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Global distribution of Fst between DPL, LW, and three Western pig breeds on autosomes. DPL-DLY represents DPL-three Western pig breeds, while LW-DLY means DPL-three Western pig breeds.
Source publication
Shandong indigenous pig breeds are an invaluable source of data on genetics in Chinese pigs. However, information on the genetic basis of these breeds remains limited. In this study, we used specific-locus amplified fragment sequencing to conduct whole-genome screening to investigate genetic diversity in Shandong indigenous breeds and Western pig b...
Citations
... Using SLAF-seq-based GWAS, several SNPs and potential genes have been found for a variety of economic traits in various animals [9][10][11][12][13]. SLAF-seq for pig genotyping effectively found numerous new mutation sites [14][15][16]. ...
Background
Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET).
Results
A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10− 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs.
Conclusions
The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
... We used sequencing data to evaluate the three populations' genetic relationships and population structure. The population differentiation coefficient, Fst, can reveal the degree of differentiation between populations (Qin et al., 2019). In this study, the degree of differentiation between AS and the other two populations was relatively high, and the Fst values were all >0.05, indicating a moderate degree of genetic differentiation between AS and the other two populations (Weir and Cockerham, 1984). ...
The broad-banded velvetchin Hapalogenys analis is an economically and scientifically important global temperate and tropical nearshore marine fish. To understand the genetic evolution mechanism of H. analis, simplified genome sequencing analysis was conducted on 82 samples of H. analis from three populations (Akashi, Zhoushan, and Shantou) in the northwestern Pacific Ocean using double-digest restriction site-associated DNA sequencing. Genetic characteristics were identified using single-nucleotide polymorphism loci, and a small fragment library (250–450 bp long) was constructed for double-end sequencing. Single-nucleotide polymorphisms (SNPs) were detected using Stacks software and analyzed. The phylogenetic tree was constructed to analyze the population structure characteristics and the genetic evolutionary relationships between individuals in different regions at the genetic level. The sequencing library constructed for 82 samples of H. analis using double-digest restriction site-associated DNA sequencing possessed an average of 7,931,195 sequencing sequences and an average of 1,141,560,806 bases in the 82 samples. A total of 3,204,106 SNP loci were obtained from the three populations of H. analis, indicating rich genetic diversity. The transition to transversion ratio of SNPs was >1.5, indicating transformational reversal bias in H. analis. The observed heterozygosity of the various populations was 0.186–0.199, with an expected heterozygosity of 0.253–0.268. High diversity in all three populations was detected using nucleotide diversity analysis. AS and ZS had the highest degree of differentiation. The H. analis samples shared two gene libraries; some populations were closely related, whereas others had a distant genetic relationship. The results of genetic statistics, genetic differentiation, population structure, principal component, phylogenetic, and genetic relationship analyses supported independent clustering of the AS population, which can be used as a new genetic resource for conserving H. analis. These results provide a reference basis for comparative genomics studies of H. analis and rational utilization of Hapalogenys resources.
... Regions associated with meat and carcass quality were also identified among the indigenous breeds. For example, the indigenous Kolbroek and Windsnyer breeds included the JPH1 gene observed on chromosome 4, which has previously been linked to meat and carcass quality in pigs [54,55]. Furthermore, Hoffman et al. [56] observed that meat from Kolbroek pigs can be processed into bacon, ham, and chops. ...
... Crossbreeding with commercial pigs has allowed for the introduction of genetic variants that are advantageous for these traits in not only village pigs but also indigenous pigs. For example, regions displaying selection signatures included genes for meat and carcass quality in pigs in the village (e.g., SCPEP1 and SAMD4A) and indigenous (e.g., JPH1) populations [54,55,69]. The admixed genomes that result from the interbreeding of previously isolated populations can carry genetic signatures that resemble signals of positive selection. ...
South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer’s extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations’ ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations.
... Specific-Locus Amplified Fragment Sequencing (SLAF) technology, independently developed by Biomarker Technologies Co., Ltd, has been successfully applied to animal and plant research. For instance, Qin et al. (2020) employed SLAF-seq to investigate the genetic structure and relatedness of ten pig breeds in Shandong Province, discovering candidate genes associated with economic traits. Li et al. (2017) utilized SLAF-seq to study the genetic structure and kinship between landrace pigs and two local breeds. ...
The Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients ( F ST ) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining F ST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between F HOM and F GRM , and the lowest between F ROH >1.5Mb and F ROH <500kb . A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.
... The reduced-representation genome sequencing (RRGS) technique can detect widely covered genetic markers throughout the whole genome, and it has advantages such as high throughput and low cost [7,8]. It has been widely used in selective sweep analysis and population genetic analysis [9,10]. In fish genomics research, the RAD-seq technique has been widely used for fish species differentiation, genetic maps, population genetics, and adaptive evolution [11][12][13][14]. ...
Larimichthys crocea (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker.
... Using SLAF-seq-based GWAS, several SNPs and potential genes have been found for a variety of economic traits in various animals [9][10][11][12][13]. SLAF-seq for pig genotyping effectively found numerous new mutation sites [14][15][16]. ...
Background
Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs.
Results A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 53 SNPs were identified for seven carcass traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The heritability estimates based on SNP for seven carcass traits ranged from 0.23 (loin eye thickness) to 0.48 (dressing percentage). Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found to be associated with carcass traits in pigs.
Conclusions A total of 30 significant SNPs, two QTLs on SSC8and SSC10, and 11 candidate genes were identified as being associated with carcasstraits of pigs. The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
... Specific-Locus Amplified Fragment sequencing (SLAFseq) is a high throughput, high-resolution, and low-cost marker development technology that has emerged recently (Sun et al., 2013). This technique focuses on finding single nucleotide polymorphisms (SNPs), an abundant form of genetic variation, in an economical way Wang et al., 2016;Ali et al., 2018;Qin et al., 2019). SNPs are found throughout the genome, and their distribution can reflect the population's genetic variation. ...
... SNPs are found throughout the genome, and their distribution can reflect the population's genetic variation. SLAF-seq has been used to analyze several species' genetic diversity and phylogenetic structure Chang et al., 2019;Qin et al., 2019;Zhang J. et al., 2020a;Fang et al., 2020;Ababaikeri et al., 2021). In addition, mtDNA provides a different perspective of population genetic structure because it is maternally inherited and generally lacks intermolecular recombination (Allendorf, 2017). ...
The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.
... As a consequence, SLAF-seq-based GWAS was successfully applied to detect SNP loci for important quantitative traits in rabbits , chickens (Wang et al., 2015;Wang et al., 2019;Li et al., 2021), ducks (Xi et al., 2021), and geese (Melak et al., 2021). SLAFseq has also been successfully used for genotyping of pigs and detected abundant novel mutation sites (Li et al., 2017;Qin et al., 2020). Furthermore, we also identified some genomic regions and several candidate genes for porcine fatness-related and growthrelated traits using GWAS based on SLAF-seq technology in our previous studies (Wang et al., 2022a;Wang et al., 2022b). ...
... Frontiers in Genetics frontiersin.org advantage of the SLAF-seq method in the GWAS, genetic diversities analysis, and construction of genetic map for animals and plants (Qi et al., 2014;Li et al., 2017;Qin et al., 2020;Yang et al., 2020;Li et al., 2021;Mandozai et al., 2021). SLAF-seq technology can obtain more genomic variation sites than SNP chips, detect novel mutation sites and provide high SNP coverage at a low cost. ...
Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07–0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
... The analysis of cold tolerance of the Min pig revealed that transient receptor potential cation channel subfamily V member 5 (TRPV5) was selected and could be a responsible gene candidate [11]. In terms of meat quality, the genetic basis of high intramuscular fat (IMF) content in Laiwu pig has been identified via whole genome resequencing [12,13]. These studies indicate that the identification of selection signatures in pigs is important for pig breeding. ...
Wanbei pig (WBP) is one of the indigenous pig resources in China and has many germplasm characteristics. However, research on its genome is lacking. To assess the genomic variation, population structure, and selection signatures, we resequenced 18 WBP for the first time and performed a comprehensive analysis with resequenced data of 10 Asian wild boars. In total, 590.03 Gb of data and approximately 41 million variants were obtained. Polymorphism level (θπ) ratio and genetic differentiation (fixation index)-based cross approaches were applied, and 539 regions, which harbored 176 genes, were selected. Functional analysis of the selected genes revealed that they were associated with lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), and reproduction (CABS1). Overall, our results provide a valuable resource for characterizing the uniqueness of WBP and a basis for future breeding.
... These results suggested that the Prevalence of pathogenic factors and antagonistic factors. In the process of longterm evolution, hosts have developed different survival strategies to resist E. coli (39)(40)(41). For this reason, we investigated the relationships between colicin B and colicin M in different pig breeds. ...
Gut microbes can affect host adaptation to various environment conditions. Escherichia coli is a common gut species, including pathogenic strains and nonpathogenic strains. This study was conducted to investigate the effects of different E. coli strains in the gut on the health of pigs. In this study, the complete genomes of two E. coli strains isolated from pigs were sequenced. The whole genomes of Y18J and the enterotoxigenic E. coli strain W25K were compared to determine their roles in pig adaptation to disease. Y18J was isolated from feces of healthy piglets and showed strong antimicrobial activity against W25K in vitro. Gene knockout experiments and complementation analysis followed by modeling the microbe-microbe interactions demonstrated that the antagonistic mechanism of Y18J against W25K relied on the bacteriocins colicin B and colicin M. Compared to W25K, Y18J is devoid of exotoxin-coding genes and has more secondary-metabolite-biosynthetic gene clusters. W25K carries more genes involved in genome replication, in accordance with a shorter cell cycle observed during a growth experiment. The analysis of gut metagenomes in different pig breeds showed that colicins B and M were enriched in Laiwu pigs, a Chinese local breed, but were scarce in boars and Duroc pigs.
IMPORTANCE This study revealed the heterogeneity of E. coli strains from pigs, including two strains studied by both in silico and wet experiments in detail and 14 strains studied by bioinformatics analysis. E. coli Y18J may improve the adaptability of pigs toward disease resistance through the production of colicins B and M. Our findings could shed light on the pathogenic and harmless roles of E. coli in modern animal husbandry, leading to a better understanding of intestinal-microbe–pathogen interactions in the course of evolution.
