Maximizing the number of SNPs within any collection of genotypes will increase the likelihood of finding associations with a target phenotype in the full collection or a subset of the genotypes. A MLM GWAS analysis was performed in separate heat and drought environments in PR in 2016 using the BASE_Meso population. doi: 10.1371/journal.pgen.1009089. 7. Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder, and major depressive disorder. File S4 and S5 are text files containing un-imputed HapMap genetic data for Andean and MA genotypes respectively. This trait appeared to be under different controls under the two conditions. 2011b). Thank you for sharing this G3: Genes | Genomes | Genetics article. Because of resource constraints for field research in these target regions, the panels were designed to be modest in size (n∼120 lines). 2015).  |  A mixed-model approach for genome-wide association studies of correlated traits in structured populations. For the full MTMM model, eight genomic regions passed the –log10(P) > 5.0 threshold. To consider that correlation in terms of the strong DTF genetic effect discovered in this analysis, the allelic effects of the major SNP for DTF (Pv03: 40,504,942 bp) on yield was evaluated. The genotypes used to develop the HapMaps represent many of genotypes used for production purposes over the last 50 years in the USA and elsewhere. The highest level of expression for this gene was noted in flower buds relative to other developmental and anatomical tissues (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris). Table S1 contains the list of BASE genotype names. The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling. 2016), nutritional (Mafi Moghaddam et al. Days to flower GWAS results for the panel grown under heat in Honduras and Puerto Rico in 2016. Major consumers of common bean in these countries often live on less than two U.S. dollars per day, where beans are grown primarily by smallholder farmers on less than two hectares (McClean and Raatz 2017). The phenotypic and genotypic data were then analyzed using single trait mixed linear model (MLM; Yu et al. Principal component analysis (PCA) was performed using the Prcom function in R, and relatedness was measured using the EMMA algorithm implemented in GAPIT. The peak SNP in each analysis was located at Pv04:4,665,828 bp and accounted for 8.9 and 7.8% of the variation, respectively, for the heat and drought trials. The tree was bootstrapped with 1,000 iterations using MEGA7 (Kumar et al. Multi-trait mixed model GWAS. 2015) and discovered several quantitative trait loci (QTL) for each agronomic trait evaluated under drought and/or heat stress. The range of SNPs per Mb is consistent across both and heterochromatic of the and Andean SNP data sets (Table S3). We do not retain these email addresses. (2016)] of were remapped, and SNPs were called. []. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. The previous observation that chitinase genes are involved in both leaf development and senescence (Quirino et al. 2016), and available database resources (http://phaseolusgenes.bioinformatics.ucdavis.edu/) are enabling the discovery of genetic factors associated with the abiotic stress response. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. 2006) or multi-trait mixed model (MTMM; Korte et al. 2012). This model contains a DUF538 domain that is a key signature of the DUF538 superfamily whose members are well-known stress-related proteins in plants (Gholizadeh 2016). Green are the BASE_Meso genotypes and purple and the BASE_Anjdean genotypes. 2015 Nov;47(11):1236-41. doi: 10.1038/ng.3406. 2018 Dec;53:9-14. doi: 10.1016/j.gde.2018.05.012. This site needs JavaScript to work properly. Since the three locations were considered different environments with potentially different heat stress conditions, the phenotypic data were transformed using the Z transformation, and the data were combined into a single MLM GWAS analysis (Figure 3A). 2011a). SPL8 acts together with the brassinosteroid-signaling component BIM1 in controlling Arabidopsis thaliana male fertility. Ray D(1), Boehnke M(1). The peak SNP discovered in a joint MLM analysis for yield over years in the HN and PR heat stress environments is located in gene model Phvul.003G187400. B. ML phylogenetic tree of BASE genotypes. Additional SNPs were located at Pv04:25,282,114 bp (P = 5.04E-5) and Pv10: 32,029,428 bp (P = 5.04E-5) in the combined analysis. One component of the project was to develop appropriate sized populations that can be managed by research teams with limited resources yet large enough to discover genetic factors of moderate to large effects. 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. As mentioned above, both Nacome, HN and Juana Diaz, PR are high heat stress environments. A. These HapMaps were based on 381,092,199 GBS reads across 469 MA genotypes and 280,085,901 GBS reads across 325 Andean genotypes. GWAS analysis for SPAD rating for BASE_Meso grown under heat (D) and drought (E) in Puerto Rico in separate trials in 2016. 3. It is appealing to develop novel multi-trait association test methods that need only GWAS summary data, since it is generally very hard to access the individual-level GWAS phenotype and genotype data. 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. Those libraries were constructed using genotypes of the MDP, ADP, BASE_120, BASE_Meso, and BASE_Andean populations. 2020 Nov 19;8(1):196. doi: 10.1186/s40478-020-01072-8. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Cattaneo A, Suderman M, Cattane N, Mazzelli M, Begni V, Maj C, D'Aprile I, Pariante CM, Luoni A, Berry A, Wurst K, Hommers L, Domschke K, Cirulli F, Szyf M, Menke A, Riva MA. 2012) is demonstrated as a method to identify statistically robust genetic factors in smaller-sized populations. For the MA SNP collection, there are 1.79x SNPs in the heterochromatic region compare to the euchromatic region, while that ratio for the Andean SNP collection is 1.51x. C. Allelic performance for SNP S03_ 40504942 for days to flower (red) and yield (green) grown under heat in Honduras and Puerto Rico in 2016. We apply MTAG to summary statistics for depressive symptoms (Neff= 354,862), neuroticism (N= … Social Science Genetic Association Consortium. 2013; Schmutz et al. The individual GWAS results for the two years were consistent, and the same major locus was discovered at Pv04/4.64-4.84 Mb (Figure 4A, 4B). Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction. The Sequence alignment/map (SAM) format and SAMtools. Supplemental material available at Figshare: https://doi.org/10.25387/g3.7965305. That population was used to identify candidate genes for production (Moghaddam et al. The MTMM analysis of DTF data from the BASE_Meso population grown in HN and PR under heat in 2016 showed the full joint analysis out-performed individual marginal analyses (Figure S2). Loading multiple GWAS summary statistics Prior to loading the summary association statistics, you need names of a set of independent SNPs. 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. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Repeated studies have shown genetic diversity is greater among domesticated MA beans than domesticated Andean beans (Velasquez and Gepts 1994; Mamidi et al. The A allele at the peak SNP was associated with lower disease incidence in the two trials. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Several common bean breeding programs that are partners in this project have been developing cultivars and lines for tolerance to a variety of abiotic stresses. These two are significant common factors and had the same positive effect at both locations (Figure 5A). Leaf senescence and the associated loss of greening is a result of multiple stresses on the plant including excessive heat (Lim et al. 2014). Marginal effects of a magnitude of –log10(P) > 5.0 were only observed for DTM. Epub 2017 Dec 10. For example, a MA diversity panel (MDP; n∼300) was developed for the USDA funded BeanCAP project that consisted of germplasm grown in the major US production regions from the 1930s to the 2000s (Moghaddam et al. SPAD readings are a general indicator of greenness of the plant. Within these regions, significant SNPs were located in three candidate gene models (Phvul.003G179500, Phvul.003G187400, and Phvul.011G159200). This platform proved useful for the discovery of many important agronomic traits primarily with bi-parental mapping studies of common bean (Mukeshimana et al. Oxidative Stress Responses and Nutrient Starvation in MCHM Treated, http://phaseolusgenes.bioinformatics.ucdavis.edu/, https://plantscience.psu.edu/research/labs/roots/projects/usaid-crb, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris, http://creativecommons.org/licenses/by/4.0/, Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments. This important molecular link to yield is suggested by the fact that the SNP in this gene accounts for 13.7% of the variation in yield. Genome-wide linkage and association mapping of halo blight resistance in common bean to race 6 of the globally important bacterial pathogen. And when the same gene is involved in the domestication, recent research has shown convergent evolution produced unique alleles in each gene pool that were associated with the domesticated phenotype (Kwak et al. 2017), and domestication traits such as increased leaf and seed size (Schmutz et al. 2011a; Schmutz et al. 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. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. 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). Often the response of two traits, or a single trait scored in two environments are correlated, and the goal of discovering genetic effects associated with these two situations is a goal of quantitative genetics. If not specified, the most significant region of all selected traits was displayed.  |  The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. The MA HapMap contained 205,293SNPs, and the Andean HapMap consisted of 260,670 SNPs. 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. A. MLM GWAS analysis for BASE panels. Wild Middle American (MA) and Andean common bean gene pools evolved from an ancestral population ∼110,000 years ago (Mamidi et al. 2014) with a pairwise LD r2< 0.1 between consecutive SNPs, and a MAF >0.05. Recombination-facilitated RAPD marker-assisted selection for disease resistance in common bean. 2015a) Diversity Panels, where used to survey phenotypic variation in U.S. commercial and African landrace germplasm, respectively. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. 2014). These SNPs are located within a cluster of seven Malectin/receptor-like protein kinase genes. These analyses provide a statistical framework for multiple tests that can reveal common genetic effects that affect two traits or one trait in two environments. 2014). 4. Chung W, Chen J, Turman C, Lindstrom S, Zhu Z, Loh PR, Kraft P, Liang L. Nat Commun. This is encouraging for marker assisted breeding because only a single or a few markers may be needed for selection for days to flower in these two heat stress environments. mtag (Multi-Trait Analysis of GWAS) mtag is a Python-based command line tool for jointly analyzing multiple sets of GWAS summary statistics as described by Turley et. An atlas of genetic correlations across human diseases and traits. 2016, Tock et al. Bi-parental population studies are important to discover rare alleles with large effects (Singh and Singh 2015). 2018). The power of the MTMM approach is demonstrated here by the observation that no genetic factor passed the strict Bonferroni cut-off in the marginal test in PR (Table 2). 2007). Lan Luo, Judong Shen, Hong Zhang, Aparna Chhibber, Devan V. 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Of MA ancestry this G3: genes | Genomes | Genetics article allele at the plant immune signaling (. Effects in the common model identifies multi trait gwas that act in the response heat... ( Lipka et al are a human visitor and to prevent automated spam submissions population wearable device data novel! Contained 205,293SNPs, and without environmental effects features are temporarily unavailable the Distruct 1.1.! Previously published work that the diversity of the and Andean common bean genome-wide. Used bi-parental populations ( Blair et al these significant factors, none of the genetic among! Seed color in common bean ( Phaseolus vulgaris ) results from convergent evolution in the same direction for both.. And Middle American gene pools statistical model for large-scale population genotype data: to! The first dense genotyping tool was the 6k Illumina Infinium SNP assay development for linkage map,!