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Improving seed oil quality in peanut (Arachis hypogaea) has long been an aim of breeding programs worldwide. The genetic resources to achieve this goal are limited. We used an advanced recombinant inbred line (RIL) population derived from JH5 × KX01-6 to explore quantitative trait loci (QTL) affecting peanut oil quality and their additive effects, epistatic effects, and QTL × environment interactions. Gas chromatography (GC) analysis suggested seven fatty acids components were obviously detected in both parents and analyzed in a follow-up QTL analysis. The major components, palmitic acid (C16:0), oleic acid (C18:1), and linoleic acid (C18:2), exhibited considerable phenotypic variation and fit the two major gene and minor gene mixed-inheritance model. Seventeen QTL explained 2.57–38.72% of the phenotypic variation in these major components, with LOD values of 4.12–37.56 in six environments, and thirty-five QTL explained 0.94–32.21% of the phenotypic variation, with LOD values of 5.99–150.38 in multiple environments. Sixteen of these QTL were detected in both individual and multiple environments. Among these, qFA_08_1 was a novel QTL with stable, valuable and major effect. Two other major-effect QTL, qFA_09_2 and qFA_19_3, share the same physical position as FAD2A and FAD2B, respectively. Eleven stable epistatic QTL involving nine loci explained 1.30–34.97% of the phenotypic variation, with epistatic effects ranging from 0.09 to 6.13. These QTL could be valuable for breeding varieties with improved oil quality. [ABSTRACT FROM AUTHOR]

Introduction: Barley (Hordeum vulgare L.) is known as the fourth most important grain crop in the world. Drought stress is also one of the main factors that reduce the growth and yield of barley, and grain yield is directly related to the morphological characteristics of the flag leaf.. Materials and methods: In order to identify the main and epistatic genomic regions and investigate their interaction with the environment for morphological traits related to flag leaf, including length, width, area, and flag leaf sheath length, an experiment was conducted with 136 doubled haploid lines of barley along with their parents 'Nure' and 'Tremois' using an alpha lattice design with two replications under normal and drought stress conditions at the Zabol Agricultural Research Station, Iran, in 2015-16 growing season. The genetic map of the target population comprised 543 markers (including DArT, SSR, SNP, and AFLP markers) for the QTL analysis. In this study, single-locus and two-locus QTL analyses were performed using the composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) methods, respectively. Results: Based on a single-locus analysis, five QTLs were identified, including three putative QTLs, Q1FLW-1H.SZ, Q1SHFLL1H.NZ and Q2SHFLL-1H.NZ at bPb-6343-bPb-8081, bPb-1419-bPb-9180, and bPb-9108-bPb-6343 marker intervals, and two suggestive QTLs, on chromosomes 1H and 5H for the traits of flag leaf width (FLW, cm) and flag leaf sheath length (SHFLL, cm). Based on a two-locus analysis, eight additive (M-QTL) QTLs and 15 pairs of epistatic effects (E-QTL) were detected for different traits, among which two pairs of epistatic QTLs for the FLW trait showed significant QTL × environment interactions (AAEI). All detected M-QTLs for flag-leaf-related traits across two environments, without additive × environment interactions (AEI), were identified as stable QTLs, and the highest number of stable QTLs was associated with chromosome 1H. In this study, drought stress-tolerant QTLs were identified in all barley chromosomes except chromosome 2H. Conclusion: Most of the QTLs associated with the investigated traits in the Nure/Tremois population in the present study have not been reported previously and, therefore, are novel. The stable and putative QTLs controlling flag-leaf-related traits in this study, along with the markers linked to these QTLs, can be utilized in marker-assisted selection (MAS) and gene pyramiding breeding programs after confirmation and validation in different environmental conditions and genetic backgrounds to create high-yielding and drought-tolerant barley cultivars. Additionally, these findings will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level. [ABSTRACT FROM AUTHOR]

In this study, we performed all-atom MD simulations of RBD–ACE2 complexes for BA.1, BA.1.1, BA.2, and BA.3 Omicron subvariants, conducted a systematic mutational scanning of the RBD–ACE2 binding interfaces and analysis of electrostatic effects. The binding free energy computations of the Omicron RBD–ACE2 complexes and comprehensive examination of the electrostatic interactions quantify the driving forces of binding and provide new insights into energetic mechanisms underlying evolutionary differences between Omicron variants. A systematic mutational scanning of the RBD residues determines the protein stability centers and binding energy hotpots in the Omicron RBD–ACE2 complexes. By employing the ensemble-based global network analysis, we propose a community-based topological model of the Omicron RBD interactions that characterized functional roles of the Omicron mutational sites in mediating non-additive epistatic effects of mutations. Our findings suggest that non-additive contributions to the binding affinity may be mediated by R493, Y498, and Y501 sites and are greater for the Omicron BA.1.1 and BA.2 complexes that display the strongest ACE2 binding affinity among the Omicron subvariants. A network-centric adaptation model of the reversed allosteric communication is unveiled in this study, which established a robust connection between allosteric network hotspots and potential allosteric binding pockets. Using this approach, we demonstrated that mediating centers of long-range interactions could anchor the experimentally validated allosteric binding pockets. Through an array of complementary approaches and proposed models, this comprehensive and multi-faceted computational study revealed and quantified multiple functional roles of the key Omicron mutational site R493, R498, and Y501 acting as binding energy hotspots, drivers of electrostatic interactions as well as mediators of epistatic effects and long-range communications with the allosteric pockets. [ABSTRACT FROM AUTHOR]

Epistasis strongly affects the performance of superior maize hybrids. In this study, a multiple-hybrid population, consisting of three hybrid maize sets with varied interparental divergence, was generated by crossing 28 temperate and 23 tropical inbred lines with diverse genetic backgrounds. We obtained 1,154 tested hybrids. Among these tested hybrids, heterosis increased steadily as the heterotic genetic distance increased. Midparent heterosis was significantly higher in the temperate by tropical hybrids than in the temperate by temperate hybrids. Genome-wide prediction and association mapping was performed for grain weight per plant (GWPP) and days to silking (DTS) using 20K high-quality SNPs, showing that epistatic effects played a more prominent role than dominance effects in temperate by tropical maize hybrids. A total of 33 and 420 epistatic QTL were identified for GWPP and DTS, respectively, in the temperate by tropical hybrids. Protein–protein interaction network and gene-set enrichment analyses showed that epistatic genes were involved in protein interactions, which play an important role in photosynthesis, biological transcription pathways, and protein synthesis. We showed that the interaction of many minor-effect genes in the hybrids could activate the transcription activators of epistatic genes, resulting in a cascade of amplified yield heterosis. The multiple-hybrid population design enhanced our understanding of heterosis in maize, providing an insight into the acceleration of hybrid maize breeding by activating epistatic effects. [ABSTRACT FROM AUTHOR]

Summary: Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein−protein interactions specific to F1 hybrids (F1‐specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter‐subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four‐thousand, six‐hundred and twelve F1‐specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1‐specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1‐specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1‐specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1‐specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1‐specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large‐scale protein interactome datasets are generated in hybrid rice in the future. Significance Statement: Based on a simulated protein interactome in hybrid rice, inter‐subspecies protein interactions specific to F1 hybrids were proven to play an epistatic role in yield heterosis. [ABSTRACT FROM AUTHOR]

Tassel branch number (TBN) is the principal component of maize tassel inflorescence architecture and is a typical quantitative trait controlled by multiple genes. The main objective of this research was to detect quantitative trait loci (QTLs) for TBN. The maize inbred line SICAU1212 was used as the common parent to develop BC1S1 and recombinant inbred line (RIL) populations with inbred lines 3237 and B73, respectively. The two related populations consisted of 123 and 238 lines, respectively. Each population was grown and phenotyped for TBN in two environments. Eleven QTLs were detected in the BC1S1 population, located on chromosomes 2, 3, 5, and 7, accounted for 4.45–26.58% of the phenotypic variation. Two QTLs (qB11Jtbn2-1, qB12Ctbn2-1, qBJtbn2-1; q11JBtbn5-1, qB12Ctbn5-1, qBJtbn5-1) that accounted for more than 10% of the phenotypic variation were identified. Three QTLs located on chromosomes 2, 3 and 5, exhibited stable expression in the two environments. Ten QTLs were detected in the RIL population, located on chromosomes 2, 3, 5, 8, and 10, accounted for 2.69–13.58% of the TBN variation. One QTL (qR14Dtbn2-2) explained >10% of the phenotypic variation. One common QTL (qB12Ctbn2-2, qR14Dtbn2-2, qRJtbn2-2) was detected between the two related populations. Three pairs of epistatic effects were identified between two loci with or without additive effects and accounted for 1.19–4.26% of the phenotypic variance. These results demonstrated that TBN variation was mainly caused by major effects, minor effects and slightly modified by epistatic effects. Thus, identification of QTL for TBN may help elucidate the genetic basis of TBN and also facilitate map-based cloning and marker-assisted selection (MAS) in maize breeding programs.

Soybean is an important crops in the world due to its high seed protein and oil contents, while the contents of seed protein and oil attributed to the quantitative traits which were controlled by multiple minor-genes. Though there were many related QTLs reported, most of them only focused on the single additive QTLs, and few of them payed attentions to the epistatic QTLs. In this paper, a soybean RIL population (ZL) was used to study the epistatic QTLs of seed protein and oil contents by analyzing ZL population using Illumina BARCSoySNP6K Beadchip and detecting the phenotypes under four different environments. The results showed that there were 48 pairs of epistatic QTLs associated with protein content and 55 pairs of epistatic QTLs related to oil content in soybean seeds. Furthermore, there were 19 pairs of co-located epistatic QTLs controlling the protein and oil contents simultaneously. Among these co-located epistatic QTLs, 12 pairs of them shared the same QTL mapping regions, 2 pairs of them shared one same marker and five pairs of them had the QTLs regions not above 5 cM genetic distance, which could be regarded as the same QTL. Meanwhile, the results also showed that these epistatic QTLs located on nineteen chromosomes of soybean except for the chromosome 11. Thus, this study identified many epistatic QTLs for soybean seed protein and oil contents, which not only could be used for soybean quality genetic improvements in future, but also offered some evidences for reveal the negative relationships between seed protein and oil contents in soybean. [ABSTRACT FROM AUTHOR]

Objectives. To seek the genetic mechanisms of impairments to the recognition of emotions, which is a sign of schizophrenia which degrades social adaptation of patients. This search was based on the view that the interaction between the dopaminergic and glutamatergic systems has a role in the pathogenesis of schizophrenia. The effects of the interaction between the polymorphic C366G locus in the gene encoding the NR2B subunit of the NMDA receptor - GRIN2B - the polymorphic loci in the dopamine receptor genes ANKK1/DRD2 Taq1A and DRD4 48-VNTR on the recognition of emotional expressions were studied. Materials and methods. The effects of the interaction between GRIN2B and DRD2 were studied in cohorts of 237 patients and 235 healthy subjects; those between GRIN2B and DRD4 were studied in cohorts of 268 and 208, respectively. Results and conclusions. Both effects reached significance in the combined cohorts of patients and healthy subjects (GRIN2B × DRD2, F = 4.12, p = 0.043; GRIN2B × DRD4, F = 6.43, p = 0.012). The effect of the interaction between the polymorphic loci in the GRIN2B and DRD2 genes on the recognition of expressed emotions in schizophrenia patients was confirmed. In patients with the less effective allele of the DRD2 gene and not bearing the minor allele of the GRIN2B gene, results were close to normal, while the genotype containing the minor alleles of both genes produced the worst results. This result is consistent with concepts of the possible role of the hypofunction of NMDA receptors and D2-mediated regulation of their activity in the production of schizophrenia endotypes such as the recognition of expressed emotions. [ABSTRACT FROM AUTHOR]

Heading date (HD) and flowering date (FD) are critical for yield potential and stability, so understanding their genetic foundation is of great significance in wheat breeding. Three related recombinant inbred line populations with a common female parent were developed to identify quantitative trait loci (QTL) for HD and FD in four environments. In total, 25 putative additive QTL and 20 pairwise epistatic effect QTL were detected in four environments. The additive QTL were distributed across 17 wheat chromosomes. Of these, QHd-1A , QHd-1D , QHd-2B , QHd-3B , QHd-4A , QHd-4B and QHd-6D were major and stable QTL for HD. QFd-1A , QFd-2B , QFd-4A and QFd-4B were major and stable QTL for FD. In addition, an epistatic interaction test showed that epistasis played important roles in controlling wheat HD and FD. Genetic relationships between HD/FD and five yield-related traits (YRTs) were characterized and ten QTL clusters (C1–C10) simultaneously controlling YRTs and HD/FD were identified. The present work laid a genetic foundation for improving yield potential in wheat molecular breeding programmes. [ABSTRACT FROM AUTHOR]

Abstract: Understanding of mungbean yellow mosaic disease resistance is crucial to develop resistant varieties to combat worldwide threat of the disease epidemics. This study was aimed to determine nature of disease resistance in terms of number of genes governing it and genetics of related traits. Experimental site was located on 31.43°N and 73.06°E with an elevation of 186 m, and evaluation trials were conducted during spring season due to high disease epidemics in this season. Two contrasting genotypes, that is, NM 6‐68‐2 (resistant) and NM 1‐32‐1 (highly susceptible), were crossed to raise six populations, that is, P1, P2, F1, F2, BC1 and BC2 for evaluation under protected and unprotected field conditions using chi‐square test and generation mean and variance analysis. It was discovered that disease resistance was governed by two major genes with additive effects. Disease resistance can easily be incorporated through backcrossing and direct selection following hybridization. Direct selection should be practised at earlier generation for plant height, chlorophyll contents and number of seeds per pod due to preponderance of additive effects whereas at later generations for seed yield per plant, 100 seed weight, harvest index, number of pods per plant and pod length due to involvement of duplicate epistasis. [ABSTRACT FROM AUTHOR]

Background: Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 lines derived from intercrossing eight recently released European winter wheat cultivars. Results: Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59.7% between MAGIC lines. WM-800 harbours distinct genomic regions exposed to segregation distortion. These are mainly located on chromosomes 2 to 6 of the wheat B genome where founder specific DNA segments were positively or negatively selected. This suggests adaptive selection of individual founder alleles during population development. The application of a genome-wide association study identified 14 quantitative trait loci (QTL) controlling plant height in WM-800, including the known semi-dwarf genes Rht-B1 and Rht-D1 and a potentially novel QTL on chromosome 5A. Additionally, epistatic effects controlled plant height. For example, two loci on chromosomes 2B and 7B gave rise to an additive epistatic effect of 13.7 cm. Conclusion: The present study demonstrates that plant height in the MAGIC-WHEAT population WM-800 is mainly determined by large-effect QTL and di-genic epistatic interactions. As a proof of concept, our study confirms that WM-800 is a valuable tool to dissect the genetic architecture of important agronomic traits. [ABSTRACT FROM AUTHOR]

Abstract: Leaf‐related traits (leaf length, leaf width, leaf area and leaf angle) are very important for the yield of maize (Zea mays L) due to their influence on plant type. Therefore, it is necessary to identify quantitative trait loci (QTLs) for leaf‐related traits. In this report, 221 doubled haploid lines (DHLs) of an IBM Syn10 DH population were provided for QTL mapping. In total, 54 QTLs were detected for leaf‐related traits in single environments using a high‐density genetic linkage map. Among them, only eight common QTLs were identified across two or three environments, and the common QTLs for the four traits explained 4.38%–19.99% of the phenotypic variation. qLL‐2‐1 (bin 2.09), qLW‐2‐2 (bin 2.09), qLW‐6‐3 (bin 6.07) and qLA‐5‐2 (bin 2.09) were detected in previous studies, and qLL‐1‐1, qLAr‐1‐1, qLAr‐2‐1 and qLA‐7‐1 may be new QTLs. Notably, qLW‐6‐3 and qLA‐5‐2 were found to be major QTLs explaining 19.99% and 10.96% of the phenotypic variation, respectively. Interestingly, we found three pairs of QTLs (qLW‐2‐2 and qLAr‐2‐1, qLW‐8‐1 and qLL‐8‐2, qLL‐3‐3 and qLAr‐3‐3) that control different traits and that were located on the same chromosome or in a nearby location. Moreover, nine pairs of loci with epistatic effects were identified for the four traits. These results may provide the foundation for QTL fine mapping and for an understanding of the genetic basis of variation in leaf‐related traits. [ABSTRACT FROM AUTHOR]

The amino acid glutamate (Glu) acts as a fast excitatory neurotransmitter in mammals. Its importance in plant signalling was recognized with the discovery of channel proteins similar to mammalian Glu receptors, as well as distinct changes in root-system architecture in response to very small amounts of soil Glu. Based on natural genetic variation within Arabidopsis, Walch-Liu et al. (2017) have now identified a major locus underpinning this root response, as well as several loci controlling it through gene by environment interactions with nitrate and temperature. It is a significant step towards unraveling crosstalk between signalling pathways that enable plants to adjust their growth and development to multiple environmental stimuli. [ABSTRACT FROM AUTHOR]

Primary root growth in Arabidopsis and a number of other species has previously been shown to be remarkably sensitive to the presence of external glutamate, with glutamate signalling eliciting major changes in root architecture. Using two recombinant inbred lines from reciprocal crosses between Arabidopsis accessions C24 and Col-0, we have identified one large-effect quantitative trait locus (QTL), GluSI, and two minor QTLs, GluS2 and GluS3, which together accounted for 41% of the phenotypic variance in glutamate sensitivity. The presence of the GluSI locus on chromosome 3 was confirmed using a set of C24/Col-0 isogenic lines. GluSI was mapped to an interval between genes At3g44830-At3g46880. When QTL mapping was repeated under a range of environmental conditions, including temperature, shading and nitrate supply, a strong genotype-by-environment interaction in the controls for the glutamate response was identified. Major differences in the loci controlling this trait were found under different environmental conditions. Here we present evidence for the existence of loci on chromosomes 1 and 5 epistatically controlling the response of the GluSI locus to variations in ambient temperature, between 20°C and 26°C. In addition, a locus on the long arm of chromosome 1 was found to play a major role in controlling the ability of external nitrate signals to antagonize the glutamate effect. We conclude that there are multiple loci controlling natural variation in glutamate sensitivity in Arabidopsis roots and that epistatic interactions play an important role in modulating glutamate sensitivity in response to changes in environmental conditions. [ABSTRACT FROM AUTHOR]

Efeitos genético aditivo, de dominância e de recombinação em cruzamentos entre as raças Santa Inês (SI), Somalis Brasileira (So), Dorper (Do) e Poll Dorset (Po) foram estimados para as características de crescimento, reprodutivas e de habilidade materna. Os dados foram obtidos da Gaasa e Alimentos LTDA, uma empresa que participa do Programa de Melhoramento Genético de Caprinos e Ovinos (GENECOC) da Embrapa Caprinos. Inicialmente, 3.573 registros foram analisados por meio do procedimento MIXED do pacote estatístico SAS (1999). As análises foram realizadas considerando os efeitos da diferença genética aditiva entre as raças, de dominância e de recombinação. O peso ao nascer foi influenciado pelos efeitos genéticos aditivos, enquanto o peso ao desmame e o ganho de peso pré-desmame foram influenciados por efeitos genéticos não-aditivos. A estimativa de herdabilidade direta para o peso ao nascer foi moderada, o que indica a existência de variabilidade genética passível de ser explorada por meio da seleção individual. Do mesmo modo, as estimativas de herdabilidade das características idade ao primeiro parto e peso total das crias ao nascer indicaram a existência de variabilidade genética para obter ganhos genéticos por meio da seleção. Os genes das raças Poll Dorset e Dorper tiveram papel importante para melhor desempenho ponderal, portanto, essas raças podem ser indicadas como paternas no cruzamento terminal. A utilização de matrizes F1 Santa Inês x Somalis Brasileira em cruzamentos com reprodutores Poll Dorset pode levar a maior eficiência reprodutiva.Additive genetic, dominance and recombination effects in breedings among Santa Inês (SI), Brazilian Somali (So), Dorper (Do) and Poll Dorset (Po) breeds were estimated for growth, reproductive and maternal hability traits. Data were obtained from Gaasa e Alimentos LTDA, a company that participates on the Programa de Melhoramento Genético de Caprinos e Ovinos (GENECOC) coordinated by Embrapa Caprinos. Initially, 3,573 records were analyzed using the MIXED procedure of the statistical package SAS (1999). The analyses were carried out considering the effects of additive genetic difference among breeds, dominance and recombination effects. Birth weight was mainly influenced by additive genetic effects, while weaning weight and pre-weaning weight gain were influenced by non-additive genetic effects. Direct heritability estimates for birth weight was moderate indicating that there is genetic variability believable to be exploited by individual selection. In the same way, heritability estimates for the traits age at first lambing and litter total weight at birth indicated the existence of genetic variability to obtain genetic gains through selection. Genes of the Poll Dorset and Dorper breeds had an important role for a better growth performance, therefore, these breeds can be indicated as sires in the terminal breeds. The use of F1 Santa Inês x Brazilian Somali females on crossbreeding with Poll Dorset rams can lead to a better reproductive efficiency.

Breeding programs for acid-soil tolerance are desirable as a relatively inexpensive and permanent way for increasing maize (Zea mays L.) yield on these soils. Our objective was to compare the genetic effects controlling the expression of maize traits in acid and non-acid soils. Seven related and one unrelated inbred lines, with different levels of tolerance to acid soil, and their F1, F2, BC1, and BC2 generations were evaluated in four acid and two non-acid soils. Estimates of additive, dominance, and epistatic effects were computed for grain yield, plant height, days to mid-silk, and prolificacy, using the generation means analysis procedure. For all traits the major part of the variation was accounted for by additive and dominance effects, with dominance effects being more important than additive and epistatic effects for both acid and non-acid soils. Epistatic effects were significant for some crosses only, being more pronounced for plant height than for the other traits. Furthermore, epistatic effects were randomly distributed among the crosses and were not related to the grain yield of the single-crosses (F1's) and to the genetic relationships of the inbreds in either type of soil. The results suggest that similar pooled gene effects control the expression of the traits assessed in both acid and non-acid soils.

Tendo em vista a grande importância dos bovinos mestiços Holandês x Gir (H x G) nos sistemas de produção de leite no Brasil e a íntima relação entre a reprodução e a produtividade destes sistemas, foram obtidos registros de partos e datas de nascimento junto à Associação Brasileira dos Criadores de Girolando, no intuito de avaliar o desempenho reprodutivo de vários grupos genéticos HxG. Os dados, num total de 2.600 registros de idade ao primeiro parto (IPP) e 3.763 de intervalos de partos (IDP), foram analisados por meio do procedimento GLM do pacote estatístico SAS (1999). As comparações do desempenho dos grupos genéticos foram feitas por meio de modelos classificatórios incluindo o efeito de grupo genético. Foram feitas estimativas dos efeitos genéticos, isto é, da diferença aditiva entre Holandês e Gir, do efeito de dominância e do efeito epistático aditivo x aditivo, utilizando-se modelos de regressão. O grupo meio-sangue apresentou desempenho superior, ou seja, menores IPP e IDP. Foi observada tendência de elevação do IDP com o aumento da proporção de genes da raça Holandesa. O efeito de dominância influenciou significativamente as duas características estudadas, enquanto o efeito de interação epistática do tipo aditivo x aditivo influenciou significativamente apenas a IPP. Os resultados indicaram que a perda de interações epistáticas favoráveis contribuiu para a alta IPP no grupo 5/8 Holandês.Reproduction efficiency of Holstein x Gir crossbred animals in Brazilian dairy farms were evaluated using data provided by the Brazilian Association of Girolando. A total of 2,600 records of age at first calving (IPP) and 3,763 records of calving intervals (IDP) were analyzed using the SAS® GLM procedure. Estimates of genetics effects: additive difference between Holstein and Gir breeds, dominance and additive x additive epistatic effects were obtained by regression models including genetic groups to model the performance of crossbred groups. The genetic group 1/2 showed better performance: lower averages for IPP and IDP than the other groups. It was observed a trend of increasing IDP as the proportion of Holstein genes increased. The dominance effect influenced significantly both traits, while the additive x additive epistatic effects significantly influenced only IPP. The results indicated that loss of favorable epistatic interactions contributed to high IPP average in the 5/8 group.

We conducted a genome-wide scan using variance components linkage analysis to localize quantitative-trait loci (QTLs) influencing triglyceride (TG), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol, and total cholesterol (TC) levels in 3,071 subjects from 459 families with atherogenic dyslipidemia. The most significant evidence for linkage to TG levels was found in a subset of Turkish families at 11q22 [logarithm of the odds ratio (LOD) = 3.34] and at 17q12 (LOD = 3.44). We performed sequential oligogenic linkage analysis to examine whether multiple QTLs jointly influence TG levels in the Turkish families. These analyses revealed loci at 20q13 that showed strong epistatic effects with 11q22 (conditional LOD = 3.15) and at 7q36 that showed strong epistatic effects with 17q12 (conditional LOD = 3.21). We also found linkage on the 8p21 region for TG in the entire group of families (LOD = 3.08). For HDL-C levels, evidence of linkage was identified on chromosome 15 in the Turkish families (LOD = 3.05) and on chromosome 5 in the entire group of families (LOD = 2.83). Linkage to QTLs for TC was found at 8p23 in the entire group of families (LOD = 4.05) and at 5q13 in a subset of Turkish and Mediterranean families (LOD = 3.72).These QTLs provide important clues for the further investigation of genes responsible for these complex lipid phenotypes. These data also indicate that a large proportion of the variance of TG levels in the Turkish population is explained by the interaction of multiple genetic loci.

Continuous improvement in grain yield is one of the major challenges for wheat ( Triticum aestivum L.) breeding worldwide. This study characterized quantitative trait loci (QTL) underlying wheat grain yield and its components using a high-density genetic linkage map developed from a recombinant inbred line (RIL) population derived from 'Ning7840' × 'Clark'. The map consisted of 594 single nucleotide polymorphism and 404 simple sequence repeat markers covering a genetic distance of 4225.7 cM. The RIL population was evaluated for grain yield (GY), spike number per m (SNPM), kernel number per spike (KNPS), and thousand-kernel weight (TKW) in three Oklahoma locations from 2001 to 2003. A total of 29 additive QTL (eight for GY, two for SNPM, five for KNPS, and 14 for TKW) were mapped on 13 chromosomes. Eight pairs of epistatic QTL were detected for different yield components: four for GY, two for KNPS, and two for TKW. Four additive QTL, including two for GY and two for KNPS, showed additive × environment interactions. QTL that were repeatable in multiple environments were identified for all traits except SNPM. Positive alleles were dispersed between the two parents for all traits, with 'Clark' contributing slightly more. Seven pleiotropic loci were co-localized for at least two traits. Interestingly, all co-localized loci overlapped for TKW, and four of them overlapped for GY. Thus, selecting QTL for TKW may simultaneously select for or against yield or other yield components in breeding. [ABSTRACT FROM AUTHOR]

The relation between high molecular weight glutenin subunit alleles and flour quality traits have been studied for 117 recombinant inbred lines (RILs) derived by single seed descend to F7 from a cross of Anza, a low quality cultivar, and Inia, a high quality cultivar, containing different alleles at 3 GLU-1 seed storage protein loci. RILs were classified by SDS-PAGE for the 8 possible combinations of the alleles. The allelic variation at the GLU-D1 locus accounted for most of the variation observed in SDS-sedimentation, mixing time and tolerance, and protein content. The GLU-D1 allele encoding the subunits 5+10 was superior to its allelic counterpart, encoding 2+ 12. All three loci had significant single locus additive effects for SDS-sedimentation volume and mixing tolerance. The additive effects of GLU-D1 locus on mixing time and protein content were also significant. The epistatic additive effects were mostly negative and with the exception of αAB and αAD for SDS-sedimentation volume were not significant.

To locate multiple interacting quantitative trait loci (QTL) influencing a trait of interest within experimental populations, usually methods as the Cockerham's model are applied. Within this framework, interactions are understood as the part of the joined effect of several genes which cannot be explained as the sum of their additive effects. However, if a change in the phenotype (as disease) is caused by Boolean combinations of genotypes of several QTLs, this Cockerham's approach is often not capable to identify them properly. To detect such interactions more efficiently, we propose a logic regression framework. Even though with the logic regression approach a larger number of models has to be considered (requiring more stringent multiple testing correction) the efficient representation of higher order logic interactions in logic regression models leads to a significant increase of power to detect such interactions as compared to a Cockerham's approach. The increase in power is demonstrated analytically for a simple two-way interaction model and illustrated in more complex settings with simulation study and real data analysis. [ABSTRACT FROM AUTHOR]

Background: Complex binary traits are influenced by many factors including the main effects of many quantitative trait loci (QTLs), the epistatic effects involving more than one QTLs, environmental effects and the effects of geneenvironment interactions. Although a number of QTL mapping methods for binary traits have been developed, there still lacks an efficient and powerful method that can handle both main and epistatic effects of a relatively large number of possible QTLs. Results: In this paper, we use a Bayesian logistic regression model as the QTL model for binary traits that includes both main and epistatic effects. Our logistic regression model employs hierarchical priors for regression coefficients similar to the ones used in the Bayesian LASSO linear model for multiple QTL mapping for continuous traits. We develop efficient empirical Bayesian algorithms to infer the logistic regression model. Our simulation study shows that our algorithms can easily handle a QTL model with a large number of main and epistatic effects on a personal computer, and outperform five other methods examined including the LASSO, HyperLasso, BhGLM, RVM and the single-QTL mapping method based on logistic regression in terms of power of detection and false positive rate. The utility of our algorithms is also demonstrated through analysis of a real data set. A software package implementing the empirical Bayesian algorithms in this paper is freely available upon request. Conclusions: The EBLASSO logistic regression method can handle a large number of effects possibly including the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTLs mapping for complex binary traits. [ABSTRACT FROM AUTHOR]

The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that nonadditive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and nonadditive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include nonadditive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and nonadditive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and nonadditive genetic effects, the broad-sense heritability (0.17 to 0.43) was more than twice as high as the narrow-sense heritability (0.04 to 0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07 to 0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of nonadditive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for nonadditive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including nonadditive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although nonadditive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The epistatic effects and genotype x environment interaction played an important role of plant genetics, evolution and heterosis, which had been confirmed by a large number of research. 100 - seed weight (100 - SW) was an important parameter in measuring soybean [ Glycine max (L) . Merr. ] yield and controlled by multiple genes. Soybean 100 quantitative trait loci (QTLs) were analyzed from 2006 to 2010 via recombination inbred lines ( RIL) population derived from a cross between Charleston and Dongnong 594. The objective of this study was to investigate epistatic effects and QE interaction effects of QTLs for 100 - SW by Inclusive Composite Interval Mapping (ICIM) and the mixed linear model. Finally, 16 QTLs were mapped. Among them, five 100 - SW QTLs with QE interaction contributed 0.11% ~0. 52% . And 8 QTLs pairs with epistatic effects were detected, accounting for 1.15% ~2. 59% of the general phenotypic variation. [ABSTRACT FROM AUTHOR]

The protein content of cultivated wheat ( Triticum aestivum L.) is an important determinant factor of the nutritional value of the grain and the technological properties and rheological properties of flour. In order to examine the genetic basis of protein content, we searched for grain protein content quantitative trait loci (QTLs) and flour protein content QTLs in a newly developed doubled haploid (DH) line and identified the genetic correlation between grain protein content and flour protein content in the same DH population. Both the DH population and its parental lines were evaluated for grain protein content and flour protein content in three field trials. Four additive effect QTLs, two pairs of epistatic QTLs, and two QTLs × environment (QE) interaction for grain protein content were identified. The model explained 51.52% of the phenotypic variation (PVE), with epistatic effects being better explained by the higher PVE than additive effects. Four additive effect QTLs, five pairs of epistatic QTLs, and one QE were detected for flour protein content. The model explained 45.8% of the PVE. Of the 15 QTLs identified, three additive QTLs and one pair of epistatic QTLs were determined for both grain protein content and flour protein content; of these, the QTLs for protein content were considered to be more 'stable' than those detected for only grain protein content or for only flour protein content. The data reported here may be useful for manipulating the QTLs for protein content by marker-assisted selection in future wheat breeding programs. [ABSTRACT FROM AUTHOR]

Grain chalkiness is one of the important appearance qualities in rice marketing. But it is a complex trait, controlled by polygenes and easily influenced by the environment. Genetic analysis and QTL detection was carried out on six characteristics of grain chalkiness consisting of the percentage of chalkiness (PGC), white belly (PWB) and white core grains (PWC), and the area of chalkiness (CA), white belly (WBA) and white core (WCA) in brown rice. A total of 16 main-effect QTLs associated with chalkiness characteristics of brown rice were mapped on seven chromosomes over two years. Among them, qPGC7.1 and qPWB7.2 were simultaneously located on chromosome 7 flanked by 7038 and 7042 at LOD scores 4.34 and 3.76, while qPWC2.1 and qWCA2.1 were simultaneously located on chromosome 2 flanked by RM492 and RM324 with LOD scores of 2.50 and 3.39. Twelve epistatic combinations were detected for five chalkiness characteristics except for CA. Results indicated that WBA was mainly influenced by the additive effects of main-effect QTLs. PGC and PWC were affected by the effects of epistatic QTLs and the interactions between additive-by-additive effects and the environment. The effects of epistatic QTLs and the main-effect QTLs played important roles on CA, PWB and WCA. For the genetic improvement of grain chalkiness in breeding system, more attention should be paid to epistatic effects and the additive effects of main-effect QTLs. [ABSTRACT FROM AUTHOR]

Cooking quality in rice grains is a complex trait which requires improvement. Earlier reports show varying genetic influence on these traits, except for a common agreement on waxy ( Wx) and alkali degeneration ( Alk) loci on chromosome 6. The present study involved 86 doubled haploid lines derived from an indica × japonica cross involving IR64 and Azucena. Grain parameters viz., raw grain length (RGL), raw grain breadth (RGB), cooked grain length (CGL), cooked grain breadth (CGB), gelatinization temperature (GT), grain shape (RGS), length elongation ratio (LER) and breadth expansion ratio (BER) were subjected to mixed model mapping of quantitative trait loci (QTL). Segregation data of 175 markers covering a distance of 2395.5 cM spanning the entire genome were used. Fifteen main effect QTLs were detected spread over the genome, except on chromosomes 4, 8 and 11. Thirty epistatic interactions significantly influencing the traits were detected. Twelve of the main effect QTLs were involved in epistatic interactions. One main effect QTL associated with LER was detected near Alk locus. QTLs located for grain length on chromosomes 9 and 10 are reported for the first time. Detection of many epistatic loci and involvement of main effect QTLs in interactions demand for judicious selection of QTLs in marker-assisted selection programmes. [ABSTRACT FROM AUTHOR]

Flour color is an important trait in the assessment of flour quality for the production of many end products. In this study, quantitative trait loci (QTLs) with additive effects, epistatic effects, and QTL × environment (QE) interactions for flour color in bread wheat ( Triticum aestivum L.) were studied, using a set of 168 doubled haploid (DH) lines derived from a Huapei 3 × Yumai 57 cross. A genetic map was constructed using 283 simple sequence repeats (SSR) and 22 expressed sequence tags (EST)-SSR markers. The DH and parents were evaluated for flour color in three environments. QTL analyses were performed using QTLNetwork 2.0 software based on a mixed linear model approach. A total of 18 additive QTLs and 24 pairs of epistatic QTLs were detected for flour color, which were distributed on 19 of the 21 chromosomes. One major QTL, qa1B, closely linked to barc372 0.1 cM, could account for 25.64% of the phenotypic variation of a* without any influence from the environments. So qa1B could be used in the molecular marker-assisted selection (MAS) in wheat breeding programs. The results showed that both additive and epistatic effects were important genetic basis for flour color, and were also sometimes subject to environmental modifications. The information obtained in this study should be useful for manipulating the QTLs for flour color by MAS in wheat breeding programs. [ABSTRACT FROM AUTHOR]

Quantitative trait loci (QTL) and their additive, dominance and epistatic effects play a critical role in complex trait variation. It is often infeasible to detect multiple interacting QTL due to main effects often being confounded by interaction effects. Positioning interacting QTL within a small region is even more difficult. We present a variance component approach nested in an empirical Bayesian method, which simultancously takes into account additive, dominance and epistatic effects due to multiple interacting QTL. The covariance structure used in the variance component approach is based on combined linkage disequilibrium and linkage (LDL) information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously fine map interacting QTL using the proposed approach. The present method combined with LDL information can efficiently detect QTL and their dominance and epistatic effects, making it possible to simultaneously fine map main and epistatic QTL. [ABSTRACT FROM AUTHOR]

Abstract: Early simulation studies have showed that the inclusion of epistatic components (especially the additive-by-additive effects) into marker-assisted selection (MAS) can improve selection efficiency for a short-term breeding program. In this study I extend Lande and Thompson''s theory to incorporate both additive and non-additive effects into MAS with reference to the mass selection case. Four different indices are analytically examined in terms of the type of genetic components involved in the marker scores: phenotype-, general combining ability (GCA)-, and GCA and reciprocal effects-based marker scores. The phenotype-based marker index is applicable to any population of non-random mating, while the other three indices are applicable to the synthetic population derived from diallel crosses. All these indices may have higher selection efficiencies than the index with solely additive effects-associated markers as long as the detectable transient non-additive effects are present. The improvement in selection efficiency depends on the magnitude of non-additive variances and the proportion of them explained by markers. The index with the phenotype-based marker scores operates on the whole of the additive and non-additive effects, and has the largest selection efficiency. The indices with the GCA-based marker scores operate only on additive and additive-by-additive genetic variation and have relatively small selection efficiencies. Inclusion of the markers from organelle genomes can also increase selection efficiency, depending upon the proportion of the total genetic variation attributable to organelle genomes and the proportion of them explained by organelle genomic markers. Sharing of markers among different marker scores does not facilitate the improvement of selection efficiency. [Copyright &y& Elsevier]

QTLs with epistatic effects and environmental interaction effects for the developmental behavior of plant height in rice were studied by conventional and conditional methods for quantitative trait loci (QTLs) by mapping with a doubled-haploid population of 123 lines from IR64/Azucena in three environments. The results showed that epistatic effects were important and most epistasis could be detected only by conditional QTL mapping, while most non–epistatic QTLs could be detected by both conventional and conditional methods. Many modificative QTLs showed only epistatic effects without their own additive effects at some stages. QTL×environment (QE) interaction effects were detected more often than QTL main effects for plant-height behavior, which might indicate that gene expression could be greatly affected by the environment. No QTLs had effects during the whole of ontogeny. Conditional QTL mapping might be a valid way to reveal dynamic gene expression for the development of quantitative traits, especially for epistatic effects. [ABSTRACT FROM AUTHOR]

The pathophysiology of sickle (SS) cell vasoocclusion is derived from the presence of hemoglobin S (HbS) which forms polymeric fibers in the deoxygenated state. Nevertheless, phenotypic expression of sickle cell disease (i.e., clinical severity) shows marked individual variations and is influenced by genetic modifiers such as epistatic effects of linked and unlinked genes. Furthermore, the polymerization of HbS is central but not the only event, and is more likely a consequence of disruptions of the steady state of flow. The available evidence indicates that the vasoocclusive crisis is a microcirculatory event in which multiple factors could be involved. We present a model of vasoocclusion as a two step process in which adhesion of deformable cells occurs first, followed by obstruction induced by less deformable SS cells. This review discusses, in addition, rheologic and microcirculatory behavior of SS erythrocytes and the interacting role of vascular factors, red cell heterogeneity, deoxygenation rates, and red cell-endothelial interactions in the pathophysiology of SS cell vasoocclusion. [ABSTRACT FROM AUTHOR]

The development of molecular markers has recently raised expectations for their application in selection programs. However, some questions related to quantitative trait loci (QTL) identification are still unanswered. The objectives of this paper are (1) to develop statistical genetic models for detecting and locating on the genome multi-QTL with additive, dominance and epistatic effects using multiple linear regression analysis in the backcross and F generations from the cross of two inbred lines; and (2) to discuss the bias caused by linked and unlinked QTL on the genetic estimates. Non-linear models were developed for different backcross and F generations when both epistasis and no epistasis were assumed. Generation analysis of marked progenies is suggested as a way of increasing the number of observations for the estimates without additional cost for molecular scoring. Some groups of progenies can be created in different generations from the same scored individuals. The non-linear models were transformed into approximate multivariate linear models to which combined stepwise and standard regression analysis could be applied. Expressions for the biases of the marker classes from linked QTL were obtained when no epistasis was assumed. When epistasis was assumed, these expressions increased in complexity, and the biases were caused by both linked and unlinked QTL. [ABSTRACT FROM AUTHOR]

• Tomato germination performance was tested at 25 °C and 15 °C. • Nine additive-effect QTLs for germination speed were detected on chromosomes 1–3. • QTLs on chr. 1 and 2 were affected by temperature; QTLs on chr. 3 were stable. • An additive QTL with environmental interaction was found on chr. 1. • An epistatic QTL with no additive effect was found on chr. 4. Rapid germination and early establishment of seedlings under unfavorable environmental conditions are desirable traits for seedling production. Quantitative trait locus (QTL) analysis of germination speed was conducted at 15 and 25 °C using a backcross inbred line family. Final germination percentage (FGP), days to 50 % and 90 % of FGP (GT 50 and GT 90 , respectively), mean germination time (MGT), and covariance of germination time were determined. The results indicated 11 additive germination-related QTLs on chromosomes 1–3, and 11. GT 50 , GT 90 , and MGT QTLs detected on chromosomes 1–3 were co-located, of which, gt 50 1 , gt 90 1 , and mgt1 had positive additive effects. A single epistatic QTL was detected, but no QTL with additive effect was found on chromosome 4 in the present study, which was not consistent with the results of previous studies. To reexamine the effect of QTLs on chromosomes 1 and 4, we constructed one and three near-isogenic lines (NILs) carrying a substituted chromosome segment from Solanum pimpinellifolium (SP) in which putative QTLs were detected on chromosomes 1 and 4. NIL experiment results indicated that a chromosomal segment from SP between TGS0308 and C2_At5g49480 markers on chromosome 1 shortened and prolonged germination time at 15 °C and 25 °C, respectively, due to QTL-by-environmental interactions. However, the substituted segment between SSR603 and TGS0411 markers on chromosome 4 did not affect seed germination. In conclusion, the QTL on chromosome 1 is useful for breeding cultivars that are able to germinate at low temperatures. [ABSTRACT FROM AUTHOR]

Aim: To search for genetic mechanisms of facial emotion recognition (FER) impairment, one of the features of schizophrenia that affects social adaptation of patients. Based on the view implicating the interplay between dopaminergic and glutamatergic systems into the pathogenesis of schizophrenia, authors explored the interaction effects of the C366G polymorphism in the GRIN2B gene encoding NMDA receptor subunit NR2B with ANKK1/DRD2 Taq1A and 48-VNTR DRD4 polymorphisms on FER., Material and Methods: GRIN2B -DRD2 interaction effects were studied in a sample of 237 patients and 235 healthy controls, GRIN2B - DRD4 in 268 patients and 208 controls., Results and Conclusion: Both effects were significant in combined samples of patients and controls (GRIN2B X DRD2, F=4.12, p=0.043; GRIN2B X DRD4, F=6.43, p=0.012). Further analysis confirmed the interaction effect of GRIN2B and DRD2 polymorphisms on FER in patients with schizophrenia. In patients with a less efficient allele of the DRD2 in the absence of the minor allele of the GRIN2B C366G polymorphism, the results were close to normal values while patients with minor alleles of both polymorphisms showed the worst results. This finding is in line with the conceptions on a possible role of NMDA-receptor hypofunction and D2-mediated regulation of NMDA-receptor activity in FER impairments in schizophrenia.