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Mahar K, Gurao A, Kumar A, Pratap Singh L, Chitkara M, Gowane GR, Ahlawat S, Niranjan SK, Pundir RK, Kataria RS, Dige MS. Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations. Gene 2024; 928:148787. [PMID: 39053660 DOI: 10.1016/j.gene.2024.148787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.
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Affiliation(s)
- Karan Mahar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Ankita Gurao
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Lalit Pratap Singh
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Meenakshi Chitkara
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Gopal R Gowane
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S K Niranjan
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R K Pundir
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R S Kataria
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - M S Dige
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Liu SQ, Xu YJ, Chen ZT, Li H, Zhang Z, Wang QS, Pan YC. Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs. Animal 2024; 18:101236. [PMID: 39096602 DOI: 10.1016/j.animal.2024.101236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/05/2024] Open
Abstract
Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.
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Affiliation(s)
- S Q Liu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Y J Xu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Z T Chen
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China
| | - H Li
- Hainan Longjian Animal Husbandry Development Co. Ltd, Lantian Road, Haikou 570203, China
| | - Z Zhang
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China
| | - Q S Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Y C Pan
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China.
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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024:1-13. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, China
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Zhao F, Xie R, Fang L, Xiang R, Yuan Z, Liu Y, Wang L. Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep. Evol Appl 2024; 17:e13697. [PMID: 38911262 PMCID: PMC11192971 DOI: 10.1111/eva.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 01/02/2024] [Accepted: 04/13/2024] [Indexed: 06/25/2024] Open
Abstract
As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1-5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.
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Affiliation(s)
- Fuping Zhao
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Rui Xie
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Lingzhao Fang
- Center for Quantitative Genetics and GenomicsAarhus UniversityAarhusDenmark
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural ScienceThe University of MelbourneParkvilleVictoriaAustralia
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of EducationYangzhou UniversityYangzhouChina
| | - Yang Liu
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Lixian Wang
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
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Tan X, Liu L, Dong J, Huang M, Zhang J, Li Q, Wang H, Bai L, Cui M, Zhou Z, Wu D, Xiang Y, Li W, Wang D. Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens. BMC Genomics 2024; 25:485. [PMID: 38755540 PMCID: PMC11097469 DOI: 10.1186/s12864-024-10349-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. RESULTS To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. CONCLUSION Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, Zhejiang, 321000, China
| | - Yun Xiang
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China.
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Ma KY, Song JJ, Li DP, Wu Y, Wang CH, Liu ZL, Li TT, Ma YJ. Genomic structure analysis and construction of DNA fingerprint for four sheep populations. Animal 2024; 18:101116. [PMID: 38484632 DOI: 10.1016/j.animal.2024.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/20/2024] Open
Abstract
The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was constructed for the four populations using 349 highly polymorphic SNPs. In summary, our research delves into the genetic diversity and population structure of QS population. The construction of DNA fingerprint profiles for each population can provide valuable references for the identification of sheep breeds both domestically and internationally.
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Affiliation(s)
- Ke-Yan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Juan-Juan Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Deng-Pan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Yi Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Chun-Hui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Zi-Long Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Tao-Tao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - You-Ji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China.
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Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals (Basel) 2024; 14:444. [PMID: 38338087 PMCID: PMC10854784 DOI: 10.3390/ani14030444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
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Affiliation(s)
- Xueliang Sun
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yifei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, No. 7, Niusha Road, Chengdu 610066, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
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Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
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10
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Zhao F, Zhang P, Wang X, Akdemir D, Garrick D, He J, Wang L. Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement. J Anim Sci Biotechnol 2023; 14:87. [PMID: 37309010 DOI: 10.1186/s40104-023-00872-x] [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: 05/19/2022] [Accepted: 04/02/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values (GEBV) to accelerate the speed of genetic improvement in domestic animals. But after multi-generation selection, the rate of inbreeding and the occurrence of homozygous harmful alleles might increase, which would reduce performance and genetic diversity. To mitigate the above problems, we can utilize genomic mating (GM) based upon optimal mate allocation to construct the best genotypic combinations in the next generation. In this study, we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population. These factors included: the algorithm used to derive inbreeding coefficients; the trait heritability (0.1, 0.3 or 0.5); the kind of GM scheme (focused average GEBV or inbreeding); the approach for computing the genomic relationship matrix (by SNP or runs of homozygosity (ROH)). The outcomes were compared to three traditional mating schemes (random, positive assortative or negative assortative matings). In addition, the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population. RESULTS Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain. The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs. The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6% higher rates of genetic gain ΔG, and 13%-83.3% lower ΔF than positive assortative mating regardless of heritability. The rates of inbreeding were always the fastest with positive assortative mating. Results from a purebred Large White pig population, confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes. CONCLUSION Compared with traditional mating schemes, genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population. Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.
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Affiliation(s)
- Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Pengfei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoqing Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Deniz Akdemir
- Center for Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, 3240, New Zealand
| | - Jun He
- College of Animal Science and Biotechnology, Hunnan Agricultural University, Changsha, 410128, China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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11
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Wang Q, Zhang J, Wang H, Wang Z, Li Q, Zhao G, Zheng M, Wen J. Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations. Anim Genet 2023; 54:155-165. [PMID: 36541281 DOI: 10.1111/age.13286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH = 0.0798) was higher than that of BY_R1 (FROH = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jin Zhang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Hailong Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Zixuan Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guiping Zhao
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jie Wen
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
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12
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Gaspar D, Usié A, Leão C, Guimarães S, Pires AE, Matos C, Ramos AM, Ginja C. Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds. Front Genet 2023; 14:1109490. [PMID: 36713074 PMCID: PMC9880275 DOI: 10.3389/fgene.2023.1109490] [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: 11/27/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10-3 ≤ π ≤ 3.1 × 10-3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.
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Affiliation(s)
- Daniel Gaspar
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,*Correspondence: Daniel Gaspar, ; Catarina Ginja,
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Célia Leão
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Sílvia Guimarães
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ana Elisabete Pires
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | | | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Catarina Ginja
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,*Correspondence: Daniel Gaspar, ; Catarina Ginja,
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Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 2023; 17:100690. [PMID: 36566708 DOI: 10.1016/j.animal.2022.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic.
| | - Héctor Marina
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Juan Jose Arranz
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Rocío Pelayo
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Jana Rychtářová
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Michal Milerski
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Luboš Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic
| | - Aroa Suárez-Vega
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens. BMC Genomics 2022; 23:91. [PMID: 35100979 PMCID: PMC8805376 DOI: 10.1186/s12864-021-08280-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/23/2021] [Indexed: 01/12/2023] Open
Abstract
Background In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. Results Our results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) of 0.11 was observed in LZ. In other populations, the FROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation. Conclusions High genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08280-z.
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