Recovering Frequencies of Known Haplotype Blocks From Single-Nucleotide Polymorphism Allele Frequencies

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 2001-2006
Author(s):  
Itsik Pe’er ◽  
Jacques S Beckmann
Keyword(s):  
Large Scale ◽  
Haplotype Analysis ◽  
Association Studies ◽  
Allele Frequencies ◽  
Mathematical Framework ◽  
Single Nucleotide Polymorphism Allele ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Haplotype Blocks ◽  
Pooled Dna

Abstract Prospects for large-scale association studies rely on economical methods and powerful analysis. Representing available SNPs by small subsets and measuring allele frequencies on pooled DNA samples each improve genotyping cost effectiveness, while haplotype analysis may highlight associations in otherwise underpowered studies. This manuscript provides the mathematical framework to integrate these methodologies.

scholarly journals Single nucleotide polymorphism of the β-lactoglobulin gene in sheep breeds reared in Bulgaria

2020 ◽  
Vol 23 (3) ◽  
pp. 295-303
Author(s):  
D. Gencheva
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Polymorphic Locus ◽  
Association Studies ◽  
Allele Frequencies ◽  
Production Traits ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Sheep Population ◽  
Sheep Breeds ◽  
Β Lactoglobulin

In the present study, single nucleotide polymorphism in exon II of the β-lactoglobulin gene was investigated in four Bulgarian sheep breeds: Bulgarian Dairy Synthetic Population sheep (BDSP), Copper-red Shumen sheep (CRSH), Stara Zagora sheep (STZG) and Pleven Blackhead sheep (PLBH). Two genetic variants of β-LG gene (A and B) have been identified through PCR-RFLP assay. A 103 bp fragment of the polymorphic β-LG locus were amplified and digested with endonuclease enzyme RsaI. The obtained restriction fragments revealed three genotypes: AA, AB and BB, observed in 31%, 65.5% and 3.5% of the BDSP population and in 48%, 28% and 24% of CRSH sheep population, respectively, with departure from the Hardy-Weinberg equilibrium (P<0.05) in these groups. The allele frequencies demonstrated a prevalence of the A allele (0.638 and 0.620) over the B allele (0.362 and 0.380) in both populations. On the contrary, the distribution of allele frequencies in STZG and PLBH was 0.240 and 0.100 for allele A, respectively and 0.760 and 0.900 for allele B. Therefore, the homozygous BB genotype in these sheep populations was more frequently encountered (0.520 and 0.800) than the heterozygous AB genotype (0.480 and 0.200), with HWE correspondence (P>0.1). The homozygous genotype AA was absent in STZG and PLBH sheep populations. The greatest Nei’s genetic distance calculated by UPGMA method was found between the populations BDSPand PLBH (0.5334), while the closest relationship (0.0006) was established between CRSH and BDSP. The results obtained from the present investigation confirmed the presence of the SNP polymorphism in exon II of the β-lactoglobulin gene. Therefore, the genetic variability established in this polymorphic locus could be applied in further association studies with milk production traits in sheep.

scholarly journals Genome-wide Association of Single Nucleotide Polymorphism Loci and Candidate Genes for Frogeye Leaf Spot (Cercospora Sojina) Resistance in Soybean

2021 ◽  
Author(s):  
Xin Gu ◽  
Shanshan Huang ◽  
Yansong Ma ◽  
Xiaohe Yang ◽  
Liangliang Yao ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Protein Kinase ◽  
Candidate Genes ◽  
Leaf Spot ◽  
Genome Wide Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cercospora Sojina ◽  
Haplotype Blocks ◽  
Genome Wide

Abstract Background: Frogeye leaf spot (FLS) is a destructive fungal disease in soybean production. The most economical and effective strategy to control FLS is to use resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new, and more virulent, Cercospora sojina races. Thus, we identified quantitative trait loci (QTL) that control resistance to FLS and identified novel resistant genes using a genome-wide association study (GWAS) on 234 Chinese soybean cultivars.Results: A total of 30,890 single nucleotide polymorphism (SNP) markers were used to estimate linkage disequilibrium (LD) and population structure. The GWAS results identified six loci (p<0.001) distributed over chromosomes (Chr.) 2, 5, 20 comprising 69 SNPs significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 55 genes in three resistance-related haplotype blocks were annotated. Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980 encoding mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding the calcium-dependent protein kinase 4(CDPK4) in the haplotype blocks were found to be associated with FLS resistance.Conclusions: The proteins encoded by these four genes directly, or indirectly participate in the biological pathway of salicylic acid (SA) and jasmonic acid (JA). These two plant hormones can induce the expression of disease resistance related genes and are essential for plant systemic acquired resistance (SAR). Therefore, the novel loci and candidate genes provide genomic location information for further advances in FLS resistance gene cloning and molecular breeding.

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