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1.
R. Pelayo M. C. T. Penedo M. Valera A. Molina L. Millon C. Ginja L. J. Royo 《Animal genetics》2017,48(4):450-454
The aim of this work was to perform a thorough analysis of the diversity of Y‐haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y‐specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y‐haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle. 相似文献
2.
Mitochondrial DNA (mtDNA) diversity in European and Asian pigs was assessed using 1536 samples representing 45 European and 21 Chinese breeds. Diagnostic nucleotide differences in the cytochrome b (Cytb) gene between the European and Asian mtDNA variants were determined by pyrosequencing as a rapid screening method. Subsequently, 637bp of the hypervariable control region was sequenced to further characterize mtDNA diversity. All sequences belonged to the D1 and D2 clusters of pig mtDNA originating from ancestral wild boar populations in Europe and Asia, respectively. The average frequency of Asian mtDNA haplotypes was 29% across European breeds, but varied from 0 to 100% within individual breeds. A neighbour-joining (NJ) tree of control region sequences showed that European and Asian haplotypes form distinct clusters consistent with the independent domestication of pigs in Asia and Europe. The Asian haplotypes found in the European pigs were identical or closely related to those found in domestic pigs from Southeast China. The star-like pattern detected by network analysis for both the European and Asian haplotypes was consistent with a previous demographic expansion. Mismatch analysis supported this notion and suggested that the expansion was initiated before domestication. 相似文献
3.
M. Ferencakovic I. Curik L. Pérez‐Pardal L. J. Royo V. Cubric‐Curik I. Fernández I. Álvarez A. Kostelic N. Sprem K. Krapinec F. Goyache 《Animal genetics》2013,44(2):184-192
Variation in mitochondrial DNA (mtDNA) and Y‐chromosome haplotypes was analysed in nine domestic sheep breeds (159 rams) and 21 mouflon ( Ovis musimon) sampled in the East Adriatic. Mitochondrial DNA analyses revealed a high frequency of type B haplotypes, predominantly in European breeds, and a very low frequency of type A haplotypes, which are more frequent in some Asian breeds. Mitochondrial haplotype Hmt‐3 was the most frequent (26.4%), and 37.1%, 20.8% and 7.6% of rams had haplotypes one, two and three mutations remote from Hmt‐3 respectively. In contrast, Y‐chromosome analyses revealed extraordinary paternal allelic richness: HY‐6, 89.3%; HY‐8, 5.0%; HY‐18, 3.1%; HY‐7, 1.3%; and HY‐5, 1.3%. In fact, the number of haplotypes observed is comparable to the number found in Turkish breeds and greater than the number found in European breeds so far. Haplotype HY‐18 (A‐oY1/135‐SRYM18), identified here for the first time, provides a link between the haplotype HY‐12 (A‐oY1/139‐SRYM18) found in a few rams in Turkey and haplotype HY‐9 (A‐oY1/131‐SRYM18) found in one ram in Ethiopia. All mouflons had type B mtDNA haplotypes, including the private haplotype (Hmt‐55), and all were paternally monomorphic for haplotype HY‐6. Our data support a quite homogeneous maternal origin of East Adriatic sheep, which is a characteristic of European breeds. At the same time, the high number of haplotypes found was surprising and intriguing, and it begs for further analysis. Simultaneous analysis of mtDNA and Y‐chromosome information allowed us to detect a large discrepancy between maternal and paternal lineages in some populations. This is most likely the result of breeder efforts to ‘upgrade’ local populations using rams with different paternal origins. 相似文献
4.
Guang‐Li Yang Feng‐Hua Lv Ming‐Jun Liu Wen‐Rong Li Yong‐Gang Liu Jin‐Quan Li Feng Wang Zhi‐Qiang Shen Sheng‐Guo Zhao EEr Hehua Nurbiy Marzanov Maziek Murawski Juha Kantanen Meng‐Hua Li 《Animal genetics》2014,45(6):903-907
Variation in two SNPs and one microsatellite on the Y chromosome was analyzed in a total of 663 rams representing 59 breeds from a large geographic range in northern Eurasia. SNPA‐oY1 showed the highest allele frequency (91.55%) across the breeds, whereas SNPG‐oY1 was present in only 56 samples. Combined genotypes established seven haplotypes (H4, H5, H6, H7, H8, H12 and H19). H6 dominated in northern Eurasia, and H8 showed the second‐highest frequency. H4, which had been earlier reported to be absent in European breeds, was detected in one European breed (Swiniarka), whereas H7, which had been previously identified to be unique to European breeds, was present in two Chinese breeds (Ninglang Black and Large‐tailed Han), one Buryatian (Transbaikal Finewool) and two Russian breeds (North Caucasus Mutton‐Wool and Kuibyshev). H12, which had been detected only in Turkish breeds, was also found in Chinese breeds in this work. An overall low level of haplotype diversity (median h = 0.1288) was observed across the breeds with relatively higher median values in breeds from the regions neighboring the Near Eastern domestication center of sheep. H6 is the dominant haplotype in northwestern and eastern China, in which the haplotype distribution could be explained by the historical translocations of the H4 and H8 Y chromosomes to China via the Mongol invasions followed by expansions to northwestern and eastern China. Our findings extend previous results of sheep Y chromosomal genetic variability and indicate probably recent paternal gene flows between sheep breeds from distinct major geographic regions. 相似文献
5.
6.
The Toll-like receptor 5 (TLR5) recognizes flagellin of Gram-positive and -negative bacteria and plays an important role in the host defense system. Here, we surveyed single nucleotide polymorphisms (SNPs) in the coding sequence of the porcine TLR5 gene in 83 individuals from five pig breeds, these including Chinese local populations and Western commercial pig breeds. A total of 19 medium polymorphic SNPs (0.25 < PIC < 0.5) were identified, three of which were missense mutations that clustered within the extracellular domain of TLR5. One of the non-synonymous SNPs fell within a 228-amino acid region which has been shown to be important for flagellin recognition. Four SNPs were only found with high frequencies in Oriental pig breeds. The 19 SNPs were found in 30 haplotypes, one of which segregated at high frequency in all samples. Compared with Western pig breeds, Chinese local populations had higher genetic diversity and more haplotypes. Tajima’s test showed no evidence for deviation from neutrality. The data provide useful information for future genetic marker characterization by means of disease association analysis and/or stimulating the mutation carrier with relevant ligands. 相似文献
7.
Amandine Marty Yves Amigues Bertrand Servin Gilles Renand Hubert Levéziel Dominique Rocha 《Molecular biotechnology》2010,44(3):190-197
Correlation between expression level of the bovine DNAJA1 gene and meat tenderness was recently found in Charolais longissimus thoracis muscle samples, suggesting that this gene could play an important role in meat tenderness. Here, we report the validation
of polymorphisms within the bovine DNAJA1 gene, and the haplotype variability and extent of linkage disequilibrium in the three main French beef breeds (Blonde d’Aquitaine,
Charolais, Limousin). Genotyping 18 putative SNPs revealed that 16 SNPs were polymorphic within the breeds tested. Two SNPs
were removed from further analyses as one SNP had a low genotyping call rate, while the other SNP was not in Hardy–Weinberg
equilibrium. The degree of heterozygosity observed for the remaining 14 SNPs varied between breeds, with Charolais being the
breed with the highest genetic variation and Blonde d’Aquitaine the lowest. Linkage disequilibrium and haplotype structure
of DNAJA1 were different between breeds. Eighteen different haplotypes, including three shared by all breeds, were discovered, and
two to three tag SNPs (depending on the breed) are sufficient to capture all the genetic variability seen in these haplotypes.
The results of this study will facilitate the design of optimal future association studies evaluating the role of the DNAJA1 gene in meat tenderness. 相似文献
8.
The association of the porcine Pitx2c gene with meat quality traits was investigated in the present study. A total of eight single nucleotide polymorphisms (SNPs)
were found. Allele frequencies of four SNPs were further detected in four commercial breeds and eight Chinese indigenous breeds.
Single SNP and meat quality associations were analyzed in a Yorkshire×Meishan F2 population. The SNPs c.474C>T (P<0.01) and c.636C>T (P<0.05) showed a significant association with meat color (MCV1). The SNPs c.*37G>A and c.*47G>A were significantly associated
with drip loss rate (DLR), water holding capacity (WHC) and meat color value (MCV1) consistently (P<0.05). Linkage disequilibrium (LD) analysis revealed that the adjacent SNPs were in LD. Two major haplotypes were identified,
and association analysis between haplotype combinations and meat quality indicated that the presence of two copies of haplotype
1 -CCGG- may improve meat quality. 相似文献
9.
IGFBP-5 is a member of the IGF families. Using PCR-SSCP, genotypic and allelic frequencies were analyzed in 18 pig breeds (n = 600). The association between haplotypes and production performance was analyzed in a Jinhua × Pietrain population family (n = 212, total 24 traits). Two SNPs (T199C and G485A) within the gene were analyzed. The breeds had different genotypic and allelic frequencies. Typically, the Chinese native pig breeds carried a higher allele C and G frequency (over 50%) than those of the European pigs, and only Guangdong Large White and wild boar were at Hardy–Weinberg equilibrium. The pigs carrying the CG haplotype had higher hue, loin, and thigh pH1 values than pigs with the TA haplotype, and pigs with the TA haplotype had the lowest loin pH2 value and highest color-a value among the haplotypes. It is proposed that the IGFBP-5 gene is associated with the variation in meat quality, especially in pH value together with other QTLs on chromosome 15. 相似文献
10.
Background
Mangalica breeds are indigenous to Hungary and their breeding history dates back to about 200–250 years ago. They are fat-type pigs and have a rare curly hair phenotype. The aim of our study was to establish the relationships between these unique breeds and other European breeds.Results
Based on a core sequence of 382 bp present in 2713 mitochondrial D-loop sequences from pigs belonging to 38 local breeds from nine countries, five cosmopolitan breeds and wild boars from 14 countries, we identified 164 haplotypes. More than half of the 2713 sequences belonged to either four haplotypes characteristic of continental European breeds or two haplotypes characteristic of British/cosmopolitan breeds; each haplotype is present in more than 100 individuals. Most Mangalica individuals belonged either to one of these common continental European haplotypes or to two Mangalica-specific haplotypes that were absent in all other breeds. In addition, we identified the ancestral mitochondrial D-loop signature present in these 2713 sequences and found that ~ 80% carried the European ancient signatures, ANC-Aside and ANC-Cside or their closely related signatures, while most of the remaining sequences carried a modern Asian signature, ANC-Easia. Mangalica individuals carried the ANC-Aside signature, but not the ANC-Cside or ANC-Easia signatures.Conclusions
In all the Mangalica individuals, a unique ancient European signature was found in the mitochondrial DNA D-loop region, but they belonged almost exclusively to either certain very abundant European or two Mangalica-specific D-loop haplotypes. This indicates that the present-day Mangalica population in Hungary evolved either by introgression of other European breeds and wild boars or via total isolation after the divergence of European ancient porcine bloodlines. 相似文献11.
12.
E. A. Staiger M. S. Almén M. Promerová S. Brooks E. G. Cothran F. Imsland K. Jäderkvist Fegraeus G. Lindgren H. Mehrabani Yeganeh S. Mikko J. L. Vega‐Pla T. Tozaki C. J. Rubin L. Andersson 《Animal genetics》2017,48(5):551-559
A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow‐up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3:Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits. 相似文献
13.
14.
《Animal biotechnology》2013,24(1):173-178
ABSTRACT Thirteen pairs of primers were designed for the entire porcine MSTN gene to enable PCR amplification for the detection of single nucleotide polymorphisms (SNPs) by a PCR-SSCP approach. Altogether 96.5% (1089/1128) of the encoding regions and 971?bp of the non-coding regions were screened. A total of three polymorphisms were identified with PCR-SSCP. They were located in the promoter, intron one and exon three regions of the gene. These polymorphisms were then confirmed to be point mutations (T→A transversion, G→A transition and C→T transition respectively) by sequencing. Allele frequencies were determined for all three SNPs in several different pig breed populations. The polymorphisms were found to be rare in Western breeds, but much more common in Chinese breeds. Whether they have any relationship with the marked difference in lean meat mass between Western and Chinese breeds requires further study. 相似文献
15.
Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis 总被引:1,自引:0,他引:1
A fragment of mitochondrial DNA (mtDNA) control region (approximately 700 bp) was sequenced in 104 individuals from 20 breeds (three Chinese domestic breeds, five recently derived breeds and 12 introduced breeds) of domestic rabbits, Oryctolagus cuniculus. Nineteen sites were polymorphic, with 18 transitions and one insertion/deletion, and eight haplotypes (A1, A2, A3, A4, A5, A6, A7 and A8) were identified. Haplotype A1 was the most common and occurred in 89 individuals. In the 25 Chinese rabbits, only haplotype A1 was observed, while four haplotypes (A1, A3, A5 and A6) were found in 26 recently derived individuals. Haplotype A2 was shared by seven individuals among three introduced strains. The other six haplotypes accounted for 0.96-1.92% of the animals. Combined with the published sequences of European rabbits, a reduced median-joining network was constructed. The Chinese rabbit mtDNAs were scattered into two clusters of European rabbits. These results suggest that the (so-called) Chinese rabbits were introduced from Europe. Genetic diversity in Chinese rabbits was very low. 相似文献
16.
Alex Clop Marcel Amills José Luís Noguera Ana Fernández Juan Capote Maria Misericòrdia Ramón Lucía Kelly James MH Kijas Leif Andersson Armand Sànchez 《遗传、选种与进化》2004,36(1):97-104
Mitochondrial DNA has been widely used to perform phylogenetic studies in different animal species. In pigs, genetic variability at the cytochrome B gene and the D-loop region has been used as a tool to dissect the genetic relationships between different breeds and populations. In this work, we analysed four SNP at the cytochrome B gene to infer the Asian (A1 and A2 haplotypes) or European (E1 and E2 haplotypes) origins of several European standard and local pig breeds. We found a mixture of Asian and European haplotypes in the Canarian Black pig (E1, A1 and A2), German Piétrain (E1, A1 and A2), Belgian Piétrain (E1, A1), Large White (E1 and A1) and Landrace (E1 and A1) breeds. In contrast, the Iberian (Guadyerbas, Ervideira, Caldeira, Campanario, Puebla and Torbiscal strains) and the Majorcan Black pig breeds only displayed the E1 haplotype. Our results show that the introgression of Chinese pig breeds affected most of the major European standard breeds, which harbour Asian haplotypes at diverse frequencies (15–56%). In contrast, isolated local Spanish breeds, such as the Iberian and Majorcan Black pig, only display European cytochrome B haplotypes, a feature that evidences that they were not crossed with other Chinese or European commercial populations. These findings illustrate how geographical confinement spared several local Spanish breeds from the extensive introgression event that took place during the 18th and 19th centuries in Europe. 相似文献
17.
X.P. An D. Han J.X. Hou G. Li J.G. Wang M.M. Yang Y.X. Song G.Q. Zhou Y.N. Wang L. Ling Q.M. Yan B.Y. Cao 《Small Ruminant Research》2009,85(2-3):130-134
In this study, polymorphisms in the goat GnRHR gene exon 1 were detected by PCR-SSCP and DNA sequencing methods in 786 individuals from two different goat breeds. Two haplotypes (A and B), two observed genotypes (AA and AB), and two single nucleotide polymorphisms (SNPs) were detected, which resulted in five amino acid substitutions. The frequencies of haplotypes A and B in the two goat breeds were 0.78–0.83 and 0.17–0.22, respectively. The SNP locus was in Hardy–Weinberg disequilibrium in the two goat breeds (P < 0.05). Polymorphisms of the GnRHR gene were shown to be associated with litter size in the two goat breeds. The SNPs in the goat GnRHR gene had significant effects on litter size (P < 0.05). Therefore, these results suggest that the GnRHR gene is a strong candidate gene that affects litter size in goat. 相似文献
18.
Mitochondrial DNA Cleavage Patterns Distinguish Independent Origin of Chinese Domestic Geese and Western Domestic Geese 总被引:1,自引:0,他引:1
It has generally been assumed, based on morphology, that Chinese domestic goose breeds were derived from the swan goose (Anser cygnoides) and that European and American breeds were derived from the graylag goose (Anser anser). To test the validity of this assumption, we investigated the mtDNA cleavage patterns of 16 Chinese breeds and 2 European breeds as well as hybrids produced between a Chinese breed and a European breed. After 224 mtDNAs, isolated from the Chinese and European breeds, were digested by 19 restriction endonucleases, variations of the cleavage patterns were observed for four enzymes (EcoRV, HaeII, HincII, and KpnI). All Chinese breeds and their maternal hybrids except the Yili breed showed an identical haplotype, named haplotype I or the Chinese haplotype; the European breeds and the Yili breed showed another haplotype, named haplotype II or the western haplotype. None of the haplotype found in the Chinese type was detectable in the western type and vice versa. The two haplotypes were found to differ from each other at 8.0% of the sites surveyed and with a 0.72% sequence divergence. Using 2% substitution per million years calibrated from the genera Anser and Branta, the two domestic geese haplotypes were estimated to have diverged approximately 360,000 years ago, well outside the 3000-6000 years in domestic history. Our findings provide the first molecular genetic evidence to support the dual origin assumption of domestic geese in the world. Meanwhile, the four mtDNA restriction fragment length polymorphisms can be used as maternal genetic markers to distinguish the two types of domestic geese. 相似文献
19.
SNPs in the porcine <Emphasis Type="Italic">PPARGC1a</Emphasis> gene: Interbreed differences and their phenotypic effects 总被引:1,自引:0,他引:1
Stachowiak M Szydlowski M Cieslak J Switonski M 《Cellular & molecular biology letters》2007,12(2):231-239
Due to its function, the peroxisome proliferative activated receptor-γ, coactivator-1α (PPARGC1A) gene is a candidate in the search for genes that may affect production traits in the pig. The purpose of this study was
to screen for new SNPs in exon 8 of the porcine PPARGC1A gene and to test their possible association with production traits. Altogether 736 pigs representing five breeds Polish Landrace,
n=242; Polish Large White, n=192; Hampshire, n=27; Duroc, 21; Pietrain, n=12) and synthetic line 990 (n=242) were scanned
via SSCP assay. Four SNPs were found; two new ones: C/G (His338Gln) and G/A Thr359Thr), and two previously reported ones:
C/A (Arg369Arg) and T/A Cys430Ser). The missense T/A and C/G SNPs demonstrated pronounced interbreed variability in terms
of allele frequencies, including the exclusive presence of the C/G substitution in the Hampshire breed. The tested SNPs occurred
in five putative haplotypes, and their frequency also differed substantially between breeds. The association of the SNPs with
production traits was tested for G/A (Thr359Thr), C/A (Arg369Arg) and T/A (Cys430Ser) substitutions in Polish Large White,
Polish Landrace and line 990. The analysis revealed only breed-specific associations. The T/A (Cys430Ser) SNP was related
to the feed conversion ratio in the Polish Large White (P=0.02), and the silent G/A and C/A substitutions were respectively
associated with abdominal fat in line 990 and backfat thickness in Polish Landrace (P=0.04). The combined effects of the substitutions
were estimated as haplotype effects. Three significant contrasts between haplotypes were calculated, but the observed associations
were again only breed-specific. 相似文献
20.
Marianna Niemi Auli Bl?uer Terhi Iso-Touru Veronica Nystr?m Janne Harjula Jussi-Pekka Taavitsainen Jan Stor? Kerstin Lidén Juha Kantanen 《遗传、选种与进化》2013,45(1):2