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Becker GM, Thorne JW, Burke JM, Lewis RM, Notter DR, Morgan JLM, Schauer CS, Stewart WC, Redden RR, Murdoch BM. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genet Sel Evol 2024; 56:56. [PMID: 39080565 PMCID: PMC11290166 DOI: 10.1186/s12711-024-00905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/23/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
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Affiliation(s)
- Gabrielle M Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
| | - Jacob W Thorne
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David R Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Christopher S Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, USA
| | - Whit C Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - R R Redden
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA.
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Ramljak J, Špehar M, Ceranac D, Držaić V, Pocrnić I, Barać D, Mioč B, Širić I, Barać Z, Ivanković A, Kasap A. Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection. Animals (Basel) 2024; 14:1928. [PMID: 38998043 PMCID: PMC11240672 DOI: 10.3390/ani14131928] [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: 06/05/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2-4, FROH4-8, FROH8-16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440-38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection.
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Affiliation(s)
- Jelena Ramljak
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
| | - Marija Špehar
- Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia; (M.Š.); (D.C.); (D.B.)
| | - Dora Ceranac
- Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia; (M.Š.); (D.C.); (D.B.)
| | - Valentino Držaić
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
| | - Ivan Pocrnić
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK;
| | - Dolores Barać
- Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia; (M.Š.); (D.C.); (D.B.)
| | - Boro Mioč
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
| | - Ivan Širić
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
| | | | - Ante Ivanković
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
| | - Ante Kasap
- Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (V.D.); (B.M.); (I.Š.); (A.I.); (A.K.)
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Li D, Zhang L, Wang Y, Chen X, Li F, Yang L, Cui J, Li R, Cao B, An X, Song Y. FecB mutation and litter size are associated with a 90-base pair deletion in BMPR1B in East Friesian and Hu crossbred sheep. Anim Biotechnol 2023; 34:1314-1323. [PMID: 34985398 DOI: 10.1080/10495398.2021.2020805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Litter size is a critical economic trait in livestock, but only a few studies have focused on associated indel mutations in BMPR1B, a key regulator of ovulation and litter size in sheep. We evaluated the effects of BMPR1B mutations on the reproductive performance of sheep. We used Hu, East Friesian, and East Friesian/Hu crossbred sheep as experimental subjects and identified a novel 90 bp deletion in BMPR1B, which coincides with the c.746A > G (FecB mutation) genotype. The correlation between the two loci and litter size was then evaluated. We identified three genotypes for the Del-90bp locus, namely, II, ID, and DD, and three genotypes for the c.746A > G locus, namely ++, B+, and BB. Both Del-90bp and c.746A > G significantly affected the litter size of Hu and East Friesian/Hu crossbred sheep. Linkage disequilibrium analysis revealed a strong linkage disequilibrium between these loci in Hu sheep and the F1 population (r2 > 0.33), which suggests that detecting this 90 bp deletion might be a simple method to identify the likely carriers of c.746A > G. However, the function of this 90-bp deletion still needs further exploration. We provide genetic data that can be used as a reference for the breeding of improved prolific traits in sheep.
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Affiliation(s)
- Danni Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuchen Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xingzhuo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lichun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiuzeng Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Yousuf S, Malik WA, Feng H, Liu T, Xie L, Miao X. Genome wide identification and characterization of fertility associated novel CircRNAs as ceRNA reveal their regulatory roles in sheep fecundity. J Ovarian Res 2023; 16:115. [PMID: 37340323 DOI: 10.1186/s13048-023-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/29/2023] [Indexed: 06/22/2023] Open
Abstract
Reproductive traits play a vital role in determining the production efficiency of sheep. Maximizing the production is of paramount importance for breeders worldwide due to the growing population. Circular RNAs (circRNAs) act as miRNA sponges by absorbing miRNA activity through miRNA response elements (MREs) and participate in ceRNA regulatory networks (ceRNETs) to regulate mRNA expression. Despite of extensive research on role of circRNAs as miRNA sponges in various species, their specific regulatory roles and mechanism in sheep ovarian tissue are still not well understood. In this study, we performed whole genome sequencing of circRNAs, miRNA and mRNA employing bioinformatic techniques on ovine tissues of two contrasting sheep breeds "Small tail Han (X_LC) and Dolang sheep (D_LC)", which results into identification of 9,878 circRNAs with a total length of 23,522,667 nt and an average length of 2,381.32 nt. Among them, 44 differentially expressed circRNAs (DECs) were identified. Moreover, correlation between miRNA-mRNA and lncRNA-miRNA provided us with to prediction of miRNA binding sites on nine differentially expressed circRNAs and 165 differentially expressed mRNAs using miRanda. miRNA-mRNA and lncRNA-miRNA pairs with negative correlation were selected to determine the ceRNA score along with positively correlated pairs from lncRNA and mRNA network. Integration of ceRNA score and positively correlated pairs exhibit a significant ternary relationship among circRNAs-miRNA-mRNA demonestrated by ceRNA, comprising of 50 regulatory pairs sharring common nodes and predicted potential differentially expressed circRNAs-miRNAs-mRNAs regulatory axis. Based on functional enrichment analysis shortlisted key ceRNA regulatory pairs associated with reproduction including circRNA_3257-novel579_mature-EPHA3, circRNA_8396-novel130_mature-LOC101102473, circRNA_4140- novel34_mature > novel661_mature-KCNK9, and circRNA_8312-novel339_mature-LOC101110545. Furthermore, expression profiling, functional enrichments and qRT-PCR analysis of key target genes infer their implication in reproduction and metabolism. ceRNA target mRNAs evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations following genomic organizations will provide new insights underlying molecular mechanisms of reproduction, and establish a solid foundation for future research. Graphical abstract summarizing the scheme of study.
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Affiliation(s)
- Salsabeel Yousuf
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Waqar Afzal Malik
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hui Feng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianyi Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingli Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C. Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 2023; 13:ani13020272. [PMID: 36670812 PMCID: PMC9854690 DOI: 10.3390/ani13020272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (FST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.
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Affiliation(s)
- Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | | | - Jaime Gallegos-Sánchez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
| | - Carlos Miguel Becerril-Pérez
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Agroecosistemas Tropicales, Colegio de Postgraduados, Campus Veracruz, Carretera Xalapa-Veracruz Km. 88.5, Manlio Favio Altamirano, Veracruz 91690, Mexico
| | - Said Cadena-Villegas
- Producción Agroalimentaria en Trópico, Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Ranchería Rio Seco y Montaña, Heroica Cárdenas 86500, Mexico
| | - César Cortez-Romero
- Recursos Genéticos y Productividad-Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km. 36.5, Texcoco 56264, Mexico
- Innovación en Manejo de Recursos Naturales, Colegio de Postgraduados, Campus San Luis Potosí, Agustín de Iturbide No. 73, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
- Correspondence: ; Tel.: +52-5959-520-200 (ext. 4000)
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Chessari G, Criscione A, Tolone M, Bordonaro S, Rizzuto I, Riggio S, Macaluso V, Moscarelli A, Portolano B, Sardina MT, Mastrangelo S. High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context. Front Vet Sci 2023; 10:1127354. [PMID: 37205231 PMCID: PMC10185747 DOI: 10.3389/fvets.2023.1127354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Bordonaro
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Catania, Italy
| | - Ilaria Rizzuto
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Silvia Riggio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Vito Macaluso
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
- *Correspondence: Salvatore Mastrangelo,
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Zsolnai A, Egerszegi I, Rózsa L, Mezőszentgyörgyi D, Anton I. Position of Hungarian Merino among other Merinos, within-breed genetic similarity network and markers associated with daily weight gain. Anim Biosci 2023; 36:10-18. [PMID: 35760405 PMCID: PMC9834658 DOI: 10.5713/ab.21.0459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE In this study, we aimed to position the Hungarian Merino among other Merino-derived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. METHODS Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. RESULTS Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise FST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log10P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log10P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. CONCLUSION The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.
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Affiliation(s)
- Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary,National Centre for Biodiversity and Gene Conservation, Gödöllő, 2100,
Hungary,Corresponding Author: Attila Zsolnai, Tel: +36-70-491-7824, E-mail:
| | - István Egerszegi
- Department of Animal Husbandry Technology and Animal Welfare, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Gödöllő, 2100,
Hungary
| | - László Rózsa
- Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360,
Hungary
| | - Dávid Mezőszentgyörgyi
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
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Pan Y, Wang M, Wu H, Akhatayeva Z, Lan X, Fei P, Mao C, Jiang F. Indel mutations of sheep PLAG1 gene and their associations with growth traits. Anim Biotechnol 2022; 33:1459-1465. [PMID: 33825658 DOI: 10.1080/10495398.2021.1906265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pleiomorphic adenoma gene 1 (PLAG1) is mainly expressed in embryonic development, and it is reported to take an effect on the growth performance of mice, cattle, pigs, and sheep. To explore how conservative the PLAG1 is in different sheep breeds, the effects of the two indel variants on the growth traits of the Chinese Luxi blackhead (LXBH) sheep were firstly detected. The P2-del 30 bp and P4-del 45 bp indel loci of the sheep PLAG1 gene were significantly related to 15 growth traits (P < 0.05). Genotype ID and genotype II were dominant for the P2-del 30 bp and P4-del 45 bp loci, respectively. The above findings indicated that the two indel mutations in the ovine PLAG1 gene were suggested to become the molecular markers for the selection of economic traits in sheep.
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Affiliation(s)
- Yun Pan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Min Wang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Wu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Panfeng Fei
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Cui Mao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
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10
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Talebi R, Ghaffari MR, Zeinalabedini M, Abdoli R, Mardi M. Genetic basis of muscle‐related traits in sheep: A review. Anim Genet 2022; 53:723-739. [DOI: 10.1111/age.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/06/2022] [Accepted: 09/10/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Reza Talebi
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
- Department of Animal Sciences, Faculty of Agriculture Bu‐Ali Sina University Hamedan Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
| | - Ramin Abdoli
- Iran Silk Research Center Agricultural Research, Education and Extension Organization (AREEO) Gilan Iran
| | - Mohsen Mardi
- Seed and Plant Certification and Registration Institute of Iran Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
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11
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Ghanem N, Zayed M, Mohamed I, Mohammady M, Shehata MF. Co-expression of candidate genes regulating growth performance and carcass traits of Barki lambs in Egypt. Trop Anim Health Prod 2022; 54:260. [PMID: 35953554 PMCID: PMC9372007 DOI: 10.1007/s11250-022-03263-y] [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: 07/14/2021] [Accepted: 07/29/2022] [Indexed: 12/02/2022]
Abstract
Sheep are considered one of the main sources of animal protein in Egypt and the producers of sheep mutton eagers to find biological criteria for selecting fast-growing lambs that reach market weight early. Therefore, the present study aimed to find a link between the expression profile of selected candidate genes with growth performance and carcass traits of Barki lambs. Thirty-eight Barki lambs were kept and fed individually after weaning till 12 months of age and were divided into 3 groups according to growth performance (fast, intermediate, and slow-growing). Three samples were taken from different body tissues (eye muscle, liver, and fat tail) of each group, directly during slaughtering and stored at − 80 °C until RNA isolation. Real-time PCR was used to profile selected candidate genes (RPL7, CTP1, FABP4, ADIPOQ, and CAPN3) and GAPDH was used as a housekeeping gene. The results indicated that the final body weight was significantly (P ≤ 0.05) greater in the fast (49.9 kg) and intermediate (40.7 kg) compared to slow-growing animals (30.8 kg). The hot carcass weight was heavier (P ≤ 0.05) in the fast and intermediate-growing (24.57 and 19.07 kg) than slow-growing lambs (15.10 kg). The blood profiles of T3 and T4 hormones in addition to other parameters such as total protein, total lipids, and calcium level showed no clear variations among different experimental groups. At the molecular level, our data demonstrated upregulation of genes involved in protein biosynthesis (RPL7), fatty acid oxidation (CPT1), and lipolysis (FABP4) in the fast and intermediate-growing lambs in all studied tissues which facilitate protein accretion, energy expenditure, and fatty acid partitioning required for muscle building up. Moreover, the expression profile of the gene involved in muscle development (CAPN3) was increased in fast and intermediate-growing compared to slow-growing lambs in order to support muscle proper development. On the other hand, a candidate gene involved in lipogenesis (ADIPOQ) was expressed similarly in fat and liver tissues; however, its expression was increased in muscles of fast and intermediate-growing lambs compared to slow-growing animals. In conclusion, the current study indicated that the expression profile of genes involved in metabolic activities of liver, muscle, and adipose tissue is linked with the growth performance of lambs although no variations were detected in blood parameters. This provides an evidence for the importance of co-expression of these genes in body tissues to determine the final body weight and carcass characteristics of Barki sheep.
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Affiliation(s)
- Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamaa Street, Giza, 12613, Egypt. .,Faculty of Agriculture, Cairo University Research Park, Cairo University, Cairo, Egypt.
| | - Mohamed Zayed
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - Ismail Mohamed
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - Mona Mohammady
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
| | - M F Shehata
- Department of Animal and Poultry Breeding, Animal and Poultry Division, Desert Research Center, Cairo, Egypt
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12
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Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. Sci Rep 2022; 12:12264. [PMID: 35851076 PMCID: PMC9293982 DOI: 10.1038/s41598-022-15986-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.
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13
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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14
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Li X, Ding N, Zhang Z, Tian D, Han B, Liu D, Liu S, Tian F, Fu D, Song X, Zhao K. Identification of SSTR5 Gene Polymorphisms and Their Association With Growth Traits in Hulun Buir Sheep. Front Genet 2022; 13:831599. [PMID: 35559027 PMCID: PMC9086292 DOI: 10.3389/fgene.2022.831599] [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: 12/08/2021] [Accepted: 03/10/2022] [Indexed: 11/15/2022] Open
Abstract
The aim of this study was to locate SSTR5 polymorphisms and evaluate their association with growth traits in Hulun Buir sheep. The study followed up 884 Hulun Buir sheep from birth to 16 months of age, which were born in the same pasture and the same year, and a consistent grazing management strategy was maintained. The birth weight (BRW) was recorded at birth, and body weight (BW), body height (BH), body length (BL), chest circumference (ChC), chest depth (ChD), chest width (ChW), hip width (HW), and cannon circumference (CaC) were measured at 4 and 9 months of age. BW, BH, BL, ChD, HW, and CaC were also recorded at 16 months of age. Based on the growth traits, 233 sheep were selected as experimental animals. Sanger sequencing was performed, and seven single-nucleotide polymorphisms (SNPs) were identified. Association analyses of the SNPs and the growth traits were then conducted. Seven SNPs of the SSTR5 exhibited moderate polymorphism (0.25
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Affiliation(s)
- Xue Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning Ding
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhichao Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dehong Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Buying Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dehui Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Dejun Fu
- Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
| | - Xiaoliang Song
- Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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15
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Identification of Somatostatin Receptor Subtype 1 (SSTR1) Gene Polymorphism and Their Association with Growth Traits in Hulun Buir Sheep. Genes (Basel) 2021; 13:genes13010077. [PMID: 35052417 PMCID: PMC8775034 DOI: 10.3390/genes13010077] [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: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022] Open
Abstract
This study was conducted to evaluate SSTR1 gene polymorphisms and their association with growth traits in Hulun Buir sheep. We followed 233 Hulun Buir sheep from birth to 16 months of age, born in the same pasture and on the same year under a consistent grazing conditions. The body weight (BW), body height (BH), body length (BL), chest circumference (ChC), chest depth (ChD), chest width (ChW), hip width (HW), and cannon circumference (CaC) were measured and recorded at birth, 4 months, 9 months, and 16 months of age. The polymorphisms of the SSTR1 gene in Hulun Buir sheep were excavated using exon sequencing, and association analyses of between SNPs and growth traits at each growth stage were conducted. The results showed that there were four SNPs in Exon 2 of the SSTR1 gene, SNP1, SNP2, and SNP3 were low mutation sites, and SNP4 was a moderate mutation site. Four SNPs were consistent with Hardy–Weinberg equilibrium, and all of them were synonymous mutations. The association analyses found that the genotypes of SNP2 were significantly associated with WW and BH at 4 months of age, BW, BL, ChC, and HW at 9 months of age (p < 0.05), and extremely significantly associated with ChD at 4 and 9 months of age (p < 0.01). There were significant associations between SNP3 and BH at 9 months of age, between SNP4 and ChD, ChW, and CaC at 9 months of age, and BW and ChC at 16 months of age (p < 0.05). There were no detectable associations with growth traits among the seven haplotypes between the SNP1, 3, and 4 of a strong linkage disequilibrium (p > 0.05). These results indicated that SNP2, SNP3, and SNP4 may be used as molecular markers for growth traits of Hulun Buir sheep.
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16
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Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Ghanatsaman Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H. Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 2021; 17:369. [PMID: 34861880 PMCID: PMC8641187 DOI: 10.1186/s12917-021-03077-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.
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Affiliation(s)
| | | | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz, Iran
| | - Olena Babenko
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Ruslana Stavetska
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Oleksandr Kalashnik
- Department of Animal Science, Sumy National Agrarian University, Sumy, Ukraine
| | - Dmytro Kucher
- Department of Breeding, Animal Genetics and Biotechnology, Polissia National University, Zhytomyr, Ukraine
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17
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Ran J, Li J, Yin L, Zhang D, Yu C, Du H, Jiang X, Yang C, Liu Y. Comparative Analysis of Skeletal Muscle DNA Methylation and Transcriptome of the Chicken Embryo at Different Developmental Stages. Front Physiol 2021; 12:697121. [PMID: 34276416 PMCID: PMC8283280 DOI: 10.3389/fphys.2021.697121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/31/2021] [Indexed: 11/26/2022] Open
Abstract
DNA methylation is a key epigenetic mechanism involved in embryonic muscle development and plays an important role in early muscle development. In this study, we sought to investigate the effects of genome-wide DNA methylation by combining the expression profiles of the chicken embryonic muscle. Genome-wide DNA methylation maps and transcriptomes of muscle tissues collected from different embryonic development points (E7, E11, E17, and D1) were used for whole-genome bisulfite sequencing (WGBS) and RNA sequencing, respectively. We found that the differentially methylated genes (DMGs) were significantly associated with muscle organ development, regulation of skeletal muscle satellite cell proliferation, and actin filament depolymerization. Furthermore, genes TBX1, MEF2D, SPEG, CFL2, and TWF2 were strongly correlated with the methylation-caused expression switch. Therefore, we chose the CFL2 gene to explore its function in skeletal muscle satellite cells, and the in vitro experiments showed that CFL2 acts as a negative regulator of chicken skeletal muscle satellite cell proliferation and can induce cell apoptosis. These results provide valuable data for future genome and epigenome studies of chicken skeletal muscle and may help reveal the molecular mechanisms of potential economic traits.
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Affiliation(s)
- Jinshan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Donghao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chunlin Yu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Huarui Du
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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18
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Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals. Animals (Basel) 2021; 11:ani11030835. [PMID: 33809500 PMCID: PMC7999090 DOI: 10.3390/ani11030835] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Skeletal muscle mass is an important economic trait, and muscle development and growth is a crucial factor to supply enough meat for human consumption. Thus, understanding (candidate) genes regulating skeletal muscle development is crucial for understanding molecular genetic regulation of muscle growth and can be benefit the meat industry toward the goal of increasing meat yields. During the past years, significant progress has been made for understanding these mechanisms, and thus, we decided to write a comprehensive review covering regulators and (candidate) genes crucial for muscle development and growth in farm animals. Detection of these genes and factors increases our understanding of muscle growth and development and is a great help for breeders to satisfy demands for meat production on a global scale. Abstract Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.
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19
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Guo T, Zhao H, Yuan C, Huang S, Zhou S, Lu Z, Niu C, Liu J, Zhu S, Yue Y, Yang Y, Wang X, Chen Y, Yang B. Selective Sweeps Uncovering the Genetic Basis of Horn and Adaptability Traits on Fine-Wool Sheep in China. Front Genet 2021; 12:604235. [PMID: 33708236 PMCID: PMC7940688 DOI: 10.3389/fgene.2021.604235] [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: 09/09/2020] [Accepted: 02/01/2021] [Indexed: 11/23/2022] Open
Abstract
Long-term natural and artificial selection leads to change in certain regions of the genome, resulting in selection signatures that can reveal genes associated with selected traits, such as horns (i.e., polled/horned), high-quality wool traits, and high-altitude hypoxia adaptability. These are complex traits determined by multiple genes, regulatory pathways, and environmental factors. A list of genes with considerable effects on horn and adaptability traits has not been found, although multiple quantitative trait loci (QTL) have been identified. Selection signatures could be identified using genetic differentiation (FST), polymorphism levels θπ, and Tajima’s D. This study aimed to identify selection signatures in fine-wool sheep and to investigate the genes annotated in these regions, as well as the biological pathways involved in horn and adaptability traits. For this purpose, the whole-genome sequence of 120 individuals from four breeds, which come from different elevations and habitats in China, was used to analyze selection signatures for horn and adaptability traits. Annotation of the consensus regions of FST and θπ ratios revealed a list of identified genes associated with polled/horned and high-altitude hypoxia adaptability traits, such as RXPF2, EERFC4, MSH6, PP1R12A, THBS1, ATP1B2, RYR2, and PLA2G2E. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified genes related primarily to mismatch repair, metabolism, vascular smooth muscle contraction, and cardiac muscle contraction. This is the first study to demonstrate that selection signatures play an important role in the polled/horned and high-altitude hypoxia adaptability traits of fine-wool sheep breeds that have undergone high-intensity selection and adapted to different ecological environments in China. Changes observed in the genome of fine-wool sheep may have acted on genomic regions that affect performance traits and provide a reference for genome design and breeding.
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Affiliation(s)
- Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Zengkui Lu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chun'e Niu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yaojing Yue
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuxin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Xianyang, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Engineering Research Center of Sheep and Goat Breeding, Chinese Academy of Agricultural Sciences, Lanzhou, China
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20
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Duan X, An B, Du L, Chang T, Liang M, Yang BG, Xu L, Zhang L, Li J, E G, Gao H. Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle. Animals (Basel) 2021; 11:ani11010192. [PMID: 33467455 PMCID: PMC7830728 DOI: 10.3390/ani11010192] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight-age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters' mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.
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Affiliation(s)
- Xinghai Duan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Bai-Gao Yang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China;
- Correspondence: (G.E); (H.G.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.D.); (B.A.); (L.D.); (T.C.); (M.L.); (L.X.); (L.Z.); (J.L.)
- Correspondence: (G.E); (H.G.)
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21
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Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
Female fertility is an important trait that contributes to cow’s profitability and it can be improved by genomic information. The objective of this study was to detect genomic regions and variants affecting fertility traits in Iranian Holstein cattle. A data set comprised of female fertility records and 3,452,730 pedigree information from Iranian Holstein cattle were used to predict the breeding values, which were then employed to estimate the de-regressed proofs (DRP) of genotyped animals. A total of 878 animals with DRP records and 54k SNP markers were utilized in the genome-wide association study (GWAS). The GWAS was performed using a linear regression model with SNP genotype as a linear covariate. The results showed that an SNP on BTA19, ARS-BFGL-NGS-33473, was the most significant SNP associated with days from calving to first service. In total, [69] significant SNPs were located within 27 candidate genes. Novel potential candidate genes include OSTN, DPP6, EphA5, CADPS2, Rfc1, ADGRB3, Myo3a, C10H14orf93, KIAA1217, RBPJL, SLC18A2, GARNL3, NCALD, ASPH, ASIC2, OR3A1, CHRNB4, CACNA2D2, DLGAP1, GRIN2A and ME3. These genes are involved in different pathways relevant to female fertility and other characteristics in mammals. Gene set enrichment analysis showed that thirteen GO terms had significant overrepresentation of genes statistically associated with female fertility traits. The results of network analysis identified CCNB1 gene as a hub gene in the progesterone-mediated oocyte maturation pathway, significantly associated with age at first calving. The candidate genes identified in this study can be utilized in genomic tests to improve reproductive performance in Holstein cattle.
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22
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Huang X, Otecko NO, Peng M, Weng Z, Li W, Chen J, Zhong M, Zhong F, Jin S, Geng Z, Luo W, He D, Ma C, Han J, Ommeh SC, Zhang Y, Zhang X, Du B. Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds. BMC Genomics 2020; 21:316. [PMID: 32312230 PMCID: PMC7171827 DOI: 10.1186/s12864-020-6736-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration. RESULTS The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein (RALY), leucine rich repeat containing G protein-coupled receptor 4 (LGR4), solute carrier family 23 member 2 (SLC23A2), and solute carrier family 2 member 14 (SLC2A14), besides the classical beta-carotene dioxygenase 2 (BCDO2), as major candidates pigment determining genes in the YFCs. CONCLUSION We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.
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Affiliation(s)
- Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Minsheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Weina Li
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China
| | - Jiebo Chen
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China
| | - Ming Zhong
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China
| | - Fusheng Zhong
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Luo
- College of Animal Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Danlin He
- College of Animal Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Cheng Ma
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,International Livestock Research Institute (ILRI), Nairobi, 30709-00100, Kenya
| | - Sheila C Ommeh
- Animal Biotechnology Group, Institute For Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya
| | - Yaping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China. .,State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, 650091, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xiquan Zhang
- College of Animal Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Bingwang Du
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science of Jiaying University, Meizhou, 514015, China.
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23
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Yang H, Ma J, Wang Z, Yao X, Zhao J, Zhao X, Wang F, Zhang Y. Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation. Genes (Basel) 2020; 11:E320. [PMID: 32192168 PMCID: PMC7140784 DOI: 10.3390/genes11030320] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction.
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Affiliation(s)
| | | | | | | | | | | | | | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (J.M.); (Z.W.); (X.Y.); (J.Z.); (X.Z.); (F.W.)
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24
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Álvarez I, Fernández I, Traoré A, Pérez-Pardal L, Menéndez-Arias NA, Goyache F. Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Rep 2020; 10:2824. [PMID: 32071365 PMCID: PMC7028950 DOI: 10.1038/s41598-020-59839-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
The Djallonké (West African Dwarf) sheep is a small-sized haired sheep resulting from a costly evolutionary process of natural adaptation to the harsh environment of West Africa including trypanosome challenge. However, genomic studies carried out in this sheep are scant. In this research, genomic data of 184 Djallonké sheep (and 12 Burkina-Sahel sheep as an outgroup) generated using medium-density SNP Chips were analyzed. Three different statistics (iHS, XP-EHH and nSL) were applied to identify candidate selection sweep regions spanning genes putatively associated with adaptation of sheep to the West African environment. A total of 207 candidate selection sweep regions were defined. Gene-annotation enrichment and functional annotation analyses allowed to identify three statistically significant functional clusters involving 12 candidate genes. Genes included in Functional Clusters associated to selection signatures were mainly related to metabolic response to stress, including regulation of oxidative and metabolic stress and thermotolerance. The bovine chromosomal areas carrying QTLs for cattle trypanotolerance were compared with the regions on which the orthologous functional candidate cattle genes were located. The importance of cattle BTA4 for trypanotolerant response might have been conserved between species. The current research provides new insights on the genomic basis for adaptation and highlights the importance of obtaining information from non-cosmopolite livestock populations managed in harsh environments.
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Affiliation(s)
- Isabel Álvarez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Iván Fernández
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain
| | - Amadou Traoré
- Institut de l'Environnement et des Recherches Agricoles (INERA), Ouagadougou, 04 BP 8645, Burkina Faso
| | | | | | - Félix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario, E-33394, Gijón, Spain.
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25
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Cheng S, Wang X, Zhang Q, He Y, Zhang X, Yang L, Shi J. Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep. Genes (Basel) 2020; 11:E183. [PMID: 32050672 PMCID: PMC7074365 DOI: 10.3390/genes11020183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/24/2022] Open
Abstract
Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.
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Affiliation(s)
- Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Yuqin He
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Xia Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China; (Y.H.); (X.Z.)
| | - Lei Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (L.Y.); (J.S.)
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26
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Davenport KM, Hiemke C, McKay SD, Thorne JW, Lewis RM, Taylor T, Murdoch BM. Genetic structure and admixture in sheep from terminal breeds in the United States. Anim Genet 2020; 51:284-291. [PMID: 31970815 PMCID: PMC7065203 DOI: 10.1111/age.12905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 11/29/2022]
Abstract
Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross‐validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.
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Affiliation(s)
- K M Davenport
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA
| | - C Hiemke
- Niman Ranch and Mapleton Mynd Shropshires, Stoughton, MA, 53589, USA
| | - S D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - J W Thorne
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA.,Texas A&M AgriLife Extension, San Angelo, TX, 76901, USA
| | - R M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - T Taylor
- Department of Animal Science, Arlington Research Station, University of Wisconsin-Madison, Arlington, WI, 53911, USA
| | - B M Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, 83844, USA
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27
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Gebreselassie G, Berihulay H, Jiang L, Ma Y. Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep ( Ovies aries). Animals (Basel) 2019; 10:E33. [PMID: 31877963 PMCID: PMC7022721 DOI: 10.3390/ani10010033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.
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Affiliation(s)
- Gebremedhin Gebreselassie
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Department of Agricultural Biotechnology, Biotechnology Center, Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa 1000, Ethiopia
| | - Haile Berihulay
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Lin Jiang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuehui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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Guo J, Qu L, Dou TC, Shen MM, Hu YP, Ma M, Wang KH. Genome-wide association study provides insights into the genetic architecture of bone size and mass in chickens. Genome 2019; 63:133-143. [PMID: 31794256 DOI: 10.1139/gen-2019-0022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bone size is an important trait for chickens because of its association with osteoporosis in layers and meat production in broilers. Here, we employed high density genotyping platforms to detect candidate genes for bone traits. Estimates of the narrow heritabilities ranged from 0.37 ± 0.04 for shank length to 0.59 ± 0.04 for tibia length. The dominance heritability was 0.12 ± 0.04 for shank length. Using a linear mixed model approach, we identified a promising locus within NCAPG on chromosome 4, which was associated with tibia length and mass, femur length and area, and shank length. In addition, three other loci were associated with bone size or mass at a Bonferroni-corrected genome-wide significance threshold of 1%. One region on chicken chromosome 1 between 168.38 and 171.82 Mb harbored HTR2A, LPAR6, CAB39L, and TRPC4. A second region that accounted for 2.2% of the phenotypic variance was located around WNT9A on chromosome 2, where allele substitution was predicted to be associated with tibia length. Four candidate genes identified on chromosome 27 comprising SPOP, NGFR, GIP, and HOXB3 were associated with tibia length and mass, femur length and area, and shank length. Genome partitioning analysis indicated that the variance explained by each chromosome was proportional to its length.
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Affiliation(s)
- Jun Guo
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Tao-Cun Dou
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Man-Man Shen
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Yu-Ping Hu
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
| | - Ke-Hua Wang
- Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China.,Jiangsu Institute of Poultry Science, Key Laboratory for Poultry Genetics and Breeding of Jiangsu province, Yangzhou, Jiangsu, 225125, China
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
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Zlobin A, Volkova N, Borodin P, Aksenovich T, Tsepilov Y. Recent advances in understanding genetic variants associated with growth, carcass and meat productivity traits in sheep ( Ovis aries): an update. Arch Anim Breed 2019; 62:579-583. [PMID: 31893215 PMCID: PMC6904904 DOI: 10.5194/aab-62-579-2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 09/17/2019] [Indexed: 12/17/2022] Open
Abstract
Identification of quantitative trait loci (QTLs) and candidate genes that affect growth intensity is a prerequisite for the marker-assisted selection of economically important traits. The number of QTL studies on sheep is relatively small in comparison to those on cattle and pigs. The current QTL sheep database - Sheep QTLdb - contains information on 1658 QTLs for 225 different traits. A few genes and markers associated with growth, carcass and meat productivity traits have been reported. The information about QTLs from the Sheep QTLdb cannot be directly used in marker-assisted selection due to the lack of essential information such as effective and reference alleles, the effect direction etc., and it requires manual curation and validation. In this study we performed a comprehensive search for QTLs focusing on single nucleotide polymorphisms (SNPs) associated with growth and meat traits in sheep. The database contains information about 156 SNP-trait associations (123 unique SNPs) and a list of 165 associated genes. The updated information is freely available at https://github.com/Defrag1236/Ovines_2018 (last access: 18 September 2019). This information can be useful for further association studies and preliminary estimation of genetic variability for economically important traits in different breeds.
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Affiliation(s)
- Alexander S. Zlobin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
| | - Natalia A. Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana I. Aksenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Nosrati M, Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Esmailizadeh A. Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reprod Domest Anim 2018; 54:358-364. [PMID: 30359467 DOI: 10.1111/rda.13368] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022]
Abstract
Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein-coding genes under positive selection from FST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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32
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Dettori ML, Pazzola M, Paschino P, Amills M, Vacca GM. Association between the GHR, GHRHR, and IGF1 gene polymorphisms and milk yield and quality traits in Sarda sheep. J Dairy Sci 2018; 101:9978-9986. [PMID: 30146276 DOI: 10.3168/jds.2018-14914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/01/2018] [Indexed: 11/19/2022]
Abstract
The growth hormone receptor (GHR), the growth hormone releasing hormone receptor (GHRHR), and the insulin-like growth factor 1 (IGF1) genes are known to modulate growth, reproduction, and lactation traits in livestock. The aim of the current work was to investigate if the variation of the sheep GHR, GHRHR, and IGF1 genes is associated with milk yield and quality traits. Three hundred eighty dairy Sarda sheep were genotyped for 36 single nucleotide polymorphisms (SNP) mapping to these 3 loci, and records for milk yield and daily fat and protein yield, as well as for fat, protein, casein, lactose, and milk urea contents, pH, somatic cell score, logarithmic bacterial count, and milk energy were obtained. The linkage disequilibrium analysis was performed only for GHR, as both GHRHR and IGF1 had only 1 polymorphic SNP. Haplotype analysis revealed the existence of 7 haplotype blocks in GHR. Two haplotype blocks, including part of the intron 1 and the upstream region, were clearly separated from the remaining 5 blocks by SNP rs412986330, which may be a recombination hotspot. The latter 5 blocks were contiguous, spanning from intron 2 to exon 10. Statistical analysis revealed that the GHR polymorphism is significantly associated with milk traits for daily fat and protein yield and fat, milk urea, and lactose content. Moreover, variation in IGF1 was associated with milk protein and casein content. Data generated in this research provide new insights into the allelic effects of the ovine GHRHR, GHR, and IGF1 genes on milk production and quality traits, information that may be useful in gene-assisted selection programs.
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Affiliation(s)
- Maria L Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.
| | - Pietro Paschino
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Giuseppe M Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
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Ilie DE, Kusza S, Sauer M, Gavojdian D. Genetic characterization of indigenous goat breeds in Romania and Hungary with a special focus on genetic resistance to mastitis and gastrointestinal parasitism based on 40 SNPs. PLoS One 2018; 13:e0197051. [PMID: 29742137 PMCID: PMC5942826 DOI: 10.1371/journal.pone.0197051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/25/2018] [Indexed: 11/18/2022] Open
Abstract
Goat breeding has become an important sector in Eastern Europe, with Romania and Hungary being among the major producer countries. Given the limited number of research done up-to-date concerning genetic studies of indigenous goat breeds reared in Romania and Hungary, the current preliminary study aimed to analyze the variability of genes related to mastitis and gastrointestinal parasitism by using Kompetitive Allele Specific PCR (KASP™). We studied 52 single nucleotide polymorphisms (SNPs) belonging to 19 genes in indigenous breeds from both countries, namely Banat's White (n = 36), Carpatina (n = 35) from Romania and Hungarian Milking (n = 79) and identified 16 polymorphic SNPs among 10 genes (PTX3, IL6, CLEC4E, IL8, IL1RN, IL15RA, TNFSF13, SOCS3, TNF and TLR3) in 150 animals. Furthermore, the diversity of the studied breeds was investigated. The PIC values ranged from 0.042 to 0.691. The mean values of observed and expected heterozygosity were 0.235 and 0.246 respectively. The highest observed heterozygosity was obtained for IL15RA g.10343904C>T in Banat's White (0.464), IL15RA g.10354813C>T in Carpatina (0.577) and SOCS3 g.52626440T>G in Hungarian Milking (0.588). Pairwise FST values between the Romanian breeds and Romanian and Hungarian breeds were small (0.009 and 0.015), indicating the close relationship among the studied goat populations. From all the polymorphic SNPs identified, the Hungarian Milking breed showed the highest proportion of polymorphisms (100%), whereas the Carpatina breed had the lowest percentage (87.5%). The highest value of MAF was obtained for SOCS3 g.52626440T>G (0.46), IL15RA g.10343904C>T (0.47), IL15RA g.10344025C>T (0.45), and IL15RA g.10354813C>T (0.42). The 16 polymorphic SNPs identified in a panel of 150 unrelated individuals belonging to three Romanian and Hungarian indigenous goat breeds could be used in future genomic based breeding schemes as markers for genetic resistance to mastitis and gastrointestinal parasitism in goat breeds found in Eastern and Central Europe.
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Affiliation(s)
- Daniela Elena Ilie
- Department of Research, Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
- Department of Research, Research and Development Station for Bovine Arad, Academy for Agricultural and Forestry Sciences, Arad, Romania
- * E-mail:
| | - Szilvia Kusza
- Department of Research, Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
- Animal Genetics Laboratory, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Maria Sauer
- Department of Research, Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
| | - Dinu Gavojdian
- Department of Research, Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
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Kusza S, Cziszter LT, Ilie DE, Sauer M, Padeanu I, Gavojdian D. Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition. PeerJ 2018; 6:e4416. [PMID: 29492347 PMCID: PMC5827040 DOI: 10.7717/peerj.4416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/05/2018] [Indexed: 11/20/2022] Open
Abstract
Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine (n = 24) and Saanen (n = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13. The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) (P < 0.05). The results showed that four SNPs rs671391101 (GHRHR), rs640582069 (IL1RN) rs635583012 (SOCS3) and rs635969404 (IL15RA) out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the GHRHR, IL1RN, SOCS3, and IL15RA genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.
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Affiliation(s)
- Szilvia Kusza
- Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania.,Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, Debrecen, Hungary
| | - Ludovic Toma Cziszter
- Banat's University of Agricultural Sciences and Veterinary Medicine 'King Michael I' from Timisoara, Timisoara, Romania
| | - Daniela Elena Ilie
- Research and Development Station for Bovine Arad, Academy for Agricultural and Forestry Sciences, Arad, Romania
| | - Maria Sauer
- Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
| | - Ioan Padeanu
- Banat's University of Agricultural Sciences and Veterinary Medicine 'King Michael I' from Timisoara, Timisoara, Romania
| | - Dinu Gavojdian
- Research and Development Station for Sheep and Goats Caransebes, Academy for Agricultural and Forestry Sciences, Caransebes, Romania
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Wang W, La Y, Zhou X, Zhang X, Li F, Liu B. The genetic polymorphisms of TGFβ superfamily genes are associated with litter size in a Chinese indigenous sheep breed (Hu sheep). Anim Reprod Sci 2018; 189:19-29. [DOI: 10.1016/j.anireprosci.2017.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 12/20/2022]
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36
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Mastrangelo S, Ciani E, Sardina MT, Sottile G, Pilla F, Portolano B. Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds. Anim Genet 2018; 49:71-81. [PMID: 29333609 DOI: 10.1111/age.12634] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 02/03/2023]
Abstract
The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del Belice). The average length of ROH across breeds was 4.55 Mb and ranged from 3.85 Mb (Biellese) to 5.51 Mb (Leccese). Valle del Belice showed the highest value of inbreeding on the basis of ROH (FROH = 0.099), whereas Comisana showed the lowest (FROH = 0.016), and high standard deviation values revealed high variability in autozygosity levels within each breed. Differences also existed in the length of ROH. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were <10 Mb in length, with a few long ROH >25 Mb. The levels of ROH that we estimated here reflect the inbreeding history of the investigated sheep breeds. These results also highlight that ancient and recent inbreeding have had an impact on the genome of the Italian sheep breeds and suggest that several animals have experienced recent autozygosity events. Comisana and Bergamasca appeared as the less consanguineous breeds, whereas Barbaresca, Leccese and Valle del Belice showed ROH patterns typically produced by recent inbreeding. Moreover, within the genomic regions most commonly associated with ROH, several candidate genes were detected.
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Affiliation(s)
- S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - E Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica University of Bari, 70124, Bari, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - G Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, 90128, Palermo, Italy
| | - F Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
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Seroussi E, Rosov A, Shirak A, Lam A, Gootwine E. Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed. Genet Sel Evol 2017; 49:19. [PMID: 28187715 PMCID: PMC5301402 DOI: 10.1186/s12711-017-0296-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene. RESULTS Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes. CONCLUSIONS Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alexander Rosov
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Andrey Shirak
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alon Lam
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Elisha Gootwine
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
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