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Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Finocchiaro R, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputation genotypes: Assessing the effect of ancestral genotyping in Holstein-Friesian dairy cows. J Dairy Sci 2024; 107:5869-5880. [PMID: 38490541 DOI: 10.3168/jds.2024-24042] [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: 08/02/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
The objective of this study was to assess the effect of using or not using the genotypes of the parents of a cow for imputing SNPs on the estimation of genomic inbreeding coefficients of cows. Imputation (i.e., genotyped plus imputed) genotypes from 68,127 Italian Holstein dairy cows registered in the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed. Cows were genotyped with the high-density (HD) Illumina Infinium BovineHD BeadChip and GeneSeek Genomic Profiler HD-150K, and the medium-density (MD) GeneSeek Genomic Profiler 3, GeneSeek Genomic Profiler 4, GeneSeek MD, and the Labogena MD. To assess differences among estimators, genomic inbreeding coefficients were estimated with 4 PLINK v1.9 estimators (F, Fhat1,Fhat2, andFhat3), 2 genomic relationship matrix- (grm) based estimators (Fgrm and Fgrm2, with the latter including also pedigree information), and one estimator of runs of homozygosity (ROH; FROH). Assuming that the correct genomic inbreeding coefficients should be those estimated from genotyped SNPs, a comparison of the genomic inbreeding coefficients estimated either with the genotyped SNPs or the SNPs after imputation was made. Information on the presence or absence of genotypic information from sire, dam, and maternal grandsire during the imputation was investigated. Genomic inbreeding coefficients estimated with genotyped SNPs or SNPs after imputation were consistent for F, Fhat3, Fgrm2, and FROH, when at least one of the parents was genotyped. Biased (mainly higher) genomic inbreeding coefficients of imputation SNPs were observed in cows that were genotyped with MD SNP panels whose SNPs were poorly represented in the selected imputation SNP dataset and also did not have their parents genotyped, when compared with what would be expected based on actual genotype data. For cows genotyped with MD the estimators Fhat1, Fhat2, and Fgrm provided higher genomic inbreeding coefficients of imputation SNPs even with both parents and the maternal grandsire genotyped. Overall, FROH was the most robust estimator, followed by F and Fhat3. Our findings suggest that SNPs selection, parental genotyping and estimator should be considered for designing imputation strategies in dairy cattle for estimating genomic inbreeding with imputation SNPs. For computing genomic inbreeding coefficients, it is recommendable to have at least one parent genotyped and use an ROH-based estimator.
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Affiliation(s)
- Christos Dadousis
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | | | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
| | - Maurizio Marusi
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
| | - Martino Cassandro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy; Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro (PD), Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
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Shen Z, Zhang T, Twumasi G, Zhang J, Wang J, Xi Y, Wang R, Wang J, Zhang R, Liu H. Genetic analysis of a Kaijiang duck conservation population through genome-wide scan. Br Poult Sci 2024; 65:378-386. [PMID: 38738932 DOI: 10.1080/00071668.2024.2335937] [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: 09/02/2023] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management.2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population.3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity.4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction.5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts.
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Affiliation(s)
- Z Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - T Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - G Twumasi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Y Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - H Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Mulim HA, Pedrosa VB, Pinto LFB, Tiezzi F, Maltecca C, Schenkel FS, Brito LF. Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data. BMC Genomics 2024; 25:726. [PMID: 39060982 PMCID: PMC11282608 DOI: 10.1186/s12864-024-10642-2] [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: 10/28/2023] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data. RESULTS The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds. CONCLUSIONS The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.
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Affiliation(s)
- Henrique A Mulim
- Department of Animal Sciences, Federal University of Bahia, Salvador, Bahia, 40110-909, Brazil.
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Parana, 84010-330, Brazil
| | | | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50121, Florence, Italy
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Ontario, N1G 2W1, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
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Mahar K, Gurao A, Kumar A, Pratap Singh L, Chitkara M, Gowane GR, Ahlawat S, Niranjan SK, Pundir RK, Kataria RS, Dige MS. Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations. Gene 2024; 928:148787. [PMID: 39053660 DOI: 10.1016/j.gene.2024.148787] [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: 01/15/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.
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Affiliation(s)
- Karan Mahar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Ankita Gurao
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Lalit Pratap Singh
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Meenakshi Chitkara
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Gopal R Gowane
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S K Niranjan
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R K Pundir
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R S Kataria
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - M S Dige
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Zhang X, Yang L, Xie Z, Gan J, Zhu P, Song J, Kang H, Zhang Z, Liu L, Xiang H, Li H. Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity. BMC Genomics 2024; 25:577. [PMID: 38858651 PMCID: PMC11163754 DOI: 10.1186/s12864-024-10492-y] [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: 10/17/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.
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Affiliation(s)
- Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Liu Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Key Laboratory of National Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant, China Conservation and Research Centre for the Giant Panda, Panda National Park, Chengdu, 611830, China
| | - Zhuojun Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiankang Gan
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiani Song
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Zhengfen Zhang
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China.
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Abdelmanova AA, Deniskova TE, Kharzinova VR, Chinarov RY, Boronetskaya OI, Sölkner J, Brem G, Ai H, Huang L, Trukhachev VI, Zinovieva NA. Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples. Animals (Basel) 2024; 14:1629. [PMID: 38891676 PMCID: PMC11171240 DOI: 10.3390/ani14111629] [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: 04/24/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.
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Affiliation(s)
- Alexandra A. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Veronika R. Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Roman Yu Chinarov
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Oksana I. Boronetskaya
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine (VMU), Veterinärplatz, 1210 Vienna, Austria;
| | - Huashui Ai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Vladimir I. Trukhachev
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
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Sheriff O, Ahbara AM, Haile A, Alemayehu K, Han JL, Mwacharo JM. Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Front Genet 2024; 15:1353026. [PMID: 38854428 PMCID: PMC11156998 DOI: 10.3389/fgene.2024.1353026] [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: 12/09/2023] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.
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Affiliation(s)
- Oumer Sheriff
- Department of Animal Science, Assosa University, Assosa, Ethiopia
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abulgasim M. Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
| | - Aynalem Haile
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Kefyalew Alemayehu
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
- Ethiopian Agricultural Transformation Institute, Amhara Agricultural Transformation Center, Bahir Dar, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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Tan X, Liu L, Dong J, Huang M, Zhang J, Li Q, Wang H, Bai L, Cui M, Zhou Z, Wu D, Xiang Y, Li W, Wang D. Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens. BMC Genomics 2024; 25:485. [PMID: 38755540 PMCID: PMC11097469 DOI: 10.1186/s12864-024-10349-4] [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: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. RESULTS To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. CONCLUSION Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, Zhejiang, 321000, China
| | - Yun Xiang
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China.
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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9
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Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [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: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
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Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
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10
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Romanov MN, Shakhin AV, Abdelmanova AS, Volkova NA, Efimov DN, Fisinin VI, Korshunova LG, Anshakov DV, Dotsev AV, Griffin DK, Zinovieva NA. Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka. Genes (Basel) 2024; 15:524. [PMID: 38674458 PMCID: PMC11050503 DOI: 10.3390/genes15040524] [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: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.
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Affiliation(s)
- Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Dmitry N. Efimov
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Vladimir I. Fisinin
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Liudmila G. Korshunova
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Arsen V. Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | | | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
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11
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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024. [PMID: 38520124 DOI: 10.1111/jbg.12862] [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: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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12
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Ojeda-Marín C, Gutiérrez JP, Formoso-Rafferty N, Goyache F, Cervantes I. Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight. J Anim Breed Genet 2024; 141:193-206. [PMID: 37990938 DOI: 10.1111/jbg.12835] [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: 05/24/2023] [Revised: 09/11/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED ) information, on ROH identified using the SW method (FROHSW ) and on ROH identified using the CR method (FROHCR ). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW . Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED . Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.
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Affiliation(s)
- Candela Ojeda-Marín
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Félix Goyache
- Departamento de Producción Agraria, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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13
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Kar D, Ganguly I, Singh S, Bhatia AK, Dixit SP. Genome-wide runs of homozygosity signatures in diverse Indian goat breeds. 3 Biotech 2024; 14:81. [PMID: 38375512 PMCID: PMC10874352 DOI: 10.1007/s13205-024-03921-y] [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: 08/22/2023] [Accepted: 01/05/2024] [Indexed: 02/21/2024] Open
Abstract
The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat (Capra hircus) breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (ALROH) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding (FROH) was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. FROH of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher FROH than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall FROH compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03921-y.
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Affiliation(s)
- Dibyasha Kar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Indrajit Ganguly
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Sanjeev Singh
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Avnish Kumar Bhatia
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - S. P. Dixit
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
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14
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Bayraktar M, Cebeci Z, Gökçe G. Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data. Reprod Domest Anim 2024; 59:e14545. [PMID: 38426375 DOI: 10.1111/rda.14545] [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: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.
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Affiliation(s)
- Mervan Bayraktar
- Division of Biometry and Genetics, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Zeynel Cebeci
- Division of Biometry and Genetics, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Gökhan Gökçe
- Division of Animal Husbandry and Breeding, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
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Ristanic M, Zorc M, Glavinic U, Stevanovic J, Blagojevic J, Maletic M, Stanimirovic Z. Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle. Animals (Basel) 2024; 14:669. [PMID: 38473054 DOI: 10.3390/ani14050669] [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: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.
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Affiliation(s)
- Marko Ristanic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Minja Zorc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1000 Ljubljana, Slovenia
| | - Uros Glavinic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Jevrosima Stevanovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Jovan Blagojevic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Milan Maletic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
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16
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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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Fabbri MC, Lozada-Soto E, Tiezzi F, Čandek-Potokar M, Bovo S, Schiavo G, Fontanesi L, Muñoz M, Ovilo C, Bozzi R. Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study. Animal 2024; 18:101070. [PMID: 38401921 DOI: 10.1016/j.animal.2023.101070] [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: 09/15/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/26/2024] Open
Abstract
Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbreeding is implemented when leveraging autochthonous and cosmopolitan breeds to obtain most of the hybrid vigor.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, United States
| | - Francesco Tiezzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| | | | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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18
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Illa SK, Mumtaz S, Nath S, Mukherjee S, Mukherjee A. Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle. J Appl Genet 2024; 65:167-180. [PMID: 38110827 DOI: 10.1007/s13353-023-00816-1] [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: 02/10/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.
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Affiliation(s)
- Satish Kumar Illa
- Livestock Research Station, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Shabahat Mumtaz
- Animal Husbandry Department, Kolkata, West Bengal State, India
| | - Sapna Nath
- College of Veterinary Science, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Sabyasachi Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
| | - Anupama Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
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Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals (Basel) 2024; 14:444. [PMID: 38338087 PMCID: PMC10854784 DOI: 10.3390/ani14030444] [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: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
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Affiliation(s)
- Xueliang Sun
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yifei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, No. 7, Niusha Road, Chengdu 610066, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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20
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Wang Z, Zhong Z, Xie X, Wang F, Pan D, Wang Q, Pan Y, Xiao Q, Tan Z. Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs. Animals (Basel) 2024; 14:201. [PMID: 38254370 PMCID: PMC10812771 DOI: 10.3390/ani14020201] [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: 11/03/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Tunchang pigs are an indigenous pig population in China known for their high tolerance to roughage, delicious meat, and fecundity. However, the number of Tunchang pigs has been declining due to the influence of commercial breeds and African swine fever, which could potentially lead to inbreeding. To assess the inbreeding level and the genetic basis of important traits in Tunchang pigs, our research investigated the patterns in "runs of homozygosity" (ROHs) using whole genome resequencing data from 32 Tunchang pigs. The study aimed to determine the length, number, coverage, and distribution model of ROHs in Tunchang pigs, as well as genomic regions with high ROH frequencies. The results of the study revealed that a total of 20,499,374 single-nucleotide polymorphisms (SNPs) and 1953 ROH fragments were recognized in 32 individuals. The ROH fragments in Tunchang pigs were predominantly short, ranging from 0.5 to 1 megabases (Mb) in length. Furthermore, the coverage of ROHs varied across chromosomes, with chromosome 3 having the highest coverage and chromosome 11 having the lowest coverage. The genetic diversity of Tunchang pigs was found to be relatively high based on the values of HE (expected heterozygosity), HO (observed heterozygosity), pi (nucleotide diversity), Ne (effective population size), and MAF (minor allele frequency). The average inbreeding coefficients of Tunchang pigs, as determined by three different methods (FHOM, FGRM, and FROH), were 0.019, 0.0138, and 0.0304, respectively. These values indicate that the level of inbreeding in Tunchang pigs is currently low. Additionally, the study identified a total of 13 ROH islands on all chromosomes, which in total contained 38,913 SNPs and 120 genes. These ROH islands included genes associated with economically important traits, including meat quality (GYS1, PHLPP1, SLC27A5, and CRTC1), growth and development (ANKS1A, TAF11, SPDEF, LHB, and PACSIN1), and environmental adaptation (SLC26A7). The findings of this research offer valuable perspectives on the present status of Tunchang pig resources and offer a reference for breeding conservation plans and the efficient utilization of Tunchang pigs in the future. By understanding the inbreeding level and genetic basis of important traits in Tunchang pigs, conservation efforts can be targeted towards maintaining genetic diversity and promoting the sustainable development of this indigenous pig population.
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Affiliation(s)
- Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Deyou Pan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Zhen Tan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
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21
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Falchi L, Cesarani A, Criscione A, Hidalgo J, Garcia A, Mastrangelo S, Macciotta NPP. Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle. J Anim Sci 2024; 102:skae147. [PMID: 38798158 PMCID: PMC11197001 DOI: 10.1093/jas/skae147] [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: 01/24/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024] Open
Abstract
Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs). The present study aimed to test the effect of chip density in detecting ROHom and ROHet in the Italian Simmental cattle breed. A sample of 897 animals were genotyped at low density (50k SNP; 397 individuals), medium density (140k SNP; 348 individuals), or high density (800k SNP; 152 individuals). The number of ROHom and ROHet per animal (nROHom and nROHet, respectively) and their average length were calculated. ROHom or ROHet shared by more than one animal and the number of times a particular SNP was inside a run were also computed (SNPROHom and SNPROHet). As the chip density increased, the nROHom increased, whereas their average length decreased. In contrast, the nROHet decreased and the average length increased as the chip density increased. The most repeated ROHom harbored no genes, whereas in the most repeated ROHet four genes (SNRPN, SNURF, UBE3A, and ATP10A) previously associated with reproductive traits were found. Across the 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, and 37 SNP (located on BTA21) exceeded the 99th percentile in the distribution of the SNPROHom and SNPROHet, respectively. The genomic region on BTA6 mapped the SLIT2, PACRGL, and KCNIP4 genes, whereas 19 and 18 genes were mapped on BTA16 and BTA21, respectively. Interestingly, most of genes found through the ROHet analysis were previously reported to be related to health, reproduction, and fitness traits. The results of the present study confirm that the detection of ROHom is more reliable when the chip density increases, whereas the ROHet trend seems to be the opposite. Genes and quantitative trait loci (QTL) mapped in the highlighted regions confirm that ROHet can be due to balancing selection, thus related to fitness traits, health, and reproduction, whereas ROHom are mainly involved in production traits. The results of the present study strengthened the usefulness of these parameters in analyzing the genomes of livestock and their biological meaning.
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Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, USA
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania 95123, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, USA
| | - Andre Garcia
- American Angus Association, Angus Genetics Inc., Saint Joseph, MO, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari, e Forestali, Università degli Studi di Palermo, Palermo 90128, Italy
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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet 2023; 140:583-595. [PMID: 37282810 DOI: 10.1111/jbg.12812] [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: 10/03/2022] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Camila B Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Welder A Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Luis Artur L Chardulo
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
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24
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Smaragdov MG. Identification of homozygosity-rich regions in the Holstein genome. Vavilovskii Zhurnal Genet Selektsii 2023; 27:471-479. [PMID: 37808215 PMCID: PMC10556852 DOI: 10.18699/vjgb-23-57] [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: 12/04/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 10/10/2023] Open
Abstract
In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.
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Affiliation(s)
- M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia
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25
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. BIOLOGY 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
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Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
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26
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Pacheco HA, Rossoni A, Cecchinato A, Peñagaricano F. Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle. Front Genet 2023; 14:1227310. [PMID: 37485336 PMCID: PMC10356982 DOI: 10.3389/fgene.2023.1227310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Intensive selection for improved productivity has been accompanied by an increase in inbreeding rates and a reduction in genetic diversity. The increase in inbreeding tends to impact performance, especially fitness-related traits such as male fertility. Inbreeding can be monitored using runs of homozygosity (ROH), defined as contiguous lengths of homozygous genotypes observed in an individual's chromosome. The goal of this study was to evaluate the presence of ROH in Italian Brown Swiss cattle and assess its association with bull fertility. First, we evaluated the association between ROH and male fertility using 1,102 Italian Brown Swiss bulls with sire conception rate records and 572 K SNPs spanning the entire genome. Second, we split the entire population into 100 high-fertility and 100 low-fertility bulls to investigate the potential enrichment of ROH segments in the low-fertility group. Finally, we mapped the significant ROH regions to the bovine genome to identify candidate genes associated with sperm biology and male fertility. Notably, there was a negative association between bull fertility and the amount of homozygosity. Four different ROH regions located in chromosomes 6, 10, 11, and 24 were significantly overrepresented in low-fertility bulls (Fisher's exact test, p-value <0.01). Remarkably, these four genomic regions harbor many genes such as WDR19, RPL9, LIAS, UBE2K, DPF3, 5S-rRNA, 7SK, U6, and WDR7 that are related to sperm biology and male fertility. Overall, our findings suggest that inbreeding and increased homozygosity have a negative impact on male fertility in Italian Brown Swiss cattle. The quantification of ROH can contribute to minimizing the inbreeding rate and avoid its negative effect on fitness-related traits, such as male fertility.
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Affiliation(s)
- Hendyel A. Pacheco
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, Zamani P, Moradi MH, Ferdosi MH, Sargolzaei M, Gondro C. Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep. Heredity (Edinb) 2023; 130:358-367. [PMID: 37016136 PMCID: PMC10238534 DOI: 10.1038/s41437-023-00611-y] [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: 12/03/2021] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.
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Affiliation(s)
- Ramin Abdoli
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran.
| | - Seyed Ziaeddin Mirhoseini
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran.
| | - Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
| | - Pouya Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, 65178-33131, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arāk, 38156-8-8349, Iran
| | - Mohammad Hossein Ferdosi
- AGBU, a joint venture of NSW Department of Primary Industries and University of New England, University of New England, Armidale, NSW, 2351, Australia
| | - Mehdi Sargolzaei
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Cedric Gondro
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
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Jourdain J, Barasc H, Faraut T, Calgaro A, Bonnet N, Marcuzzo C, Suin A, Barbat A, Hozé C, Besnard F, Taussat S, Grohs C, Kuchly C, Iampietro C, Donnadieu C, Pinton A, Boichard D, Capitan A. Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets. Genome Res 2023; 33:957-971. [PMID: 37414574 PMCID: PMC10519396 DOI: 10.1101/gr.277787.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 07/08/2023]
Abstract
In this paper, we developed a highly sensitive approach to detect interchromosomal rearrangements in cattle by searching for abnormal linkage disequilibrium patterns between markers located on different chromosomes in large paternal half-sib families genotyped as part of routine genomic evaluations. We screened 5571 families of artificial insemination sires from 15 breeds and revealed 13 putative interchromosomal rearrangements, 12 of which were validated by cytogenetic analysis and long-read sequencing. These consisted of one Robertsonian fusion, 10 reciprocal translocations, and the first case of insertional translocation reported in cattle. Taking advantage of the wealth of data available in cattle, we performed a series of complementary analyses to define the exact nature of these rearrangements, investigate their origins, and search for factors that may have favored their occurrence. We also evaluated the risks to the livestock industry and showed significant negative effects on several traits in the sires and in their balanced or aneuploid progeny compared with wild-type controls. Thus, we present the most comprehensive and thorough screen for interchromosomal rearrangements compatible with normal spermatogenesis in livestock species. This approach is readily applicable to any population that benefits from large genotype data sets, and will have direct applications in animal breeding. Finally, it also offers interesting prospects for basic research by allowing the detection of smaller and rarer types of chromosomal rearrangements than GTG banding, which are interesting models for studying gene regulation and the organization of genome structure.
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Affiliation(s)
- Jeanlin Jourdain
- Eliance, 75012 Paris, France;
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Harmonie Barasc
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Anne Calgaro
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Nathalie Bonnet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Camille Marcuzzo
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Amandine Suin
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Anne Barbat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Chris Hozé
- Eliance, 75012 Paris, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Florian Besnard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
- Idele, 75012 Paris, France
| | - Sébastien Taussat
- Eliance, 75012 Paris, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Carole Iampietro
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Cécile Donnadieu
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Génomique, Université Fédérale de Toulouse, 31320 Castanet-Tolosan, France
| | - Alain Pinton
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320 Castanet-Tolosan, France
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
| | - Aurélien Capitan
- Eliance, 75012 Paris, France;
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, G2B, 78350 Jouy-en-Josas, France
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Matsumoto Y, Konno A, Ishihara G, Inoue-Murayama M. Genetic dissection of behavioral traits related to successful training of drug detection dogs. Sci Rep 2023; 13:7326. [PMID: 37147374 PMCID: PMC10163243 DOI: 10.1038/s41598-023-33638-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/16/2023] [Indexed: 05/07/2023] Open
Abstract
Drug detection dogs play integral roles in society. However, the interplay between their behaviors and genetic characteristics underlying their performance remains uninvestigated. Herein, more than 120,000 genetic variants were evaluated in 326 German Shepherd or Labrador Retriever dogs to profile the genetic traits associated with various behavioral traits related to the successful training of drug detection dogs. Behavioral breed differences were observed in 'friendliness to humans' and 'tolerance to dogs.' A genome-wide association study within both breeds identified 11 regions potentially associated with drug detection dog characteristics as well as 'interest in the target' and 'friendliness to humans,' which are related to drug detection abilities. Among them, 63 protein-coding genes, including Atat1 and Pfn2 known to be associated with anxiety-related or exploration behavior in mice, respectively, were located surrounding the identified candidate polymorphisms. This study highlights genetic characteristics associated with behavioral traits that are important for the successful training of drug detection dogs. Thus, these findings may facilitate improved breeding and training of these dogs.
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Affiliation(s)
- Yuki Matsumoto
- Anicom Specialty Medical Institute Inc., Yokohama, Kanagawa, 231-0033, Japan
| | - Akitsugu Konno
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, 409-0193, Japan
| | - Genki Ishihara
- Anicom Specialty Medical Institute Inc., Yokohama, Kanagawa, 231-0033, Japan
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Wang Q, Zhang J, Wang H, Wang Z, Li Q, Zhao G, Zheng M, Wen J. Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations. Anim Genet 2023; 54:155-165. [PMID: 36541281 DOI: 10.1111/age.13286] [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: 04/12/2022] [Revised: 10/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH = 0.0798) was higher than that of BY_R1 (FROH = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jin Zhang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Hailong Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Zixuan Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guiping Zhao
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jie Wen
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
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31
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Rocha RDFB, Garcia AO, Otto PI, da Silva MVB, Martins MF, Machado MA, Panetto JCDC, Guimarães SEF. Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle. Mamm Genome 2023:10.1007/s00335-023-09989-w. [PMID: 37000236 DOI: 10.1007/s00335-023-09989-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.
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Affiliation(s)
| | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Rio Grande Do Sul, Brazil
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32
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Dash S, Singh A, Dixit SP, Kumar A, Behera R. Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India. Trop Anim Health Prod 2023; 55:129. [PMID: 36952060 DOI: 10.1007/s11250-023-03534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.
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Affiliation(s)
- Soumya Dash
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
- School of Crop Health Policy Support Research, ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India.
| | - Avtar Singh
- Animal Genetics and Breeding Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Avnish Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Rajalaxmi Behera
- Regional Centre, ICAR-Directorate of Poultry Research, Bhubaneswar, 751003, Odisha, India
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33
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Visser C, Lashmar SF, Reding J, Berry DP, van Marle-Köster E. Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds. Front Genet 2023; 14:1136078. [PMID: 37007942 PMCID: PMC10063850 DOI: 10.3389/fgene.2023.1136078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.
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Affiliation(s)
- Carina Visser
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Carina Visser,
| | - Simon Frederick Lashmar
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Jason Reding
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Donagh P. Berry
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Animal and Grassland Research and Innovation Centre, Teagasc, Co. Cork, Ireland
| | - Esté van Marle-Köster
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Koshkina OA, Rodionov AN, Vetokh AN, Gusev IV, Anshakov DV, Stanishevskaya OI, Dotsev AV, Griffin DK, Zinovieva NA. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol 2023; 14:35. [PMID: 36829208 PMCID: PMC9951459 DOI: 10.1186/s40104-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/27/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.
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Affiliation(s)
- Michael N. Romanov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia ,grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Vladimir I. Fisinin
- grid.4886.20000 0001 2192 9124Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Olga A. Koshkina
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Igor V. Gusev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Dmitry V. Anshakov
- grid.4886.20000 0001 2192 9124Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Olga I. Stanishevskaya
- grid.473314.6Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Darren K. Griffin
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [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: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Finocchiaro R, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows. Front Vet Sci 2023; 10:1142476. [PMID: 37187928 PMCID: PMC10180025 DOI: 10.3389/fvets.2023.1142476] [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: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to evaluate the effect of imputation of single nucleotide polymorphisms (SNP) on the estimation of genomic inbreeding coefficients. Imputed genotypes of 68,127 Italian Holstein dairy cows were analyzed. Cows were initially genotyped with two high density (HD) SNP panels, namely the Illumina Infinium BovineHD BeadChip (678 cows; 777,962 SNP) and the Genomic Profiler HD-150K (641 cows; 139,914 SNP), and four medium density (MD): GeneSeek Genomic Profiler 3 (10,679 cows; 26,151 SNP), GeneSeek Genomic Profiler 4 (33,394 cows; 30,113 SNP), GeneSeek MD (12,030 cows; 47,850 SNP) and the Labogena MD (10,705 cows; 41,911 SNP). After imputation, all cows had genomic information on 84,445 SNP. Seven genomic inbreeding estimators were tested: (i) four PLINK v1.9 estimators (F, Fhat1,2,3), (ii) two genomic relationship matrix (grm) estimators [VanRaden's 1st method, but with observed allele frequencies (Fgrm) and VanRaden's 3rd method that is allelic free and pedigree dependent (Fgrm2)], and (iii) a runs of homozygosity (roh) - based estimator (Froh). Genomic inbreeding coefficients of each SNP panel were compared with genomic inbreeding coefficients derived from the 84,445 imputation SNP. Coefficients of the HD SNP panels were consistent between genotyped-imputed SNP (Pearson correlations ~99%), while variability across SNP panels and estimators was observed in the MD SNP panels, with Labogena MD providing, on average, more consistent estimates. The robustness of Labogena MD, can be partly explained by the fact that 97.85% of the SNP of this panel is included in the 84,445 SNP selected by ANAFIBJ for routine genomic imputations, while this percentage for the other MD SNP panels varied between 55 and 60%. Runs of homozygosity was the most robust estimator. Genomic inbreeding estimates using imputation SNP are influenced by the SNP number of the SNP panel that are included in the imputed SNP, and performance of genomic inbreeding estimators depends on the imputation.
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Affiliation(s)
- Christos Dadousis
- Department of Veterinary Science, University of Parma, Parma, Italy
- *Correspondence: Christos Dadousis
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, Italy
| | | | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), Cremona, Italy
| | - Maurizio Marusi
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), Cremona, Italy
| | - Martino Cassandro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), Cremona, Italy
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Legnaro, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, Parma, Italy
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Cesarani A, Mastrangelo S, Congiu M, Portolano B, Gaspa G, Tolone M, Macciotta NPP. Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds. J Anim Breed Genet 2023; 140:28-38. [PMID: 36239218 PMCID: PMC10092622 DOI: 10.1111/jbg.12741] [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: 04/22/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022]
Abstract
The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED ), or runs of homozygosity (ROH; FROH ) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of FROH . The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.
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Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Michele Congiu
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Giustino Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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Dedato MN, Robert C, Taillon J, Shafer ABA, Côté SD. Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec. Evol Appl 2022; 15:2043-2053. [PMID: 36540642 PMCID: PMC9753816 DOI: 10.1111/eva.13495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/31/2022] [Accepted: 10/06/2022] [Indexed: 08/04/2023] Open
Abstract
The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θ π and estimated the coalescent or ancestral effective population size (N e), which ranged from 12,030 to 15,513. When compared to the census size, N C, the endangered Gaspésie Mountain caribou population had the highest ancestral N e:N C ratio which is consistent with recent work suggesting high ancestral N e:N C is of conservation concern. In contrast, values of contemporary N e, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e:N C ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral N e and Tajima's D into management decisions.
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Affiliation(s)
- Morgan N. Dedato
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Claude Robert
- Département des Sciences AnimalesUniversité LavalQuébecQuébecCanada
| | - Joëlle Taillon
- Direction de l'expertise sur la Faune Terrestre, l'herpétofaune et l'avifaune, Ministère des Forêts, de la faune et des parcsGouvernement du QuébecQuébecQuébecCanada
| | - Aaron B. A. Shafer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Forensics DepartmentTrent UniversityPeterboroughOntarioCanada
| | - Steeve D. Côté
- Département de Biologie, Caribou Ungava and Centre d'Études NordiquesUniversité LavalQuébecQuébecCanada
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Lashmar SF, Visser C, Okpeku M, Muchadeyi FC, Mapholi NO, van Marle-Köster E. A within- and across-country assessment of the genomic diversity and autozygosity of South African and eSwatini Nguni cattle. Trop Anim Health Prod 2022; 54:365. [DOI: 10.1007/s11250-022-03373-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
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Ballan M, Schiavo G, Bovo S, Schiavitto M, Negrini R, Frabetti A, Fornasini D, Fontanesi L. Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds. Anim Genet 2022; 53:849-862. [PMID: 36073189 PMCID: PMC9826494 DOI: 10.1111/age.13264] [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: 01/24/2022] [Revised: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.
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Affiliation(s)
- Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Michele Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Contrada Giancola SncVolturara AppulaItaly
| | | | | | | | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
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Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types. Animals (Basel) 2022; 12:ani12233293. [PMID: 36496815 PMCID: PMC9736150 DOI: 10.3390/ani12233293] [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: 09/28/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.
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Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
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Lozada-Soto EA, Tiezzi F, Jiang J, Cole JB, VanRaden PM, Maltecca C. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. J Dairy Sci 2022; 105:8956-8971. [PMID: 36153159 DOI: 10.3168/jds.2022-22116] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022]
Abstract
Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (FPED), marker-based using a genomic relationship matrix (FGRM), and segment-based using ROH (FROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using FPED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using FGRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using FROH. In addition, the effective population size at past generations (5-100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.
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Affiliation(s)
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50144 Florence, Italy
| | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh 27607
| | | | - Paul M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh 27607
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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
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Wu X, Zhou R, Wang Y, Zhang W, Zheng X, Zhao G, Zhang X, Yin Z, Ding Y. Genome‐wide scan for runs of homozygosity in Asian wild boars and Anqing six‐end‐white pigs. Anim Genet 2022; 53:867-871. [DOI: 10.1111/age.13250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/26/2022] [Accepted: 08/02/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Ren Zhou
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yuanlang Wang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Wei Zhang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Xianrui Zheng
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Guiying Zhao
- College of Animal Science and Technology Yunnan Agricultural University Kunming China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
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Chokoe TC, Hadebe K, Muchadeyi FC, Nephawe KA, Dzomba EF, Mphahlele TD, Matelele TC, Mtileni BJ. Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker. Front Genet 2022; 13:909472. [PMID: 36017496 PMCID: PMC9395594 DOI: 10.3389/fgene.2022.909472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.
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Affiliation(s)
- T. C. Chokoe
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
- School of Agriculture & Environmental Sciences, University of Limpopo, Polokwane, South Africa
- *Correspondence: T. C. Chokoe,
| | - K. Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - K. A. Nephawe
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of Kwazulu-Natal, Scottsville, South African
| | - T. D. Mphahlele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - T. C. Matelele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - B. J. Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
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Mulim HA, Brito LF, Batista Pinto LF, Moletta JL, Da Silva LR, Pedrosa VB. Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems. Front Genet 2022; 13:858970. [PMID: 35923708 PMCID: PMC9341487 DOI: 10.3389/fgene.2022.858970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.
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Affiliation(s)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | | | | | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, Brazil
- *Correspondence: Victor Breno Pedrosa,
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Toro-Ospina AM, Herrera Rios AC, Pimenta Schettini G, Vallejo Aristizabal VH, Bizarria dos Santos W, Zapata CA, Ortiz Morea EG. Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia). Genes (Basel) 2022; 13:genes13071232. [PMID: 35886015 PMCID: PMC9318017 DOI: 10.3390/genes13071232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.
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Affiliation(s)
- Alejandra M. Toro-Ospina
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Correspondence:
| | - Ana C. Herrera Rios
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia
| | - Gustavo Pimenta Schettini
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA;
| | - Viviana H. Vallejo Aristizabal
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil;
| | - Cesar A. Zapata
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Edna Gicela Ortiz Morea
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
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Breeding Sustainable Beef Cows: Reducing Weight and Increasing Productivity. Animals (Basel) 2022; 12:ani12141745. [PMID: 35883292 PMCID: PMC9311566 DOI: 10.3390/ani12141745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions. Cumulative weight weaned reflects reproductive performance and avoidance of premature culling for characteristics related to animal health, welfare, and worker safety. Both traits were evaluated with random regression models with records from a crossbred population representing 18 breeds that conduct US national cattle evaluations. The genomic REML analyses included additive and dominance components, with relationships among 22,776 animals constructed from genotypes of 181,286 potentially functional variants imputed from a low-pass sequence. Projected to 8 years of age, the additive heritability estimate for CW was 0.57 and 0.11 for WtW. Dominance heritability was 0.02 for CW and 0.19 for WtW. Many variants with significant associations with CW were within previously described quantitative trait loci (QTL) for growth-related production, meat, and carcass traits. Significant additive WtW variants were covered by QTL for traits related to reproduction and structural soundness. All breeds contributed to groups of cows with high and low total genetic values (additive + dominance effects) for both traits. The high WtW cows and cows above the WtW mean but below the CW mean had larger heterosis values and fewer bases in runs of homozygosity. The high additive heritability of CW and dominance effects on WtW indicate that breeding to improve beef cow sustainability should involve selection to reduce CW and mate selection to maintain heterosis and reduce runs of homozygosity.
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