Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs
Abstract This research aimed to characterize the mitochondrial genome of the Ghoongroo (GH) pig, a notable breed in India, along with its crossbred varieties, to elucidate their matrilineal components, evolutionary history, and implications for conservation. Seven pigs (5 GH, 2 crossbred, namely Ran...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-024-81205-4 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832594862908637184 |
|---|---|
| author | Pranab Jyoti Das Satish Kumar Manasee Choudhury Seema Rani Pegu K. Meera Rajib Deb Sunil Kumar Santanu Banik Vivek Kumar Gupta |
| author_facet | Pranab Jyoti Das Satish Kumar Manasee Choudhury Seema Rani Pegu K. Meera Rajib Deb Sunil Kumar Santanu Banik Vivek Kumar Gupta |
| author_sort | Pranab Jyoti Das |
| collection | DOAJ |
| description | Abstract This research aimed to characterize the mitochondrial genome of the Ghoongroo (GH) pig, a notable breed in India, along with its crossbred varieties, to elucidate their matrilineal components, evolutionary history, and implications for conservation. Seven pigs (5 GH, 2 crossbred, namely Rani and Asha) were sequenced for complete mitochondrial genome, while 24 pigs (11 GH, 6 Rani, and 7 Asha) were sequenced for the complete D-loop of the mitochondrial genome. The genome size of these pigs was determined to be 16,690 bp. Analysis of the mitochondrial sequences and phylogenetics uncovered two distinct matrilineal components within the GH population, a phenomenon also observed in its crossbred counterparts, Rani and Asha. Phylogenetic analysis demonstrated a clear clustering of GH sequences into two clades, indicating the presence of two independent maternal lineages. The phylogenetic study using complete mitogenome also indicated that GH pigs were originated locally from Indian wild boar independently from Asian and European pig population. Haplotype analysis from complete D-loop sequences revealed 10 different haplotypes, with some sequences shared among GH, Rani, and Asha, while others differed due to varying matrilineal origins. The haplotype analysis using complete mitogenome sequences revealed 16 different haplotypes with some shared sequences among GH. Furthermore, examination of tRNA genes and nucleotide composition of different genes namely rRNAs, COX1, COX2, ATP6, ND4, ND5, ND6, Cytb offered insights into genetic diversity within these pigs. The findings suggest that geographical isolation and historical events likely contributed to the emergence of distinct maternal lineages within the GH breed. This study underscores the significance of mitochondrial DNA analysis in uncovering hidden genetic diversity within seemingly uniform populations. The molecular insights gained into the genetic makeup of GH pigs could aid in designing effective breeding programs for conservation efforts and highlight its significance in understanding the broader context of pig domestication in India. |
| format | Article |
| id | doaj-art-d4accb61a7844ce3840df029741910f4 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-d4accb61a7844ce3840df029741910f42025-01-19T12:18:54ZengNature PortfolioScientific Reports2045-23222025-01-0115111810.1038/s41598-024-81205-4Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigsPranab Jyoti Das0Satish Kumar1Manasee Choudhury2Seema Rani Pegu3K. Meera4Rajib Deb5Sunil Kumar6Santanu Banik7Vivek Kumar Gupta8Animal Genetics and Breeding, ICAR-National Research Centre on PigAnimal Genetics and Breeding, ICAR-National Research Centre on PigAnimal Genetics and Breeding, ICAR-National Research Centre on PigAnimal Health, ICAR-National Research Centre on PigAnimal Genetics and Breeding, ICAR-National Research Centre on PigAnimal Health, ICAR-National Research Centre on PigAnimal Reproduction, ICAR-National Research Centre on PigAnimal Genetics and Breeding, ICAR-National Research Centre on PigAnimal Health, ICAR-National Research Centre on PigAbstract This research aimed to characterize the mitochondrial genome of the Ghoongroo (GH) pig, a notable breed in India, along with its crossbred varieties, to elucidate their matrilineal components, evolutionary history, and implications for conservation. Seven pigs (5 GH, 2 crossbred, namely Rani and Asha) were sequenced for complete mitochondrial genome, while 24 pigs (11 GH, 6 Rani, and 7 Asha) were sequenced for the complete D-loop of the mitochondrial genome. The genome size of these pigs was determined to be 16,690 bp. Analysis of the mitochondrial sequences and phylogenetics uncovered two distinct matrilineal components within the GH population, a phenomenon also observed in its crossbred counterparts, Rani and Asha. Phylogenetic analysis demonstrated a clear clustering of GH sequences into two clades, indicating the presence of two independent maternal lineages. The phylogenetic study using complete mitogenome also indicated that GH pigs were originated locally from Indian wild boar independently from Asian and European pig population. Haplotype analysis from complete D-loop sequences revealed 10 different haplotypes, with some sequences shared among GH, Rani, and Asha, while others differed due to varying matrilineal origins. The haplotype analysis using complete mitogenome sequences revealed 16 different haplotypes with some shared sequences among GH. Furthermore, examination of tRNA genes and nucleotide composition of different genes namely rRNAs, COX1, COX2, ATP6, ND4, ND5, ND6, Cytb offered insights into genetic diversity within these pigs. The findings suggest that geographical isolation and historical events likely contributed to the emergence of distinct maternal lineages within the GH breed. This study underscores the significance of mitochondrial DNA analysis in uncovering hidden genetic diversity within seemingly uniform populations. The molecular insights gained into the genetic makeup of GH pigs could aid in designing effective breeding programs for conservation efforts and highlight its significance in understanding the broader context of pig domestication in India.https://doi.org/10.1038/s41598-024-81205-4Indian Ghoongroo pigMitochondrial genomeD-loopDouble matrilinealPhylogeny |
| spellingShingle | Pranab Jyoti Das Satish Kumar Manasee Choudhury Seema Rani Pegu K. Meera Rajib Deb Sunil Kumar Santanu Banik Vivek Kumar Gupta Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs Scientific Reports Indian Ghoongroo pig Mitochondrial genome D-loop Double matrilineal Phylogeny |
| title | Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs |
| title_full | Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs |
| title_fullStr | Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs |
| title_full_unstemmed | Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs |
| title_short | Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs |
| title_sort | complete mitochondrial genome sequence analysis revealed double matrilineal components in indian ghoongroo pigs |
| topic | Indian Ghoongroo pig Mitochondrial genome D-loop Double matrilineal Phylogeny |
| url | https://doi.org/10.1038/s41598-024-81205-4 |
| work_keys_str_mv | AT pranabjyotidas completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT satishkumar completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT manaseechoudhury completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT seemaranipegu completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT kmeera completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT rajibdeb completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT sunilkumar completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT santanubanik completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs AT vivekkumargupta completemitochondrialgenomesequenceanalysisrevealeddoublematrilinealcomponentsinindianghoongroopigs |