Phenotypic and molecular screening of dry bean (Phaseolus vulgaris L.) breeding lines for resistance to bean common mosaic virus and bean common mosaic necrosis virus

Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) are among the most economically important virus species infecting common bean. The use of resistant plant cultivars is the most effective way to control these viruses. National dry bean breeding studies have been conducted by seven different governmental agricultural research institutes in Turkey, and advanced breeding lines have been developed by using the selected local dry bean populations and crossing studies. In this study, 204 breeding lines were tested for resistance levels to BCMV and BCMNV. Initially, BCMNV NL-3 and BCMV NL-4 strains were individually sap-inoculated onto the leaves of bean plants belonging to each breeding lines with 10 replications, and the reactions of plants were evaluated for symptomatic appearance of virus infection 21 days after inoculation. Additionally, phenotypic evaluation was confirmed by molecular markers linked to resistance genes. As a result of the study, 153 breeding lines were found to involve the dominant I gene whereas four and five of the tested lines had the recessive genes bc-1² and bc-2², respectively. In conclusion, it was emphasized that these breeding lines could be registered after evaluating them in terms of yield and quality. Also, the use of seeds of the resistant lines to supply the source of virus-resistance in breeding studies and maintaining their seeds at the national genebank were recommended.

Development of a marker panel for genotyping of domestic soybean cultivars for genes controlling the duration of vegetation and response to photoperiod

Soybean, Glycine max L., is one of the most important agricultural crops grown in a wide range of latitude. In this regard, in soybean breeding, it is necessary to pay attention to the set of genes that control the transition to the flowering stage, which will make it possible to adapt genotypes to local growing conditions as accurately as possible. The possibilities of soybean breeding for this trait have now significantly expanded due to identification of the main genes (E1–E4, GmFT2a, GmFT5a) that control the processes of flowering and maturation in soybean, depending on the day length. The aim of this work was to develop a panel of markers for these genes, which could be used for a rapid and efficient genotyping of domestic soybean cultivars and selection of plant material based on sensitivity to photoperiod and the duration of vegetation. Combinations of 10 primers, both previously developed and our own, were tested to identify different alleles of the E1–E4, GmFT2a, and GmFT5a genes using 10 soybean cultivars from different maturity groups. As a result, 5 combinations of dominant and recessive alleles for the E1–E4 genes were identified: (1) e1-nl(e1-as)/ e2-ns/e3-tr(e3-fs)/e4; (2) e1-as/e2-ns/e3-tr/E4; (3) e1-as/e2-ns/E3-Ha/e4; (4) E1/e2-ns/e3-tr/E4; (5) e1-nl/e2-ns/E3-Ha/E4. The studied cultivars contained the most common alleles of the GmFT2a and GmFT5a genes, with the exception of the ‘Cassidi’ cultivar having a rare dominant allele GmFT5a-H4. The degree of earliness of cultivars positively correlated with the number of recessive genes E1–E4, which is consistent with the data of foreign authors on different sets of cultivars from Japan and North China. Thus, the developed panel of markers can

A novel locus (Bnsdt2) in a TFL1 homologue sustaining determinate growth in Brassica napus

Background The determinate growth habits is beneficial for plant architecture modification and the development of crops cultivars suited to mechanized production systems. Which play an important role in the genetic improvement of crops. In Brassica napus, a determinate inflorescence strain (4769) has been discovered among doubled haploid (DH) lines obtained from a spring B. napus × winter B. napus cross, but there are few reports on it. We fine mapped a determinate inflorescence locus, and evaluated the effect of the determinate growth habit on agronomic traits. Results In this study, we assessed the effect of the determinate growth habit on agronomic traits. The results showed that determinacy is beneficial for reducing plant height and flowering time, advancing maturity, enhancing lodging resistance, increasing plant branches and maintaining productivity. Genetic analysis in the determinate (4769) and indeterminate (2982) genotypes revealed that two independently inherited recessive genes (Bnsdt1, Bnsdt2) are responsible for this determinate growth trait. Bnsdt2 was subsequently mapped in BC2 and BC3 populations derived from the combination 2982 × 4769. Bnsdt2 could be delimited to an approximately 122.9 kb region between 68,586.2 kb and 68,709.1 kb on C09. BLAST analysis of these candidate intervals showed that chrC09g006434 (BnaC09.TFL1) is homologous to TFL1 of A. thaliana. Sequence analysis of two alleles identified two non-synonymous SNPs (T136C, G141C) in the first exon of BnaC09.TFL1, resulting in two amino acid substitutions (Phe46Leu, Leu47Phe). Subsequently, qRT-PCR revealed that BnaC09.TFL1 expression in shoot apexes was significantly higher in NIL-4769 than in 4769, suggesting its essential role in sustaining the indeterminate growth habit. Conclusions In this study, the novel locus Bnsdt2, a recessive genes for determinate inflorescence in B. napus, was fine-mapped to a 68,586.2 kb - 68,709.1 kb interval on C09. The annotated genes chrC09g006434 (BnaC09.TFL1) that may be responsible for inflorescence traits were found.

Case Report: A Novel In-Frame Deletion of GLIS2 Leading to Nephronophthisis and Early Onset Kidney Failure

Variants in the GLIS family zinc finger protein 2 (GLIS2) are a rare cause of nephronophthisis-related ciliopathies (NPHP-RC). A reduction in urinary concentration and a progressive chronic tubulointerstitial nephropathy with corticomedullary cysts are the major characteristic features of NPHP. NPHP demonstrates phenotypic and genetic heterogeneity with at least 25 different recessive genes associated with the disease. We report a female, from a consanguineous family, who presented age 9 years with echogenic kidneys with loss of cortico-medullary differentiation and progressive chronic kidney disease reaching kidney failure by 10 years of age. A novel homozygous in-frame deletion (NM_032,575.3: c.560_574delACCATGTCAACGATT, p.H188_Y192del) in GLIS2 was identified using whole exome sequencing (WES) that segregated from each parent. The five amino acid deletion disrupts the alpha-helix of GLIS2 zinc-finger motif with predicted misfolding of the protein leading to its predicted pathogenicity. This study broadens the variant spectrum of GLIS2 variants leading to NPHP-RC. WES is a suitable molecular tool for children with kidney failure suggestive of NPHP-RC and should be part of routine diagnostics in kidney failure of unknown cause, especially in consanguineous families.

The impact of linkage disequilibrium and epistasis in the studies of inheritance based on Hayman’s diallel and generation mean analysis

This simulation-based study assessed the impact of linkage disequilibrium (LD) and epistasis on Hayman’s diallel and generation mean analysis, assuming hundreds of genes, variable degree of dominance, and seven types of digenic epistasis. The diallel parents were 15 doubled-haploid lines from a high LD population. The generation mean analysis was based on seven generations, assuming association. Under low LD and no epistasis, the diallel analysis provided confident results about the inheritance of the quantitative trait and high correlation between number of recessive genes and Wr + Vr, but biased estimates of the dominance components and genetic parameters. The additional consequences of high LD under no epistasis were rejection of the additive-dominance model assuming high heritability and lower correlation. Assuming 100% of epistatic genes, for four epistasis types there was evidence of inadequacy of the additive-dominance model. Assuming 30% of epistatic genes, there was a tendency for accepting the additive-dominance model for low heritability traits and for rejecting for high heritability traits. Linkage and epistasis affects the estimates of the genetic components of the generation means. Even assuming 100% of interacting genes, for most epistasis types there was no statistical evidence of epistasis. Assuming positive partial dominance, the signs of the epistatic components do not allow discriminate complementary, recessive, dominant and recessive, duplicate genes with cumulative effects, and non-epistatic genic interaction. Negative epistatic components evidence dominant epistasis. When the additive x additive and dominance x dominance components are positive and the additive x dominance component is negative, there is duplicate epistasis.

Association between CSF alpha-synuclein seeding activity and genetic status in Parkinson’s disease and dementia with Lewy bodies

The clinicopathological heterogeneity in Lewy-body diseases (LBD) highlights the need for pathology-driven biomarkers in-vivo. Misfolded alpha-synuclein (α-Syn) is a lead candidate based on its crucial role in disease pathophysiology. Real-time quaking-induced conversion (RT-QuIC) analysis of CSF has recently shown high sensitivity and specificity for the detection of misfolded α-Syn in patients with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). In this study we performed the CSF RT-QuIC assay in 236 PD and 49 DLB patients enriched for different genetic forms with mutations in GBA, parkin, PINK1, DJ1, and LRRK2. A subgroup of 100 PD patients was also analysed longitudinally. We correlated kinetic seeding parameters of RT-QuIC with genetic status and CSF protein levels of molecular pathways linked to α-Syn proteostasis. Overall, 85% of PD and 86% of DLB patients showed positive RT-QuIC α-Syn seeding activity. Seeding profiles were significantly associated with mutation status across the spectrum of genetic LBD. In PD patients, we detected positive α-Syn seeding in 93% of patients carrying severe GBA mutations, in 78% with LRRK2 mutations, in 59% carrying heterozygous mutations in recessive genes, and in none of those with bi-allelic mutations in recessive genes. Among PD patients, those with severe GBA mutations showed the highest seeding activity based on RT-QuIC kinetic parameters and the highest proportion of samples with 4 out of 4 positive replicates. In DLB patients, 100% with GBA mutations showed positive α-Syn seeding compared to 79% of wildtype DLB. Moreover, we found an association between α-Syn seeding activity and reduced CSF levels of proteins linked to α-Syn proteostasis, specifically lysosome-associated membrane glycoprotein 2 and neurosecretory protein VGF.These findings highlight the value of α-Syn seeding activity as an in-vivo marker of Lewy-body pathology and support its use for patient stratification in clinical trials targeting α-Syn.

Inheritance of Compact Growth Habit, and Investigation of Linkage to Weeping Architecture and Purple Leaf Color in Eastern Redbud (Cercis canadensis L.)

Eastern redbud (Cercis canadensis L.) is a commonly used small landscape tree. Compact growth, purple leaf color, and weeping architecture are three popular ornamental phenotypes. Inheritances of weeping architecture and purple leaves have been reported previously. Inheritance of compact growth habit and its genetic linkage with the weeping and purple leaf genes have not been reported. In the present research, the inheritance of compact growth derived from ‘Ace of Hearts’ was explored in the F1, F2, and reciprocal backcross families resulting from the controlled hybridization of ‘Ruby Falls’ (normal growth/weeping architecture/purple leaf) × ‘Ace of Hearts’ (compact growth/nonweeping architecture/green leaf). All 27 F1 individuals were nonweeping, green-leaved, and noncompact. A total of 572 F2 progeny were obtained, and subsequent analysis of segregation revealed a single recessive gene controlled compact growth habit. Analysis of reciprocal backcross families confirmed this result as well. Weeping architecture and purple leaf color were also controlled by single recessive genes, confirming findings presented in previous studies in another redbud family. No linkage between the three genes was detected. This research is the first to report the inheritance of compact growth in eastern redbud and confirms independent assortment between the compact, purple leaf, and weeping genes.

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes

Background DNA sequencing is increasingly incorporated into the routine care of cancer patients, many of whom also carry inherited, moderate/high-penetrance variants associated with other diseases. Yet, the prevalence and consequence of such variants remain unclear. Methods We analyzed the germline genomes of 10,389 adult cancer cases in the TCGA cohort, identifying pathogenic/likely pathogenic variants in autosomal-dominant genes, autosomal-recessive genes, and 59 medically actionable genes curated by the American College of Molecular Genetics (i.e., the ACMG 59 genes). We also analyzed variant- and gene-level expression consequences in carriers. Results The affected genes exhibited varying pan-ancestry and population-specific patterns, and overall, the European population showed the highest frequency of pathogenic/likely pathogenic variants. We further identified genes showing expression consequence supporting variant functionality, including altered gene expression, allelic specific expression, and mis-splicing determined by a massively parallel splicing assay. Conclusions Our results demonstrate that expression-altering variants are found in a substantial fraction of cases and illustrate the yield of genomic risk assessments for a wide range of diseases across diverse populations.

MICRONUTRITIENT VARIABILITY IN MAIZE INBRED LINES

Development of micronutrienten riched staple plant foods through plant breeding holds promise for sustainable and cost-effective food-based solutions to combat micronutrient deficiencies. The first step in this process is screening aviable germplasm for micronutritient content, so the aim of this study was determination of carotenoids and tocopherols content in set of maize inbred lines. Carotenoids (lutein, zeaxanthin and β-carotene) and tocopherols (α, β+γ and δ) content in 101 maize inbred lines with different kernel type (37 orange, 29 yellow, 4 white,19 sweetcorn and 12 popcorn) were determined by HPLC-DAD. The mean values of L+Z, β-carotene, α-tocopherol, β+γ tocopherol, and δ-tocopherol, were 31.34, 8.72, 10.22, 49.17 and 1.81 μg/ g, respectively. Content of α -tocopherol was in the range from 2.22 to 38.14 μg/g and β+γ tocopherols from 12.10 to 105.52 μg/g, β-carotene 1.20 to 39.37 μg/g and lutein+zeaxanthin 11.28 to 69.31 μg/g. White maize lacked carotenoids in the endosperm due to the presence of recessive genes. The highest value of β-carotene had inbred line H, L+Z inbred W-4, γ-tocopherols KRW 803-3-1-2-1 and α –tocopherol P21. Orange kernel inbred lines had the highest value of L+Z and β-carotene, yellow kernel inbred lines α –tocopherol, whereas sweetcorn inbreds had the highest value of γ-tocopherols. The genetic background undoubtedly influences chemical quality and line with high content of particularly micronutritients may be used in breeding program to improve nutritional value.

Variability and genetic control of the “seedlings-earing” interphase period in spring barley under water deficit

Purpose. To determine the variability and genetic control of the “seedlings–earing” interphase period in spring barley under water deficit, to theoretically substantiate generations for selection in the diallel crossing design using cultivars bred at different breeding institutions and of different ecotypes, thereby solving the problem of shortening the spring barley breeding process. Material and methods. The study was conducted at Donetsk State Agricultural Station of NAAS of Ukraine. In 2018–2019, hybridization was performed and over 150 grains for each combination were obtained. In 2019–2020, the field experiments were laid out; cultivars and hybrids were sown within the optimal timeframe. The plots were arranged as per a P1 F1 P2 scheme. The row length was 1.5 m. A cassette seeder SKS-6-10 was used. The nutrition area was 10 cm x 20 cm. The experiments were carried out in three replications. The predecessor was black fallow. Data were processed using the package of applications for processing genetic and breeding experiments "EliteSystems gr." developed by the PPI nd.a. V.Ya. Yuriev NAASU. Based on genetic analysis, the Hayman parameters were determined. Results and discussion. The “seedlings–earing” interphase period in the cultivars varied 42.8 days to 49.1 days. In F1 hybrids, the “seedlings–earing” interphase period varied significantly, depending on crossing of cultivars of different ecotypes. Significant influence and SCA variance, the effects of allelic and non-allelic interactions were higher in a less favorable year: 18% vs. 14.5%. Analysis of the hybrid combinations indicates that the female effect, which increases the earing time, was seen in the hybrid combinations Partner/Komandor, Komandor/Baskak, Bohun/Baskak, and Bohun/Komandor. Baskak and Svarozhych reduced the earing time, while Komandor and Bohun increased it, and the GCA effects were most pronounced in the latter. Evaluation of the Wr–Vr difference homogeneity using t-test revealed no epistatic interaction (t = 0.21 and 0.10 insignificant). The regression line passes above the origin, indicating the leading role of dominance in the genetic control of the “seedlings–earing” period. This is confirmed by the indicator of medium degree of dominance. The divergence of the cultivar points along the regression line is significant, indicating the differentiation of the genotypes by the presence of dominant and recessive genes. In 2019, Partner and Komander were in the dominant zone, Baskak, Svarozhych and Bohun – in the recessive one. In 2020, Svarozhych and Komandor were in the recessive zone, and Bohun moved from the recessive zone to the dominant one. In general, the location of the cultivars along the regression line is relatively stable. In the loci that show dominance, the product of the frequencies of positive and negative alleles was asymmetric, and the ratio of the total number of dominant genes to the total number of recessive ones, proceeding from the values of >1, indicates prevalence of the former. In the genetic control of the “seedlings–earing” interphase period, incomplete intra-locus dominance and inter-locus additivity were recorded. Conclusions. Cultivars of different ecotypes bred at different breeding institutions, with due account for their competitiveness in terms of performance, were taken as initial components. Of crossing designs, we preferred diallel crossing for the following reasons: it allows obtaining the full range of combinatorics of the parents’ genetic information. The assemblage of F1 hybrids and parental cultivars gives a typical segregation. Starting selection, we have an idea about the trait inheritance and can determine from which generation to start it. Positive correlation coefficients between Wr + Vr and Xp (P3 = 0.32 ± 40 and 0.52 ± 0.32) indicate the stability of genetic systems determining the barley earing time, but they are insignificant, indicating the dominance direction, i.e. both dominant and recessive genes can reduce or increase this trait. The trait is controlled by a single genetic system, so selection can be based both on dominant alleles and on recessive ones, regardless of whether or not they reduce “seedlings-earing” interphase period. One should prefer recessive alleles, because they can be manifested in F2. Svarozhych can be used as a source to reduce the “seedlings-earing” interphase period, while Bohun can lengthen it