Significant Epistatic Effects Research Articles

Genome-Wide Network Analysis of Above- and Below-Ground Co-growth in Populus euphratica.

Tree growth is the consequence of developmental interactions between above- and below-ground compartments. However, a comprehensive view of the genetic architecture of growth as a cohesive whole is poorly understood. We propose a systems biology approach for mapping growth trajectories in genome-wide association studies viewing growth as a complex (phenotypic) system in which above- and below-ground components (or traits) interact with each other to mediate systems behavior. We further assume that trait-trait interactions are controlled by a genetic system composed of many different interactive genes and integrate the Lotka-Volterra predator-prey model to dissect phenotypic and genetic systems into pleiotropic and epistatic interaction components by which the detailed genetic mechanism of above- and below-ground co-growth can be charted. We apply the approach to analyze linkage mapping data of Populus euphratica, which is the only tree species that can grow in the desert, and characterize several loci that govern how above- and below-ground growth is cooperated or competed over development. We reconstruct multilayer and multiplex genetic interactome networks for the developmental trajectories of each trait and their developmental covariation. Many significant loci and epistatic effects detected can be annotated to candidate genes for growth and developmental processes. The results from our model may potentially be useful for marker-assisted selection and genetic editing in applied tree breeding programs. The model provides a general tool to characterize a complete picture of pleiotropic and epistatic genetic architecture in growth traits in forest trees and any other organisms.

Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies.

Mate-allocation strategies in breeding programs can improve progeny performance by harnessing non-additive genetic effects. These approaches prioritise predicted progeny merit over parental breeding value, making them particularly appealing for clonally propagated crops such as sugarcane. We conducted a comparative analysis of mate-allocation strategies, exploring utilising non-additive and heterozygosity effects to maximise clonal performance with schemes that solely consider additive effects to optimise breeding value. Using phenotypic and genotypic data from a population of 2,909 clones evaluated in final assessment trials of Australian sugarcane breeding programs, we focused on three important traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and Fibre. By simulating families from all possible crosses (1,225) with 50 progenies each, we predicted the breeding and clonal values of progeny using two models: GBLUP (considering additive effects only) and extended-GBLUP (incorporating additive, non-additive, and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among selected parents. Compared to breeding value-based approaches, mate-allocation strategies based on clonal performance yielded substantial improvements, with predicted progeny values increasing by 57% for TCH, 12% for CCS, and 16% for fibre. Our simulation study highlights the effectiveness of mate-allocation approaches that exploit non-additive and heterozygosity effects, resulting in superior clonal performance. However, there was a notable decline in additive gain, particularly for TCH, likely due to significant epistatic effects. When selecting crosses based on clonal performance for TCH, the inbreeding coefficient of progeny was significantly lower compared to random mating, underscoring the advantages of leveraging non-additive and heterozygosity effects in mitigating inbreeding depression. Thus, mate-allocation strategies are recommended in clonally propagated crops to enhance clonal performance and reduce the negative impacts of inbreeding.

Genome-wide association studies for epistatic genetic effects on fertility and reproduction traits in Holstein cattle.

Non-additive genetic effects are well known to play an important role in the phenotypic expression of complex traits, such as fertility and reproduction. In this study, a genome scan was performed using 41,640 single nucleotide polymorphism (SNP) markers to identify genomic regions associated with epistatic (additive-by-additive) effects in fertility and reproduction traits in Holstein cattle. Nine fertility and reproduction traits were analysed on 5825 and 6090 Holstein heifers and cows with phenotypes and genotypes, respectively. The Marginal Epistasis Test (MAPIT) was used to identify SNPs with significant marginal epistatic effects at a chromosome-wise 5% and 10% false discovery rate (FDR) level. The -log10 (p) values were adjusted by the genomic inflation factor (λ) to correct for the potential bias on the p-values and minimize the possible effects of population stratification. After adjustments, MAPIT enabled the identification of genomic regions with significant marginal epistatic effects for heifers on BTA5 for age at first insemination, BTA3 and BTA24 for non-return rate (NRR); BTA16 and BTA28 for gestation length (GL); BTA1, BTA4 and BTA17 for stillbirth (SB). For the cow traits, MAPIT enabled the identification of regions on BTA11 for GL, BTA11 and BTA16 for SB and BTA19 for calf size (CZ). An additional approach for mapping epistasis in a genome-wide association study was also proposed, in which the genome scan was performed using estimates of epistatic values as the input pseudo-phenotypes, computed using single-trait animal models. Significant SNPs were identified at the chromosome-wise 5% and 10% FDR levels for all traits. For the heifer traits, significant regions were found on BTA7 for AFS; BTA12 for NRR; BTA14 and BTA19 for GL; BTA19 for calving ease (CE); BTA5, BTA24, BTA25 and in the X chromosome for SB; BTA23 and in the X chromosome for CZ and in the X chromosome for the number of services (NS). For the cow traits, significant regions were found on BTA29 and in the X chromosome for NRR, BTA11, BTA16 and in the X chromosome for SB, BTA2 for GL, BTA28 for CZ, BTA19 for calving to first insemination, and in the X chromosome for NS and first insemination to conception. The results suggest that the epistatic genetic effects are likely due to many loci with a small effect rather than few loci with a large effect and/or a single SNP marker alone do not capture the epistatic effects well. The genomic architecture of fertility and reproduction traits is complex, and these results should be validated in independent dairy cattle populations and using alternative statistical models.

The control of genetic parameters on grain yield and its components in hexaploid wheat

Controlling of genetical parameters on grain yield and its components were study in six generation (P1,P2,F1,F2,B1 and B2) for two crosses of hexaploid wheat, Triticum aestivum L. (Iba-99 x Reyna-27) and (Abochareeb-3 x Jawaher-20) to estimate: gene action parameters, components of genetic variance, environmental variance, average degree of dominance, broad sense heritability, narrow sense heritability and expected genetic advance from selection in F2. Two models were applied in analyzing the component of generation means and the total phenotypic variance for studied traits in six generations for each cross were analyzed. The results showed that: The three parameter genetics models were adequate for the inheritance of spike number and grain yield in tow crosses and there were significant additive, dominance and epistatic effects on the other traits. Over dominance for studied traits, but partial for 100 grain weight in the first cross, plant height and spike length in the second cross. Narrow sense heritability and expected genetic advance were high for most traits.

Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs.

Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.

Genetic mapping of powdery mildew resistance genes in wheat landrace Guizi 1 via genotyping by sequencing.

Wheat (Triticum aestivum L.) powdery mildew (Pm), which caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease worldwide that causes severe yield losses in wheat. Resistant wheat cultivars easily lose their ability to effectively resist newly emerged Bgt strains; therefore, identifying new resistance genes is necessary for breeding resistant cultivars. Guizi 1 (GZ1) is a Chinese wheat cultivar with moderate and stable resistance to Pm. Genetic analysis indicated that the Pm resistance of GZ1 was controlled by a single dominant gene, designated PmGZ1. In total, 110 F2 individual plants and their 2 parents were subjected to genotyping by sequencing (GBS), which yielded 23,134 high-quality single-nucleotide polymorphisms (SNPs). The SNP distributions across the 21 chromosomes ranged from 134 on chromosome 6D to 6288 on chromosome 3B. Chromosome 6A has 1866 SNPs, among which 16 are physically located between positions 307,802,221 and 309,885,836 in an approximate 2.3-cM region; this region also had the greatest SNP density. The average map distance between SNP markers was 0.1cM. A quantitative trait locus (QTL) with a significant epistatic effect on Pm resistance was mapped to chromosome 6A. The logarithm of odds (LOD) value of PmGZ1 was 34.8, and PmGZ1 was located within the confidence interval marked by chr6a-307802221 and chr6a-309885836. Moreover, 74.7% of the phenotypic variance was explained by PmGZ1. Four candidate genes (which encoded two TaAP2-A and two actin proteins) were annotated maybe as resistance genes. The present results provide valuable information for wheat genetic improvement, QTL fine mapping, and candidate gene validation.

Precise mapping of QTL for Hessian fly resistance in the hard winter wheat cultivar 'Overland'.

A major QTL for Hessian fly resistance was precisely mapped to a 2.32 Mb region on chromosome 3B of the US hard winter wheat cultivar 'Overland'. The Hessian fly (HF, Mayetiola destructor) is a destructive insect pest of wheat in the USA and worldwide. Deploying HF-resistant cultivars is the most effective and economical approach to control this insect pest. A population of 186 recombinant inbred lines (RILs) was developed from 'Overland' × 'Overley' and phenotyped for responses to HF attack using the HF biotype 'Great Plains'. A high-density genetic linkage map was constructed using 1,576 single nucleotide polymorphism (SNP)markers generated by genotyping-by-sequencing(GBS). Two quantitative trait loci (QTLs) with a significant epistatic effect on HF resistance were mapped to chromosomes 3B (QHf.hwwg-3B) and 7A (QHf.hwwg-7A) in Overland, which are located in similar chromosome regions as found for H35 and H36 in the cultivar 'SD06165', respectively. QHf.hwwg-3B showed a much larger effect on HF resistance than QHf.hwwg-7A. Five and four GBS-SNPs, respectively, in the QHf.hwwg-3B and QHf.hwwg-7A QTL intervals were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. QHf.hwwg-3B was precisely mapped to a 2.32Mb interval (2,479,314-4,799,538bp) using near-isogenic lines (NILs) and RILs that have recombination within the QTL interval. The US winter wheat accessions carrying contrasting alleles at KASP markers KASP-3B4525164, KASP-7A47772047 and KASP-7A65090410 showed significant difference in HF resistance. The combination of the two KASP markers KASP-3B3797431 and KASP-3B4525164 is near-diagnostic for the detection ofQHf.hwwg-3B in a US winter wheat panel and can be potentially used for screening the QTL in breeding programs.

The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach

The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. Understanding and manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (β/⍺)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.

Epistatic Effects of Six Candidate Genes on Fatty Acid Composition in Korean Native Chicken

Fatty acid composition is an important economic trait that affects meat flavor. Several genes that influence fatty acid composition in meat have been investigated. In a previous study, we identified 51 significant SNP × SNP interactions (<i>P</i>≤0.05) between nine SNPs of six candidate genes (<i>DEGS1</i>, <i>ELOVL6</i>, <i>FABP3</i>, <i>FABP4</i>, <i>FASN</i>, and <i>SCD</i>) on meat fatty acid composition in Korean native chicken. This study further investigated the patterns of the SNP × SNP interactions to understand how they affect the fatty acid content in thigh and breast meat of Korean native chicken. The significant epistatic effects of SNP combinations showed various patterns for each fatty acid trait. The results of this study suggest that the respective additive effects of each SNP on polygenic traits, such as fatty acid composition, should be considered in combination with the epistatic effect of SNP combinations in animal breeding programs. The findings of this study have provided new genetic information for improving meat quality, especially the fatty acid composition, of Korean native chicken.

Marsh Spot Disease and Its Causal Factor, Manganese Deficiency in Plants: A Historical and Prospective Review

This review provides an examination of the marsh spot disease in beans and the roles played by its causal factor, manganese (Mn) deficiency. The discovery of the marsh spot disease, its relation with Mn deficiency, and how it can be treated are discussed. Mn serves as a cofactor and a catalyst in various metabolic processes in different cell compartments, such as the oxygen-evolving complex of photosystem II (PSII) or reactive oxygen species scavenging. Some major quantitative trait loci (QTL) and putative candidate genes associated with Mn content in plants, especially in plant seeds, have been identified. Marsh spot disease in cranberry common bean is controlled by several major genes with significant additive and epistatic effects. They provide valuable clues for QTL candidate gene prediction and an improved understanding of the genetic mechanisms responsible for marsh spot resistance in plants.

Genetic Studies on the Inheritance of Storage-Induced Cooking Time in Cowpeas [Vigna unguiculata (L.) Walp

Cowpeas provide food and income for many small-holder farmers in Africa. Cowpea grains contain substantial quantities of protein, carbohydrates, vitamins, and fiber. In areas where subsistence farming is practiced, cowpea’s protein is cheaper than that obtained from other sources such as fish, meat, poultry or dairy products and combines well with cereal grains in diets. However, long-cooking times, typical of many grain legumes, is a major limitation to the utilization of cowpeas especially among the low-income and growing middle-income population of Africa. Long periods of cooking cowpeas lead to loss of nutrients, loss of useful time and increased greenhouse gas emission through increased burning of firewood. Fast-cooking cowpeas has the potential to deliver highly nutritious food to the hungry within shorter periods, encourage less use of firewood, improve gender equity, increase the consumption of cowpeas, trigger an increase in demand for cowpeas and thus incentivize cowpea production by smallholder farmers in Sub-Saharan Africa. In this study, the inheritance of storage-induced cooking time in cowpeas was investigated. Two sets of bi-parental crosses were conducted involving three cowpea genotypes: CRI-11(1)-1, C9P(B) and TVu7687. Generation means from six generations were used to determine the phenotypic and genotypic variances and coefficients of variation. Broad and narrow sense heritabilities and genetic advance percentage of mean were estimated. Generation mean analysis showed that additive, dominant, additive–additive, additive–dominant, and dominant–dominant gene actions were significant (p < 0.001). Fast-cooking trait was dominant over the long-cooking trait. Broad sense heritability for crosses C9P(B) × CRI-11(1)-1 and TVu7687 × CRI-11(1)-1 were 0.94 and 0.99 respectively while narrow sense heritabilities were 0.84 and 0.88 respectively. Genetic advances were 27.09 and 40.40 respectively. High narrow-sense heritabilities and moderate genetic advance for the fast-cooking trait indicated the presence of additive genes in the trait and the possibility of introgressing the trait into farmer-preferred varieties using conventional selection methods. However, due to significant epistatic gene effects observed, effective selection for fast-cooking trait would be appropriate at advanced generations.

Genetic dissection of stem WSC accumulation and remobilization in wheat (Triticum aestivum L.) under terminal drought stress

BackgroundThe accumulation and remobilization of stem water soluble carbohydrates (WSC) are determinant physiological traits highly influencing yield potential in wheat against drought stress. However, knowledge gains of the genetic control are still limited. A hexaploid wheat population of 120 recombinant inbred lines were developed to identify quantitative trait loci (QTLs) and to dissect the genetic basis underlying eight traits related to stem WSC under drought stress (DS) and well-watered (WW) conditions across three environments.ResultsAnalysis of variance (ANOVA) revealed larger environmental and genotypic effects on stem WSC-related traits, indicating moderate heritabilities of 0.51–0.72. A total of 95 additive and 88 pairs of epistatic QTLs were identified with significant additive and epistatic effects, as well as QTL× water environmental interaction (QEI) effects. Most of additive QTLs and additive QEIs associated with drought-stressed environments functioned genetic effects promoting pre-anthesis WSC levels and stem WSC remobilization to developing grains. Compared to other genetic components, both genetic effects were performed exclusive contributions to phenotypic variations in stem WSC-related traits. Nineteen QTL clusters were identified on chromosomes 1B, 2A, 2B, 2D, 3B, 4B, 5A, 6A, 6B and 7A, suggestive of the genetic linkage or pleiotropy. Thirteen additive QTLs were detectable repeatedly across two of the three water environments, indicating features of stable expressions. Some loci were consistent with those reported early and were further discussed.ConclusionStem WSC-related traits were inherited predominantly by additive and QEI effects with a moderate heritability. QTL cluster regions were suggestive of tight linkage or pleiotropy in the inheritance of these traits. Some stable and common loci, as well as closely linked molecular markers, had great potential in marker-assisted selection to improve stem WSC-related traits in wheat, especially under drought-stressed environments.

Association analysis of loci implied in "buffering" epistasis.

The existence of buffering mechanisms is an emerging property of biological networks, and this results in the buildup of robustness through evolution. So far, there are no explicit methods to find loci implied in buffering mechanisms. However, buffering can be seen as interaction with genetic background. Here we develop this idea into a tractable model for quantitative genetics, in which the buffering effect of one locus with many other loci is condensed into a single statistical effect, multiplicative on the total additive genetic effect. This allows easier interpretation of the results and simplifies the problem of detecting epistasis from quadratic to linear in the number of loci. Using this formulation, we construct a linear model for genome-wide association studies that estimates and declares the significance of multiplicative epistatic effects at single loci. The model has the form of a variance components, norm reaction model and likelihood ratio tests are used for significance. This model is a generalization and explanation of previous ones. We test our model using bovine data: Brahman and Tropical Composite animals, phenotyped for body weight at yearling and genotyped at high density. After association analysis, we find a number of loci with buffering action in one, the other, or both breeds; these loci do not have a significant statistical additive effect. Most of these loci have been reported in previous studies, either with an additive effect or as footprints of selection. We identify buffering epistatic SNPs present in or near genes reported in the context of signatures of selection in multi-breed cattle population studies. Prominent among these genes are those associated with fertility (INHBA, TSHR, ESRRG, PRLR, and PPARG), growth (MSTN, GHR), coat characteristics (KIT, MITF, PRLR), and heat resistance (HSPA6 and HSPA1A). In these populations, we found loci that have a nonsignificant statistical additive effect but a significant epistatic effect. We argue that the discovery and study of loci associated with buffering effects allow attacking the difficult problems, among others, of the release of maintenance variance in artificial and natural selection, of quick adaptation to the environment, and of opposite signs of marker effects in different backgrounds. We conclude that our method and our results generate promising new perspectives for research in evolutionary and quantitative genetics based on the study of loci that buffer effect of other loci.

A Joint Segregation Analysis of the Inheritance of Fertility Restoration for Cytoplasmic Male Sterility in Pepper

A cytoplasmic male sterility (CMS) system is one of the most efficient ways to produce F1 hybrid seeds in pepper (Capsicum annuum). Restorer-of-fertility (Rf) genes are a critical component within the CMS/Rf system. The inheritance of Rf genes in pepper by joint segregation analysis was examined. The inheritance of Rf genes in the two progenies was controlled by two major additive-dominant epistatic genes and additive-dominant epistasis polygene. The two major genes had high additive effects and dominant effects. In addition, there existed significant epistatic effects between the two major genes. The major genes had high heritability in F2, BC1, and BC2 generations. Also, the fertility restorer characteristic can be selected during early generations of the breeding cycle.

TaVrt2, an SVP-like gene, cooperates with TaVrn1 to regulate vernalization-induced flowering in wheat.

TaVrn1, encoding a MADS-box transcription factor (TF), is the central regulator of wheat vernalization-induced flowering. Considering that the MADS-box TF usually works by forming hetero- or homodimers, we conducted yeast-two-hybrid screening and identified an SVP-like MADS-box protein TaVrt2 interacting with TaVrn1. However, the specific function of TaVrt2 and the biological implication of its interaction with TaVrn1 remained unknown. We validated the function of TaVrt2 and TaVrn1 by wheat transgenic experiments and their interaction through multiple protein-binding assays. Population genetic analysis also was used to display their interplay. Transcriptomic sequencing and chromatin immunoprecipitation assays were performed to identify their common targets. TaVrt2 and TaVrn1 are flowering promoters in the vernalization pathway and interact physically in vitro, in planta and in wheat cells. Additionally, TaVrt2 and TaVrn1 were significantly induced in leaves by vernalization, suggesting their spatio-temporal interaction during vernalization. Genetic analysis indicated that TaVrt2 and TaVrn1 had significant epistatic effects on flowering time. Furthermore, native TaVrn1 was up-regulated significantly in TaVrn1-OE (overexpression) and TaVrt2-OE lines. Moreover, TaVrt2 could bind with TaVrn1 promoter directly. A TaVrt2-mediated positive feedback loop of TaVrn1 during vernalization was proposed, providing additional understanding on the regulatory mechanism underlying vernalization-induced flowering.

Identification of quantitative trait loci underlying resistance of soybean to Fusarium graminearum

AbstractFusarium graminearum could cause serious yield loss of soybean. Host resistance could offer an economical and effective way to control F. graminearum. The aims of this study were to identify and confirm quantitative trait loci (QTLs) underlying resistance to F. graminearum, and to analyse the genetic effects of pyramid resistance QTL on resistance level. A total of 140 F2:14 recombinant inbred lines (RILs) were constructed via the cross between 'Hefeng 25' (moderate resistance to F. graminearum) and 'Conrad' (resistance to F. graminearum). The molecular genetic linkage map was constructed based on 164 simple sequence repeat (SSR) markers. A total of seven QTLs underlying F. graminearum resistance, located on six chromosomes, were identified. Among these seven identified QTLs, beneficial allele of qFG‐1, qFG‐2 and qFG‐3 derived from 'Hefeng 25' and beneficial allele of qFG‐4, qFG‐5, qFG‐6, qFG‐7 derived from 'Conrad'. Of these seven identified QTLs, qFG‐1, qFG‐3, qFG‐4 and qFG‐5 were novel for F. graminearum resistance. Four pairs of QTLs with significant epistatic effects were found. The accumulation of resistance QTL was positively correlated with decreases in disease severity index, which was valuable for improving efficiency of marker‐assistant breeding in F. graminearum resistance.

Estimation of additive and epistatic gene effects for phenotypic and biochemical traits in double hyploid lines of winter rape seed ,(Brassica napus L.)

In this paper 60 doubled haploid lines of winter oilseed rape (Brassica napus L.) were studied. Genetic parameters as additive and epistatic effects were estimated for 24 traits. The results indicate the importance of both these effects for number of branches per plant, number of siliques per plant, linoleic acid, total of glucosinolates, total of alkenyl glucosinolates, gluconapin, glucobrassicanapin, progoitryn, napoleiferin and indolyl in both years of this study. Statistically significant epistatic effect and non-significant additive effect for thousand seed weight means that this trait was determined by genes with small individual effects but strong gene by gene interaction effects. Confounding epistatic effects in models suggested that inheritance of this trait is complex and polygenic.

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders.

Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C > T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by >94% of Tibetans but absent or in low frequencies (<3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10−5), red blood cell count (p = 5.72 × 10−7) and hematocrit (p = 2.57 × 10−6). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.

Mapping QTLs with main and epistatic effect on Seri ‘M82 × Babax‘wheat population under salt stress

The population of this research included 167 recombinant inbred lines (RILs) derived from a Seri/Babax cross. In order to map and visualize the genetic architecture of the agricultural traits, an experiment was conducted in an alpha lattice under normal (2 ds m−1) and saline (12–14 ds m−1) conditions at the Research Farm of Agricultural and Natural Resource Station of Zabol, Iran for 2 years (2012–2013). in this study, a total of 20 QTLs with additive effects and of 24 QTLs with epistatic effects for these traits were identified and distributed across all 21 chromosomes of wheat. Twenty stable QTL regions were detected on chromosomes 1B, 1D, 2A, 3B, 4A, 6A, 7A and 7D, which could significantly affect traits in all experiments. The QTLs detected on chromosomes 7D and 1D were not only significant and consistent but also co-localized for days to heading and days to anthesis. Several colocalized and additive QTLs with variability in QTL regions of chromosome 3B were also identified, which included the QTLs for final dry biomass (BY, straw + grain), grain yield and water-soluble carbohydrate content. The only two QTLs on chromosome 1B identified for the two traits were chlorophyll Florence (FV/FM) and thousand grain weight in different regions. Most of the identified QTLs had significant additive and epistatic effects with QTL and environments (QEIs) interactions.

Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans.

Previous studies have found that fecundity is a multigenic trait regulated, in part, by mitochondrial-nuclear (mit-n) genetic interactions. However, the identification of specific nuclear genetic loci or genes interacting with the mitochondrial genome and contributing to the quantitative trait fecundity is an unsolved issue. Here, a panel of recombinant inbred advanced intercrossed lines (RIAILs), established from a cross between the N2 and CB4856 strains of C. elegans, were used to characterize the underlying genetic basis of mit-n genetic interactions related to fecundity. Sixty-seven single nucleotide polymorphisms (SNPs) were identified by association mapping to be linked with fecundity among 115 SNPs linked to mitotype. This indicated significant epistatic effects between nuclear and mitochondria genetics on fecundity. In addition, two specific nuclear genetic loci interacting with the mitochondrial genome and contributing to fecundity were identified. A significant reduction in fecundity was observed in the RIAILs that carried CB4856 mitochondria and a N2 genotype at locus 1 or a CB4856 genotype at locus 2 relative to the wild-type strains. Then, a hybrid strain (CNC10) was established, which was bred as homoplasmic for the CB4856 mtDNA genome and N2 genotype at locus 1 in the CB4856 nuclear background. The mean fecundity of CNC10 was half the fecundity of the control strain. Several functional characteristics of the mitochondria in CNC10 were also influenced by mit-n interactions. Overall, experimental evidence was presented that specific nuclear genetic loci or genes have interactions with the mitochondrial genome and are associated with fecundity. In total, 18 genes were identified using integrative approaches to have interactions with the mitochondrial genome and to contribute to fecundity.