Genetic parameters controlling the inheritance of glaucousness and yield traits in bread wheat

Wheat breeders frequently use generation mean analysis to obtain information on the type of gene action involved in inheriting a trait to choose the helpful breeding procedure for trait improvement. The present study was carried out to study the inter-allelic and intra-allelic gene action and inheritance of glaucousness, earliness and yield traits in a bread wheat cross between divergent parents in glaucousness and yield traits; namely Mut-2 (P1) and Sakha 93 (P2). The experimental material included six populations, i.e. P1, P2, F1, F2, BC1, and BC2 for this wheat cross. A randomized complete block design with three replications was used, and a six parameters model was applied. Additive effects were generally more critical than dominance for all studied traits, except for plant height (PH) and grain yield/plant (GYPP). The duplicate epistasis was observed in spike length; SL, spikes/plant; SPP and days to heading; DTH. All six types of allelic and non-allelic interaction effects controlled SL, GYPP, DTH and glaucousness. All three types of epistasis, i.e. additive x additive, additive x dominance, and dominance x dominance, are essential in determining the inheritance of four traits (SL, GYPP, DTH and glaucousness). Dominance × dominance effects were higher in magnitude than additive × dominance and additive × additive in most traits. The average degree of dominance was minor than unity in six traits (glaucousness, grains/spike, spike weight, days to maturity, 100-grain weight and SL), indicating partial dominance and selection for these traits might be more effective in early generations. Meanwhile, the remaining traits (PH, SPP, GYPP and DTH) had a degree of dominance more than unity, indicating that overdominance gene effects control such traits and it is preferable to postpone selection to later generations. The highest values of narrow-sense heritability and genetic advance were recorded by glaucousness trait followed by SL and SPP, indicating that selection in segregating generations would be more effective than other traits.

Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice

Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.

LRFN5 locus structure is influenced by the individual’s sex and associated with autism

BackgroundLRFN5 is a brain-specific gene needed for synaptic development and plasticity. It is the only gene in a large 5.4 Mb topologically associating domain (TAD) on chromosome 14, which we term the LRFN5 locus. This locus is highly conserved, but has extensive copy number variation. MethodsLocus structure was studied by chromatin immunoprecipitation (chIP-onchip) in fibroblasts from individuals with autism and controls, supplemented with a capture-HiC determination of TAD structures in a family trio. LRFN5 expression was studied in foetal brain cell cultures. In addition, locus interaction was studied in four large and independent cohorts by measuring deviations from Hardy-Weinberg equilibrium of a common deletion polymorphism. ResultsWe found that locus structural changes are associated with developmental delay (DD) and autism spectrum disorders (ASD). In a large family, ASD in males segregated with a chromosome 14 haplotype carrying a 172 kb deletion upstream of LRFN5 . In a fibroblast capture-HiC study on an ASD-patient-parent trio, the ASDsusceptible haplotype (in the mother and her autistic son) had a TAD pattern different from both the father and a female control. When the trimethylated histone-3-lysine-9 chromatin (H3K9me3) profiles in fibroblasts from control males (n=6) and females (n=7) were compared, a male-female difference was observed around the LRFN5 gene itself (p<0.01). Intriguingly, in three cohorts of individuals with DD (n=8757), the number of heterozygotes of a common deletion polymorphism upstream of LRFN5 was 20-26% lower than expected from Hardy-Weinberg equilibrium. This indicates early allelic interaction, and the genomic conversions from heterozygosity to wildtype or deletion homozygosity were of equal magnitudes. In a control group of medical students (n=1416), such conversions were three times more common than in the DD-patient cohorts (p=0.00001). Hypothetically, such allelic interaction is needed to establish monoallelic expression, which we found in foetal brain cell cultures. LimitationsThe male-female difference in H3K9me3 profiles was based on fibroblast data from a small number of individuals, and the monoallelic expression data on a single experiment. ConclusionsTaken together, allelic interaction, monoallelic expression and sexdependent differences make the LRFN5 locus attractive for exploring the genetic basis of synaptic memory and high-functioning male autism.

Two Nicotiana occidentalis accessions enable gene identification for Type II hybrid lethality by the cross to N. sylvestris

Hybrid lethality, meaning the death of F1 hybrid seedlings, has been observed in many plant species, including Nicotiana. Previously, we have revealed that hybrids of the selected Nicotiana occidentalis accession and N. tabacum, an allotetraploid with S and T genomes, exhibited lethality characterized by the fading of shoot color. The lethality was suggested to be controlled by alleles of loci on the S and T genomes derived from N. sylvestris and N. tomentosiformis, respectively. Here, we extended the analysis of hybrid lethality using other two accessions of N. occidentalis identified from the five tested accessions. The two accessions were crossed with N. tabacum and its two progenitors, N. sylvestris and N. tomentosiformis. After crosses with N. tabacum, the two N. occidentalis accessions yielded inviable hybrid seedlings whose lethality was characterized by the fading of shoot color, but only the T genome of N. tabacum was responsible for hybrid lethality. Genetic analysis indicated that first-mentioned N. occidentalis accession carries a single gene causing hybrid lethality by allelic interaction with the S genome.

Generation Mean Analysis for Seed Yield and Wilt Resistance in Castor (Ricinus communis L.)

Background: Castor is an important non-edible oil seeds crop of Gujarat state. Yield potentiality of this crop has been considerably improved through several breeding techniques. Now days, a wilt (Fusarium oxysporum f. sp. ricini) of castor has become a serious problem. The present study therefore, was under taken to use populations of P1, P2, F1, F2, BC1 and BC2 generations in each of six crosses of castor. The six crosses were selected in such a way that two crosses in each group of resistance × resistance, resistance × susceptible and susceptible × susceptible made available for detail study of gene effects for wilt resistance.Methods: The experiment was laid out in a compact family block design with three replications during kharif, 2017. The experimental materials consisted of four pistillate lines viz., VP-1, Geeta, SKP-84 and SKP-106 and six inbred lines viz., VI-9, JI-35, 48-1, SH-72, SKI-215 and PCS-124 selected from the germplasm maintained at the Castor and Mustard Research Station, S.D. Agricultural University, Sardarkrushinagar. Each entry was planted in a single row of 10 dibbles maintaining 120 cm row to row and 60 cm plant to plant distances.Result: The analysis of variance revealed significant difference among different generations for wilt incidence and seed yield indicating considerable variability in the material tested. The estimation of the gene effects revealed that additive as well as non-additive gene effects were observed for wilt incidence and seed yield in all the six cross. In the cross, VP - 1 × JI- 35 the wilt incidence estimation of scaling test and gene effect was observed non-significant indicating non-allelic interaction was absent for this character, while for seed yield, all the crosses have significant scaling test indicating the presence of non-allelic interactions for this trait.

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

Paramutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploid Arabidopsis thaliana. Our data suggest that different types of small RNA are derived from paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation.

Oncogenic allelic interaction inXiphophorushighlights hybrid incompatibility

Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations makeXiphophorusone of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene,rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role ofegfrregulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.