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1.
QTL analysis of white blood cell, platelet and red blood cell-related traits in an F2 intercross between Landrace and Korean native pigs 总被引:1,自引:0,他引:1
Cho IC Park HB Yoo CK Lee GJ Lim HT Lee JB Jung EJ Ko MS Lee JH Jeon JT 《Animal genetics》2011,42(6):621-626
Haematological traits play important roles in disease resistance and defence functions. The objective of this study was to locate quantitative trait loci (QTL) and the associated positional candidate genes influencing haematological traits in an F2 intercross between Landrace and Korean native pigs. Eight blood‐related traits (six erythrocyte traits, one leucocyte trait and one platelet trait) were measured in 816 F2 progeny. All experimental animals were genotyped with 173 informative microsatellite markers located throughout the pig genome. We report that nine chromosomes harboured QTL for the baseline blood parameters: genomic regions on SSC 1, 4, 5, 6, 8, 9, 11, 13 and 17. Eight of twenty identified QTL reached genome‐wide significance. In addition, we evaluated the KIT locus, an obvious candidate gene locus affecting variation in blood‐related traits. Using dense single nucleotide polymorphism marker data on SSC 8 and the marker‐assisted association test, the strong association of the KIT locus with blood phenotypes was confirmed. In conclusion, our study identified both previously reported and novel QTL affecting baseline haematological parameters in pigs. Additionally, the positional candidate genes identified here could play an important role in elucidating the genetic architecture of haematological phenotype variation in swine and in humans. 相似文献
2.
To detect quantitative trait loci (QTL) for litter size related traits, the total number of born piglets (TNB), the number of born alive piglets (NBA), the number of stillborn piglets (NSB) and the number of mummies (NM) at the first parity were recorded in 299 F2 sows in a White Duroc × Chinese Erhualian intercross resource population. A whole genome scan was performed with 183 microsatellites distributed across 19 porcine chromosomes in the resource population, and the QTL analysis was performed with a least-squares method. A 5% genome-wide significant QTL was detected at 88 cM on pig chromosome (SSC) 15 for NBA, which also showed suggestive effect on TNB. In addition, four suggestive QTL were detected on SSC 6, 7, 8 and 15 for TNB, NBA or NSB. Two of the five QTL detected showed accordance with previous reports. No QTL was found for NM. 相似文献
3.
This study provides 53 new fluorescent in situ hybridization cytogenetic assignments for microsatellite markers linked on the swine genetic map. Forty microsatellites are physically assigned for the first time. The chromosomal locations of eight markers were either confirmed or refined, while five loci were assigned to locations different from those given in previous reports. Markers were selected to provide physical anchors based on their presumed proximity to centromeres or telomeres and at approximately 30 cM intervals across the genetic map. The number of physical anchors for pig (SSC) chromosomes 8, 15, and 18 linkage groups was significantly improved. Centromeric regions were localized to areas less than 10 cM for SSC 1, 2, 3, 6, 7, 8, and 9. Although the recombination rate was generally higher across small biarmed chromosomes and lowest for large acrocentric chromosomes, two regions with particularly low (1q2.1-->q2.9 and 13q2.3-->q4.1) and three regions with extremely high (5p1.5-->p1.2, 6p1.4-->p1.3, and 12p1.5-->p1.4) rates of recombination were detected. These assignments represent an overall 10% increase in the number of physically assigned markers in Sus scrofa and more than a 20% increase in the number of Type II loci assigned to the pig cytogenetic map. 相似文献
4.
在猪数量性状位点的定位研究中,标记的使用和图谱的构建是很重要的。本研究从猪的第4、6、7、8和13染色体上选取39个微卫星标记,在来源于约克夏和梅山214头猪组成的资源群中,分析了遗传特征并构建了图谱。研究表明,平均等位基因数、平均观察杂合度(Ho)和平均多态信息含量(PIC)在F1和F2代中分别为:3.2,0.528,0.463和3.2,0.496,0.447。结果表明大多数微卫星标记位点表现为中高度杂合性。在资源群体中,平均有信息减数分裂数是217.4(44-316),而各染色体上两性平均图谱的长度分别是:172.3cM(SSC4),168.7cM(SSC6),191.7cM(SSC7),197.3cM(SSC8),178.3cM(SSC13)。与USDA-MARC的参考图谱相比,标记位点的顺序相同,但长度均较长。雌雄两性图谱相比,第4和第6染色体上雌性图谱长于雄性图谱;而在另外3条染色体上,则雄性图谱长于雌性图谱。结果显示了标记位点在资源猪群的遗传特征和遗传关系,其连锁图谱可用于今后的QTL定位。 相似文献
5.
Arthur Bob Karnuah Hirohide Uenishi Sachiko Kiuchi Misaki Kojima Akira Onishi Hiroshi Yasue Tadayoshi Mitsuhashi 《Mammalian genome》2001,12(7):518-523
A swine resource family was constructed at the National Institute of Animal Industry, Japan, in order to determine the genetic
regions responsible for economically important traits, including fetus development. To identify genes expressed in the early
stage of embryo development, we cataloged and mapped genes expressed in a 28-day-old normal pig embryo. In this effort, we
have mapped 64 genes, which have map information in human genome onto a swine radiation hybrid (RH) map, IMpRH. These mappings
provided additional chromosomal homologies between swine and human to improve the comparative map between the two species.
The distribution of the genes assigned to swine chromosomes are as follows: 9 genes were assigned on SSC6; 6 genes each assigned
on SSC5 and SSC14; 5 genes each assigned on SSC3, SSC4, and SSC8; 4 genes each assigned on SSC1, SSC7, SSC9, and SSC15; 3
genes each assigned on SSC2, SSC13 and SSCX; and 1 gene each assigned on SSC10, SSC11, and SSC16. Moreover, the present findings
revealed 18 new chromosomal homologies between pig and human. Briefly, SSC3 regions were indicated to correspond with HSA1
and HSA10; SSC4 with HSA6; SSC5 with HSA2, HSA15, and HSA16; SSC6 with HSA3, HSA6, and HSA20; SSC7 with HSA11; SSC8 with HSA3,
HSA6, and HSA7; SSC9 with HSA8; SSC13 with HSA1; SSC14 with HSA13; SSC15 with HSA19; SSC16 with HSA9.
Received: 19 December 2000 / Accepted: 13 March 2001 相似文献
6.
Genome scan reveals new coat color loci in exotic pig cross 总被引:2,自引:0,他引:2
Hirooka H de Koning DJ van Arendonk JA Harlizius B de Groot PN Bovenhuis H 《The Journal of heredity》2002,93(1):1-8
The porcine genome was scanned to identify loci affecting coat color in an experimental cross between the Meishan breed and Dutch commercial lines. Linkage was studied in 1181 F(2) animals for 132 microsatellite markers and seven binary coat color scores: White, Black spotting, Speckle, Gray, Black, and specific color phenotypes for head and legs. The analyses were performed using interval mapping under various models. The study confirmed the existence of coat color loci on chromosome 8 and chromosome 6. One additional locus affecting White was detected on chromosome 5, possibly representing the porcine equivalent of the steel factor. Two new loci affecting Black were detected on chromosome 2. One of these showed exclusive maternal expression and mapped to a region where imprinted genes have been reported. The effect of the binary coding was tested by additional analyses excluding the white animals (>50% of F(2) animals). This showed that Black spotting was strongly influenced by the locus on chromosome 6 and the other color phenotypes were mainly influenced by the locus on chromosome 8. Epistatic effects were found between the loci on chromosomes 6 and 8 for Black spotting. For Black color, all combinations among chromosomes 2, 6, and 8 showed epistatic effects. 相似文献
7.
Regine Preissler Jens Tetens Kerstin Reiners Holger Looft Nicole Kemper 《Animal genetics》2013,44(5):502-508
Postpartum dysgalactia syndrome (PDS) in sows is an important disease after parturition with a relevant economic impact, affecting the health and welfare of both sows and piglets. The genetic background of this disease has been discussed and its heritability estimated, but further genetic analyses are lacking in detail. The aim of the current study was to detect loci affecting the susceptibility to PDS through a genome‐wide association approach. The study was designed as a family‐based association study with matched sampling of affected sows and healthy half‐ or full‐sib control sows on six farms. For the study, 597 sows (322 affected vs. 275 healthy control sows) were genotyped on 62 163 single nucleotide polymorphisms (SNPs) using the Illumina PorcineSNP60 BeadChip. After quality control, 585 sows (314 affected vs. 271 healthy control sows) and 49 740 SNPs remained for further analysis. Statistics were performed mainly with the r package genabel and included a principal component analysis. A statistically significant genome‐wide associated SNP was identified on porcine chromosome (SSC) 17. Further promising results with moderate significance were detected on SSC 13 and on an unplaced scaffold with an older annotation on SSC 15. The PRICKLE2 and NRP2 genes were identified as candidate genes near associated SNPs. Several quantitative trait loci (QTL) have been previously described in these genomic regions, including QTL for mammary gland condition, as teat number and non‐functional nipples QTL, as well as QTL for body temperature and gestation length. 相似文献
8.
Mikawa S Shimanuki S Morozumi T Domukai M Shinkai H Uchida Y Mikawa A Miyake M Miyake Y Hayashi N Kusumoto H Uenishi H Hayashi T Awata T 《Animal genetics》2004,35(6):445-450
Several quantitative trait loci (QTL) have been detected on SSC1qter (Sus scrofa chromosome 1qter), including QTL for the number of vertebrae, as reported in our previous study. To provide the tools for analysis of QTLs on SSC1qter, we constructed a comparative map of swine and human. In addition, we identified 26 swine STSs and mapped 16 of them on SSC1qter using the INRA - University of Minnesota porcine radiation hybrid (IMpRH) panel. We screened a BAC library using these swine STSs and developed 35 new polymorphic microsatellite markers from the BAC clones, of which 26 were informative in our reference family. We also mapped nine microsatellite markers we had isolated previously. Consequently a total of 44 new polymorphic microsatellite markers were located within a 60-cM region of SSC1qter, spanning from SW1092 to the telomere. 相似文献
9.
Maintaining pH and blood gases in a narrow range is essential to sustain normal biochemical reactions. Decreased oxygenation, poor tissue perfusion, disturbance to CO2 expiration, and shortage of HCO3 − can lead to metabolic acidosis. This is a common situation in swine, and originates from a broad range of medical conditions. pH and blood gases appear to be under genetic control, and populations with physiological traits closer to the pathological thresholds may be more susceptible to developing pathological conditions. However, little is known about the genetic basis of such traits. We have therefore estimated phenotypic and genetic variability and identified quantitative trait loci (QTL) for pH and blood gases in blood samples from 139 F2 pigs from the Meishan/Pietrain family. Samples were taken before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. Twenty-seven QTL influencing pH and blood gases were identified on nine chromosomes. Five of the QTL were significant on a genome-wide level; 22 QTL were significant on a chromosome-wide level. QTL for pH-associated traits have been mapped to SSC3, 18 and X. QTL associated with CO2 have been detected on SSC6, 7, 8 and 9, and QTL associated with O2 on SSC2 and SSC8. QTL showed specific health/disease patterns that were related to the physiological state of the pigs from day 0, to acute disease (day 14), convalescence (day 28) and chronic disease (day 42). The results demonstrate that pH and blood gases are influenced by multiple chromosomal areas, each with relatively small effects. 相似文献
10.
Chen CY Guo YM Zhang ZY Ren J Huang LS 《Animal : an international journal of animal bioscience》2010,4(6):861-866
Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F2 sows from a White Duroc × Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r = -0.13, P < 0.05). Three QTL were detected on pig chromosome (SSC)2, 8 and 12 for gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13. 相似文献
11.
Nii M Hayashi T Tani F Niki A Mori N Fujishima-Kanaya N Komatsu M Aikawa K Awata T Mikawa S 《Animal genetics》2006,37(4):342-347
Here, we analysed quantitative trait loci (QTL) for fatty acid composition, one of the factors affecting fat quality, in a Japanese wild boar x Large White cross. We found 25 significant effects for 17 traits at 13 positions at the 5% genome-wise level, of which 16 effects for 12 traits at 10 positions were significant at the 1% level. QTL for saturated fatty acids (SFA) in back fat were mapped to swine (Sus scrofa) chromosomes (SSC) 1p, 9 and 15. QTL for unsaturated fatty acids in back fat were mapped to SSC1p, 1q, 4, 5, 9, 15 and 17. Using a regression model that fits back fat thickness as a covariate, two of the QTL for linoleic acid content on SSC4 and SSC17 were not significant, but one QTL for total SFA composition was detected on SSC5 with correction for back fat thickness. Wild boar alleles at six of seven QTL tended to increase SFAs and to decrease unsaturated fatty acids. QTL for fatty acid composition in perirenal fat were mapped on SSC2, 3, 4, 5, 6, 14, 16 and X. QTL for melting point (in back fat samples) were mapped on SSC1, 2 and 15. Wild boar alleles in QTL on SSC1 and SSC15 were associated with elevated melting points whereas those on SSC2 were associated with lower melting point measurements. 相似文献
12.
13.
Thierry Tribout Nathalie Iannuccelli Tom Druet Hélène Gilbert Riquet Juliette Gueblez Ronan Marie-José Mercat Jean-Pierre Bidanel Denis Milan Pascale Le Roy 《遗传、选种与进化》2008,40(1):61-78
A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL. 相似文献
14.
Since the distal half of swine chromosome (SSC) 10q was shown to contain a quantitative trait locus (QTL) influencing swine growth, the precise correspondence between this chromosome region and the orthologous human chromosome region (HSA10p) was investigated using chromosomal fluorescence in situ hybridization and RH mapping of type I loci spanning the growth QTL. The goal was to align this critical region of swine with the corresponding region in human for the purpose of identifying candidate genes. The HSA10p type I loci mapped in swine were VIM, MRC1, GAD2, and IL2RA. Locus order on SSC10q was shown to be centromere-VIM-MRC1-GAD2-IL2RA, while in human the order is centromere-GAD2-MRC1-VIM--IL2RA, indicating that the chromosome segment marked by VIM, MRC1 and GAD2 has been inverted relative to the centromere and IL2RA. 相似文献
15.
G. Reiner F. Köhler T. Berge R. Fischer K. Hübner-Weitz J. Scholl H. Willems 《Animal genetics》2009,40(4):366-376
Behavioural indices in vertebrates are under genetic control at least to some extent. In spite of significant behavioural problems in farm animals, information on the genetic background of behaviour is sparse. The aim of this study was to map QTL for behavioural indices in swine under healthy conditions and after infection with Sarcocystis miescheriana , as behaviour can be significantly influenced by disease . This well-described parasite model subsequently leads to acute (day 14 p.i.), subclinical (day 28 p.i.) and chronic disease (day 42 p.i.), allowing the study and comparison of the behaviour of pigs under four different states of health or disease. The study was based on a well-described Pietrain/Meishan F2 family that has recently allowed the detection of QTL for disease resistance. We have mapped six genome-wide significant and 24 chromosome-wide significant QTL for six behavioural indices in swine. Six of these QTL (i.e. 20% of total QTL) showed effects on behavioural traits of the healthy pigs (day 0). Some of them (QTL on SSC11 and 18) lost influence on behavioural activities during disease, while the effects of others (QTL on SSC5, SSC8) partly remained during the whole experiment, although with different effects on the distinct behavioural indices. The disease model has been of high relevance to detect effects of gene loci on behavioural indices. Considering the importance of segregating alleles and environmental conditions that allow the identification of the phenotype, we conclude that there are indeed QTL with interesting effects on behavioural indices in swine. 相似文献
16.
A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines. 相似文献
17.
In vivo effect of a TLR5 SNP (C1205T) on Salmonella enterica serovar Typhimurium infection in weaned,specific pathogen‐free Landrace piglets
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Yoshihiro Muneta Nobuo Arai Yoko Yakabe Masahiro Eguchi Tomoyuki Shibahara Akiko Sakuma Hiroki Shinkai Hirohide Uenishi Kensuke Hirose Masato Akiba 《Microbiology and immunology》2018,62(6):380-387
18.
Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle 总被引:3,自引:0,他引:3
Sodeland M Kent MP Olsen HG Opsal MA Svendsen M Sehested E Hayes BJ Lien S 《Animal genetics》2011,42(5):457-465
Mastitis is the most frequent and costly disease in dairy production and solutions leading to a reduction in the incidence of mastitis are highly demanded. Here a genome-wide association study was performed to identify polymorphisms affecting susceptibility to mastitis. Genotypes for 17 349 SNPs distributed across the 29 bovine autosomal chromosomes from a total of 2589 sires with 1 389 776 daughters with records on clinical mastitis were included in the analysis. Records of occurrence of clinical mastitis were divided into seven time periods in the first three lactations in order to identify quantitative trait loci affecting mastitis susceptibility in particular phases of lactation. The most convincing results from the association mapping were followed up and validated by a combined linkage disequilibrium and linkage analysis. The study revealed quantitative trait loci affecting occurrence of clinical mastitis in the periparturient period on chromosomes 2, 6 and 20 and a quantitative trait locus affecting occurrence of clinical mastitis in late lactation on chromosome 14. None of the quantitative trait loci for clinical mastitis detected in the study seemed to affect lactation average of somatic cell score. The SNPs highly associated with clinical mastitis lie near both the gene encoding interleukin 8 on chromosome 6 and the genes encoding the two interleukin 8 receptors on chromosome 2. 相似文献
19.
A A Paszek P J Wilkie G H Flickinger L M Miller C F Louis G A Rohrer L J Alexander C W Beattie L B Schook 《Animal biotechnology》2001,12(2):155-165
An autosomal scan of the swine genome with 119 polymorphic microsatellite (ms) markers and data from 116 F2 barrows of the University of Illinois Meishan x Yorkshire Swine Resource Families identified genomic regions with effects on variance in carcass composition and meat quality at nominal significance (p-value <0.05). Marker intervals on chromosomes 1, 6, 7, 8 and 12 (SSC1, SSC6, SSC7, SSC8, SSC12) with phenotypic effects on carcass length, 10th rib backfat thickness, average backfat thickness, leaf fat, loin eye area and intramuscular fat content confirm QTL effects identified previously based on genome wide significance (p-value <0.05). Several marker intervals included nominally significant (p-value <0.05) dominance effects on leaf fat, 10th rib backfat thickness, loin eye area, muscle pH and intramuscular fat content. 相似文献
20.
A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea 总被引:9,自引:0,他引:9
P.J. Wilkie A.A. Paszek C.W. Beattie L.J. Alexander M.B. Wheeler L.B. Schook 《Mammalian genome》1999,10(6):573-578
Reproductive traits have low heritabilities, are expressed in only one sex, and are not measurable until sexual maturity
(Avalos and Smith, Anim Prod 44:153, 1987). Using traditional methods, selection for reproductive traits is relatively less
effective than selecting for growth or carcass traits. Traits most affected by a small number of genes with major effects
rather than many genes with small effects are most amenable to MAS. As part of our porcine genome scan to identify quantitative
trait loci (QTLs) of economic importance in marker-assisted selective (MAS) breeding programs, we examined 8 reproductive
and farrowing traits in the University of Illinois (UI) Meishan × Yorkshire Resource Family. Gilts were genotyped with 119
microsatellite markers (MS) with intervals averaging 24 cM over all 18 porcine autosomes. F-ratios supporting QTL location
were calculated by the least squares regression method. Results suggestive of linkage at the 5% genome-wide level were observed
for the number of stillborn piglets on Chromosome (Chr) 4 (SSC4) (p-value = 0.0001), corpora lutea on SSC8 (p-value = 0.00027), and gestation length on SSC9 (p-value = 0.00019). Results for additional loci relevant to litter size, number of corpora lutea on SSC15 and 7 (p-value = 0.0029 and 0.0028 at 107 and 150 cM, respectively), gestation length on SSC15 and 1 (p-value = 0.0017 and 0.0069 at 96 and 166 cM, respectively), uterine length on SSC7 and 5 (p-value = 0.0044 and 0.0075 at 148 and 1 cM, respectively) and piglets born per litter on SSC6 (p-value = 0.0075 at 102 cM), were not statistically significant at the 5% genome-wide level. Thus, the use of a linked marker
to facilitate selection for reproductive traits has considerable potential. By using linked markers, selection can be applied
to both sexes before sexual maturity, making genetic selection considerably more efficient and less costly.
Received: 24 June 1998 / Accepted 29 January 1999 相似文献