scholarly journals Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

2020 ◽  
Author(s):  
Lirong Hu ◽  
Dong Li ◽  
Qin Chu ◽  
Yachun Wang ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Low Cost ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Cattle Population ◽  
Crossbred Cattle ◽  
Dna Pooling ◽  
Flight Mass Spectrometry ◽  
Pcr Products

Abstract Combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel consisting of 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively. Knowledge of these results, we provided one low-cost and efficient method of SNP assays for running paternity testing in crossbred cattle population of Simmental and Holstein in China.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals Genotyping Single-Nucleotide Polymorphisms by the Invader Assay with Dual-Color Fluorescence Polarization Detection

2001 ◽  
Vol 47 (8) ◽  
pp. 1373-1377 ◽  
Author(s):  
Tony M Hsu ◽  
Scott M Law ◽  
Shenghui Duan ◽  
Bruce P Neri ◽  
Pui-Yan Kwok
Keyword(s):  
Fluorescence Polarization ◽  
Cost Effective ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Clear Cut ◽  
Pcr Product ◽  
Invader Assay ◽  
Pcr Products ◽  
Incorporation Assay

Abstract Background: The PCR-Invader® assay is a robust, homogeneous assay that has been shown to be highly sensitive and specific in genotyping single-nucleotide polymorphism (SNP) markers. In this study, we introduce two changes to improve the assay: (a) we streamline the PCR-Invader method by assaying both alleles for each SNP in one reaction; and (b) we reduce the cost of the method by adopting fluorescence polarization (FP) as the detection method. Methods: PCR product was incubated with Invader oligonucleotide and two primary probes at 93 °C for 5 min. Signal probes corresponding to the cleaved flaps of the primary probes [labeled with fluorescein and 6-carboxytetramethylrhodamine (TAMRA) dye] and Cleavase® VIII enzyme (a flap endonuclease) were then added to the mixture. This reaction mixture was incubated at 63 °C for 5 min. FP measurements were made with a fluorescence plate reader. Results: Eighty-eight individuals were genotyped across a panel of 10 SNPs, using PCR product as template, for a total of 880 genotypes. An average “no call” rate of 3.2% was observed after first round of experiments. PCR products were remade in those samples that failed to produce any genotype in the first round, and all gave clear-cut genotypes. When the genotypes determined by the PCR-Invader assay and template-directed dye-terminator incorporation assay with FP were compared, they were in 100% concordance for all SNP markers and experiments. Conclusions: The improvements introduced in this study make PCR-Invader assay simpler and more cost-effective, and therefore more suitable for high-throughput genotyping.

scholarly journals Population and individual identification of coho salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

2017 ◽  
Vol 74 (9) ◽  
pp. 1391-1410 ◽  
Author(s):  
Terry D. Beacham ◽  
Colin Wallace ◽  
Cathy MacConnachie ◽  
Kim Jonsen ◽  
Brenda McIntosh ◽  
...  
Keyword(s):  
Coho Salmon ◽  
Direct Sequencing ◽  
Parentage Analysis ◽  
Individual Identification ◽  
Parental Genotype ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Genetic Stock ◽  
Genetic Stock Identification ◽  
Assignment Probability

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program.

scholarly journals Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

2020 ◽  
Author(s):  
Lirong Hu ◽  
Dong Li ◽  
Qin Chu ◽  
Yachun Wang ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Parentage Analysis ◽  
Breeding Systems ◽  
Parentage Assignment ◽  
Cattle Population ◽  
Crossbred Cattle ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Parentage Testing ◽  
Snp Panel

Abstract Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle

scholarly journals Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

2021 ◽  
Author(s):  
Paul Flynn ◽  
Romy Morrin-O'Donnell ◽  
Rebecca Weld ◽  
Laura M Gargan ◽  
Jens Carlsson ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Thoroughbred Horses ◽  
Snp Panels ◽  
Average Sample ◽  
Short Tandem

Short tandem repeat (STR), also known as microsatellite markers are currently used for genetic parentage verification within equine. Transitioning from STR to single nucleotide polymorphism (SNP) markers to perform equine parentage verification is now a potentially feasible prospect and a key area requiring evaluation is parentage testing accuracies when using SNP based methods, in comparison to STRs. To investigate, we utilised a targeted equine genotyping by sequencing (GBS) panel of 562 SNPs to SNP genotype 309 Thoroughbred horses - inclusive of 55 previously parentage verified offspring. Availability of STR profiles for all 309 horses, enabled comparison of parentage accuracies between SNP and STR panels. An average sample call rate of 97.2% was initially observed, and subsequent removal of underperforming SNPs realised a pruned final panel of 516 SNPs. Simulated trio and partial parentage scenarios were tested across 12-STR, 16-STR, 147-SNP and 516-SNP panels. False-positives (i.e. expected to fail parentage, but pass) ranged from 0% for 147-SNP and 516-SNP panels to 0.003% when using 12-STRs within trio parentage scenarios, and 0% for 516-SNPs to 1.6% for 12-STRs within partial parentage scenarios. Our study leverages targeted GBS methods to generate low-density equine SNP profiles and demonstrates the value of SNP based equine parentage analysis in comparison to STRs - particularly when performing partial parentage discovery.

scholarly journals Polymorphism and molecular characteristics of the <i>CSN1S2</i> gene in river and swamp buffalo

2020 ◽  
Vol 63 (2) ◽  
pp. 345-354
Author(s):  
Xinyang Fan ◽  
Shanshan Gao ◽  
Lin Fu ◽  
Lihua Qiu ◽  
Yongwang Miao
Keyword(s):  
Direct Sequencing ◽  
Physicochemical Characteristics ◽  
Molecular Characteristics ◽  
Nucleotide Polymorphisms ◽  
Milk Traits ◽  
Single Nucleotide ◽  
Pcr Products ◽  
Variation Characteristics ◽  
Polymerase Chain ◽  
Swamp Buffalo

Abstract. The αS2-casein (αS2-CN) is a member of the casein family associated with milk traits in ruminants, but so far the buffalo CSN1S2 gene has not been well understood. In this work, the polymorphisms of CSN1S2 in river and swamp buffalo were detected using direct sequencing of polymerase chain reaction (PCR) products. As a result, 13 single nucleotide polymorphisms (SNPs) were identified in the coding sequence (CDS) of CSN1S2 in two types of buffalo, of which eight SNPs were non-synonymous. The amino acid changes caused by c.580T>C and c.642C>G may affect the function of buffalo αS2-CN. A total of 11 CSN1S2 CDS haplotypes were defined, and accordingly 11 variants of buffalo αS2-CN were inferred and named. The CSN1S2 CDSs of both types of buffalo were 669 nucleotides, which encoded a precursor of 222 amino acids (AAs), and the first 15 AAs constitute a signal peptide. The composition and physicochemical characteristics of two types of buffalo αS2-CNs were similar but slightly different from those of cattle αS2-CN. The αS2-CN mature peptides of buffalo and the species of Bos genus contained a casein domain, and their secondary structures were highly consistent, indicating that they are functionally similar. The results here provide initial insights into the variation, characteristics and biological function of buffalo CSN1S2.

scholarly journals Identification of genetic variants in differentially expressed sequences in cattle of different metabolic type – potential genetic markers of nutrient utilization

2005 ◽  
Vol 48 (4) ◽  
pp. 324-333 ◽  
Author(s):  
M. Schwerin ◽  
T. Goldammer ◽  
C. Kuehn ◽  
C. Walz ◽  
S. Ponsuksili
Keyword(s):  
Genetic Variants ◽  
Growth Traits ◽  
Direct Sequencing ◽  
Nutrient Utilization ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Cattle Breeds ◽  
Specific Distribution ◽  
Genomic Regions ◽  
Body Parameters

Abstract. Two cattle breeds serve as a model to identify genes and genetic variants, respectively, that are potentially associated with nutrient transformation: Holsteins bred for high milk production mainly, and Charolais bred for high body weight with outstanding muscular growth. The major differences between Charolais and Holstein regarding many general body parameters originate from differences in pathways and deposition of nutrients. In an initial experiment, expressed sequence tags (ESTs) differentially displayed between both cattle breeds were isolated by mRNA differential display in liver and intestine. Of the in total identified 277 ESTs, 79 showing the most prominent differences, were screened for single nucleotide polymorphisms (SNPs). Thirty four SNPs were detected in 30 ESTs In a direct sequencing approach based on the comparative sequencing of the corresponding amplicons generated by PCR from genomic DNA pools of 20 animals each of both cattle breeds,. Eighteen of these SNPs showed breed specific distribution of allelic variants. Occurrence of ESTs with a breed specific SNP distribution and localisation of the respective ESTs to chromosome regions known to be affecting carcass and growth traits in cattle suggest a trait association of the respective SNPs. The polymorphic nature of the SNP markers suggests that they will be useful for evaluating whether variation in these genomic regions influences nutrient pathways in cattle.

scholarly journals Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinkwan Jo ◽  
Youngin Kim ◽  
Geon Woo Kim ◽  
Jin-Kyung Kwon ◽  
Byoung-Cheorl Kang
Keyword(s):  
Multiplex Pcr ◽  
Low Cost ◽  
Genotyping By Sequencing ◽  
Illumina Miseq ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Loci ◽  
Sequencing Method ◽  
Pcr Conditions

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.

scholarly journals Association between the rs8028440 polymorphism of CYFIP 1 gene in autism patients

2021 ◽  
Vol 1 (3) ◽  
Author(s):  
Hossein Ghahramani Almanghadim ◽  
Marjan Assefi ◽  
Shahab Masoumi ◽  
Parisa Vakili, ◽  
Zinat Shams ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Autism Spectrum ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Interacting Protein ◽  
Homozygous Genotype ◽  
Significant Difference ◽  
Pcr Products ◽  
Healthy Control ◽  
Neurodevelopmental Abnormalities

Demonstrated no association between ASD and rs8028440 polymorphism of the CYFIP1 gene, which needs further studies in a larger population of ASD subjects to find the contribution of rs8028440 polymorphism in CYFIP1 gene with ASD in Iranian patients. Introduction: Given the importance of the Cytoplasmic FMR1 Interacting Protein 1 (CYFIP1 gene) in relation to neurodevelopmental abnormalities such as autism spectrum disorder (ASD), recognizing the interaction between single nucleotide polymorphisms (SNPs) of this gene in autism cases is important. In this study, we evaluated the probable association of rs8028440 polymorphism of the CYFIP1 gene with ASD disorder in Iranian subjects. Methods and patients: The CYFIP1 gene were amplified with specific primers and the PCR products were digested with RsaI restriction enzyme to obtain the rs8028440 polymorphism in 100 ASD patients and 100 healthy control cases. Finally, the samples were genotyped using direct sequencing to identify CC, CT, and TT genotypes. Results: The Hardy-Weinberg equilibrium showed no significant deviation in the subjected population. According to our results, the frequency of the C allele was higher in ASD groups than in the control group. The full length of PCR was 662 bp and through RFLP‐PCR, normal genotype (C/C), heterozygote genotype (T/C), and homozygous genotype (T/T) was detected. Ten PCR products were sequenced and the corresponded alleles A/T and Y (C or T) were determined. It was revealed no significant difference was found between ASD subjects and controls with respect to the frequency of the rs8028440 gene allele

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