Discovery and characterization of single nucleotide polymorphisms in coho salmon,Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population‐ and pedigree‐based analyses across the southern part of the species native range.     

Molecular genetic variation of boll weevil populations in North America estimated with microsatellites: Implications for patterns of dispersal

The boll weevil (Anthonomus grandis Boheman) is an insect pest of cotton that underwent a well-documented range expansion across the southeastern U.S. from Mexico beginning about 110 years ago. Eleven microsatellite loci were surveyed to infer the magnitude and pattern of genetic differentiation among boll weevil populations from 18 locations across eight U.S. states and northeast Mexico. Estimates of genetic diversity (allelic diversity and heterozygosity) were greater in Southern than Northern populations, and were greater in the west than the east among Northern populations. Boll weevil populations were genetically structured as a whole across the geographic range sampled, with a global F _ST of 0.241. South-central populations exhibit classic isolation by distance, but evidence suggests that populations within the Eastern and Western regions have not yet reached genetic equilibrium. Gene flow appears to be relatively high among populations within the Eastern region. Population assignment data and estimates of gene flow indicate that migration between locations separated by < 300 km is frequent. The database of microsatellite genotypes generated in this study now makes it possible, through population assignment techniques, to identify the most likely geographic source of a boll weevil reintroduced to an eradication zone, which will help action agencies decide the most appropriate mitigation response. Kyung Seok Kim - Formerly: USDA-ARS, Areawide Pest Management Research Unit, 2771 F & B Rd., College Station,TX 77845, USA.     

Polymerase chain reaction multiplexing of microsatellites and single nucleotide polymorphism markers for quantitative trait loci mapping of wild house mice

We tested 96 microsatellites and 10 single nucleotide polymorphisms for their allelic distribution in two subspecies of the house mouse, Mus musculus musculus and M. m. domesticus. Sixty‐two microsatellites discriminated strain‐specific differences among nine wild‐derived ‘musculus’ and ‘domesticus’ and three ‘classical’ laboratory strains. For efficient genotyping, we optimized multiplex conditions using five microsatellites per polymerase chain reaction. All 10 single nucleotide polymorphisms were also optimized for simultaneous analysis in one reaction using SNaPshot multiplex. The uniform distribution of markers on autosomes and on the X chromosome makes these panels potentially useful tools for quantitative trait loci mapping of wild house mice.     

Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellites

1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species.
2. Eight polymorphic allozyme loci ( ACO-1, ACO-2 , EST-D, GPI, IDH-2, MDH, OPDH and PGM ) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples.
3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci.
4. Pairwise comparisons, using Fisher's exact tests and F _ST values, revealed significant genetic differentiation among populations. The overall multilocus F _ST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study.
5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2 , IDH-2 and MDH, which contributed most to the significant differentiation between samples.     

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.     

Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses

Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 < or = FST < or = 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 < or = FST < or = 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050-0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (> or = 20 animals per population) and fairly variable loci were used.     

Genetic diversity of north Okhotsk Sea chum salmon populations with natural and artificial reproduction

The variability of 32 enzyme loci was studied in chum salmon populations with different types of reproduction—natural, mixed, and artificial—in some Magadan Region rivers. Among the populations studied, the values of mean heterozygosity and allele number per locus did not differ significantly. We found evidence of definite temporal stability of the populations, and also found that their genetic variability was expressed only slightly but still remained in spite of periodic egg transplantations between rivers. Statistically significant spatial genetic differentiation of the populations accounted for 0.55 to 0.76% of the total variation and the mean inter-year differentiation accounted for 0.30% of the total. Significant temporal (seasonal) genetic subdivision was revealed in chum salmon of the Tauy River. The populations of the Okhotsk Sea coast are very similar genetically to the east Sakhalin populations. The industrial chum salmon population founded and reproduced artificially in the Kulkuty River preserves the genetic similarity of the donor Yama River chum salmon. In the industrial population, we observed a tendency toward reduction of genetic variation over time. The contribution of the Yama population to the gene pool of the Ola chum salmon, (both by natural reproduction and by farming) is small in spite of many large-scale transplantations. However, the consequences of those transplantations are revealed by means of linkage disequilibrium analysis.     

Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays

Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction‐site associated DNA (ddRAD) reads using 454‐Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183 bp) detecting a total of 5399 contigs (mean contig length: 396 ± 91 bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty‐two of these SNPs were successfully validated and 61 were polymorphic: 14 in P. falkneri, 21 in P. motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.     

Frequency distribution of single nucleotide polymorphisms in P-selectin gene in Chinese Tibetan and Han populations

Background

Chinese Tibetans have a series of distinctive physiological traits which enable them to tolerate the extreme environment of the Tibetan plateau. P-selectin gene has been proved to be highly polymorphic in Europeans and Americans. Nevertheless, studies on either the frequency distributions of single nucleotide polymorphisms (SNPs) or haplotype diversity and linkage disequilibrium of P-selectin gene in Chinese Tibetan population are still unavailable.

Methods

The frequency distributions of 3 SNPs in P-selectin gene promoter (− 2123C/G, − 1969A/G, − 1817T/C) and 3 SNPs in exon region (Ser290Asn, Val599Leu, Thr715Pro) were investigated by real-time PCR and high-resolution melting method among 314 Chinese Tibetans and 328 age- and sex-matched Han people.

Results

The frequencies of the − 2123G and − 1817T alleles among the Tibetan population had no significant differences from those of the Han population. Among the Tibetan population, the G allele frequency of − 1969A/G and Ser290Asn were both higher than those of the Han population. Val599Leu and Thr715Pro did not show any polymorphism in the two populations. In the Tibetan population, − 2123C/G, − 1969A/G, − 1817T/C and Ser290Asn were in tight linkage disequilibrium with each other.

Conclusions

The frequency distributions of − 1969A/G and Ser290Asn polymorphisms in the Tibetan population were different from those in the Han population.     

特发性少精子症和无精子症与Pygo2基因蛋白编码区SNPs的相关性

男性不育常伴随精子数量减少。Pygo2基因在染色质重塑的伸长精细胞中表达, 其功能受损会导致精子形成阻滞和精子生成减少而引发不育。文章旨在检测引起人特发性少精子症和无精子症的Pygo2基因突变。从77例正常生育力男性和195例特发性少精子症和无精子症患者静脉血提取DNA, 采用聚合酶链式反应-测序方法对Pygo2基因3个蛋白质编码区进行测序对比, 非同义单核苷酸多态性(Single nucleotide polymorphisms, SNPs)位点分别用SIFT、Polyphen-2和 Mutation Taster软件进行诱发蛋白质结构和表型改变的检测和分析。结果表明, 195例患者中, 178例(30例轻度或中度少精子症, 57例重度少精子症和91例无精子症)基因序列分析报告完好, 无精子症中3例患者分别在2个位点(rs61758740, rs141722381)发生了非同义突变SNPs, 重度少精子症中1例患者在位点rs61758741发生了非同义突变, 3个突变位点在SNPs基因数据库都已有报道, 轻度或中度少精子症患者以及正常生育力男性中不存在SNPs。rs61758740可使PYGO2蛋白第141位蛋氨酸(M)变为异亮氨酸(I), rs61758741使PYGO2蛋白第261位碱性赖氨酸(K)变为酸性谷氨酸(E), rs141722381使PYGO2蛋白第240位亲水侧链天冬酰胺(N)变为疏水侧链异亮氨酸(I)。软件分析表明, 在所发现的3个SNP非同义突变位点中, rs141722381引起的单个氨基酸改变会导致PYGO2蛋白空间结构破坏和诱发相关疾病。因此, Pygo2基因蛋白质编码序列区SNPs可能是特发性少精子症和无精子症的诱发因素之一, 导致男性不育。     

Bimodal size distributions in wild juvenile Atlantic salmon populations and their relationship with age at smolt migration

A bimodal length distribution developed in an Atlantic salmon population planted as start-fed fry in a Norwegian stream. The earliest fish to smolt were from the upper modal group.     

The single nucleotide polymorphisms of the chicken myostatin gene are associated with skeletal muscle and adipose growth

Myostatin, a new member of the TGF-ß superfamily, is predominantly expressed in skeletal muscle cells and functions as a negative regulator of skeletal muscle growth in animals. Recently, we have reported three single nucleotide polymorphisms (SNPs) in the chicken myostatin gene. Herein, we investigate the association of those SNPs with the production traits in a F₂ chicken line derived from Broilers crossing to Silky with the least square analysis. The results show that the BB and AA genotypes are strongly associated with abdominal fat weight (AFW), abdominal fat percentage (AFP), and birth weight (BW) (P < 0.05). Breast muscle percentage (BMP) of the AA type is higher than that of the AB type. The breast muscle weight and breast muscle percentages of F₂ individuals have significant difference between CC and DD genotypes (P < 0.05). Breast muscle weight (BMW) of EF birds is higher than that of EE birds (P < 0.05). In this report, we present the first genetic evidence to show that chicken myostatin not only plays an important role in controlling skeletal muscle growth and differentiation, but also may be involved in regulation of adipose growth in chicken.     

The single nucleotide polymorphisms of the chicken myostatin gene are associated with skeletal muscle and adipose growth

Myostatin, a new member of the TGF-p superfamily, is predominantly expressed in skeletal muscle cells and functions as a negative regulator of skeletal muscle growth in animals. Recently, we have reported three single nucleotide polymorphisms (SNPs) in the chicken my-ostatin gene. Herein, we investigate the association of those SNPs with the production traits in a F2 chicken line derived from Broilers crossing to Silky with the least square analysis. The results show that the BB and AA genotypes are strongly associated with abdominal fat weight (AFW), abdominal fat percentage (AFP), and birth weight (BW) (P < 0.05). Breast muscle percentage (BMP) of the AA type is higher than that of the AB type. The breast muscle weight and breast muscle percentages of F2 individuals have significant difference between CC and DD genotypes (P< 0.05). Breast muscle weight (BMW) of EF birds is higher than that of EE birds (P< 0.05). In this report, we present the first genetic evidence to show that chicken myostatin not o     

Association study of single nucleotide polymorphisms in JAK2 and STAT5B genes and their differential mRNA expression with mastitis susceptibility in Chinese Holstein cattle

The JAK–STAT pathway plays a key role in mediating immune responses. The genetic effects of single nucleotide polymorphisms (SNPs) in JAK2 and STAT5B were investigated for serum cytokines, mastitis indicators and productions traits in a population of 468 Chinese Holstein cattle. Pooled DNA sequencing revealed one SNP (BTA8:g.39645396A>G) in JAK2 and two SNPs (BTA19:g.43673888A>G and BTA19:g.43660093T>C) in STAT5B. A fixed effect model considering the effects of SNPs, parity, herd, season and year of calving was used by way of the general linear model procedure of sas . Genotype frequencies of these SNPs in the population were in Hardy–Weinberg equilibrium (P > 0.05). A novel SNP (g.39645396A>G) in JAK2 was predicted to change the amino acid from lysine to asparagine and was significantly associated with the somatic cell count (SCC) and somatic cell score (SCS), whereas g.43673888A>G in STAT5B was significantly associated with SCC, SCS and interleukin‐4 (IL‐4) (P < 0.05). The dominant effect of g.39645396A>G in JAK2 was significant for SCS, and its additive effect was significant for SCC, whereas the dominant effect of g.43673888A>G in STAT5B was significant for SCS and IL‐4 (P < 0.05). The combination of g.39645396A>G in JAK2 and g.43673888A>G in STAT5B showed a significant effect on SCC, SCS, IL‐4 and TNF‐α (P < 0.05). As for mRNA expression analysis, the AA genotype g.39645396A>G and GG genotype g.43673888A>G indicated higher mRNA expression level and were significantly different from other genotypes (P < 0.05). The results imply that JAK2 and STAT5B genes could be useful candidate genes, and the identified polymorphisms might potentially be strong genetic markers for selection of dairy cattle against mastitis development.