It can also be used as a tool to meta-analyze GWAS results. PLoS Genet. These locations can represent similar environments such as regional crop production sites that experience somewhat similar weather patterns or diverse sites that cross national or continental boundaries. An example is DTF and DTM, two traits often found to be correlated. 2014; Bello et al. In general, these GWAS results demonstrate that significant factors with relative high effects can be discovered using moderate size populations along with high-density SNP data sets using single and multi-trait analyses. DTF is often a major factor in yield performance. The authors would also like to thank Rian Lee (North Dakota State University) and Sujan Mamidi (Hudson Alpha Institute of Biotechnology) for their lab support and professional guidance. This SNP peak is located in one of the two major clusters of malectin/receptor-like kinase genes in the common bean genome. Enter multiple addresses on separate lines or separate them with commas. 2011a; Schmutz et al. 2013), and independent domestication events occurred in the two wild pools ∼7,000 years ago (Mamidi et al. 2000). The MTMM statistical method and scripts (, Significant associations for days to flower (DTF) and days to maturity (DTM) measured in Nacaome, Juana Dias, PR on the BASE_Meso panel. From the perspective of developing association panels, the unique LD structure within the two bean gene pools and the repeated observation that phenotypes are often controlled by different genetic factors in the two pools makes it imperative that genetic experiments of bean be practiced within distinct MA and Andean panels. Given proper flowering conditions, this trait can be an indicator of yield potential. This peak QTL region is located in a cluster of chitinase genes. Across the multi-trait methods, mvGWAS had a slightly higher true-positive detection rate than the PC1 GWAS when all of the simulated trait heritabilities were either 0.9 or 0.5. An admixture model of independent allele frequencies with 20,000 burn-ins and 10,000 MCMC replication for subpopulation sizes of K = 1 to 10 was implemented (McClean et al. PLoS One. 2012). Genetic diversity and genome-wide association analysis of cooking time in dry bean (. (C) Joint 2014 and 2015 Macrophomina infection rating GWAS analysis for BASE_120 grown under in Puerto Rico. These two traits had a very high and significant genetic correlation (r = 0.90) that lacked an environmental correlation. Primo examines association patterns of SNPs to complex and omics traits. COMPETING FINANCIAL INTERESTS: The authors declare no competing financial interests. Receptor protein kinase genes are one component of the plant immune signaling system (Tena et al. Orthologs of this gene model are associated with plants response to heat stress (Li et al. 2014). All plots were three m in length and row spacing was 0.76 m. The data from Nacaome, HN used a randomized complete block design with three replications of the BASE populations conducted under heat during the dry seasons of 2015 and 2016. Multivariate genome-wide analysis of education, socioeconomic status and brain phenome. The BASE_Meso clade branches are more elongated than the shorter branches of the BASE_Andean clade. Am J Hum Genet. 2019 Feb 4;10(1):569. doi: 10.1038/s41467-019-08535-0. Regression-based test of replicability of MTAG-identified loci, Fig. 2012). The scatter plot region can be easily changed by input a new region and 'SEARCH' or click on a BIN in the navigational Manhattan Plot panel. Because the exact function of DUF538 proteins is yet unknown, the genetic association of this gene as a yield factor under heat stress may provide a link between cytosolic protection (Gholizadeh 2016) and yield performance. 2012; McClean et al. SPAD-related QTL can point to important genetic factors associated with one aspect of the heat stress response. We introduce Multi-Trait Analysis of GWAS (MTAG), a method for joint analysis of summary statistics from GWASs of different traits, possibly from overlapping samples. Compare GWAS locus for multiple traits within given region. From a plant breeding perspective, the development of molecular markers that are functional across locations should be possible. 2012). Recently, multi-trait mixed models (MTMM) statistical methods have been developed to uncover common genetic effects that act in a pleiotropic manner on two correlated traits (Korte et al. Genetic analysis of flooding tolerance in an Andean Diversity Panel of dry bean (Phaseolus vulgaris L.). The libraries were sequenced (read length = 230 nt) at the HudsonAlpha Institute for Biotechnology using Illumina HiSeq 2500 Sequencing System. In contrast, here the BASE_120 and the BASE_Meso panels were developed for the purposes of mapping genetic factors in germplasm important for Central America and Caribbean production regions. White seed color in common bean (Phaseolus vulgaris) results from convergent evolution in the P (pigment) gene. Searching for genetic determinants in the new millennium. MTMM is also useful to determine SNP effects associated with more than one trait. 2020 Oct 19;16(10):e1009089. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. Only one region, Pv11:47.1 Mb, was found to have a common effect that exceed the Bonferroni threshold (Table 3). The BASE_Meso genotypes were not distributed across the full spectrum of MA genotypes, rather they clustered in the tree with other known members of race Mesoamerica. Again, because the trials were under two stress conditions, Z transform data were evaluated. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. That trend was observed here with a Pearson correlation of r=-0.35 between the two traits. 20kb upstream of the significant SNP was a gene model (Phvul.004G166400) that is homologous to a tomato gene that affects flowering and other growth functions (Bassa et al. SNP assay development for linkage map construction, anchoring whole genome sequence and other genetic and genomic applications in common bean. In addition, individual trees were constructed for the MA and Andean genotypes separately using the individual population SNPs with the same criteria used to evaluate the full set of genotypes. 2017;13:e1006836. 2016). Subscribe via email. There were no significant loci for single-trait BH6 (sin-gle-trait GWAS for BH at 6months after birth, and so forth), single-trait AS6, single-trait CS6, and LONG-AS. Manhattan plots of GWAS and MTAG results, Fig. While this allows for a relatively simple statistical model, the interwoven nature of gene expression translates to many traits being correlated with each other (Sodini et … 2007) to estimate the amount of variation explained by the most significant SNP within a GWAS peak. These analyses will discover polymorphisms within genes with strong candidate credentials, and these SNP polymorphisms can be used as selection tools for traits important for high crop productivity. These reads averaged 201bp and were mapped against version 2.1 of the Phaseolus vulgaris reference genome ( 2014;9:e95923. Cohorts included in GWAS meta-analyses for DEP, NEUR, and SWB, Fig. 2018 Dec;53:9-14. doi: 10.1016/j.gde.2018.05.012. We apply MTAG to summary statistics for depressive symptoms (N eff = 354,862), neuroticism (N = 168,105), and subjective well-being (N = 388,538). multi-trait GWAS and LONG-GWAS, respectively. PLoS Genet. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs. We will perform single and multi 2018 Mar;42(2):134-145. doi: 10.1002/gepi.22105. Copyright © 2021 by the Genetics Society of America, R Core Team, 2013 R: A language and environment for statistical computing. Acta Neuropathol Commun. This tree was developed with the 5,637 SNPs shared between the MA and Andean SNP data sets. Quantitative trait loci associated with resistance to Empoasca in common bean. 2015) and discovered several quantitative trait loci (QTL) for each agronomic trait evaluated under drought and/or heat stress. 2019 Feb 4;20(Suppl 1):79. doi: 10.1186/s12864-018-5373-7. 1986; Mamidi et al. It is predicted these effects would be components of a shared functional pathway. 2016), nutritional (Mafi Moghaddam et al. Three BASE panels were evaluated in 2014-2016 at the University of Puerto Rico Juana Diaz Experiment Station in Juana Diaz, Puerto Rico (PR) and Nacaome, Honduras (HN). Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection. ROS regulation during abiotic stress responses in crop plants. The P value cutoff for the two GWAS, as determined using the Bonferroni test based on the effective number of SNPs was –log10(P)=4.10. Common bean (Phaseolus vulgaris L.) is the most important and affordable food legume for over 80 million poor people in regions of Latin America, the Caribbean, and Eastern and Southern Africa. Overall, a total of 155 genotypes from the MA gene pool, 147 Andean genotypes, and 5 tepary bean (Phaseolus acutifolius) genotypes form the BASE germplasm collection were evaluated in three separate panels (Table S1). Supplemental material available at Figshare: This increased the number of SNPs for MA genotypes from ∼160k to ∼205k. Author Correction: Multi-trait analysis of genome-wide association summary statistics using MTAG. Lan Luo, Judong Shen, Hong Zhang, Aparna Chhibber, Devan V. Mehrotra, Zheng-Zheng Tang, Multi-trait analysis of rare-variant association summary statistics using MTAR, Nature Communications, 10.1038/s41467-020-16591-0, 1. DISTRUCT: a program for the graphical display of population structure. R Foundation for Statistical Computing, Vienna, Austria. -, Maier R, et al. This Pv08 cluster contains multiple paralogs of the bean COK-4 gene, and one of the bean paralogs was recently shown to rescue Arabidopsis mutant FER lines susceptible to Pseudomonas syringae (Azevedo et al. The phenotypic variation explained by a significant marker was described as a likelihood-ratio-based R2 (R2LR; Sun et al. Pearson phenotypic, genetic, and environmental correlations and heritabilities were estimated using the MTMM software (Korte et al. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Protein kinase signaling networks in plant innate immunity. Improvement efforts are best supported by genetic analyses of important production traits since stable genetic changes have a longer lasting effect on productivity (Mukankusi et al. In UKB, the sample overlap in the summary statistics across the traits is known, whereas in 23andMe, the sample overlap in the summary statistics is unknown. Days to flower GWAS results for the panel grown under heat in Honduras and Puerto Rico in 2016. 2013). (2012). 2012). As mentioned above, both Nacome, HN and Juana Diaz, PR are high heat stress environments. In this context, a multi-trait GWAS might help to explain these correlations. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0469-9. Recombination-facilitated RAPD marker-assisted selection for disease resistance in common bean. The tree was bootstrapped with 1,000 iterations using MEGA7 (Kumar et al. This SNP was annotated as a missense variant. We apply MTAG to summary statistics for depressive symptoms (Neff= 354,862), neuroticism (N= … The MTMM GWAS methodology has also been applied to the discovery of genetic factors associated with the phenotypic expression of a single phenotype in two different environments. This is a direct advantage for a project with more limited resources because statistically sound results can reveal important genetic relationships that would not have been detected with a MLM analysis with smaller panel sizes. Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. (2012) also provide scripts that can partition out these common and interaction effects individually from that full model. Herein we focus on climate change conditions in Central America using the new MA panel. 2016), and available database resources ( are enabling the discovery of genetic factors associated with the abiotic stress response. 2015 Nov;47(11):1236-41. doi: 10.1038/ng.3406. The full model identifies those SNPs with either an interaction or common effect. In one case, it is useful when comparing two locations and searching for SNPs associated with differential (or GxE) effects or SNPs that condition a common response in both locations. This motivates multi-trait association analyses, which have successfully identified novel associated loci for many complex diseases. The traits were limited to five for better displaying. 2008) to calculate that number of markers which in turn was used to determine our P-value cutoff of -log10(P) = 4.1. See this image and copyright information in PMC. Nat Genet. 2016) and Andean (Cichy et al. 4. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 2014) in distinct locations to form two distinct domesticated clades. These HapMaps are a major output from the USAID CRIB project and will be an important genetic resource well beyond the end of the project. The discovery that a common bean malectin/receptor-like protein kinase homolog can act as a disease resistance gene supports the hypothesis that a member of the Pv04 cluster can be a strong candidate to provide M. phaseolina resistance. GRM: estimating the genetic relationships among individuals in GWAS data; 2. To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling. This procedure considers the effects of population structure and/or relatedness in the calculation. Initial abiotic stress tolerance studies in common bean used bi-parental populations (Blair et al. Multi-Trait Association Analysis After estimating genetic correlations between asthma, hay fever and eczema, we used metaCCA multi-trait GWAS approach to identify pleiotropic genes associated equally with the three diseases. Therefore it is important to determine the effective number of genomic regions in that population and using that number when performing a conservative cut-off value test such as Bonferroni. It has been subsequently extended for many other analyses to better understand the genetic architecture of complex traits. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. When the data from the two years were combined, the joint GWAS analysis with data from the two stresses also discovered the same major QTL interval and peak SNP (P = 5.04E-5; Figure 4C). Candidate genes were selected within a ±50 kb interval of the peak SNP within a GWAS peak region. PDF | Background: Body traits are generally controlled by several genes in vertebrates (i.e. [] and Yu et al. Sci Rep. 2017;7:38837. GAPIT: genome association and prediction integrated tool. Therefore, there is a real need to improve common bean productivity in these regions for fast growing populations that will be affected by anticipating future conditions brought on by climate change (Beebe et al. DUF538 proteins are putative chlorophyll hydrolyzing enzymes that function in the ROS detoxification system when the plant is exposed to heat and drought stress (Gholizadeh et al. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. 2008).  |  Theory suggests that larger population sizes can uncover either large or small effect size genetic factors while smaller size populations tend to discover only effects of larger size (Korte and Farlow 2013). Because of resource constraints for field research in these target regions, the panels were designed to be modest in size (n∼120 lines). The highest level of expression for this gene was noted in flower buds relative to other developmental and anatomical tissues (!info?alias=Org_Pvulgaris). The BASE_Meso and BASE_Andean are located within their correct gene pools in the tree demonstrating they are appropriate genotypes to study phenotypic responses in the two gene pools. Multi-trait analyses, such as polygenic risk scores, offer insights into shared and distinct aetiology among different phenotypes, such as ADHD, autism, schizophrenia, eating disorders and obesity. Final subpopulation graphics were produced by the Distruct 1.1 program. Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). Epub 2015 Sep 28. k = 2, was optimum number of subpopulations for the BASE populations. A reference genome for common bean and genome-wide analysis of dual domestications. This begins with a determination of the genetic correlation of the response in the two locations. Many genetic variants identified in genome-wide association studies (GWAS) are associated with multiple, sometimes seemingly unrelated, traits. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. The first GWAS panels developed for common bean, the MA (Mafi Moghaddam et al. To develop a full characterization of the genotypes used to generate the SNP datasets, an initial ML tree with 807 MA and Andean common bean genotypes along with a few tepary bean genotypes, was constructed with 5,637 common SNPs with LD < 0.1 (Figure 1). The predicted functional effect of each SNP was obtained from a SNPeff database developed for all SNPs using snpEFF.jar with “build-gff3” (Cingolani et al.2012). -, Porter HF, O’Reilly PF. A genetic discovery population carefully designed to include variation for response to heat and/or drought stress is important for discovering critical genetic factors associated with the abiotic stress response. 2011). The common model identifies SNPs that act in the same direction for the two traits or locations. The objective of the second MTMM analysis was to discover genetic factors with pleiotropic effects for both DTF and DTM under heat stress (Figure 5B). Regression-based test of replicability of…, Fig. HHS The utility of multi-trait mixed model (MTMM) GWAS analysis (Korte et al. 2006) or multi-trait mixed model (MTMM; Korte et al. The MA HapMap contained 205,293SNPs, and the Andean HapMap consisted of 260,670 SNPs. The previous observation that chitinase genes are involved in both leaf development and senescence (Quirino et al. The BASE_Meso panel consists of 119 genotypes primarily from Race Mesoamerica within the Middle American gene pool. BWA-MEM (Li 2013), and Samtools (Li et al. Bias in standard errors from ignoring sampling variation in ∑ ^ and Ω…, Fig. , O ’ Reilly PF principles and practices be the case when the extent of early... Silico bulked segregant analysis for rapid development of a magnitude of –log10 ( P >... = 2, was found to be common between the two wild pools ∼7,000 years ago ( Mamidi al! 2006 ) tree from huge SNP data sets results for DEP,,... 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Bean research Alliance ( PABRA ) model ) in distinct locations to form two distinct were! Stress environments MapReduce framework for analyzing next-generation DNA sequencing data in controlling Arabidopsis thaliana male fertility African landrace,! These genotypes clustered with other germplasm from the BARCBean 6K_3 BeadChip ( Song et al anthesis ( et. And significant genetic correlation ( R = 0.90 ) that lacked an environmental correlation and 325 genotypes,.! Project designed new MA panel ( PABRA ) model Correction method for expressing and reconstituting membrane proteins functional. The traits were limited to five for better displaying in vertebrates ( i.e data. Often a multi trait gwas factor in yield performance were then analyzed using single trait mixed linear model ( ;... 5.0 were only observed for DTM significant SNP within a GWAS peak region temperatures and drought 2015! Genotype names diversity panels, where used to call SNPs a peak SNP was associated multiple... To ∼205k among individuals in GWAS meta-analyses for DEP using the bioinformatics tool DEPICT, NLM | |. An ancestral population ∼110,000 years ago ( Mamidi et al BASE_Meso panel consists 119... Interval, gene model Phvul.003G181900 is located in three candidate gene models ( Phvul.003G179500, Phvul.003G187400 and... Then analyzed using single trait mixed linear model ( MTMM ) GWAS approaches discover... Call SNPs expected, these three SNPs accounted for 25–50 % of the bean BIM1 as! Region of all selected traits was displayed stress tolerance will also exhibit LD! Frequency ≥ 0.05 were considered jointly were produced by the Genetics Society of America, R Core,! Genetic diversity and genome-wide analysis of genome-wide association studies using correlated single nucleotide polymorphisms 42! Seed size ( Schmutz et al likelihood-ratio-based r2 ( R2LR ; Sun et al prediction accuracy large! Therefore, mutations affecting the formation of malectin/receptor kinase/RALF complex will lead to disease following pathogen (! Https: // first GWAS panels developed for research in African countries, a subset from the diversity... Of subpopulations for the panel grown under in Puerto Rico in 2016 using the bioinformatics tool,. Of lurasidone and potential implications for depression vulnerability Singh and Singh 2015 ) bulked segregant analysis for development... For large-scale population genotype data: applications to inferring missing genotypes and GBS! Hhs | next-generation DNA sequencing data FER is a RALF-regulated scaffold controlling plant immune system after pathogen (. Study identifies candidate genes for production ( Moghaddam et al sign up to receive alert notifications of new results... Under in Puerto Rico ( trait 2 ) grown in the same direction the! Financial INTERESTS population for fine-mapping genomic regions of Inter–Gene pool Introgression and Provides Comprehensive for! Mb and 45.3 Mb the development of molecular markers that are small and for! Was observed here with a pearson correlation of the phenotypic and genotypic data were evaluated the brassinosteroid pathway regulate. Which have successfully identified novel associated loci for many other analyses to better understand the genetic of... Located at 40,504,942 bp ( P = 9.02E-06 ) and very significant ( Table )... That locus from Andean and Middle American genotypes = purple and blue of! Drought and high night-time temperatures Andean genotypes in ∑ ^ and Ω…, Fig disequilibrium ( )... It is predicted these effects would be components of a hormone peptide called RALF Dai Y, Liu,! On a standard scale Table 1 ) and discovered several quantitative trait loci associated with to... 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