scholarly journals Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding

2020 ◽  
Vol 33 (5) ◽  
pp. 712-721
Author(s):  
Wei Zhang ◽  
Min Yang ◽  
Yuanlang Wang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
High Fertility ◽  
Selection Signatures ◽  
Single Nucleotide Variants ◽  
Genetic Characteristics ◽  
Genome Variation ◽  
Wild Boars ◽  
Pig Breeds

Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding.Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios.Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions.Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.

scholarly journals Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication

2019 ◽  
Author(s):  
Wei Zhang ◽  
Yuanlang Wang ◽  
Min Yang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
X Chromosome ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Sweat Glands ◽  
Whole Genome Sequencing Data ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Long Time

AbstractYucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and π ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.

scholarly journals A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

animal ◽  
2019 ◽  
Vol 13 (4) ◽  
pp. 683-693 ◽  
Author(s):  
Z. Wang ◽  
H. Sun ◽  
Q. Chen ◽  
X. Zhang ◽  
Q. Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Scan ◽  
Next Generation ◽  
Selection Signatures ◽  
Pig Breeds ◽  
A Genome ◽  
Generation Sequencing

149 Integration of Selection Signatures Analyses and Weighted Single-step GWAS to Prioritize Candidate Genes for Body Conformation Traits in Pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-77
Author(s):  
Seyed Milad Vahedi ◽  
Siavash Salek Ardestani ◽  
Duy Ngoc Do ◽  
Karim Karimi ◽  
Younes Miar
Keyword(s):  
Candidate Genes ◽  
Complex Traits ◽  
Body Height ◽  
Single Step ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Selection Signatures ◽  
Body Conformation ◽  
Yorkshire Pigs ◽  
Estimated Breeding Values

Abstract Body conformation traits such as body height (BH) and body length (BL) have been included in the swine industry’s selection criteria. The objective of this study was to identify the quantitative trait loci (QTLs) and candidate genes for pig conformation traits using an integration of selection signatures analyses and weighted single-step GWAS (WssGWAS). Body measurement records of 5,593 Yorkshire pigs of which 598 animals were genotyped with Illumina 50K panel were used. Estimated breeding values (EBVs) for BH and BL were computed using univariate animal models. Genotyped animals were grouped into top 5% and bottom 5% based on their EBVs, and selection signatures analyses were performed using fixation index (Fst), FLK, hapFLK, and Rsb statistics, which were then combined as a Mahalanobis distance (Md) framework. The WssGWAS was conducted to detect the single nucleotide polymorphisms (SNPs) associated with the studied traits. The top 1% SNPs (n=530) from Md distribution that overlapped with the top 1% SNPs from WssGWAS (n = 530) were used to detect the candidate genes. A total of 31 and six overlapped SNPs were found to be associated with BH and BL, respectively. Several candidate genes were identified for BH (PARVA, DCDC1, SYT1, CASTOR2, RGSL1, RGS8, RBMS3, TGFBR2, and HS6ST1) and BL (SNTB1, AK7, PAPOLA, KSR1, CHODL, and BMP2), explaining 2.58% and 0.42% of the trait’s genetic variation, respectively. Our results indicated that integrating data from the signatures of selection tests with WssGWAS could help elucidate genomic regions underlying complex traits.

scholarly journals Genetic Relationships Among Representatives of Dasypyrum, Secale and Triticum Species Revealed with RAPD and ISSR Markers

2014 ◽  
Vol 42 (2) ◽  
pp. 420-430
Author(s):  
Agnieszka GRADZIELEWSKA ◽  
Mirosław TYRKA ◽  
Justyna LESNIOWSKA-NOWAK ◽  
Justyna NAZARUK
Keyword(s):  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
Fixation Index ◽  
Triticum Species ◽  
The Difference ◽  
Bridge Species ◽  
Differentiation Gene ◽  
Rapd And Issr

In this study the genetic similarity among Dasypyrum, Secale andTriticum species with RAPDs and ISSRs was analyzed. To show a level of similarity between the species, 12 populations of Dasypyrum (11 D. villosum and 1 D. breviaristatum), together with 12 accessions belonging to 3 Secale species and 12 accessions from 4 Triticum species were used. Genetic distances (GD) and bootstrap values were calculated and PCA analysis was conducted to present the relationships among the species. To estimate the genetic structure among and inside genera, as well as population differentiation, gene diversity (He), total genetic variation (Ht) and Wright’s fixation index (Fst) were computed. The highest values were found in Triticum, within which Ht was equal to 0.332±0.023 and Fst was 0.42. It confirmed that the material studied was highly differentiated. Both systems found Dasypyrum more related with Triticum, as compared to Secale. With RAPDs, genetic distance (GD) between Triticum and Dasypyrum was 0.435, respectively 0.460 for Secale vs Dasypyrum. In the case of ISSRs these values were 0.374 and 0.407, respectively. Despite the fact that the difference between the two GD indices was insignificant, one should not exclude the possibility of successful hybridization of Dasypyrum and Secale, especially when using bridge species.

scholarly journals The Population Structure and Selection Signal Analysis of Shenxian Pigs Based on Genome Resequencing Technology

2021 ◽  
Author(s):  
Diao Liu ◽  
Chunlian Lu ◽  
Shang Li ◽  
Mengyu Jia ◽  
Yutao Miao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Meat Quality ◽  
Genetic Relationships ◽  
Animal Husbandry ◽  
Hebei Province ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Large White ◽  
Bioinformatics Analyses ◽  
Pig Breeds

Abstract Shenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3). However, no genes related to meat quality traits were successfully screened.

scholarly journals Candidate genes associated with athletes' skeletal muscle functions regulation

2021 ◽  
Vol 1 (2) ◽  
pp. 83-94
Author(s):  
O. V. Balberova ◽  
E. V. Bykov ◽  
G. V. Medvedev
Keyword(s):  
Candidate Genes ◽  
Skeletal Muscles ◽  
Sports Injuries ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Genetic Characteristics ◽  
Endurance Strength ◽  
Personalized Approach ◽  
And Function ◽  
Genetically Determined

It is generally recognized that an elite athlete's status is a multifactorial phenotype depending on many environmental and genetic factors. Variations in the sequence of nucleotides in deoxyribonucleic acid (DNA), in particular, single-nucleotide variants (SNVs) act as key internal factors associated with achieving high results in sports. The determination of specific individuals' genetic characteristics allows us to identify athletes who have the greatest genetically determined potential for certain sports that require speed, strength or endurance manifestation. Of course, peculiarities of the structure and function of skeletal muscles are among the most important characteristics in sports results context, in sports associated with the development of power / strength or endurance phenotypes. The composition and function of skeletal muscles are controlled by many different genes, and their SNVs can serve as strength or endurance athletes' status biomarkers. (1) Background: to conduct a thematic review of candidate genes studies and their single-nucleotide variants (SNVs) associated with the functioning of skeletal muscles in athletes. (2) Methods: A search for articles for the period from 2010 to 2020 was conducted in the databases SCOPUS, Web of Science, Google Calendar, Clinical keys, PubMed, e-LIBRARY using keywords and their combinations; (3) Conclusions: The identification of genetic biomarkers associated with muscular system regulation can help neurologists, sports doctors and coaches in developing personalized strategies for selecting children, adolescents and young adults for endurance, strength and speed sports (for example, running short, medium or long distances). Such a personalized approach will increase sports performance and reduce the risk of sports injuries of the musculoskeletal system.

scholarly journals Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

2020 ◽  
Author(s):  
Siavash Salek Ardestani ◽  
Mahmoud Amiri Roudbar ◽  
Mohammad Hossein Banabazi ◽  
Seyedeh Fatemeh Mousavi ◽  
Madhav Bhatta ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Rice Genome ◽  
Fixation Index ◽  
Biological Processes ◽  
Selection Signatures ◽  
Genomic Changes ◽  
Asian Rice ◽  
Genome Level ◽  
Window Approach ◽  
Genomic Regions

Abstract BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.

scholarly journals The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

2020 ◽  
Vol 24 (7) ◽  
pp. 747-754
Author(s):  
V. R. Kharzinova ◽  
N. A. Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Genetic Material ◽  
Animal Husbandry ◽  
Molecular Genetic Analysis ◽  
Fixation Index ◽  
Large White ◽  
Black And White ◽  
The Republic

One of the main tasks of genetics and animal breeding is the assessment of genetic diversity and the study of genetic relationships between different breeds and populations using molecular genetic analysis methods. We analysed the polymorphism of microsatellites and the information on the state of genetic diversity and the population structure of local breeds in Russia: the Kemerovo, the Berkshire, the Liven, the Mangalitsa, and the Civilian; in the Republic of Belarus: the Large White and the Black-and-White; and in Ukraine: the White Steppe, as well as commercial breeds of imported origin of domestic reproduction: the Large White, the Landrace, and the Duroc. The materials used for this study were the tissue and DNA samples extracted from 1,194 pigs and DNA of the UNU “Genetic material bank of domestic and wild animal species and birds” of the L.K. Ernst Federal Research Center for Animal Husbandry. Polymorphisms of 10 microsatellites (S0155, S0355, S0386, SW24, SO005, SW72, SW951, S0101, SW240, and SW857) were determined according to the previously developed technique using DNA analyser ABI3130xl. To estimate the allele pool of each population, the average number of alleles (NA), the effective number of alleles (NE ) based on the locus, the rarified allelic richness (AR), the observed (HO ) and expected (HE ) heterozygosity, and the fixation index (FIS) were calculated. The degree of genetic differentiation of the breeds was assessed based on the pairwise values of FST and D. The analysis of the allelic and genetic diversity parameters of the local breeds showed that the maximum and minimum levels of polymorphism were observed in pigs of the Ukrainian White Steppe breed (NA = 6.500, NE = 3.709, and AR = 6.020) and in pigs of the Duroc breed (NA = 4.875, NE = 2.119, and AR = 3.821), respectively. The highest level of genetic diversity was found in the Large White breed of the Republic of Belarus (HO = 0.707 and NE = 0.702). The minimum level of genetic diversity was found in pigs of the imported breeds – the Landrace (HO = 0.459, HE = 0.400) and the Duroc (HO = 0.480, HE = 0.469) – indicating a high selection pressure in these breeds. Based on the results of phylogenetic analysis, the genetic origin of Large White pigs, the breeds, from which the Berkshire pigs originated, and the genetic detachment of the Landrace from the Mangalitsa breeds were revealed. The cluster analysis showed a genetic consolidation of the Black-and-White, the Berkshire, and the Mangalitsa pigs. Additionally, the imported breeds with clustering depending on the origin were characterised by a genetic structure different from that of the other breeds. The information obtained from these studies can serve as a guide for the management and breeding strategies of the pig breeds studied, to allow their better use and conservation.

scholarly journals Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

2018 ◽  
Vol 53 (9) ◽  
pp. 975-984 ◽  
Author(s):  
Arnaldo Basso Rebelato ◽  
Alexandre Rodrigues Caetano
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Runs Of Homozygosity ◽  
Demographic Information ◽  
Genomic Information ◽  
Selection Signatures ◽  
Effective Population ◽  
High Frequencies ◽  
Production Animals ◽  
Genealogical Information

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

scholarly journals Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2074
Author(s):  
Ayano Hata ◽  
Atsushi Takenouchi ◽  
Keiji Kinoshita ◽  
Momomi Hirokawa ◽  
Takeshi Igawa ◽  
...  
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Genetic Relationships ◽  
Indigenous Chicken ◽  
Genetic Characteristics ◽  
Indigenous Chickens ◽  
Loop Region ◽  
Microsatellite Dna Markers ◽  
D Loop ◽  
Chicken Breeds

Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A–E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.

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