1
|
Safaa H, Khaled R, Isaac S, Mostafa R, Ragab M, Elsayed DAA, Helal M. Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks. J Genet Eng Biotechnol 2023; 21:105. [PMID: 37856056 PMCID: PMC10587045 DOI: 10.1186/s43141-023-00556-z] [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: 07/05/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.
Collapse
Affiliation(s)
- Hosam Safaa
- Department of Biology, College of Science, University of Bisha, P.O. Box 551, 61922, Bisha, Saudi Arabia.
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Rawan Khaled
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Suzy Isaac
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Rofida Mostafa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Mohamed Ragab
- Poultry Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Animal Breeding and Genetics Department, National Institute for Agricultural and Food Research and Technology (INIA), 28040, Madrid, Spain
| | - Dalia A A Elsayed
- Department of Poultry Breeding, Agriculture Research Center, Animal Production Research Institute, Dokki, Giza, Egypt
| | - Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| |
Collapse
|
2
|
Wu Z, Gong H, Zhang M, Tong X, Ai H, Xiao S, Perez-Enciso M, Yang B, Huang L. A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations. Genet Sel Evol 2021; 53:39. [PMID: 33892623 PMCID: PMC8063339 DOI: 10.1186/s12711-021-00631-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00631-4.
Collapse
Affiliation(s)
- Zhongzi Wu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingpeng Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xinkai Tong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Miguel Perez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain.,ICREA, Passeig de Lluís Companys 23, Barcelona, Spain
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| |
Collapse
|
3
|
Jiang F, Lin R, Xiao C, Xie T, Jiang Y, Chen J, Ni P, Sung WK, Han J, Du X, Li S. Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations. Genet Sel Evol 2021; 53:35. [PMID: 33849442 PMCID: PMC8042899 DOI: 10.1186/s12711-021-00627-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/26/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. RESULTS Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). CONCLUSIONS Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.
Collapse
Affiliation(s)
- Fan Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Ruiyi Lin
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Tanghui Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yaoxin Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianhai Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute for Systems Genetics, West China Hospital, Auspiciousness Peace Center, Gaopeng Avenue, Wuhou District, Chengdu, 610041 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wing-Kin Sung
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Department of Computer Science, National University of Singapore, Singapore, 117417 Singapore
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People’s Republic of China
| | - Xiaoyong Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Shijun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun, 130118 People’s Republic of China
| |
Collapse
|