An NGS-based genotyping in LQTS; minor genes are no longer minor

Resistance to stem rust (Puccinia graminis Pers. f. sp. tritici Eriks, and Henn.), particularly adult plant resisitance to race 15B-1, was studied in seven wheat (Triticum aestivum L.) cultivars or lines: 'Bonza', 'Chris', 'FKN-II-50-17', 'MRFY', 'Thatcher', 'Marquillo', and 'Hope'. Each of the seven was crossed with a susceptible parent and either F4- or F5-derived lines developed by single seed descent. All of the lines were tested with race 15B-1 in field nurseries. Lines derived from parents carrying seedling resistance to race 15B-1 were also tested as seedlings in the greenhouse with race 15B-1, and in some cases races 56, 29, and C65. The data indicated that 'Bonza' carries Sr6, probably Sr5, an unidentified gene giving resistance to race 56, two unidentified genes for resistance to race C65, and two minor genes that combine to produce intermediate adult plant resistance. 'Chris' carries Sr5, Sr7a, Sr8a, and Sr12. In addition, it may have three minor genes for adult plant resistance. 'FKN-II-50-17' carries Sr6 and may have four minor genes that combine to produce moderate adult plant resistance. 'MRFY', which is seedling susceptible to race 15B-1, carries Sr9b, possibly Sr5, plus an unidentified gene for resistance to C65. In addition, it appears to have one major gene for adult plant resistance plus two or more minor genes. 'Thatcher', 'Marquillo', and 'Hope' had only limited resistance to race 15B-1 in the field and no genetic analysis of their crosses was possible. The four parents that had good resistance to race 15B-1 in the field, 'Bonza', 'Chris', 'FKN-II-50-17', and 'MRFY', all carry minor genes for adult plant resistance that had little effect individually but produced moderate resistance when combined. The genes Sr5 and Sr9b, which have no effect on resistance to 15B-1 is seedlings, were found to significantly increase resistance in adult plants in the field.Key words: stem rust, Puccinia graminis tritici, wheat, Triticum aestivum, adult plant rust resistance.

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Analysis of Microsymptomatology in CNS Malformations

Acta geneticae medicae et gemellologiae ◽

10.1017/s1120962300023908 ◽

1974 ◽

Vol 23 (S1) ◽

pp. 265-267

Author(s):

G. Del Porto ◽

G. Brenci ◽

M. L. Tombolini

Keyword(s):

Spina Bifida ◽

Spina Bifida Occulta ◽

Major Genes ◽

Minor Genes ◽

Cns Malformations ◽

Mode Of Inheritance

A total of 105 sibships with one or more members affected by CNS malformations have been drawn from the Mendel Institute's Eugenic Counseling file and examined. The mode of inheritance and the variability of segregation have been verified according to the presence or absence of spina bifida occulta in one or both parents.The results obtained lead the authors to suggest that the expression of major genes responsible for the pathology be conditioned by minor genes responsible for localization.

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Inheritance of Resistance to Colletotrichum acutatum in Fragaria × ananassa

Phytopathology ◽

10.1094/phyto-95-0405 ◽

2005 ◽

Vol 95 (4) ◽

pp. 405-412 ◽

Cited By ~ 28

Author(s):

Béatrice Denoyes-Rothan ◽

Guy Guérin ◽

Estelle Lerceteau-Köhler ◽

Georgette Risser

Keyword(s):

Dominant Gene ◽

Resistance Breeding ◽

Intermediate Level ◽

Colletotrichum Acutatum ◽

Fragaria Ananassa ◽

Anthracnose Resistance ◽

Minor Genes ◽

Pathogenicity Group ◽

Group 2 ◽

High Level

Anthracnose, caused by Colletotrichum acutatum, is a major disease of the octoploid cultivated strawberry, Fragaria × ananassa The inheritance of high and intermediate level plant resistances to C. acutatum, pathogenicity group 2, was investigated in an 8 × 8 factorial design. A single dominant gene (Rca2) controlled the high-level resistance, although minor genes may also contribute to resistance in cultivars such as Belrubi. The intermediate level of resistance was quantitative and controlled by minor genes. Analysis of 26 genotypes and cultivars from Fragaria spp. showed that the dominant gene was not rare in the germ plasm of F. × ananassa and that anthracnose resistance was also present in other species of Fragaria. These findings have important implications for anthracnose resistance breeding.

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Breeding With Major and Minor Genes: Genomic Selection for Quantitative Disease Resistance

Frontiers in Plant Science ◽

10.3389/fpls.2021.713667 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lance F. Merrick ◽

Adrienne B. Burke ◽

Xianming Chen ◽

Arron H. Carter

Keyword(s):

Disease Resistance ◽

Genomic Selection ◽

Stripe Rust ◽

Fixed Effects ◽

Prediction Accuracy ◽

Major Gene ◽

Gene Markers ◽

Quantitative Disease Resistance ◽

Minor Genes ◽

Population Type

Disease resistance in plants is mostly quantitative, with both major and minor genes controlling resistance. This research aimed to optimize genomic selection (GS) models for use in breeding programs that are needed to select both major and minor genes for resistance. In this study, stripe rust (Puccinia striiformis Westend. f. sp. tritici Erikss.) of wheat (Triticum aestivum L.) was used as a model for quantitative disease resistance. The quantitative nature of stripe rust is usually phenotyped with two disease traits, infection type (IT) and disease severity (SEV). We compared two types of training populations composed of 2,630 breeding lines (BLs) phenotyped in single-plot trials from 4 years (2016–2020) and 475 diversity panel (DP) lines from 4 years (2013–2016), both across two locations. We also compared the accuracy of models using four different major gene markers and genome-wide association study (GWAS) markers as fixed effects. The prediction models used 31,975 markers that are replicated 50 times using a 5-fold cross-validation. We then compared GS models using a marker-assisted selection (MAS) to compare the prediction accuracy of the markers alone and in combination. GS models had higher accuracies than MAS and reached an accuracy of 0.72 for disease SEV. The major gene and GWAS markers had only a small to nil increase in the prediction accuracy more than the base GS model, with the highest accuracy increase of 0.03 for the major markers and 0.06 for the GWAS markers. There was a statistical increase in the accuracy using the disease SEV trait, BLs, population type, and combining years. There was also a statistical increase in the accuracy using the major markers in the validation sets as the mean accuracy decreased. The inclusion of fixed effects in low prediction scenarios increased the accuracy up to 0.06 for GS models using significant GWAS markers. Our results indicate that GS can accurately predict quantitative disease resistance in the presence of major and minor genes.

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Abstract 12059: Incidental Findings in Cardiomyopathy and Channelopathy Genes Among 5891 Individuals Undergoing Whole-exome Sequencing. What Should be Reported?

Circulation ◽

10.1161/circ.132.suppl_3.12059 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Elisa Mastantuono ◽

Thomas Wieland ◽

Riccardo Berutti ◽

Peter Lichtner ◽

Tim Strom ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Incidental Findings ◽

Genetic Disorders ◽

Molecular Diagnostic ◽

Minor Genes ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Whole Exome ◽

Unknown Significance

Background: Whole-exome-sequencing (WES) is becoming a common molecular diagnostic test for patients with genetic disorders. However, this technique allows the identification not only of mutations responsible for the disease under investigation, but also of variants potentially causing other diseases, the so called “incidental findings” (IFs). The American College of Medical Genetics and Genomics (ACMG) stated that IFs should be reported based on clinical validity and utility and indicated a list of 56 actionable genes. Among these, nearly half (20/56) are major genes associated with channelopathies and cardiomyopathies. Despite these recommendations, most of the studies so far published, reported also mutations in minor genes among the actionable findings. Methods: WES was performed in 5891 individuals without known channelopathies or cardiomyopathies. Exome data were first filtered based on genotype quality. Subsequently, a frequency filter was applied, considering 1000 Genomes, ExAC and our internal exome database. Variants reported as pathogenic in ClinVar or novel but expected to be pathogenic (nonsense, frameshift and splice) were further investigated, following the ACMG guidelines. Major (20) and minor (73) genes associated with channelopathies and cardiomyopathies were evaluated. Results: We identified 3514 variants in the 93 genes under investigation, after applying the quality and frequency filters. Eight variants were classified as pathogenic and 52 as likely pathogenic and they were detected in around 1% of the individuals. The vast majority (85%) of pathogenic or likely pathogenic variants were located in the 20 actionable genes indicated by ACMG. The inclusion of minor genes increased the number of variants of unknown significance (VUS), from 865 to 3454. Conclusion: Our data support the ACMG recommendations in reporting only IFs identified in the 20 major cardiac actionable genes. Indeed, the inclusion of minor genes is mainly increasing the number of VUS, without significantly impacting the number of pathogenic and likely pathogenic variants. The percentage of individuals with potentially clinical relevant variants in these genes is too high in relation to the disease-prevalence: a cardiologic evaluation is warranted.

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Abstract 3091: The Clinical and Electrocardiographic Phenotype of Unrelated Patients with Genotype-Negative Long QT Syndrome

Circulation ◽

10.1161/circ.118.suppl_18.s_813 ◽

2008 ◽

Vol 118 (suppl_18) ◽

Author(s):

Malek M El Yaman ◽

David J Tester ◽

Argelia Medeiros Domingo ◽

Carla M Haglund ◽

Michael J Ackerman

Keyword(s):

Cardiac Arrest ◽

Genetic Testing ◽

Family History ◽

Long Qt Syndrome ◽

Susceptibility Genes ◽

Long Qt ◽

Diagnostic Score ◽

Minor Genes ◽

History Of ◽

Qt Syndrome

Long QT syndrome (LQTS) is a heterogeneous group of channelopathies characterized by increased risk of potentially lethal ventricular arrhythmias. LQT1, LQT2, and LQT3 comprise 95% of genetically proven cases and exhibit a number of established genotype-phenotype correlations. The study aimed at examining the phenotypes of genotype-negative LQTS, accounting for ~25% of LQTS cases. An IRB-approved retrospective analysis was conducted on 56 patients (39 female, 25 ± 17 years) who, after genetic testing either in our sudden death genomics laboratory or with the commercially available Familion test, were negative for mutations in the 3 principal LQTS-susceptibility genes ( KCNQ1, KCNH2, and SCN5A), and the minor genes underlying LQT5 and LQT6. All had been diagnosed with LQTS, with a clinical diagnostic score of ≥ 3.5 or QTc ≥ 480 ms. The mean diagnostic score was 4.4 (95% CI 4.2 – 4.7); mean QTc was 525 ms (95% CI 508 – 543 ms). Two-thirds were symptomatic (syncope, cardiac arrest, and/or seizures) with exercise-triggered events in 10 (26%). Twenty-one (38%) had a family history of sudden cardiac arrest. ECG showed a T wave pattern suggestive of LQT1 in 32%, LQT2 in 43%, and LQT3 in 18%. In those with exercise-induced symptoms, the ECG was LQT2-like in 50% and LQT1-like in 30%. One patient had post-partum syncope with an LQT2-like ECG. None had an auditory trigger, but 3 patients, all with an LQT2-like ECG, had a family history of auditory-triggered events. One-third of the patients had received an ICD, 58% as secondary prevention. Over 2/3 were on beta-blockers. Among the 45 patients so far tested for mutations in minor LQTS-susceptibility genes, 2 had LQTS-causing mutations in ANKB (LQT4), 1 in SCN4B (LQT10), 1 in AKAP9 (LQT11) and 2 in SNTA1 (LQT12). Genotype-negative patients with a firm LQTS diagnosis show marked phenotypic heterogeneity, suggesting multiple underlying pathogenic pathways. Only a few patients have LQTS-causing mutations in minor genes after complete LQT1–12 genetic testing. Classifying genotype negative patients into LQT1-, LQT2-, or LQT3-like profiles may guide the discovery of novel genes encoding channel interacting proteins corresponding to those specific signaling pathways.

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Genes for long shelf-life in tomato

The Journal of Agriculture of the University of Puerto Rico ◽

10.46429/jaupr.v71i3.6973 ◽

1969 ◽

Vol 71 (3) ◽

pp. 313-321

Author(s):

Franklin W. Martin

Keyword(s):

Puerto Rico ◽

Shelf Life ◽

Standard Variety ◽

Minor Genes ◽

Pedigree Selection ◽

Long Life ◽

Pure Lines ◽

Different Sources ◽

Dominant Genes

One hundred eighty-four red-fruited tomato accessions from various origins were screened in Puerto Rico in 1981 for shelf-life of ripened fruit; 13 were found to have exceptionally long life (16 weeks or more). From these, six lines were selected and crossed with Kewalo from Hawaii and F1, F2 and F3 generations as well as BC1 and F2 of BC1, were grown. Long shelf-life was controlled by several genes in these crosses, and discrete ratios were not obtained. Among the hybrids longest shelf-life was found in individuals of F2 families. Both recessive and dominant genes were segregating. Individual plants with fruit of exceptional shelf-life were obtained even in the most advanced generations. Pedigree selection is suggested as a useful technique for concentrating the genes for long shelf-life in o standard variety. Pure lines can then be crossed to combine genes from different sources. Minor genes for long shelf-life in homozygous pure lines may prove more useful than simple dominant genes in hybrids.

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