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Mao Z, Betti MJ, Cedeno MA, Pedroza LA, Basaria S, Liu Q, Choi JM, Markle JG. Clinical and cellular phenotypes resulting from a founder mutation in IL10RB. Clin Exp Immunol 2024; 216:113-119. [PMID: 37503744 PMCID: PMC11036105 DOI: 10.1093/cei/uxad085] [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: 06/27/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023] Open
Abstract
Inborn errors of immunity are a group of rare genetically determined diseases that impair immune system development or function. Many of these diseases include immune dysregulation, autoimmunity, or autoinflammation as prominent clinical features. In some children diagnosed with very early onset inflammatory bowel disease (VEOIBD), monogenic inborn errors of immune dysregulation underlie disease. We report a case of VEOIBD caused by a novel homozygous loss of function mutation in IL10RB. We use cytometry by time-of-flight with a broad panel of antibodies to interrogate the immunophenotype of this patient and detect reduced frequencies of CD4 and CD8 T cells with additional defects in some populations of T helper cells, innate-like T cells, and memory B cells. Finally, we identify the patient's mutation as a founder allele in an isolated indigenous population and estimate the age of this variant by studying the shared ancestral haplotype.
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Affiliation(s)
- Zhiming Mao
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Michael J Betti
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Miguel A Cedeno
- Department of Pediatrics, Hospital de ninos Roberto Gilbert Elizalde, Guayaquil, Ecuador
| | - Luis A Pedroza
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Shamel Basaria
- Division of Molecular Pathogenesis, Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Liu
- Division of Molecular Pathogenesis, Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph M Choi
- Division of Molecular Pathogenesis, Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Janet G Markle
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Molecular Pathogenesis, Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [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: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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3
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Sarviaho K, Uimari P, Martikainen K. Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population. J Dairy Sci 2024:S0022-0302(24)00548-4. [PMID: 38490540 DOI: 10.3168/jds.2024-24105] [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: 08/21/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits, e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.
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Affiliation(s)
- Katri Sarviaho
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Katja Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J. Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. PLoS One 2024; 19:e0299109. [PMID: 38442089 PMCID: PMC10914290 DOI: 10.1371/journal.pone.0299109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.
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Affiliation(s)
- B. Bazvand
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
| | - A. Rashidi
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
| | - M. B. Zandi
- Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - M. H. Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - J. Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdishistan, Sanandaj, Kurdishistan, Iran
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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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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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Yin C, Wang Y, Zhou P, Shi H, Ma X, Yin Z, Liu Y. Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs. Int J Mol Sci 2023; 24:12914. [PMID: 37629094 PMCID: PMC10454931 DOI: 10.3390/ijms241612914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.
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Affiliation(s)
- Chang Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Yuwei Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Peng Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Haoran Shi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Xinyu Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Yang Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
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Perfilyeva A, Bespalova K, Bespalov S, Begmanova M, Kuzovleva Y, Vishnyakova O, Nazarenko I, Abylkassymova G, Perfilyeva Y, Plakhov K, Djansugurova L, Bekmanov B. Homozygosity mapping in the Kazakh national dog breed Tazy. Sci Rep 2023; 13:10735. [PMID: 37400480 DOI: 10.1038/s41598-023-37990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
The Tazy is a breed of sighthound common in Kazakhstan. The identification of runs of homozygosity (ROH) is an informative approach to assessing the history and possible patterns of directional selection pressure. To our knowledge, the present study is the first to provide an overview of the ROH pattern in the Tazy dogs from a genome-wide perspective. The ROH of the Tazy was found to be mainly composed of shorter segments (1-2 Mb), accounting for approximately 67% of the total ROH. The estimated ROH-based inbreeding coefficients (FROH) ranged from 0.028 to 0.058 with a mean of 0.057. Five genomic regions under positive selection were identified on chromosomes 18, 22, and 25. The regions on chromosomes 18 and 22 may be breed specific, while the region on chromosome 22 overlaps with regions of hunting traits in other hunting dog breeds. Among the 12 candidate genes located in these regions, the gene CAB39L may be a candidate that affects running speed and endurance of the Tazy dog. Eight genes could belong to an evolutionarily conserved complex as they were clustered in a large protein network with strong linkages. The results may enable effective interventions when incorporated into conservation planning and selection of the Tazy breed.
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Affiliation(s)
- Anastassiya Perfilyeva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Kira Bespalova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan.
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan.
| | - Sergey Bespalov
- Department of Theriology, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Mamura Begmanova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yelena Kuzovleva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Olga Vishnyakova
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 050008, Almaty, Kazakhstan
| | - Inna Nazarenko
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 020000, Astana, Kazakhstan
| | - Gulnar Abylkassymova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yuliya Perfilyeva
- Laboratory of Molecular Immunology and Immunobiotechnology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, 050012, Almaty, Kazakhstan
| | - Konstantin Plakhov
- Laboratory of Biocenology and Hunting Management, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Leyla Djansugurova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan
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Cavedon M, Neufeld L, Finnegan L, Hervieux D, Michalak A, Pelletier A, Polfus J, Schwantje H, Skinner G, Steenweg R, Thacker C, Poissant J, Musiani M. Genomics of founders for conservation breeding: the Jasper caribou case. CONSERV GENET 2023; 24:855-867. [PMID: 37969360 PMCID: PMC10638200 DOI: 10.1007/s10592-023-01540-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/07/2023] [Indexed: 11/17/2023]
Abstract
Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01540-3.
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Affiliation(s)
- Maria Cavedon
- Deparment of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Lalenia Neufeld
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Laura Finnegan
- fRI Research, 1176 Switzer Drive, Hinton, AB T7V 1V3 Canada
| | - Dave Hervieux
- Fish and Wildlife Stewardship Branch, Alberta Environment and Protected Areas, Grande Prairie, AB T8V 6J4 Canada
| | - Anita Michalak
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Agnes Pelletier
- Ministry of Land, Water and Resource Stewardship Northeast Region, 400-10003-110Th Avenue, Fort St. John, BC V1J 6M7 Canada
| | - Jean Polfus
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Helen Schwantje
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Geoff Skinner
- Jasper National Park of Canada, Parks Canada, Jasper, Canada
| | - Robin Steenweg
- Canadian Wildlife Service – Pacific Region, Environment and Climate Change Canada, 1238 Discovery Ave, Kelowna, BC V1V 1V9 Canada
| | - Caeley Thacker
- Wildlife and Habitat Branch, Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Government of British Columbia, 2080 Labieux Road, Nanaimo, BC V9T 6J 9 Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marco Musiani
- Dipartimento Scienze Biologiche Geologiche Ambientali, Università Di Bologna, Via Zamboni, 33 - 40126 Bologna, Italia
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10
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Pérez‐Pereira N, Quesada H, Caballero A. An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions. Evol Appl 2023; 16:1302-1315. [PMID: 37492144 PMCID: PMC10363801 DOI: 10.1111/eva.13568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/27/2023] Open
Abstract
Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non-inbred and unrelated individuals (F = 0) and inbred individuals (full-sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness-related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non-inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.
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Affiliation(s)
- Noelia Pérez‐Pereira
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Humberto Quesada
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Armando Caballero
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
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11
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Vahedi SM, Salek Ardetani S, Brito LF, Karimi K, Pahlavan Afshari K, Banabazi MH. Expanding the application of haplotype-based genomic predictions to the wild: A case of antibody response against Teladorsagia circumcincta in Soay sheep. BMC Genomics 2023; 24:335. [PMID: 37330501 DOI: 10.1186/s12864-023-09407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/24/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Genomic prediction of breeding values (GP) has been adopted in evolutionary genomic studies to uncover microevolutionary processes of wild populations or improve captive breeding strategies. While recent evolutionary studies applied GP with individual single nucleotide polymorphism (SNP), haplotype-based GP could outperform individual SNP predictions through better capturing the linkage disequilibrium (LD) between the SNP and quantitative trait loci (QTL). This study aimed to evaluate the accuracy and bias of haplotype-based GP of immunoglobulin (Ig) A (IgA), IgE, and IgG against Teladorsagia circumcincta in lambs of an unmanaged sheep population (Soay breed) based on Genomic Best Linear Unbiased Prediction (GBLUP) and five Bayesian [BayesA, BayesB, BayesCπ, Bayesian Lasso (BayesL), and BayesR] methods. RESULTS The accuracy and bias of GPs using SNP, haplotypic pseudo-SNP from blocks with different LD thresholds (0.15, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, and 1.00), or the combinations of pseudo-SNPs and non-LD clustered SNPs were obtained. Across methods and marker sets, higher ranges of genomic estimated breeding values (GEBV) accuracies were observed for IgA (0.20 to 0.49), followed by IgE (0.08 to 0.20) and IgG (0.05 to 0.14). Considering the methods evaluated, up to 8% gains in GP accuracy of IgG were achieved using pseudo-SNPs compared to SNPs. Up to 3% gain in GP accuracy for IgA was also obtained using the combinations of the pseudo-SNPs with non-clustered SNPs in comparison to fitting individual SNP. No improvement in GP accuracy of IgE was observed using haplotypic pseudo-SNPs or their combination with non-clustered SNPs compared to individual SNP. Bayesian methods outperformed GBLUP for all traits. Most scenarios yielded lower accuracies for all traits with an increased LD threshold. GP models using haplotypic pseudo-SNPs predicted less-biased GEBVs mainly for IgG. For this trait, lower bias was observed with higher LD thresholds, whereas no distinct trend was observed for other traits with changes in LD. CONCLUSIONS Haplotype information improves GP performance of anti-helminthic antibody traits of IgA and IgG compared to fitting individual SNP. The observed gains in the predictive performances indicate that haplotype-based methods could benefit GP of some traits in wild animal populations.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Karim Karimi
- Molecular Diagnostics Program, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Kian Pahlavan Afshari
- Department of Animal Sciences, Islamic Azad University, Varamin, Varamin-Pishva Branch3381774895, Iran
| | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden.
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj, 3146618361, Iran.
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12
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Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J. Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide. Genes (Basel) 2023; 14:1211. [PMID: 37372391 DOI: 10.3390/genes14061211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies.
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Affiliation(s)
- Chujie Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bo Zhu
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Xiangwei Tang
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bin Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Mei Liu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Ning Gao
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sheng Li
- Maxun Biotechnology Institute, Changsha 410024, China
| | - Jingjing Gu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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13
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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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14
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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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15
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Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [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: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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16
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Lavanchy E, Goudet J. Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization. Mol Ecol Resour 2023; 23:787-802. [PMID: 36626297 DOI: 10.1111/1755-0998.13755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Genomic measures of inbreeding based on identical-by-descent (IBD) segments are increasingly used to measure inbreeding and mostly estimated on SNP arrays and whole-genome sequencing (WGS) data. However, some softwares recurrently used for their estimation assume that genomic positions which have not been genotyped are nonvariant. This might be true for WGS data, but not for reduced genomic representations and can lead to spurious IBD segments estimation. In this project, we simulated the outputs of WGS, two SNP arrays of different sizes and RAD-sequencing for three populations with different sizes and histories. We compare the results of IBD segments estimation with two softwares: runs of homozygosity (ROHs) estimated with PLINK and homozygous-by-descent (HBD) segments estimated with RZooRoH. We demonstrate that to obtain meaningful estimates of inbreeding, RZooRoH requires a SNPs density 11 times smaller compared to PLINK: ranks of inbreeding coefficients were conserved among individuals above 22 SNPs/Mb for PLINK and 2 SNPs/Mb for RZooRoH. We also show that in populations with simple demographic histories, distribution of ROHs and HBD segments are correctly estimated with both SNP arrays and WGS. PLINK correctly estimated distribution of ROHs with SNP densities above 22 SNPs/Mb, while RZooRoH correctly estimated distribution of HBD segments with SNPs densities above 11 SNPs/Mb. However, in a population with a more complex demographic history, RZooRoH resulted in better distribution of IBD segments estimation compared to PLINK even with WGS data. Consequently, we advise researchers to use either methods relying on excess homozygosity averaged across SNPs or model-based HBD segments calling methods for inbreeding estimations.
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Affiliation(s)
- Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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17
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Sundell T, Kammonen JI, Mustanoja E, Biard V, Kunnasranta M, Niemi M, Nykänen M, Nyman T, Palo JU, Valtonen M, Paulin L, Jernvall J, Auvinen P. Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractFragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.
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18
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Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China. Animals (Basel) 2022; 12:ani12233239. [PMID: 36496760 PMCID: PMC9737016 DOI: 10.3390/ani12233239] [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: 08/05/2022] [Revised: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.
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19
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Hu T, Wang J, Zhu Q, Zhang Z, Hu R, Xiao L, Yang Y, Liao N, Liu S, Wang H, Niu X, Liu S. Clinical experience of noninvasive prenatal testing for rare chromosome abnormalities in singleton pregnancies. Front Genet 2022; 13:955694. [PMID: 36226167 PMCID: PMC9549601 DOI: 10.3389/fgene.2022.955694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives: The study aimed to investigate the clinical use of noninvasive prenatal testing (NIPT) for common fetal aneuploidies as a prenatal screening tool for the detection of rare chromosomal abnormalities (RCAs). Methods: Gravidas with positive NIPT results for RCAs who subsequently underwent amniocentesis for a single nucleotide polymorphism array (SNP array) were recruited. The degrees of concordance between the NIPT and SNP array were classified into full concordance, partial concordance, and discordance. The positive predictive value (PPV) was used to evaluate the performance of NIPT. Results: The screen-positivity rate of NIPT for RCAs was 0.5% (842/158,824). Of the 528 gravidas who underwent amniocentesis, 29.2% (154/528) were confirmed to have positive prenatal SNP array results. PPVs for rare autosomal trisomies (RATs) and segmental imbalances were 6.1% (7/115) and 21.1% (87/413), respectively. Regions of homozygosity/uniparental disomy (ROH/UPD) were identified in 9.5% (50/528) of gravidas. The PPV for clinically significant findings was 8.0% (42/528), including 7 cases with mosaic RATs, 30 with pathogenic/likely pathogenic copy number variants, and 5 with imprinting disorders. Conclusion: NIPT for common fetal aneuploidies yielded low PPVs for RATs, moderate PPVs for segmental imbalances, and incidental findings for ROH/UPD. Due to the low PPV for clinically significant findings, NIPT for common fetal aneuploidies need to be noticed for RCAs.
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Affiliation(s)
- Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qian Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yunyuan Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Sha Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaoyu Niu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
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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: 0] [Impact Index Per Article: 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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Meiring C, Schurz H, van Helden P, Hoal E, Tromp G, Kinnear C, Kleynhans L, Glanzmann B, van Schalkwyk L, Miller M, Möller M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 2022; 12:14979. [PMID: 36056068 PMCID: PMC9440078 DOI: 10.1038/s41598-022-19025-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
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Affiliation(s)
- Christina Meiring
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Louis van Schalkwyk
- Department of Agriculture, Land Reform and Rural Development, PO Box 12, Skukuza, 1350, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
| | - Michele Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Private bag X1, Merriman Avenue, Stellenbosch, 7600, South Africa
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Morgan AP, Hughes JJ, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, de Villena FPM. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity (Edinb) 2022; 129:183-194. [PMID: 35764696 PMCID: PMC9411160 DOI: 10.1038/s41437-022-00551-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, Duke University Hospital, Durham, NC, USA.
| | - Jonathan J Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Independent Scientist, San Diego, CA, USA
| | | | | | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
| | - Francois Bonhomme
- Institut des Sciences de l'Évolution Montpellier, Université de Montpellier, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Yuan J, Zhou X, Xu G, Xu S, Liu B. Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip. Front Genet 2022; 13:910521. [PMID: 36092902 PMCID: PMC9455598 DOI: 10.3389/fgene.2022.910521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.
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Affiliation(s)
- Jiao Yuan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
| | - Guoqiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sanping Xu
- Department of Agricultural and Rural Bureau, Xianning, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
- *Correspondence: Bang Liu,
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25
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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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26
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Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle. Animals (Basel) 2022; 12:ani12121546. [PMID: 35739882 PMCID: PMC9219517 DOI: 10.3390/ani12121546] [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: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0−5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0−5 Mb 0.929, and lowest correlation for 0−>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs.
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27
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Wang S, Yang J, Li G, Ding R, Zhuang Z, Ruan D, Wu J, Yang H, Zheng E, Cai G, Wang X, Wu Z. Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs. Front Vet Sci 2022; 9:855933. [PMID: 35573406 PMCID: PMC9096619 DOI: 10.3389/fvets.2022.855933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.
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Affiliation(s)
- Shiyuan Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Guixin Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Huaqiang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xiaopeng Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Xiaopeng Wang
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- Zhenfang Wu
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Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, Lieberman Aiden E, Osipova E, Hiller M, Morales HE, Magrath MJL, Clarke RH, Sunnucks P, Pavlova A. Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater. Gigascience 2022; 11:6554768. [PMID: 35348671 PMCID: PMC8963300 DOI: 10.1093/gigascience/giac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/13/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
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Affiliation(s)
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia.,GeneSEQ Sdn Bhd, 48300 Rawang, Selangor, Malaysia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- UWA School of Agriculture and Environment, The University of Western Australia, Perth WA 6009,Australia.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 101307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Hernán E Morales
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Denmark
| | - Michael J L Magrath
- Department of Wildlife Conservation and Science, Zoos Victoria, Parkville, VIC 3052, Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats. J Anim Sci Biotechnol 2022; 13:35. [PMID: 35264251 PMCID: PMC8908635 DOI: 10.1186/s40104-022-00684-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/19/2022] [Indexed: 12/30/2022] Open
Abstract
Background Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. Results We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK, IL27, CCL19 and CCL21. Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. Conclusions Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00684-5.
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Druet T, Gautier M. An hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors. Theor Popul Biol 2022; 145:38-51. [DOI: 10.1016/j.tpb.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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Kim YM, Seong HS, Kim YS, Hong JK, Sa SJ, Lee J, Lee JH, Cho KH, Chung WH, Choi JW, Cho ES. Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon. Front Genet 2022; 13:779152. [PMID: 35186025 PMCID: PMC8847790 DOI: 10.3389/fgene.2022.779152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/07/2022] [Indexed: 02/03/2023] Open
Abstract
A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.
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Affiliation(s)
- Yong-Min Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ha-Seung Seong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Young-Sin Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Joon-Ki Hong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Soo-Jin Sa
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Jun-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Kyu-Ho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, South Korea
| | - Jung-Woo Choi
- Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
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Weng Z, Xu Y, Zhong M, Li W, Chen J, Zhong F, Du B, Zhang B, Huang X. Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data. Br Poult Sci 2021; 63:307-315. [PMID: 34747677 DOI: 10.1080/00071668.2021.2003752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of ten YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated.2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being <1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained.3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, IFNA, IFNB, IL11RA, IL22RA1, IFNLR1, and TRIF genes were involved in disease resistance. The AMY, G6PC, SDHB, GCNT4, and ACO genes were associated with energy material metabolism; and FABPL, AQP7, ACAA2, and RYR2 were related to meat quality and flavour. The KITLG, CREB3, RYR2, and LGR4 genes, related to pigmentation, were detected.4. This ROH-based inbreeding evaluation laid the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.
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Affiliation(s)
- Zhuoxian Weng
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Yongjie Xu
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Ming Zhong
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Weina Li
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Jiebo Chen
- Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Fusheng Zhong
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Bingwang Du
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
| | - Bin Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xunhe Huang
- Jiaying University/Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou 514015, China.,Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, 514015, China
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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34
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Fabbri MC, Dadousis C, Tiezzi F, Maltecca C, Lozada-Soto E, Biffani S, Bozzi R. Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity. PLoS One 2021; 16:e0248087. [PMID: 34695128 PMCID: PMC8544844 DOI: 10.1371/journal.pone.0248087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
- * E-mail:
| | - Christos Dadousis
- Dipartimento di Scienze Medico‐Veterinarie, Università di Parma, Parma, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology (CNR), Milano, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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Koenigstein F, Boekstegers F, Wilson JF, Fuentes-Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Acuña-Alonzo V, Gallo C, Linares AR, Rothhammer F, Bermejo JL. Inbreeding, native American ancestry and child mortality: Linking human selection and paediatric medicine. Hum Mol Genet 2021; 31:975-984. [PMID: 34673976 PMCID: PMC8947305 DOI: 10.1093/hmg/ddab302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The children of related parents show increased risk of early mortality. The Native American genome typically exhibits long stretches of homozygosity, and Latin Americans are highly heterogeneous regarding the individual burden of homozygosity, the proportion, and the type of Native American ancestry. We analysed nationwide mortality and genome-wide genotype data from admixed Chileans to investigate the relationship between common causes of child mortality, homozygosity and Native American ancestry. Results from two-stage linear-Poisson regression revealed a strong association between the sum length of runs of homozygosity (SROH) above 1.5 Megabases (Mb) in each genome and mortality due to intracranial non-traumatic haemorrhage of foetus and new-born (5% increased risk of death per Mb in SROH, P = 1 × 10-3) and disorders related to short gestation and low birth weight (P = 3 × 10-4). The major indigenous populations in Chile are Aymara-Quechua in the north of the country, and the Mapuche-Huilliche in the south. The individual proportion of Aymara-Quechua ancestry was associated with an increased risk of death due to anencephaly and similar malformations (P = 4 × 10-5), and the risk of death due to Edwards and Patau trisomy syndromes decreased 4% per 1% Aymara-Quechua ancestry proportion (P = 4 × 10-4) and 5% per 1% Mapuche-Huilliche ancestry proportion (P = 2 × 10-3). The present results suggest that short gestation, low birth weight and intracranial non-traumatic haemorrhage mediate the negative effect of inbreeding on human selection. Independent validation of the identified associations between common causes of child death, homozygosity and fine-scale ancestry proportions may inform paediatric medicine.
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Affiliation(s)
- Fabienne Koenigstein
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica, Chile
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Instituto de Biología, Grupo Genmol, Universidad de Antioquía, Medellín, Colombia
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
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Hajihosseinlo A, Nejati-Javaremi A, Miraei-Ashtiani SR. Genetic structure analysis in several populations of cattle using SNP genotypes. Anim Biotechnol 2021; 34:288-300. [PMID: 34591729 DOI: 10.1080/10495398.2021.1960360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r2 decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.
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Affiliation(s)
- Abbas Hajihosseinlo
- Department of Animal Science, University of Tehran Aras International Campus, Jolfa, Iran
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37
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Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle. BMC Genomics 2021; 22:678. [PMID: 34548021 PMCID: PMC8454143 DOI: 10.1186/s12864-021-07992-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. RESULTS We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. CONCLUSIONS Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.
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38
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Investigating inbreeding in the turkey (Meleagris gallopavo) genome. Poult Sci 2021; 100:101366. [PMID: 34525446 PMCID: PMC8445901 DOI: 10.1016/j.psj.2021.101366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (FPED) with genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (FROH = 0.27; FGRM = 0.32) were higher than coefficients estimated from pedigree records (FPED = 0.14). Correlations between FROH and FPED, FROH and FGRM, and FPED and FGRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between FROH from different lengths and FPED substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.
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Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun 2021; 12:5425. [PMID: 34521843 PMCID: PMC8440622 DOI: 10.1038/s41467-021-25289-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
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40
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Sumreddee P, Hay EH, Toghiani S, Roberts A, Aggrey SE, Rekaya R. Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. BMC Genomics 2021; 22:538. [PMID: 34256689 PMCID: PMC8278650 DOI: 10.1186/s12864-021-07872-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/05/2021] [Indexed: 12/02/2022] Open
Abstract
Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07872-z.
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Affiliation(s)
- Pattarapol Sumreddee
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA.
| | - Sajjad Toghiani
- USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Samuel E Aggrey
- Department of Poultry Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA.,Department of Statistics, The University of Georgia, Athens, GA, 30602, USA
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Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW. Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi. Mol Ecol 2021; 30:6006-6020. [PMID: 34242449 DOI: 10.1111/mec.16068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal. Nat Commun 2021; 12:2972. [PMID: 34016997 PMCID: PMC8138023 DOI: 10.1038/s41467-021-23222-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/29/2021] [Indexed: 02/03/2023] Open
Abstract
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.
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Affiliation(s)
- M A Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - S E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Caivio-Nasner S, López-Herrera A, González-Herrera LG, Rincón JC. Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle. J Anim Breed Genet 2021; 138:613-627. [PMID: 33783906 DOI: 10.1111/jbg.12549] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/26/2021] [Accepted: 03/16/2021] [Indexed: 01/18/2023]
Abstract
Blanco Orejinegro (BON) cattle have 500 years of adaptation to the Colombian tropic, but little is known about their genetic history. Our aim was to estimate levels of linkage disequilibrium (LD), effective population size (Ne), genomic inbreeding for runs of homozygosity (FROH ), genomic relation matrix (FGRM ), excess of homozygotes (FHOM ) and pedigree information (FPEDCOMP ) and to characterize the runs of homozygosity (ROH), searching for selection signatures. A total of 419 BON animals were genotyped, 70 with a 150K chip and 349 with a 50K chip. Next, an imputation to 50K was performed, and, after editing, databases of 40K were obtained. The PLINK v1.90 and R programs were used to estimate LD, ROH, FROH and FHOM . The SNeP v1.1 program was used to obtain Ne, and PreGSf90 was used to elaborate the scaled G matrix. The MTDFNRM program was used to estimate FPEDCOMP . The LD mean as r2 at 1 Mb was 0.21 (r2 > 0.30 at a distance of 96.72kb), and Ne was 123 ± 1. A total of 7,652 homozygous segments were obtained, with a mean of 18.35 ± 0.55 ROH/animal. Most of the genome was covered by long ROHs (ROH>8 Mb = 4.86%), indicating significant recent inbreeding. The average inbreeding coefficient for FPEDCOM , FGRM , FHOM and FROH was 4.41%, 4.18%, 5.58% and 6.78%, respectively. The highest correlation was observed between FHOM and FROH (0.95). ROH hotspots/islands were defined using the extreme values of a box plot that was generated, and correspond to QTLs related to milk yield (55.11%), external appearance (13.47%), production (13.30%), reproduction (8.15%), health (5.24%) and meat carcass (4.74%).
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Affiliation(s)
- Sindy Caivio-Nasner
- Grupo de Investigación Biomolecular y Pecuaria (BIOPEC), Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Albeiro López-Herrera
- Universidad Nacional de Colombia sede Medellín, Medellín, Colombia.,Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia
| | - Luis G González-Herrera
- Universidad Nacional de Colombia sede Medellín, Medellín, Colombia.,Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan C Rincón
- Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia.,Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
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Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics 2021; 113:1407-1415. [PMID: 33705888 DOI: 10.1016/j.ygeno.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Arash Javanmard
- Departement of Animal Sceince, Faculty of Agriculture, University of Tabriz, PB 5166616471,Tabriz, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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Macciotta NPP, Colli L, Cesarani A, Ajmone-Marsan P, Low WY, Tearle R, Williams JL. The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events. Genet Sel Evol 2021; 53:20. [PMID: 33639853 PMCID: PMC7912491 DOI: 10.1186/s12711-021-00616-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 01/03/2023] Open
Abstract
Background Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. Results The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Conclusions Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00616-3.
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Affiliation(s)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca sulla Biodiversità e sul DNA Antico-BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italia. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italia
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Rick Tearle
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italia.,The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Aggrey SE, Rekaya R. Runs of homozygosity and analysis of inbreeding depression. J Anim Sci 2021; 98:5979489. [PMID: 33180906 DOI: 10.1093/jas/skaa361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.
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Affiliation(s)
| | - Sajjad Toghiani
- Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD
| | - El Hamidi Hay
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Andrew Roberts
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA.,Department of Statistics, University of Georgia, Athens, GA
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Hidalgo J, Cesarani A, Garcia A, Sumreddee P, Larios N, Mancin E, García JG, Núñez R, Ramírez R. Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico. Animals (Basel) 2021; 11:ani11020321. [PMID: 33525405 PMCID: PMC7911603 DOI: 10.3390/ani11020321] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The objective of this study was to evaluate the genetic background and inbreeding depression in the Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals; 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. A 1% increase in inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to sustainable breeding programs for the Mexican Romosinuano cattle breed. Abstract The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.
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Affiliation(s)
- Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Alberto Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Andre Garcia
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Pattarapol Sumreddee
- Department of Livestock Development, Bureau of Biotechnology in Livestock Production, Pathum Thani 12000, Thailand;
| | - Neon Larios
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment-DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy;
| | - José Guadalupe García
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
- Correspondence:
| | - Rafael Núñez
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
| | - Rodolfo Ramírez
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
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Kumar S, Deng CH, Hunt M, Kirk C, Wiedow C, Rowan D, Wu J, Brewer L. Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear ( Pyrus spp.). FRONTIERS IN PLANT SCIENCE 2021; 11:590846. [PMID: 33469460 PMCID: PMC7813798 DOI: 10.3389/fpls.2020.590846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (FROH) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that FROH would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.
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Affiliation(s)
- Satish Kumar
- Hawke’s Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North, New Zealand
| | - Cecilia Hong Deng
- Mount Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Martin Hunt
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Chris Kirk
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Claudia Wiedow
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Daryl Rowan
- Palmerston North Research Centre, The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Jun Wu
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Lester Brewer
- Motueka Research Centre, The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
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Gorssen W, Meyermans R, Janssens S, Buys N. A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species. Genet Sel Evol 2021; 53:2. [PMID: 33397285 PMCID: PMC7784028 DOI: 10.1186/s12711-020-00599-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/11/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. RESULTS The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). CONCLUSIONS We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.
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Affiliation(s)
- Wim Gorssen
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Roel Meyermans
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30, Box 2472, 3001, Leuven, Belgium.
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Strillacci MG, Vevey M, Blanchet V, Mantovani R, Sartori C, Bagnato A. The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System. Animals (Basel) 2020; 10:ani10122385. [PMID: 33322839 PMCID: PMC7764440 DOI: 10.3390/ani10122385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Veruska Blanchet
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
- Correspondence: ; Tel.: +39-02-5033-4583
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