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 The Population Structure and Selection Signal Analysis of Shenxian Pigs based on Genome Resequencing Technology

2021 ◽  
Author(s):  
Liu Diao ◽  
Lu Chunlian ◽  
Li Shang ◽  
Jia Mengyu ◽  
Li Sai ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signal Analysis ◽  
Genetic Resource ◽  
Genetic Relationships ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Large White ◽  
Bioinformatics Analyses ◽  
Whole Genome Resequencing ◽  
Selection Signal

ABSTRACTShenxian 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. 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).

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 Microstructure of Longissimus Lumborum Muscle and Meat Quality of Native Polish Pig Breeds: Złotnicka Sp Otted and Puławska

2016 ◽  
Vol 16 (4) ◽  
pp. 1199-1210 ◽  
Author(s):  
Joanna Bogucka ◽  
Wojciech Kapelański
Keyword(s):  
Meat Quality ◽  
The Other ◽  
Type I ◽  
Large White ◽  
Pig Breeds ◽  
Longissimus Lumborum ◽  
Fattening Pigs

Abstract In 50 fattening pigs representing two Polish native breeds: 24 Złotnicka Spotted, 10 Puławska and 16 F1 ♀ (Polish Large White × Polish Landrace) × F1 ♂ (Duroc × Pietrain) crosses microstructure of muscle, carcass and meat quality were studied. Puławska pigs had the thickest backfat, but the loin eye area was smaller only in comparison to crossbreds. Compared to the Puławska breed, the meat of Złotnicka Spotted pigs was darker, which was associated with a greater percentage of type I fibres and a smaller percentage of type IIB fibres. Puławska pigs distinguished themselves from the other groups under study by the greatest density of fibres per mm2. Smaller diameter of type IIA and IIB fibres and higher total number of fibres were found in Puławska breed pigs compared to Złotnicka Spotted, despite the absence of differences in the loin eye area. Smaller thickness of the fibres favourably affects meat quality, and might be considered an indicator of a delicate structure of meat.

scholarly journals Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Kejun Wang ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

scholarly journals Whole‐genome resequencing to identify candidate genes for the QTL for oleic acid percentage in Japanese Black cattle

2019 ◽  
Vol 90 (4) ◽  
pp. 467-472 ◽  
Author(s):  
Fuki Kawaguchi ◽  
Hiroto Kigoshi ◽  
Moriyuki Fukushima ◽  
Eiji Iwamoto ◽  
Eiji Kobayashi ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Whole Genome ◽  
Japanese Black Cattle ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Acid Percentage

scholarly journals Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Weibing Zhuang ◽  
Tianyu Liu ◽  
Shenchun Qu ◽  
Binhua Cai ◽  
Yalong Qin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Leaf Scorch ◽  
Whole Genome Resequencing ◽  
Populus Deltoids

The effect of breed on calpastatin isoforms and longissimus shear force in pigmeat

1999 ◽  
Vol 1999 ◽  
pp. 194-194 ◽  
Author(s):  
P.L. Sensky ◽  
T. Parr ◽  
R.G. Bardsley ◽  
P.J. Buttery ◽  
C. C. Warkup
Keyword(s):  
Meat Quality ◽  
Shear Force ◽  
Carotid Arteries ◽  
Enzyme System ◽  
Carcass Weight ◽  
Quality Traits ◽  
Large White ◽  
Inhibitory Component ◽  
Pig Breeds ◽  
Livestock Species

The calpain enzyme system plays an important role in the proteolytic events leading to the conversion of muscle to meat in livestock species. Increasing evidence suggests that calpastatin, the inhibitory component of the system, correlates negatively with tenderness in beef and pigs (Koohmaraieet al., 1995; Senskyet al., 1998). In this study, the immunoreactivity of calpastatin in three pig breeds with different meat quality traits have been measured.Thirty-six female pigs, comprising equal numbers of Duroc (D), Large White (LW) and Duroc x Large White (50:50 DxLW) breeds were reared under identical conditions at a commercial pig unit and slaughtered at a commercial slaughterhouse on the same day by electrical stunning and severance of the carotid arteries. Carcass weight, backfat thickness, pH45and pHuwere all monitored.

Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep

Genomics ◽  
2021 ◽  
Vol 113 (4) ◽  
pp. 2077-2084
Author(s):  
Deyin Zhang ◽  
Xiaoxue Zhang ◽  
Fadi Li ◽  
Teng Liu ◽  
Zhihong Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Hu Sheep

scholarly journals Feed Intake Behaviour of different Pig Breeds during Performance Testing on Station

2006 ◽  
Vol 49 (1) ◽  
pp. 77-88 ◽  
Author(s):  
R. Baumung ◽  
G. Lercher ◽  
A. Willam ◽  
J. Sölkner
Keyword(s):  
Meat Quality ◽  
Feed Intake ◽  
Quality Index ◽  
Consumption Rate ◽  
Performance Testing ◽  
Feed Consumption ◽  
Feeding Patterns ◽  
Large White ◽  
Pig Breeds ◽  
Feeding Station

Abstract. The aim of the study was to compare the feed intake behaviour of the two main pig breeds used as dam lines in Austria, Large White and Landrace, and to clarify whether there is an effect of MHS-type on feeding patterns in Pietrain. Feed intake behaviour of 1.593 pigs of three different breeds (618 Large White, 486 Landrace, 489 Pietrain) kept in group pens (maximum 13 pigs per pen) was analyzed. Different traits such as visits per hour and per day, time in the feeding station per hour and per day, feed intake per hour and per day and feed consumption rate were used to describe feed intake behaviour for the observation periods testing day and testing period. By using Generalized Linear Models differences in feed intake behaviour between the breeds were assessed. LS-Means were used to describe feed intake patterns for each breed. Large White and Landrace animals showed clearly different feed intake strategies: Large White can be characterized by a high number of visits in the station combined with shorter time spent in the station and lower consumption rates. Landrace animals tend to visit the feeding station less often per hour but compensate this with staying longer in the feeding station resulting in a higher feed intake per meal. The effects of MHS-type on feeding patterns of Pietrain, were small. Finally the relationships between selected growth and carcass traits (average daily gain, feed conversion ratio, lean meat content, meat quality index, intramuscular fat content) and selected feed intake behaviour traits (average feed intake per day, average time per day, average feed consumption rate) were analyzed using regression analysis. Average feed intake had a significant influence on all performance traits except the meat quality index.

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