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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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Wang J, Liu J, Lei Q, Liu Z, Han H, Zhang S, Qi C, Liu W, Li D, Li F, Cao D, Zhou Y. Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses. BMC Genomics 2024; 25:296. [PMID: 38509464 PMCID: PMC10956266 DOI: 10.1186/s12864-024-10185-6] [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: 08/10/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. METHODS We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. RESULTS We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. CONCLUSION Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens.
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Affiliation(s)
- Jie Wang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Jie Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Qiuxia Lei
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Zhihe Liu
- Sichuan agricultural university college of animal science and technology, Chengdu, 611130, China
| | - Haixia Han
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Wei Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dapeng Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Fuwei Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dingguo Cao
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Yan Zhou
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China.
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China.
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Das PJ, Kumar S, Choudhury M, Banik S, Pegu SR, Kumar S, Deb R, Gupta VK. Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig. Gene 2024; 897:148070. [PMID: 38070787 DOI: 10.1016/j.gene.2023.148070] [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: 06/08/2023] [Revised: 11/15/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090th to 1099th position, deletion of a 10 bp sequence at the 755th position, insertion of (CA) at the 137th position, and substitution of AT to GA at the 638th position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.
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Affiliation(s)
- Pranab Jyoti Das
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India.
| | - Satish Kumar
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Manasee Choudhury
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Santanu Banik
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Seema Rani Pegu
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
| | - Sunil Kumar
- Animal Reproduction, ICAR-National Research Centre on Pig, Rani, Guwahati-781131, Assam, India
| | - Rajib Deb
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
| | - Vivek Kumar Gupta
- Animal Health, ICAR-National Research Centre on Pig, Rani, Guiwahati-781131, Assam, India
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Paul K, Restoux G, Phocas F. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Genet Sel Evol 2024; 56:13. [PMID: 38389056 PMCID: PMC10882880 DOI: 10.1186/s12711-024-00884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. RESULTS Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). CONCLUSIONS Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.
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Affiliation(s)
- Katy Paul
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gwendal Restoux
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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Zhang M, Wang S, Xu R, Liu Y, Zhang H, Sun M, Wang J, Liu Z, Wu K. Managing genomic diversity in conservation programs of Chinese domestic chickens. Genet Sel Evol 2023; 55:92. [PMID: 38097971 PMCID: PMC10722821 DOI: 10.1186/s12711-023-00866-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. RESULTS Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (FST), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation. CONCLUSIONS Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.
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Affiliation(s)
- Mengmeng Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd., No. 75 Bingjiaokou Hutong, Beijing, 100088, People's Republic of China
| | - Shiwei Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ran Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yijun Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- College of Animal Science, Southwest University, Chongqing, 402460, People's Republic of China
| | - Han Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mengxia Sun
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junyan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhexi Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Keliang Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
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Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
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10
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Rajawat D, Panigrahi M, Nayak SS, Ghildiyal K, Sharma A, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Dutt T. Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection. Anim Biotechnol 2023; 34:3920-3933. [PMID: 37493405 DOI: 10.1080/10495398.2023.2240387] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Pharmacology and Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Animal Biotechnology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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11
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Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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12
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Sawicka-Zugaj W, Chabuz W, Kasprzak-Filipek K. The Role of Reproduction and Genetic Variation in Polish White-Backed Cows in the Breed Restoration Process. Animals (Basel) 2023; 13:2790. [PMID: 37685054 PMCID: PMC10486713 DOI: 10.3390/ani13172790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Local breeds are the main reservoir of biodiversity of farm animals. According to FAO, they account for 87% of all described breeds in the world. To ensure that they are adequately protected, they should be continually monitored for genetic variation. Another crucial factor is reproduction, which is the most important guarantee of population growth. In the present study, genetic variation in 372 Polish White-Backed cows was determined using DNA microsatellite sequences, taking into account their parentage. Reproductive parameters were analysed as well, based on data from 3658 lactations of 1128 Polish White-Backed cows. The results indicate that despite the small initial population and the implementation of a moderate selection of animals, the existing population of Polish White-Backed cattle has a high level of genetic variation, reflected in the degree of heterozygosity (0.761). Regarding reproductive traits, despite their late age at first calving, Polish White-Backed cows were shown to be distinguished by very good fertility parameters in comparison to other breeds raised in Poland. These findings not only confirm the value of protecting local cattle breeds around the world but may also be of importance in developing selection indices for highly productive breeds, in which reproductive functioning should be one of the most important factors considered.
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Affiliation(s)
| | - Witold Chabuz
- Department of Cattle Breeding and Genetic Resources Conservation, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (W.S.-Z.); (K.K.-F.)
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13
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Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023; 30:103741. [PMID: 37575470 PMCID: PMC10413190 DOI: 10.1016/j.sjbs.2023.103741] [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] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and Seglawi) from the previous study for phylogenetic comparison. The whole mitochondrial genome sequencing resulted in intra and inter mtDNA variations between the studied horses. Interestingly, the Hamdani horse has nucleotide substitutions similar to those of the Hadban horse, which is reflected in the phylogenetic tree as a significantly close relationship. This type of study provides a better understanding of mitogenome structure and conservation of livestock species genetic data.
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Affiliation(s)
- Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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14
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Zhang Y, Qi S, Liu L, Bao Q, Wu T, Liu W, Zhang Y, Zhao W, Xu Q, Chen G. Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene. Genes (Basel) 2023; 14:1605. [PMID: 37628656 PMCID: PMC10454708 DOI: 10.3390/genes14081605] [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: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Guohong Chen
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (S.Q.); (L.L.); (Q.B.); (T.W.); (W.L.); (Y.Z.); (W.Z.); (Q.X.)
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15
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Wang Z, Lu G, Gao Y, Yan L, Li M, Hu D, Zhang D. mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China. Animals (Basel) 2023; 13:2191. [PMID: 37443989 DOI: 10.3390/ani13132191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023] Open
Abstract
Forest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.
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Affiliation(s)
- Zhe Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Guanjie Lu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Yunyun Gao
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Mingzhe Li
- China Wildlife Conservation Association, Beijing 100714, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Qinghua East Road 35, Beijing 100083, China
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16
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Pimentel F, McManus C, Soares K, Caetano AR, de Faria DA, Paiva SR, Ianella P. Landscape Genetics for Brazilian Equines. J Equine Vet Sci 2023; 126:104251. [PMID: 36796740 DOI: 10.1016/j.jevs.2023.104251] [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: 11/14/2022] [Revised: 01/17/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Optimization of DNA collection for National gene bank and conservation programs requires information on spatial and genetic distribution of animals countrywide. The relationship between genetic and geographic distances were examined in 8 Brazilian horse breeds (Baixadeiro, Crioulo, Campeiro, Lavradeiro, Marajoara, Mangalarga Marchador, Pantaneiro and Puruca) using Single Nucleotide Polymorphism markers and collection point locations. Mantel correlations, Genetic Landscape Shape Interpolation, Allelic Aggregation Index Analyses and Spatial autocorrelation tests indicated a nonrandom distribution of horses throughout the country. Minimum collection distances for the national Gene Bank should be 530km, with clear divisions seen in genetic structure of horse populations in both North/South and East/West directions. Comparing Pantaneiro and North/Northeastern breeds, physical distance is not necessarily the defining factor for genetic differentiation. This should be considered when sampling these local breeds. These data can help optimise GenBank collection routines and conservation strategies for these breeds.
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Affiliation(s)
| | - Concepta McManus
- Departamento de Ciências Fisiológicas, Instituto de Biologia, Campus Darcy Ribeiro, Universidade de Brasilia, Asa Norte, Brasilia, DF, Brasil.
| | - Kaifer Soares
- Faculdade de Agronomia e Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, Brasil
| | | | - Danielle Assis de Faria
- Faculdade de Agronomia e Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, Brasil
| | | | - Patrícia Ianella
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
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17
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Perini F, Ceccobelli S, Crooijmans RPMA, Tiambo CK, Lasagna E. Editorial: Global green strategies and capacities to manage a sustainable animal biodiversity. Front Genet 2023; 14:1213080. [PMID: 37396045 PMCID: PMC10313107 DOI: 10.3389/fgene.2023.1213080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023] Open
Affiliation(s)
- F. Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - S. Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica Delle Marche, Ancona, Italy
| | - R. P. M. A. Crooijmans
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
| | - C. K. Tiambo
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya
| | - E. Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
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18
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Filip E, Strzała T, Stępień E, Cembrowska-Lech D. Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach. Sci Rep 2023; 13:9133. [PMID: 37277428 DOI: 10.1038/s41598-023-35637-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland.
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Edyta Stępień
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16, 70-383, Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Sanprobi Sp. z o. o. Sp. k., Kurza Stopka 5C, 70-535, Szczecin, Poland
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19
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Rannamäe E, Saarma U, Kantanen J, Bläuer A. Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds. Anim Genet 2023; 54:177-188. [PMID: 36514938 DOI: 10.1111/age.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022]
Abstract
Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.
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Affiliation(s)
- Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Auli Bläuer
- Archaeology, University of Turku, Turku, Finland
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20
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De AK, Sawhney S, Sunder J, Muthiyan R, Ponraj P, Sujatha T, Malakar D, Mondal S, Bera AK, Kumar A, Chakurkar EB, Bhattacharya D. Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling. Genes (Basel) 2023; 14:genes14040784. [PMID: 37107542 PMCID: PMC10138289 DOI: 10.3390/genes14040784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 04/29/2023] Open
Abstract
Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Ramachandran Muthiyan
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Tamilvanan Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Asit Kumar Bera
- Reservoir and Wetland Fisheries Division, ICAR-Central Inland Fishery Research Institute, Barrackpore 700120, West Bengal, India
| | - Ashish Kumar
- Centre for Technology Alternatives for Rural Areas, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Eaknath Bhanudasrao Chakurkar
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
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21
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Perini F, Cendron F, Wu Z, Sevane N, Li Z, Huang C, Smith J, Lasagna E, Cassandro M, Penasa M. Genomics of Dwarfism in Italian Local Chicken Breeds. Genes (Basel) 2023; 14:genes14030633. [PMID: 36980905 PMCID: PMC10047989 DOI: 10.3390/genes14030633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.
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Affiliation(s)
- Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Zhou Wu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid, Avenida Puerta de Hierro, 28040 Madrid, Spain
| | - Zhiqiang Li
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- Correspondence: ; Tel.: +39-075-58517102
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
- Federazione delle Associazioni Nazionali di Razza e Specie, 00187 Roma, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
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Xia J, Chang L, Xu D, Jia Y, Ding Y, Cao C, Geng Z, Jin S. Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family. Animals (Basel) 2023; 13:ani13030531. [PMID: 36766420 PMCID: PMC9913526 DOI: 10.3390/ani13030531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.
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Affiliation(s)
- Jingjing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Liang Chang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dashuang Xu
- Anhui Livestock and Poultry Genetic Resources Protection Center, Hefei 231283, China
| | - Yuqing Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanfei Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: ; Tel.:+86-551-6578-6328; Fax:+86-551-6578-6326
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Chen X, Duan X, Chong Q, Li C, Xiao H, Chen S. Genome-Wide DNA Methylation Differences between Bos indicus and Bos taurus. Animals (Basel) 2023; 13:ani13020203. [PMID: 36670743 PMCID: PMC9854497 DOI: 10.3390/ani13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Disease risk is a persistent problem in domestic cattle farming, while economic traits are the main concern. This study aimed to reveal the epigenetic basis for differences between zebu (Bos indicus) and taurine cattle (Bos taurus) in disease, disease resistance, and economic traits, and provide a theoretical basis for the genetic improvement of domestic cattle. In this study, whole genome bisulfite sequencing (WGBS) was used to analyze the whole-genome methylation of spleen and liver samples from Yunnan zebu and Holstein cattle. In the genome-wide methylation pattern analysis, it was found that the methylation pattern of all samples was dominated by the CG type, which accounted for >94.9%. The DNA methylation levels of different functional regions and transcriptional elements in the CG background varied widely. However, the methylation levels of different samples in the same functional regions or transcriptional elements did not differ significantly. In addition, we identified a large number of differentially methylation region (DMR) in both the spleen and liver groups, of which 4713 and 4663 were annotated to functional elements, and most of them were annotated to the intronic and exonic regions of genes. GO and KEGG functional analysis of the same differentially methylation region (DMG) in the spleen and liver groups revealed that significantly enriched pathways were involved in neurological, disease, and growth functions. As a result of the results of DMR localization, we screened six genes (DNM3, INPP4B, PLD, PCYT1B, KCNN2, and SLIT3) that were tissue-specific candidates for economic traits, disease, and disease resistance in Yunnan zebu. In this study, DNA methylation was used to construct links between genotypes and phenotypes in domestic cattle, providing useful information for further screening of epigenetic molecular markers in zebu and taurine cattle.
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Affiliation(s)
- Xiaona Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xinyu Duan
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Qingqing Chong
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Correspondence: ; Tel.: +86-186-8712-2260
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Falchi L, Cesarani A, Mastrangelo S, Senczuk G, Portolano B, Pilla F, Macciotta NPP. Analysis of runs of homozygosity of cattle living in different climate zones. J Anim Sci 2023; 101:skad061. [PMID: 36802370 PMCID: PMC10066727 DOI: 10.1093/jas/skad061] [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: 09/27/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
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Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, 30602 Athens, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
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Cortez T, Montenegro H, Coutinho LL, Regitano LCA, Andrade SCS. Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus). PLoS One 2022; 17:e0279091. [PMID: 36548260 PMCID: PMC9778527 DOI: 10.1371/journal.pone.0279091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families' turnover rate (λ). Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (λ = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
| | - Horácio Montenegro
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luiz L. Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luciana C. A. Regitano
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
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26
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Andaman local goat: mitochondrial genome characterization and lineage analysis. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products. Genes (Basel) 2022; 13:genes13101825. [PMID: 36292710 PMCID: PMC9601671 DOI: 10.3390/genes13101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/04/2022] Open
Abstract
The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products.
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Zhang M, Zhang C, Hu P, Shi L, Ju M, Zhang B, Li X, Han X, Wang K, Li X, Qiao R. Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds. Anim Genet 2022; 53:803-813. [PMID: 36071602 DOI: 10.1111/age.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022]
Abstract
Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.
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Affiliation(s)
- Menghao Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shanxi, China
| | - Panyang Hu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lidan Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Mingming Ju
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ben Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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Mauki DH, Tijjani A, Ma C, Ng’ang’a SI, Mark AI, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Kazwala RR, Gwakisa PS, Yin TT, Li Y, Peng MS, Adeola AC, Zhang YP. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics 2022; 23:306. [PMID: 35428239 PMCID: PMC9012019 DOI: 10.1186/s12864-022-08512-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. Results The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. Conclusion The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08512-w.
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Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars. PLoS One 2022; 17:e0254299. [PMID: 35344556 PMCID: PMC8959178 DOI: 10.1371/journal.pone.0254299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin. The results revealed considerable genetic diversity (0.900±0.016) and widespread Asian pig-ancestry (94.60%) in the phylogenetic analysis, with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine domestic pigs corroborates our hypothesis of a genetic signal that may be associated with the recently reported multiple waves of human migrations to the Philippines. The Haplogroup D7, reported to occur only in Indo-Burma Biodiversity Hotspots, included a high frequency of Philippine domestic pig haplotypes (54.08%), which poses an interesting challenge because its distribution is not consistent with the hypothesized migration route of Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes (Asian major) on several Philippine islands. The analyses of mismatch distribution and neutrality test were consistent with the Bayesian skyline plot which showed a long stationary period of effective population size. The population decline was consistent with the pronounced population bottleneck in Asian and European pigs during the interglacial periods of the Pleistocene. The results of this study will support the conservation strategies and improvements of economically important genetic resources in the Philippines.
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31
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Her C, Rezaei HR, Hughes S, Naderi S, Duffraisse M, Mashkour M, Naghash HR, Bălășescu A, Luikart G, Jordan S, Özüt D, Kence A, Bruford MW, Tresset A, Vigne JD, Taberlet P, Hänni C, Pompanon F. Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros. Anim Genet 2022; 53:452-459. [PMID: 35288946 DOI: 10.1111/age.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).
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Affiliation(s)
- Charlotte Her
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Hamid-Reza Rezaei
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Environmental Sciences Department, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Saeid Naderi
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France.,Department of Environment, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, ENSL, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marjan Mashkour
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Hamid-Reza Naghash
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - Adrian Bălășescu
- Department of Bioarchaeology, 'Vasile Pârvan' Institute of Archaeology, Romanian Academy, Bucharest, Romania
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, Montana, USA
| | - Steve Jordan
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Deniz Özüt
- Biology Department, Middle East Technical University, Ankara, Turkey
| | - Aykut Kence
- Biology Department, Middle East Technical University, Ankara, Turkey
| | | | - Anne Tresset
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Jean-Denis Vigne
- Département d'Ecologie et Gestion de la Biodiversité, CNRS, UMR 7209, Muséum National d'Histoire Naturelle, 'AASPE' Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Paris Cedex 05, France
| | - Pierre Taberlet
- The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway
| | - Catherine Hänni
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
| | - François Pompanon
- LECA, CNRS, Université Grenoble Alpes, Université Savoie Mont Blanc, Grenoble, France
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Sezgin E, Teferedegn EY, Ün C, Yaman Y. Excessive replacement changes drive evolution of global sheep prion protein (PRNP) sequences. Heredity (Edinb) 2022; 128:377-385. [PMID: 35273383 PMCID: PMC9076837 DOI: 10.1038/s41437-022-00520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Sheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.
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Affiliation(s)
- Efe Sezgin
- Department of Food Engineering, Izmir Institute of Technology, Urla, Izmir, Turkey.
| | - Eden Yitna Teferedegn
- Department of Biology, Molecular Biology Division, Ege University, Izmir, Turkey.,Armauer Hansen research institute, Biotechnology and Bioinformatic Directorate, Addis Ababa, Ethiopia
| | - Cemal Ün
- Armauer Hansen research institute, Biotechnology and Bioinformatic Directorate, Addis Ababa, Ethiopia
| | - Yalçın Yaman
- Department of Breeding and Genetics, Bandırma Sheep Breeding Research Institute, Bandırma, Balıkesir, Turkey
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Layos JKN, Godinez CJP, Liao LM, Yamamoto Y, Masangkay JS, Mannen H, Nishibori M. Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA. Front Genet 2022; 12:823364. [PMID: 35145546 PMCID: PMC8822243 DOI: 10.3389/fgene.2021.823364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.
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Affiliation(s)
- John King N. Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- College of Agriculture and Forestry, Capiz State University, Mambusao, Philippines
- *Correspondence: John King N. Layos, ; Masahide Nishibori,
| | - Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
| | - Lawrence M. Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Joseph S. Masangkay
- College of Veterinary Medicine, University of the Philippines, Los Baños, Philippines
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
- *Correspondence: John King N. Layos, ; Masahide Nishibori,
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34
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Population structure and genetic relatedness of Sri Lankan Jaffna Local sheep with major South Indian breeds. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2021.106571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Niego A, Benítez-Burraco A. Are feralization and domestication truly mirror processes? ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2021.1975314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amy Niego
- PhD Program, Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain (E-mail: )
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36
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Lewis JA, Morran LT. Advantages of laboratory natural selection in the applied sciences. J Evol Biol 2021; 35:5-22. [PMID: 34826161 DOI: 10.1111/jeb.13964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
In the past three decades, laboratory natural selection has become a widely used technique in biological research. Most studies which have utilized this technique are in the realm of basic science, often testing hypotheses related to mechanisms of evolutionary change or ecological dynamics. While laboratory natural selection is currently utilized heavily in this setting, there is a significant gap with its usage in applied studies, especially when compared to the other selection experiment methodologies like artificial selection and directed evolution. This is despite avenues of research in the applied sciences which seem well suited to laboratory natural selection. In this review, we place laboratory natural selection in context with other selection experiments, identify the characteristics which make it well suited for particular kinds of applied research and briefly cover key examples of the usefulness of selection experiments within applied science. Finally, we identify three promising areas of inquiry for laboratory natural selection in the applied sciences: bioremediation technology, identifying mechanisms of drug resistance and optimizing biofuel production. Although laboratory natural selection is currently less utilized in applied science when compared to basic research, the method has immense promise in the field moving forward.
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Affiliation(s)
- Jordan A Lewis
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Levi T Morran
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA.,Department of Biology, Emory University, Atlanta, Georgia, USA
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Vohra V, Singh NP, Chhotaray S, Raina VS, Chopra A, Kataria RS. Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India. PeerJ 2021; 9:e11846. [PMID: 34447621 PMCID: PMC8364325 DOI: 10.7717/peerj.11846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/01/2021] [Indexed: 12/02/2022] Open
Abstract
To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.
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Affiliation(s)
- Vikas Vohra
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Narendra Pratap Singh
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Varinder Singh Raina
- Department of Animal Husbandry and Dairying, Ministry of Fisheries, Animal Husbandry and Dairying, New Delhi, New Delhi, India
| | - Alka Chopra
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Ranjit Singh Kataria
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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38
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Thorne JW, Murdoch BM, Freking BA, Redden RR, Murphy TW, Taylor JB, Blackburn HD. Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century. Anim Genet 2021; 52:395-408. [PMID: 33955573 PMCID: PMC8360125 DOI: 10.1111/age.13067] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2021] [Indexed: 12/14/2022]
Abstract
The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.
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Affiliation(s)
- J. W. Thorne
- Texas A&M AgriLife ExtensionTexas A&M UniversitySan AngeloTX76901USA
- Department of Animal, Veterinary and Food ScienceUniversity of IdahoMoscowID83844USA
| | - B. M. Murdoch
- Department of Animal, Veterinary and Food ScienceUniversity of IdahoMoscowID83844USA
| | - B. A. Freking
- United States Meat Animal Research CenterUnited States Department of Agriculture, Agricultural Research ServiceClay CenterNE68933‐0166USA
| | - R. R. Redden
- Texas A&M AgriLife ExtensionTexas A&M UniversitySan AngeloTX76901USA
| | - T. W. Murphy
- United States Meat Animal Research CenterUnited States Department of Agriculture, Agricultural Research ServiceClay CenterNE68933‐0166USA
| | - J. B. Taylor
- United States Sheep Experiment StationUnited States Department of Agriculture, Agricultural Research ServiceDuboisID83423USA
| | - H. D. Blackburn
- National Animal Germplasm ProgramUnited States Department of Agriculture, Agricultural Research ServiceFort CollinsCO80521USA
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39
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Wu Z, Bortoluzzi C, Derks MFL, Liu L, Bosse M, Hiemstra SJ, Groenen MAM, Crooijmans RPMA. Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses. Evol Appl 2021; 14:1095-1108. [PMID: 33897823 PMCID: PMC8061282 DOI: 10.1111/eva.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022] Open
Abstract
The growth of animals is a complex trait, in chicken resulting in a diverse variety of forms, caused by a heterogeneous genetic basis. Bantam chicken, known as an exquisite form of dwarfism, has been used for crossbreeding to create corresponding dwarf counterparts for native fowls in the Dutch populations. Here, we demonstrate the heterogeneity of the bantam trait in Dutch chickens and reveal the underlying genetic causes, using whole-genome sequence data from matching pairs of bantam and normal-sized breeds. During the bantam-oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, and three major bantam sources were identified and clustered. The genome-wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including HMGA2 and PRDM16, genes involved in body growth and stature. The comparison of associated variants among studies illustrated differences related to divergent bantam origins, suggesting a clear heterogeneity among bantam breeds. We show that in neo-bantam breeds, the bantam-related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal-sized counterpart. The bantam heterogeneity is further confirmed by the presence of multiple haplotypes comprising associated alleles, which suggests the selection of the bantam phenotype is likely subject to a convergent direction across populations. Our study demonstrates that the diverse history of human-mediated crossbreeding has contributed to the complexity and heterogeneity of the bantam phenotype.
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Affiliation(s)
- Zhou Wu
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Chiara Bortoluzzi
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Martijn F. L. Derks
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Langqing Liu
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
| | - Sipke Joost Hiemstra
- Centre for Genetic Resources, the Netherlands (CGN) of Wageningen University & ResearchWageningenThe Netherlands
| | - Martien A. M. Groenen
- Wageningen University & Research, Animal Breeding and GenomicsWageningenThe Netherlands
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40
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Diaz-Maroto P, Rey-Iglesia A, Cartajena I, Núñez L, Westbury MV, Varas V, Moraga M, Campos PF, Orozco-terWengel P, Marin JC, Hansen AJ. Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes. eLife 2021; 10:63390. [PMID: 33724183 PMCID: PMC8032396 DOI: 10.7554/elife.63390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.
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Affiliation(s)
| | - Alba Rey-Iglesia
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isabel Cartajena
- Faculty of Social Sciences, University of Chile, Santiago de Chile, Chile
| | - Lautaro Núñez
- Institute of Archaeological Research and Museum, Católica del Norte University, San Pedro de Atacama, Chile
| | - Michael V Westbury
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Valeria Varas
- School of Science Ecology and Evolution, Faculty of Sciences, Austral of Chile University, Valdivia, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Paula F Campos
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom
| | - Juan Carlos Marin
- ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom.,Genomic and Biodiversity Laboratory, Basic Sciences Department, Faculty of Sciences, Bio-Bio University, Chillán, Chile
| | - Anders J Hansen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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The WC1 γδ T cell pathogen receptor of ruminants is preserved in the genome of ancient extinct auroch. Immunogenetics 2021; 73:419-424. [PMID: 33712898 DOI: 10.1007/s00251-021-01211-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/22/2021] [Indexed: 12/21/2022]
Abstract
The work reported here investigated the γδ T cell-specific cell surface receptor known as workshop cluster 1 (WC1) in the extinct Auroch and compared the gene sequences to those in modern cattle breeds. These molecules function as hybrid pattern recognition receptors (PRR), binders of microbial pathogens, and as signaling co-receptors of the T cell antigen receptor (TCR), directing the immune responses by γδ T cell subsets. Sequences in the Auroch genome included both WC1.1 and WC1.2-like a-patterned scavenger receptor cytsteine-rich (SRCR) domains as well as the more conserved b, c, d, and e-patterned SRCR domains. While there was much sequence homology with bovine WC1 genes, there are also unique Auroch genes based on the signature a1 SRCR domain sequences that are used to identify individual WC1 genes. There was also conservation of genes coding for Type I and II intracytoplasmic endodomains although no evidence for gene sequences for Type III endodomains or the extracellular 6 SRCR domains that are associated with this endodomain. This particular WC1 molecule has been proposed to represent the most ancient WC1, and thus, it is particularly interesting that it is apparently missing in the Auroch genome although it could be due to incomplete sequencing. Overall, the results suggest that while WC1 genes have been preserved from Ancient Auroch to modern cattle, they may have co-evolved perhaps as a result of differing pathogen or environmental antigen exposure.
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Machová K, Milerski M, Rychtářová J, Hofmanová B, Vostrá-Vydrová H, Moravčíková N, Kasarda R, Vostrý L. Assessment of the genetic diversity of Two Czech autochthonous sheep breeds. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2020.106301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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Ibrahim A, Budisatria IGS, Widayanti R, Artama WT. The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences. Vet World 2020; 13:2625-2634. [PMID: 33487980 PMCID: PMC7811546 DOI: 10.14202/vetworld.2020.2625-2634] [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: 06/30/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.
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Affiliation(s)
- Alek Ibrahim
- Veterinary Science Postgraduate Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - I Gede Suparta Budisatria
- Department of Animal Production, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Wayan Tunas Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Sharma R, Ahlawat S, Sharma H, Sharma P, Panchal P, Arora R, Tantia MS. Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India. Sci Rep 2020; 10:20422. [PMID: 33235268 PMCID: PMC7687881 DOI: 10.1038/s41598-020-77480-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
Sheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.
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Affiliation(s)
- Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Priyanka Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Poonam Panchal
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Dettori ML, Petretto E, Pazzola M, Vidal O, Amills M, Vacca GM. Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers. Animals (Basel) 2020; 10:E2194. [PMID: 33255190 PMCID: PMC7761473 DOI: 10.3390/ani10122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022] Open
Abstract
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
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Affiliation(s)
- Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Elena Petretto
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003 Girona, Spain;
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Department of Animal Genetics, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
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Moreno-Sierra AM, Cerón-Muñoz MF, Soto-Calderón ID. Population genetic structure of two herds of Aberdeen Angus cattle breed in Colombia. REV COLOMB CIENC PEC 2020. [DOI: 10.17533/udea.rccp.v34n4a05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Two biotypes of Aberdeen Angus cattle breed, known as Old Type and New Type, that differ in their origin and beef production are formally recognized. In Colombia, this breed has been commercialized for approximately 80 years. Studies on the origin, kinship and levels of genetic diversity of this breed in Colombian herds are scarce, yet important for planning crossing and management strategies. Objective: To measure the genetic diversity and structure of two Colombian herds of Old Type and New Type biotypes of Aberdeen Angus from Huila and Cundinamarca provinces and assess mitochondrial introgression with other breeds. Methods: A set of ten microsatellites and sequences of the Mitochondrial Control Region were characterized. Estimators of genetic diversity and population differentiation along with tests of population assignment were applied. Results: Nuclear loci were highly polymorphic as shown by the Polymorphic Information Content (0.599) and the Probability of Identity (1.896 10-08). Both populations were highly diverse and clearly differentiated into two groups corresponding to the Old Type and New Type phenotypes. In contrast, mitochondrial data failed to distinguish these two groups and showed extensive admixture. Conclusions: This study optimized a set of ten highly polymorphic nuclear markers that may be used for parentage and population genetic studies of Aberdeen Angus. Genetic differentiation in these loci agreed with phenotypic differences of the Old and New Types. However, mitochondrial data indicated ancestry of multiple European breeds in the origin of Colombian Aberdeen Angus.
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McManus C, Paiva SR, Caetano AR, Hermuche P, Guimarães RF, Carvalho Jr OA, Braga R, Souza Carneiro PL, Ferrugem-Moraes J, De Souza CJH, Faco O, Santos SA, Azevedo HC, De Araujo AM, Façanha DAE, Ianella P. Landscape genetics of sheep in Brazil using SNP markers. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region. Animals (Basel) 2020; 10:ani10111970. [PMID: 33120938 PMCID: PMC7692571 DOI: 10.3390/ani10111970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.
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Diwedi J, Singh AW, Ahlawat S, Sharma R, Arora R, Sharma H, Raja KN, Verma NK, Tantia MS. Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats. Gene 2020; 756:144910. [PMID: 32574758 DOI: 10.1016/j.gene.2020.144910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/01/2020] [Accepted: 06/17/2020] [Indexed: 11/18/2022]
Abstract
Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.
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Affiliation(s)
- Jyotsana Diwedi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Himani Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - K N Raja
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - N K Verma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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