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Luong NN, Ha HTT, Huy NX, Loi BV, Van NH, Quang HT, Loc NH. Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics. Animals (Basel) 2024; 14:2020. [PMID: 39061482 DOI: 10.3390/ani14142020] [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: 05/03/2024] [Revised: 06/24/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress-a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts.
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Affiliation(s)
- Nguyen Ngoc Luong
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
| | - Huynh Thi Thu Ha
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
| | - Nguyen Xuan Huy
- Department of Science, Technology and International Relations, Hue University, 4 Le Loi, Hue 530000, Vietnam
- Faculty of Biology, University of Education, Hue University, 34 Le Loi, Hue 530000, Vietnam
| | - Bui Van Loi
- Presidential Board, Hue University, 3 Le Loi, Hue 530000, Vietnam
| | - Nguyen Huu Van
- University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Hoang Tan Quang
- Institute of Biotechnology, Hue University, Tinh Lo 10, Phu Thuong, Phu Vang 536801, Vietnam
| | - Nguyen Hoang Loc
- College of Sciences, Hue University, 77 Nguyen Hue, Hue 530000, Vietnam
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Machová K, Málková A, Vostrý L. Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes. Genes (Basel) 2022; 13:genes13040613. [PMID: 35456419 PMCID: PMC9025449 DOI: 10.3390/genes13040613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/26/2022] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
- Correspondence:
| | - Anežka Málková
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Luboš Vostrý
- Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic;
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An 8.22 Mb Assembly and Annotation of the Alpaca ( Vicugna pacos) Y Chromosome. Genes (Basel) 2021; 12:genes12010105. [PMID: 33467186 PMCID: PMC7830431 DOI: 10.3390/genes12010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
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