scholarly journals A DNA test for high incidence of soft scald and soggy breakdown postharvest disorders in Malus domestica Borkh

2021 ◽  
Vol 41 (9) ◽  
Author(s):  
Baylee A. Miller ◽  
John R. Tillman ◽  
Nicholas P. Howard ◽  
Sarah A. Kostick ◽  
Kate M. Evans ◽  
...  
Keyword(s):  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Dna Test ◽  
Specific Pcr ◽  
Promising Tool ◽  
High Incidence ◽  
Allele Specific ◽  
Trait Locus ◽  
Soft Scald ◽  
Allele Specific Pcr

AbstractThe ‘Honeycrisp’ apple, an economically important cultivar and breeding parent, is prone to soft scald and soggy breakdown postharvest physiological disorders. Phenotypic evaluation of soft scald is time consuming and costly, making it an excellent target for DNA-informed breeding. The objective of this study was to develop a DNA test for a soft scald and soggy breakdown quantitative trait locus (QTL) on linkage group two (LG2) that was characterized in a previous study. ‘Honeycrisp’ is homozygous for the undesirable high disorder incidence haplotype (HDI) at this QTL. In this study, sixteen single nucleotide polymorphism markers were evaluated for their associations with the HDI haplotype in a set of 132 unique cultivars and important breeding parents. A DNA test was successfully developed utilizing KASP™ (Kompetitive Allele Specific PCR) chemistry to identify the number of HDI haplotypes in individuals. This test had a 100% accuracy for detecting homozygous unfavorable HDI individuals and has an expected 88% accuracy over all three haplotype copy groups across the evaluated germplasm. This DNA test is a promising tool for minimizing the chances of selecting individuals that exhibit high incidence of soft scald postharvest disorder in ‘Honeycrisp’-related germplasm.

scholarly journals Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

2021 ◽  
Vol 12 ◽  
Author(s):  
Patrick Obia Ongom ◽  
Christian Fatokun ◽  
Abou Togola ◽  
Stella Salvo ◽  
Oluwaseye Gideon Oyebode ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Principal Component ◽  
Snp Markers ◽  
Breeding Program ◽  
Molecular Fingerprinting ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Optimization of a breeding program for increased genetic gain requires quality assurance (QA) and quality control (QC) at key phases of the breeding process. One vital phase in a breeding program that requires QC and QA is the choice of parents and successful hybridizations to combine parental attributes and create variations. The objective of this study was to determine parental diversity and confirm hybridity of cowpea F1 progenies using KASP (Kompetitive Allele-Specific PCR)-based single nucleotide polymorphism (SNP) markers. A total of 1,436 F1 plants were derived from crossing 220 cowpea breeding lines and landraces to 2 elite sister lines IT99K-573-1-1 and IT99K-573-2-1 as male parents, constituting 225 cross combinations. The progenies and the parents were genotyped with 17 QC SNP markers via high-throughput KASP genotyping assay. The QC markers differentiated the parents with mean efficiency of 37.90% and a range of 3.4–82.8%, revealing unique fingerprints of the parents. Neighbor-Joining cladogram divided the 222 parents into 3 clusters. Genetic distances between parents ranged from 0 to 3.74 with a mean of 2.41. Principal component analysis (PCA) depicted a considerable overlap between parents and F1 progenies with more scatters among parents than the F1s. The differentiation among parents and F1s was best contributed to by 82% of the markers. As expected, parents and F1s showed a significant contrast in proportion of heterozygous individuals, with mean values of 0.02 and 0.32, respectively. KASP markers detected true hybridity with 100% success rate in 72% of the populations. Overall, 79% of the putative F1 plants were true hybrids, 14% were selfed plants, and 7% were undetermined due to missing data and lack of marker polymorphism between parents. The study demonstrated an effective application of KASP-based SNP assay in fingerprinting, confirmation of hybridity, and early detection of false F1 plants. The results further uncovered the need to deploy markers as a QC step in a breeding program.

scholarly journals Association of the rs7903146 single nucleotide polymorphism at the Transcription Factor 7-like 2 (TCF7L2) locus with type 2 diabetes in Brazilian subjects

2012 ◽  
Vol 56 (8) ◽  
pp. 479-484 ◽  
Author(s):  
Gustavo Barcelos Barra ◽  
Ludmila Alves Sanches Dutra ◽  
Sílvia Conde Watanabe ◽  
Patrícia Godoy Garcia Costa ◽  
Patrícia Sales Marques da Cruz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Odds Ratio ◽  
Genetic Model ◽  
University Hospital ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

OBJECTIVE:To investigate the association of the T allele of the single nucleotide polymorphism (SNP) rs7903146 of TCF7L2 with the occurrence of T2D in a sample of subjects followed up at the Brasilia University Hospital. SUBJECTS AND METHODS: The SNP rs7903146 of TCF7L2 was genotyped by allele-specific PCR in 113 patients with known T2D and in 139 non-diabetic controls in Brasilia, Brazil. RESULTS:We found that the T allele of the SNP rs7903146 of TCF7L2 was significantly associated with T2D risk (odds ratio of 3.92 for genotype TT in the recessive genetic model, p = 0.004 and 1.5 for T allele, p = 0.032). CONCLUSION:These results reinforce previous findings on the consistent association of this genetic factor and the risk of T2D in populations of diverse ethnic backgrounds. Arq Bras Endocrinol Metab. 2012;56(8):479-84

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