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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [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] [Indexed: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Sivalingam J, Niranjan SK, Yadav DK, Singh SP, Sukhija N, Kanaka KK, Singh PK, Singh AP. Phenotypic and genetic characterization of unexplored, potential cattle population of Madhya Pradesh. Trop Anim Health Prod 2024; 56:102. [PMID: 38478192 DOI: 10.1007/s11250-024-03946-8] [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: 06/17/2023] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
Bawri or Garri, a non-descript cattle population managed under an extensive system in Madhya Pradesh state of India, was identified and characterized both genetically and phenotypically to check whether or not it can be recognised as a breed. The cattle have white and gray colour and are medium sized with 122.5 ± 7.5 cm and 109.45 ± 0.39 cm height at withers in male and female, respectively. Double-digest restriction site associated DNA (ddRAD) sequencing was employed to identify ascertainment bias free SNPs representing the entire genome cost effectively; resulting in calling 1,156,650 high quality SNPs. Observed homozygosity was 0.76, indicating Bawri as a quite unique population. However, the inbreeding coefficient was 0.025, indicating lack of selection. SNPs found here can be used in GWAS and genetic evaluation programs. Considering the uniqueness of Bawri cattle, it can be registered as a breed for its better genetic management.
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Affiliation(s)
- Jayakumar Sivalingam
- Presently at ICAR-Directorate of Poultry Research, Hyderabad, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
| | - S K Niranjan
- Presently at ICAR-Directorate of Poultry Research, Hyderabad, India
| | | | - S P Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Nidhi Sukhija
- Krishi Vigyan Kendra, Rajmata Vijayaraje Scindia Krishi Vishwavidyalaya, Morena, MP, India
| | - K K Kanaka
- Central Tasar Research and Training Institute, Ranchi, India
| | - P K Singh
- Presently at ICAR-Directorate of Poultry Research, Hyderabad, India
| | - Ajit Pratap Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
- Nanaji Deshmukh Veterinary Science University, Jabalpur, MP, India
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Raja TV, Alex R, Singh U, Kumar S, Das AK, Sengar G, Singh AK, Ghosh A, Saha S, Mitra A. Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India. 3 Biotech 2023; 13:310. [PMID: 37621321 PMCID: PMC10444711 DOI: 10.1007/s13205-023-03701-0] [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: 03/03/2023] [Accepted: 06/26/2023] [Indexed: 08/26/2023] Open
Abstract
The Frieswal™ is a crossbred cattle evolved by ICAR-Central Institute for Research on Cattle utilizing more than 15,000 cattle maintained at more than 37 military farms spread all over the agro-climatic regions of the country. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs. The results of variant calling revealed 1,487,851 SNPs and 128,175 INDELs at a read depth of 10. A total of 3,775,079 effects were identified, and majority (66.41%) of the effects were in the intron region of the genome followed by intergenic (21.87%). Majority (99.18%) of the variants had the modifier effect. The results revealed a higher magnitude of transitions as compared to the transversion. The classification of SNPs by functional class revealed a majority of missense (43%) and silent (56%) effects. Out of 26,278 genes identified, 1841 SNPs were annotated in 207 candidate genes responsible for various milk production and reproduction traits. The observed heterozygosity was 0.2804 against the expected heterozygosity value of 0.2978. The overall average inbreeding coefficient (FIS) was 0.0604. The pathway analysis revealed that the prolactin signaling pathway (GO:0038161) was significant biological process complete for both milk production and reproduction traits. The SNP variations can be effectively used as markers for early and accurate identification of the QTLs and for formulating an efficient and effective breed improvement program in Frieswal™ cattle. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03701-0.
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Affiliation(s)
- Thiruvothur Venkatesan Raja
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Rani Alex
- National Dairy Research Institute, Karnal, Haryana India
| | - Umesh Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Sushil Kumar
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Achintya Kumar Das
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Gyanendra Sengar
- National Research Centre on Pigs, Rani (Near Airport), Guwahati, Assam 781 131 India
| | - Amit Kumar Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India
| | - Abhijit Mitra
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
- Present Address: Animal Husbandry Commissioner, Department of Animal Husbandry and Dairying, Government of India, New Delhi, India
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Lee YS, Son S, Lee HK, Lee RH, Shin D. Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds' genomic characteristics. Anim Cells Syst (Seoul) 2022; 26:338-347. [PMID: 36605594 PMCID: PMC9809348 DOI: 10.1080/19768354.2022.2141316] [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] [Indexed: 11/10/2022] Open
Abstract
Although conserving native pig breeds is important in Korea, research on the genomic aspects to identify breed-specific variations in native pig breeds is uncommon. Single nucleotide polymorphisms (SNPs) can be a powerful source for identifying breed-specific variants. We used whole genome sequencing data, including Jeju Native Pig (JNP), Korean Native Pig (KNP), Korean Wild Boar (KWB), and other western commercial pig breeds to determine native pig breed-specific SNPs. Furthermore, the goal was not only to determine the genomic specificity of native pig breeds but also to identify SNPs that carry breed-specific information (breed-informative SNPs) that can be related to breed characteristics. The representative characteristics of native pigs are their unique meat quality and disease resistance. We surveyed the gene ontology (GO) of native pigs with breed-specific SNPs. Examining the genes associated with GO may contribute to revealing the reasons for the unique characteristics of native pig breeds. The enriched GOs terms were neuron projection development, cell surface receptor signaling pathway, ion homeostasis in JNP, cell adhesion and wound healing in KNP, and DNA repair and reproduction in KWB. We expect that this study of breed-specific SNPs will enable us to gain a deeper understanding of native pigs in Korea.
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Affiliation(s)
- Young-Sup Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seungwoo Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea,Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ra Ham Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea, Ra Ham Lee Department of Animal Biotechnology, Jeonbuk National University, Jeonju54896, Republic of Korea; Donghyun Shin Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju54896, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea, Ra Ham Lee Department of Animal Biotechnology, Jeonbuk National University, Jeonju54896, Republic of Korea; Donghyun Shin Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju54896, Republic of Korea
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Devadasan MJ, Kumar DR, Vineeth MR, Choudhary A, Surya T, Niranjan SK, Verma A, Sivalingam J. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech 2020; 10:309. [PMID: 32582506 DOI: 10.1007/s13205-020-02297-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.
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Affiliation(s)
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | - M R Vineeth
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - T Surya
- ICAR-National Dairy Research Institute, Karnal, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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Genetic position of Hungarian Grey among European cattle and identification of breed-specific markers. Animal 2020; 14:1786-1792. [PMID: 32248869 DOI: 10.1017/s1751731120000634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hungarian Grey is an indigenous cattle breed that is one of the national symbols of Hungary. However, genetic description of the Hungarian Grey cattle has not yet been conducted based on whole-genome screening. Using the GeneSeek high-density Bovine SNP (single nucleotide polymorphism) 150 K BeadChip, we sampled the genome of 36 Hungarian Grey, 12 Maremmana, 13 Hungarian Fleckvieh and 5 Holstein-Friesian cattle for population studies and used data of 139 other cattle from an additional dataset created on European cattle breeds (Upadhyay et al.2017. Heredity 118, 169-176). The performance of a multidimensional scaling plot showed that Hungarian Grey clustered independently from other European cattle. The number and total length of runs of homozygosity (ROH) is similar or slightly below the value of other European cattle; FROH coefficients (proportion of the autosomal genome covered by ROH) are similar to Maremmana and Maronesa. The frequency of ROH does not show increased values as it can be noticed in Heck and Maltese. These results indicate that the Hungarian Grey cattle have been successfully maintained avoiding negative genetic effects, and reflect the uniqueness among European cattle. The identification of breed-specific loci has been aimed at differentiating Hungarian Grey (n = 136 in this case) from other cattle breeds (n = 169). Ten loci (-log10P > 5) were identified as markers capable for differentiation of Hungarian Grey. These markers are located on chromosomes 6, 14, 15, 16, 20 and 24.
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Guan D, Landi V, Luigi-Sierra MG, Delgado JV, Such X, Castelló A, Cabrera B, Mármol-Sánchez E, Fernández-Alvarez J, de la Torre Casañas JLR, Martínez A, Jordana J, Amills M. Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats. J Anim Sci Biotechnol 2020; 11:35. [PMID: 32175082 PMCID: PMC7065321 DOI: 10.1186/s40104-020-00435-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/19/2022] Open
Abstract
Background In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats. Results The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins. Conclusions The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.
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Affiliation(s)
- Dailu Guan
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vincenzo Landi
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - María Gracia Luigi-Sierra
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Xavier Such
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Castelló
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Betlem Cabrera
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Emilio Mármol-Sánchez
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Javier Fernández-Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340 Granada, Spain
| | | | - Amparo Martínez
- 2Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Jordi Jordana
- 3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- 1Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,3Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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