Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.).

Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.

Genome-wide dissection and haplotype analysis identified candidate loci for nitrogen use efficiency under drought conditions in winter wheat.

Climate change causes extreme conditions like prolonged drought, which results in yield reductions due to its effects on nutrient balances such as nitrogen uptake and utilization by plants. Nitrogen (N) is a crucial nutrient element for plant growth and productivity. Understanding the mechanistic basis of nitrogen use efficiency (NUE) under drought conditions is essential to improve wheat (Triticum aestivum L.) yield. Here, we evaluated the genetic variation of NUE-related traits and photosynthesis response in a diversity panel of 200 wheat genotypes under drought and nitrogen stress conditions to uncover the inherent genetic variation and identify quantitative trait loci (QTLs) underlying these traits. The results revealed significant genetic variations among the genotypes in response to drought stress and nitrogen deprivation. Drought impacted plant performance more than N deprivation due to its effect on water and nutrient uptake. GWAS identified a total of 27 QTLs with a significant main effect on the drought-related traits, while 10 QTLs were strongly associated with the NUE traits. Haplotype analysis revealed two different haplotype blocks within the associated region on chromosomes 1B and 5A. The two haplotypes showed contrasting effects on N uptake and use efficiency traits. The in silico and transcript analyses implicated candidate gene coding for cold shock protein. This gene was the most highly expressed gene under several stress conditions, including drought stress. Upon validation, these QTLs on 1B and 5A could be used as a diagnostic marker for NUE and drought tolerance screening in wheat.

Local and Bayesian Survival FDR Estimations to Identify Reliable Associations in Whole Genome of Bread Wheat.

Estimating the FDR significance threshold in genome-wide association studies remains a major challenge in distinguishing true positive hypotheses from false positive and negative errors. Several comparative methods for multiple testing comparison have been developed to determine the significance threshold; however, these methods may be overly conservative and lead to an increase in false negative results. The local FDR approach is suitable for testing many associations simultaneously based on the empirical Bayes perspective. In the local FDR, the maximum likelihood estimator is sensitive to bias when the GWAS model contains two or more explanatory variables as genetic parameters simultaneously. The main criticism of local FDR is that it focuses only locally on the effects of single nucleotide polymorphism (SNP) in tails of distribution, whereas the signal associations are distributed across the whole genome. The advantage of the Bayesian perspective is that knowledge of prior distribution comes from other genetic parameters included in the GWAS model, such as linkage disequilibrium (LD) analysis, minor allele frequency (MAF) and call rate of significant associations. We also proposed Bayesian survival FDR to solve the multi-collinearity and large-scale problems, respectively, in grain yield (GY) vector in bread wheat with large-scale SNP information. The objective of this study was to obtain a short list of SNPs that are reliably associated with GY under low and high levels of nitrogen (N) in the population. The five top significant SNPs were compared with different Bayesian models. Based on the time to events in the Bayesian survival analysis, the differentiation between minor and major alleles within the association panel can be identified.

Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat.

Estimation and prediction play a key role in breeding programs. Currently, phenotyping of complex traits such as nitrogen use efficiency (NUE) in wheat is still expensive, requires high-throughput technologies and is very time consuming compared to genotyping. Therefore, researchers are trying to predict phenotypes based on marker information. Genetic parameters such as population structure, genomic relationship matrix, marker density and sample size are major factors that increase the performance and accuracy of a model. However, they play an important role in adjusting the statistically significant false discovery rate (FDR) threshold in estimation. In parallel, there are many genetic hyper-parameters that are hidden and not represented in the given genomic selection (GS) model but have significant effects on the results, such as panel size, number of markers, minor allele frequency, number of call rates for each marker, number of cross validations and batch size in the training set of the genomic file. The main challenge is to ensure the reliability and accuracy of predicted breeding values (BVs) as results. Our study has confirmed the results of bias-variance tradeoff and adaptive prediction error for the ensemble-learning-based model STACK, which has the highest performance when estimating genetic parameters and hyper-parameters in a given GS model compared to other models.

Stage-specific genotype-by-environment interactions determine yield components in wheat.

In cereal crops, environmental fluctuations affect different physiological processes during various developmental phases associated with the formation of yield components. Because these effects are coupled with cultivar-specific phenology, studies investigating environmental responses in different cultivars can give contradictory results regarding key phases impacting yield performance. To dissect how genotype-by-environment interactions affect grain yield in winter wheat, we estimated the sensitivities of yield components to variation in global radiation, temperature and precipitation in 220 cultivars across 81 time-windows ranging from double ridge to seed desiccation. Environmental sensitivity responses were prominent in the short-term physiological subphases of spike and kernel development, causing phenologically dependent, stage-specific genotype-by-environment interactions. Here we reconcile contradicting findings from previous studies and show previously undetected effects; for example, the positive impact of global radiation on kernel weight during canopy senescence. This deep insight into the three-way interactions between phenology, yield formation and environmental fluctuations provides comprehensive new information for breeding and modelling cereal crops.

Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population.

Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd-H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.

Genetic dissection of root architectural plasticity and identification of candidate loci in response to drought stress in bread wheat.

BACKGROUND: The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adaptation to drought stress, however; genetic control of root systems in wheat under field conditions is not yet well understood. RESULTS: Natural variation in root architecture plasticity (phenotypic alteration due to changing environments) was dissected under field-based control (well-irrigated) and drought (rain-out shelter) conditions by a genome-wide association study using 200 diverse wheat cultivars. Our results revealed root architecture and plasticity traits were differentially responded to drought stress. A total of 25 marker-trait associations (MTAs) underlying natural variations in root architectural plasticity were identified in response to drought stress. They were abundantly distributed on chromosomes 1 A, 1B, 2 A, 2B, 3 A, 3B, 4B, 5 A, 5D, 7 A and 7B of the wheat genome. Gene ontology annotation showed that many candidate genes associated with plasticity were involved in water-transport and water channel activity, cellular response to water deprivation, scavenging reactive oxygen species, root growth and development and hormone-activated signaling pathway-transmembrane transport, indicating their response to drought stress. Further, in silico transcript abundance analysis demonstrated that root plasticity-associated candidate genes were highly expressed in roots across different root growth stages and under drought treatments. CONCLUSION: Our results suggest that root phenotypic plasticity is highly quantitative, and the corresponding loci are associated with drought stress that may provide novel ways to enable root trait breeding.

Intergenerational and transgenerational effects of drought stress on winter wheat (Triticum aestivum L.).

The environments where the progenitors are grown have the potential to affect the expression of traits in their offspring. Currently, there are various hypotheses regarding the evolutionary and ecological importance of stress memory effects. There is uncertainty regarding its occurrence, persistence, predictability, and adaptive value. In this study, 15 winter wheat cultivars were grown under drought and well-watered (control) treatments for two seasons to produce seeds with all possible combinations of drought exposure histories. A comprehensive analysis to estimate transgenerational (grandparental effects), intergenerational (parental effects), and their combined memory effects on offspring traits under both control and drought moisture treatments, was performed. There were significant memory effects in most of the evaluated traits ranging from +787% to -39.0% changes in both seed quality and plant traits. The expression of stress memory was highly dependent on the generation and number of exposures, traits, and seasons. Under drought treatment, the combination of grandparental and parental stress memories was additive in all traits, but their strengths were variable when considered separately. Stress memory enhanced the performance of offspring under similar stressful conditions: increased plant height, above-ground biomass, number of grains per plant, grain weight per plant and water potential. This study offers valuable new insights into the occurrence of drought stress memory, the complexities of the effects, possible physiological and metabolic alterations explaining the detected differences, and impacts toward a clearer understanding of their generation and context-dependency.

Stress memory and its regulation in plants experiencing recurrent drought conditions.

Developing stress-tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation is not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This ability could enable training of plants to face future challenges that increase in frequency and intensity. A better understanding of stress memory-associated mechanisms leading to alteration in gene expression and how they link to physiological, biochemical, metabolomic and morphological changes would initiate diverse opportunities to breed stress-tolerant genotypes through molecular breeding or biotechnological approaches. In this perspective, this review discusses different stress memory types and gives an overall view using general examples. Further, focusing on drought stress, we demonstrate coordinated changes in epigenetic and molecular gene expression control mechanisms, the associated transcription memory responses at the genome level and integrated biochemical and physiological responses at cellular level following recurrent drought stress exposures. Indeed, coordinated epigenetic and molecular alterations of expression of specific gene networks link to biochemical and physiological responses that facilitate acclimation and survival of an individual plant during repeated stress.

Convergently selected NPF2.12 coordinates root growth and nitrogen use efficiency in wheat and barley.

Understanding the genetic and molecular function of nitrate sensing and acquisition across crop species will accelerate breeding of cultivars with improved nitrogen use efficiency (NUE). Here, we performed a genome-wide scan using wheat and barley accessions characterized under low and high N inputs that uncovered the NPF2.12 gene, encoding a homolog of the Arabidopsis nitrate transceptor NRT1.6 and other low-affinity nitrate transporters that belong to the MAJOR FACILITATOR SUPERFAMILY. Next, it is shown that variations in the NPF2.12 promoter correlated with altered NPF2.12 transcript levels where decreased gene expression was measured under low nitrate availability. Multiple field trials revealed a significantly enhanced N content in leaves and grains and NUE in the presence of the elite allele TaNPF2.12TT grown under low N conditions. Furthermore, the nitrate reductase encoding gene NIA1 was up-regulated in npf2.12 mutant upon low nitrate concentrations, thereby resulting in elevated levels of nitric oxide (NO) production. This increase in NO correlated with the higher root growth, nitrate uptake, and N translocation observed in the mutant when compared to wild-type. The presented data indicate that the elite haplotype alleles of NPF2.12 are convergently selected in wheat and barley that by inactivation indirectly contribute to root growth and NUE by activating NO signaling under low nitrate conditions.

Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat.

BACKGROUND: The transition from vegetative to floral phase is the result of complex crosstalk of exogenous and endogenous floral integrators. This critical physiological event is the response to environmental interaction, which causes biochemical cascades of reactions at different internal tissues, organs, and releases signals that make the plant moves from vegetative status to a reproductive phase. This network controlling flowering time is not deciphered largely in bread wheat. In this study, a comparative transcriptome analysis at a transition time in combination with genetic mapping was used to identify responsible genes in a stage and tissue-specific manner. For this reason, two winter cultivars that have been bred in Germany showing contrasting and stable heading time in different environments were selected for the analysis. RESULTS: In total, 670 and 1075 differentially expressed genes in the shoot apical meristem and leaf tissue, respectively, could be identified in 23 QTL intervals for the heading date. In the transition apex, Histone methylation H3-K36 and regulation of circadian rhythm are both controlled by the same homoeolog genes mapped in QTL TaHd112, TaHd124, and TaHd137. TaAGL14 gene that identifies the floral meristem was mapped in TaHd054 in the double ridge. In the same stage, the homoeolog located on chromosome 7D of FLOWERING TIME LOCUS T mapped on chr 7B, which evolved an antagonist function and acts as a flowering repressor was uncovered. The wheat orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) was identified in the late reproductive stage and was mapped in TaHd102, which is strongly associated with heading date. Deletion of eight nucleotides in the AS1 promoter could be identified in the binding site of the SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1) gene in the late flowering cultivar. Both proteins AS1 and SOC1 are inducing flowering time in response to gibberellin biosynthesis. CONCLUSION: The global transcriptomic at the transition phase uncovered stage and tissue-specific genes mapped in QTL of heading date in winter wheat. In response to Gibberellin signaling, wheat orthologous transcription factor AS1 is expressed in the late reproductive phase of the floral transition. The locus harboring this gene is the strongest QTL associated with the heading date trait in the German cultivars. Consequently, we conclude that this is another indication of the Gibberellin biosynthesis as the mechanism behind the heading variation in wheat.

Pinpointing genomic loci for drought-induced proline and hydrogen peroxide accumulation in bread wheat under field conditions.

BACKGROUND: Proline (Pro) and hydrogen peroxide (H2O2) play a critical role in plants during drought adaptation. Genetic mapping for drought-induced Pro and H2O2 production under field conditions is very limited in crop plants since their phenotyping with large populations is labor-intensive. A genome-wide association study (GWAS) of a diversity panel comprised of 184 bread wheat cultivars grown in natural field (control) and rain-out shelter (drought) environments was performed to identify candidate loci and genes regulating Pro and H2O2 accumulation induced by drought. RESULTS: The GWAS identified top significant marker-trait associations (MTAs) on 1A and 2A chromosomes, respectively for Pro and H2O2 in response to drought. Similarly, MTAs for stress tolerance index (STI) of Pro and H2O2 were identified on 5B and 1B chromosomes, respectively. Total 143 significant MTAs were identified including 36 and 71 were linked to drought and 2 and 34 were linked to STI for Pro and H2O2, respectively. Next, linkage disequilibrium analysis revealed minor alleles of significant single-markers and haplotypes were associated with higher Pro and H2O2 accumulation under drought. Several putative candidate genes for Pro and H2O2 content encode proteins with kinase, transporter or protein-binding activities. CONCLUSIONS: The identified genetic factors associated with Pro and H2O2 biosynthesis underlying drought adaptation lay a fundamental basis for functional studies and future marker-assisted breeding programs.

Natural selection under conventional and organic cropping systems affect root architecture in spring barley.

A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore, evaluating the root system variation for breeding crop plants towards stress adaptation is critically important. Here, we phenotyped root architectural traits of naturally adapted populations from organic and conventional cropping systems under hydroponic and field trails. Long-term natural selection under these two cropping systems resulted in a microevolution of root morphological and anatomical traits. Barley lines developed under an organic system possessed longer roots with narrow root angle, larger surface area, increased root mass density, and a thinner root diameter with an increased number of metaxylem vessels. In contrast, lines adapted to the conventional system tend to have a shorter and wider root system with a larger root volume with a thicker diameter but fewer metaxylem vessels. Allometry analysis established a relationship between root traits and plant size among barley genotypes, which specifies that root angle could be a good candidate among studied root traits to determine root-borne shoot architecture. Further, multivariate analyses showed a strong tendency towards increased variability of the organically adapted population's root morphological and anatomical traits. The genotyping of ancestor populations validated the observations made in these experiments. Collectively, this results indicate significant differences in root phenotypes between conventional and organic populations, which could be useful in comparative genomics and breeding.

Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat.

Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.

Natural diversity uncovers P5CS1 regulation and its role in drought stress tolerance and yield sustainability in barley.

Proline accumulation is one of the major responses of plants to many abiotic stresses. However, the significance of proline accumulation for drought stress tolerance remains enigmatic in crop plants. First, we examined the natural variation of the pyrolline-5-carboxylate synthase (P5CS1) among 49 barley genotypes. Allele mining identified a previously unknown allelic series that showed polymorphisms at 42 cis-elements across the P5CS1 promoter. Selected haplotypes had quantitative variation in P5CS1 gene expression and proline accumulation, putatively influenced by both  abscisic acid-dependent and independent pathways under drought stress. Next, we introgressed the P5CS1 allele from a high proline accumulating wild barley accession ISR42-8 into cultivar Scarlett developing a near-isogenic line (NIL-143). NIL-143 accumulated higher proline concentrations than Scarlett under drought stress at seedling and reproductive stages. Under drought stress, NIL-143 showed less pigment damage, sustained photosynthetic health, and higher drought stress recovery compared to Scarlett. Further, the drought-induced damage to yield-related traits, mainly thousand-grain weight, was lower in NIL-143 compared with Scarlett in field conditions. Our data uncovered new variants of the P5CS1 promoter and the significance of the increased proline accumulation regulated by the P5CS1 allele of ISR42-8 in drought stress tolerance and yield stability in barley.

Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity.

The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley transcriptome and leaf chlorophyll content under 8h conditions, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. This might lead to a cascade of suspended sink-source activities, which ultimately delay organ development and differentiation in barley shoot meristems under short photoperiods.

Chromosome 3A harbors several pleiotropic and stable drought-responsive alleles for photosynthetic efficiency selected through wheat breeding.

Water deficit is the most severe stress factor in crop production threatening global food security. In this study, we evaluated the genetic variation in photosynthetic traits among 200 wheat cultivars evaluated under drought and rainfed conditions. Significant genotypic, treatments, and their interaction effects were detected for chlorophyll content and chlorophyll fluorescence parameters. Drought stress reduced the effective quantum yield of photosystem II (YII) from the anthesis growth stage on. Leaf chlorophyll content measured at anthesis growth stages was significantly correlated with YII and non-photochemical quenching under drought conditions, suggesting that high throughput chlorophyll content screening can serve as a good indicator of plant drought tolerance status in wheat. Breeding significantly increased the photosynthetic efficiency as newer released genotypes had higher YII and chlorophyll content than the older ones. GWAS identified a stable drought-responsive QTL on chromosome 3A for YII, while under rainfed conditions, it detected another QTL on chromosome 7A for chlorophyll content across both growing seasons. Molecular analysis revealed that the associated alleles of AX-158576783 (515.889 Mbp) on 3A co-segregates with the NADH-ubiquinone oxidoreductase (TraesCS3A02G287600) gene involved in ATP synthesis coupled electron transport and is proximal to WKRY transcription factor locus. This allele on 3A has been positively selected through breeding and has contributed to increasing the grain yield.

Identification of QTLs for wheat heading time across multiple-environments.

KEY MESSAGE: The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays it. A genome-wide scan of marker-trait associations with heading date detected two QTL: an adapted allele at locus TaHd102 on chromosome 5A that has a consistent effect on HD in German cultivars in multiple environments and a non-adapted allele at locus TaHd044 on chromosome 3A that accelerates flowering by 5.6 days. TaHd102 and TaHd044 explain 13.8% and 33% of the genetic variance, respectively. The interplay of the climatic variables led to the detection of environment specific association responding to temperature in lower latitudes and photoperiod in higher ones. Another locus TaHd098 on chromosome 5A showed epistatic interactions with 15 known regulators of flowering time when non-adapted cultivars from outside Germany were included in the analysis.

NeuralLasso: Neural Networks Meet Lasso in Genomic Prediction.

Prediction of complex traits based on genome-wide marker information is of central importance for both animal and plant breeding. Numerous models have been proposed for the prediction of complex traits and still considerable effort has been given to improve the prediction accuracy of these models, because various genetics factors like additive, dominance and epistasis effects can influence of the prediction accuracy of such models. Recently machine learning (ML) methods have been widely applied for prediction in both animal and plant breeding programs. In this study, we propose a new algorithm for genomic prediction which is based on neural networks, but incorporates classical elements of LASSO. Our new method is able to account for the local epistasis (higher order interaction between the neighboring markers) in the prediction. We compare the prediction accuracy of our new method with the most commonly used prediction methods, such as BayesA, BayesB, Bayesian Lasso (BL), genomic BLUP and Elastic Net (EN) using the heterogenous stock mouse and rice field data sets.