1
|
Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
Collapse
Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| |
Collapse
|
2
|
Fabbri MC, Tiezzi F, Crovetti A, Maltecca C, Bozzi R. Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity. Animal 2024; 18:101142. [PMID: 38636149 DOI: 10.1016/j.animal.2024.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
The analysis of livestock heterozygosity is less common compared to the study of homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, this study was conducted to investigate and characterize the heterozygosity patterns of four beef cattle breeds, which included two cosmopolitan breeds (Limousine and Charolaise) and two local breeds (Sarda and Sardo Bruna). Our analysis identified regions with a high degree of heterozygosity using a consecutive runs approach, the Tajima D test, nucleotide diversity estimation, and Hardy Weinberg equilibrium test. These regions exhibited recurrent heterozygosity peaks and were consistently found on specific chromosomes across all breeds, specifically autosomes 15, 16, 20, and 23. The cosmopolitan and Sardo Bruna breeds also displayed peaks on autosomes 2 and 21, respectively. Thirty-five top runs shared by more than 25% of the populations were identified. These genomic fragments encompassed 18 genes, two of which are directly linked to male fertility, while four are associated with lactation. Two other genes play roles in survival and immune response. Our study also detected a region related to growth and carcass traits in Limousine breed. Our analysis of heterozygosity-rich regions revealed particular segments of the cattle genome linked to various functional traits. It appears that balancing selection is occurring in specific regions within the four examined breeds, and unexpectedly, they are common across cosmopolitan and local breeds. The genes identified hold potential for applications in breeding programs and conservation studies to investigate the phenotypes associated with these heterozygous genotypes. In addition, Tajima D test, Nucleotide diversity, and Hardy Weinberg equilibrium test confirmed the presence of heterozygous fragments found with Heterozygous-Rich Regions analysis.
Collapse
Affiliation(s)
- M C Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.
| | - F Tiezzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| | - A Crovetti
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| | - C Maltecca
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy; Department of Animal Science, North Carolina State University, Raleigh, NC 27695, United States
| | - R Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
| |
Collapse
|
3
|
Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
Collapse
Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| |
Collapse
|
4
|
Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [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: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
Collapse
Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
| |
Collapse
|
5
|
The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
Collapse
|
6
|
Assessment of Genetic Diversity, Runs of Homozygosity, and Signatures of Selection in Tropical Milking Criollo Cattle Using Pedigree and Genomic Data. Genes (Basel) 2022; 13:genes13101896. [PMID: 36292782 PMCID: PMC9602073 DOI: 10.3390/genes13101896] [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: 09/28/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree (FPed), the genomic relationship matrix (FGRM), and runs of homozygosity (FROH) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for FPED, FGRM, and FROH, respectively. Correlation between FPED and FROH was significant only for runs of homozygosity > 4 Mb, indicating the FPED of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program.
Collapse
|
7
|
Mulim HA, Brito LF, Batista Pinto LF, Moletta JL, Da Silva LR, Pedrosa VB. Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems. Front Genet 2022; 13:858970. [PMID: 35923708 PMCID: PMC9341487 DOI: 10.3389/fgene.2022.858970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.
Collapse
Affiliation(s)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | | | | | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, Brazil
- *Correspondence: Victor Breno Pedrosa,
| |
Collapse
|
8
|
Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs. Comput Struct Biotechnol J 2022; 20:4060-4071. [PMID: 35983229 PMCID: PMC9364102 DOI: 10.1016/j.csbj.2022.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/23/2022] Open
Abstract
Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using FST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.
Collapse
|
9
|
Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
Collapse
Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
10
|
Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci 2022; 105:5926-5945. [DOI: 10.3168/jds.2021-21125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
|