Genomic insight into X chromosome dynamics in high altitude adaptation of trans-Himalayan yaks DOI Creative Commons
Mahesh Shivanand Dige,

Karan Mahar,

Rangasai Chandra Goli

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 28, 2024

Abstract This study delves into the genomic foundations of high-altitude adaptation in Indian yaks, with a specific emphasis on X chromosome and its role traits related to production, reproduction, immunity. Utilizing whole-genome resequencing, we identified 319,015 high-quality chromosomal SNPs from 30 unrelated yaks 8 Jinchuan yaks. These were analyzed through various statistical methodologies, including composite likelihood ratio (CLR) statistics, Tajima’s D, iHS, FST, XP-EHH. Our findings highlight several genes associated adaptation, such as AIFM1, APOOL, ATRX, CHST7, DACH2, DGAT2L6, DIAPH2, EIF2S3B, CLR approaches. Additionally, GPR119, HS6ST2, MAGED1, MOSPD1, PQBP1, SLC25A14, SLC35A2, TIMM17B, WDR44 exhibited common selection signatures across FST XP-EHH methods. Unique loci each yak population uncovered chromosome, which are critical for adaptability, immunity, production traits. Notably, our regions containing RLIM gene Himachali is crucial Dosage Compensation chromosome. research offers new insights X-linked different populations, enhancing understanding mechanisms underlying adaptation.

Language: Английский

Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness DOI

Rangasai Chandra Goli,

Karan Mahar,

Peela Sai Manohar

et al.

Mammalian Genome, Journal Year: 2024, Volume and Issue: 35(4), P. 657 - 672

Published: Aug. 27, 2024

Language: Английский

Citations

7
Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs DOI Creative Commons
Yinping Tian, Yu Lin, Yue Ma

et al.

Biology, Journal Year: 2025, Volume and Issue: 14(1), P. 30 - 30

Published: Jan. 2, 2025

The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during development maintenance traits desired by humans. White raccoon dogs are among most popular farmed dogs, but white more susceptible to disease have lower reproductive ability. However, accumulation deleterious this breed is largely unknown. By analyzing comparing whole-genome sequencing data 20 38 normal we detected an increased occurrence loss-of-function (LoF) compared dogs. With finding significantly higher dosage homozygous missense dog genome, greater fitness cost Although much FROH level for ROH fragments longer than 1 Mb has been reported did not detect signal purging This study provides valuable genomic resources new insights into mutation loads

Language: Английский

Citations

0
Dissecting genomes of multiple yak populations: unveiling ancestry and high-altitude adaptation through whole-genome resequencing analysis DOI Creative Commons
Sheikh Firdous Ahmad,

Munish Gangwar,

Amit Kumar

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 3, 2025

The present study was undertaken to elucidate the population structure and differentiation of Indian yak from Chinese wild cohorts on genome-wide scale by identifying selection sweeps genomic basis their adaptation across different comparisons while analyzing whole genome sequencing (WGS) data using latest bioinformatics tools. included 105 individuals three distinct populations i.e., (n = 29); 61) 15), hypothesized be related along evolutionary timescale. Efficient variant calling quality control in GATK PLINK programs resulted around 1 million (1,002,970) high-quality (LD-independent) SNPs with an average genotyping rate 96.55%. PCA, ADMIXTURE TREEMIX analysis revealed stratification groups into clusters. empirical distribution pattern minor allele frequency (MAF) also elucidated for revealing unique five bins. signature candidate genes that are important against harsh environmental conditions habitats. Under iHS analysis, several were identified under pressure including ABCA12, EXOC1, JUNB, KLF1, PRDX2, NANOS3, RFX1, RFX2, CACNG7. On other hand, like NR2F2, OSBPL10, CIDEC, WFIKKN2, ADCY, THSD7A, ADGRB3, TRPC1, VASH2, ABHD5 part selective these comparisons. A total 53 found common between intra- inter-population yak. Notably, harbouring significant traits lipidogenesis, energy metabolism, thermogenesis, hair follicle formation, oxidation–reduction reactions, hypoxia reproduction. These may evaluated as livestock further research application era climate change.

Language: Английский

Citations

0
X-linked signatures of positive selection and adaptive genetic plasticity shaping high-altitude resilience in Indian Changthangi sheep DOI

Rangasai Chandra Goli,

Karan Mahar,

Kiyevi G Chishi

et al.

Small Ruminant Research, Journal Year: 2025, Volume and Issue: unknown, P. 107492 - 107492

Published: March 1, 2025

Language: Английский

Citations

0
Splenic comparative transcriptome analysis reveals the immunological mode of undomesticated Gayal (Bos frontalis) for adapting to harsh environments DOI Creative Commons
Ye Yu,

Chunjia Jin,

Runqi Fu

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 20, 2025

The utilization of transcriptome technology in the identification pivotal regulatory genes associated with immunity is paramount importance. Previous studies have shown that undomesticated gayal (Bos frontalis) may higher humoral responses which comparable to yaks. However, research on immune function limited, and comparisons different breeds are rarely reported. objective this study was inspect status compare splenic differential expression (DEGs) through comparative analysis domesticated local cattle (Yunan yellow cattle). Serum immunological investigation showed better lower levels pro-inflammatory cytokines when compared cattle. Spleen RNA-seq 708 DEGs (365 up- 343 down-regulated genes) were obtained between Kyoto Encyclopedia Genes Genomes (KEGG) Gene Ontology (GO) enrichment system pathways, disease chemotaxis-related molecular significantly enriched, whereas T cell-related cellular component biological process downregulated gayal. Correlation CD1, CD36, CD38, CD179a, CD179b, CXCL8, IGCGAMMA, IGH, IGHG1, IGLL1, IL1R2, SERPINB, SERPINB4 had positive correlations IgA, IgD, IgE, IgG, IgM, respectively (R > 0.5, P < 0.05). ANPEP, BVD1.23, CD1E, CD3D, CD3E, CD3G, CD5, CD8 A, HBB, IDO1, LCK, MGC126945, MHC1, TRAV, TRBV, ZAP70 negative -0.5, Our results reveal mode high-level enhanced immunoglobulin gene B cell differentiation, enable adapt harsh environments.

Language: Английский

Citations

0
Hallmarks of selection located in scaffold-level polar bear genome sheds light on genomic rhythmicity DOI

K K Kanaka,

Immanual Gilwax Prabhu,

Rangasai Chandra Goli

et al.

Biological Rhythm Research, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 14

Published: May 22, 2025

Language: Английский

Citations

0
Runs of Homozygosity decipher genetic diversity in cattle breed dwelling in the colder regions of the world DOI

Karan Mahar,

Rangasai Chandra Goli,

Kiyevi G Chishi

et al.

Cytogenetic and Genome Research, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 11

Published: Oct. 5, 2024

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs homozygosity (ROHs). cattle are adapted to Siberia’s harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies this breed scanty, document genetic uniqueness in these cattle. Results: We analyzed 40 with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual an average length 9 Mb. regions were found be involved important pathways pertaining cold adaptation. Autozygosity ranged from 1% 12% genome, relatively low coefficient (F<sub>ROH</sub>) 0.057, as compared other breeds. Also, different indicators, namely, principal component analysis, heterozygosity, effective size revealed prevalence within breed. Conclusion: findings first kind that support their adaptability colder environments, evidenced by high diversity.

Language: Английский

Citations

2
Genomic insights into high-altitude adaptation and evolutionary dynamics of Indian yaks in the Trans-Himalayan region DOI

Karan Mahar,

Ankita Gurao, Amod Kumar

et al.

Conservation Genetics, Journal Year: 2024, Volume and Issue: 26(1), P. 49 - 62

Published: Oct. 25, 2024

Language: Английский

Citations

1
Genomic insight into X chromosome dynamics in high altitude adaptation of trans-Himalayan yaks DOI Creative Commons
Mahesh Shivanand Dige,

Karan Mahar,

Rangasai Chandra Goli

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 28, 2024

Abstract This study delves into the genomic foundations of high-altitude adaptation in Indian yaks, with a specific emphasis on X chromosome and its role traits related to production, reproduction, immunity. Utilizing whole-genome resequencing, we identified 319,015 high-quality chromosomal SNPs from 30 unrelated yaks 8 Jinchuan yaks. These were analyzed through various statistical methodologies, including composite likelihood ratio (CLR) statistics, Tajima’s D, iHS, FST, XP-EHH. Our findings highlight several genes associated adaptation, such as AIFM1, APOOL, ATRX, CHST7, DACH2, DGAT2L6, DIAPH2, EIF2S3B, CLR approaches. Additionally, GPR119, HS6ST2, MAGED1, MOSPD1, PQBP1, SLC25A14, SLC35A2, TIMM17B, WDR44 exhibited common selection signatures across FST XP-EHH methods. Unique loci each yak population uncovered chromosome, which are critical for adaptability, immunity, production traits. Notably, our regions containing RLIM gene Himachali is crucial Dosage Compensation chromosome. research offers new insights X-linked different populations, enhancing understanding mechanisms underlying adaptation.

Language: Английский

Citations

1