
Capital-driven animal husbandry systems undertaken in the last century led to the abandoning of many pig breeds that were not profitable. These local pig breeds and their respective production systems have great potential as they are able to respond to the high criteria and needs of modern society concerning some environmental aspects, animal-welfare, healthiness, etc. This is the case of the black pigs of Italy. The Apulo-Calabrese is a breed of black pig, known by many other names such as Nero d’Abruzzo. In order to further understand the biological differences between different types of porcine genetics (Nero d’Abruzzo and commercial-hybrid) we used a label-free LC-MS strategy and Western-blot to characterize the proteomes of muscle-exudate collected from these pigs. This proteomics approach identified 1669 proteins of which 100 changed significantly in abundance between breeds. Bioinformatics functional analysis indicated that differentially expressed proteins were involved in several biological processes related to energy-metabolism and response to oxidative stress, suggesting that these functions might distinguish between these pigs. Fatty-acid synthase, catalase and glutathione-peroxidase, involved in enzymatic activity were found to be more represented in samples obtained from the Nero d’Abruzzo. This biological information can potentially provide new biological factors that could determine the different production performances of these pigs, distinguished by their different genetic backgrounds. Full article
(This article belongs to the Special Issue Sustainable Future: Genetics and Breeding of Indigenous Breeds of Livestock)
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