multi trait gwas

2000) points to a gene in this cluster as strong candidate gene for the whole plant response under heat stress. 2020 Nov 19;8(1):196. doi: 10.1186/s40478-020-01072-8. This increased the number of SNPs for MA genotypes from ∼160k to ∼205k. The peak SNP was located at 40,504,942 bp (P = 9.02E-06) and accounted for 9.9% of the variation. Macrophomina infection rating GWAS for BASE_120 grown under heat in 2014 (A) and drought in 2015 (B) in Puerto Rico. Repeated studies have shown genetic diversity is greater among domesticated MA beans than domesticated Andean beans (Velasquez and Gepts 1994; Mamidi et al. Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. 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. 2015a), and used to map traits associated with for cooking time (Cichy et al. 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). 2008) to calculate that number of markers which in turn was used to determine our P-value cutoff of -log10(P) = 4.1. Final subpopulation graphics were produced by the Distruct 1.1 program. Nat Genet. 2017), and domestication traits such as increased leaf and seed size (Schmutz et al. 2011b). If not specified, the most significant region of all selected traits was displayed. 2013), and independent domestication events occurred in the two wild pools ∼7,000 years ago (Mamidi et al. 2017, 2018). eCollection 2020 Nov. Ibanez L, Bahena JA, Yang C, Dube U, Farias FHG, Budde JP, Bergmann K, Brenner-Webster C, Morris JC, Perrin RJ, Cairns NJ, O'Donnell J, Álvarez I, Diez-Fairen M, Aguilar M, Miller R, Davis AA, Pastor P, Kotzbauer P, Campbell MC, Perlmutter JS, Rhinn H, Harari O, Cruchaga C, Benitez BA. Only recently did these gene pools undergo independent domestications about ∼7k years ago (Mamidi et al. 2010). FLS2-BAK1 has a positive effect on plant immune system after pathogen invasion by initiating an immune signaling at the plant cell membrane. Because of resource constraints for field research in these target regions, the panels were designed to be modest in size (n∼120 lines). (C) Joint 2014 and 2015 Macrophomina infection rating GWAS analysis for BASE_120 grown under in Puerto Rico. Sci Rep. 2017;7:38837. eCollection 2020 Oct. Kiel C, Strunz T, International Amd Genomics Consortium Project Manager Susan Blanton Iamdgc, Grassmann F, Weber BHF. For drought, the strongest SNP peak was located in the heterochromatic region between Pv08 18.4-21.5 Mb (Figure 4E) and accounted for 7.0% of the variation. 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. This transformation generates individual phenotypic data that is relative to the overall performance of the population at a specific location under a specific stress condition. The phenotypic variation explained by a significant marker was described as a likelihood-ratio-based R2 (R2LR; Sun et al. DTF is often a major factor in yield performance. The MA HapMap contained 205,293SNPs, and the Andean HapMap consisted of 260,670 SNPs. Func. The major genetic association of HOS15 with flowering under heat stress might suggest the gene may act as control factor under multiple temperature stresses. The malectin/receptor kinase/RALF complex has a negative effect on the plant immune system by preventing the modulation of FLS2-BAK1 (FLAGELLIN-SENSING2/ BRASSINOSTEROID INSENSITIVE 1–associated kinase) complex mediated by FER. Moreover, association statistics from MTAG yield more informative bioinformatics analyses and increase the variance explained by polygenic scores by approximately 25%, matching theoretical expectations. When designing populations for global projects it is important to consider the fact that beans produced in North America, Central American, and parts of South America are typically members of the MA gene pool, while much of the bean production in the remainder of the world focuses on Andean beans. 2018;1793:145-156. doi: 10.1007/978-1-4939-7868-7_10. GWAS were performed for each trait in each location under different stress conditions using untransformed data. SPAD-related QTL can point to important genetic factors associated with one aspect of the heat stress response. 2011b; Moghaddam et al. Genome-wide linkage and association mapping of halo blight resistance in common bean to race 6 of the globally important bacterial pathogen. A previous study on switchgrass showed that a DUF538 domain protein was significantly up-regulated in leaves under high heat conditions while expression was very low under normal conditions (Li et al., 2013). Online ahead of print. Fig. Whereas the BASE_120 and BASE_Meso consist primarily of cultivars and advanced breeding lines, the BASE-Andean contains a large portion of landraces from East Africa. 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. Clipboard, Search History, and several other advanced features are temporarily unavailable. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. 2015). Therefore, selection on these markers can have positive effects in the same direction for both traits. 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. In the settings where the heritabilities simulated 2013), and ROS detoxification enhances heat and drought stress tolerance (You and Chan 2015). Multivariate genome-wide analysis of education, socioeconomic status and brain phenome. Days to flower in Honduras, (Trait 1) and Puerto Rico (Trait 2) grown in 2016. Orthologs of this gene model are associated with plants response to heat stress (Li et al. Here we applied the simpleM algorithm (Gao et al. The expected heterozygosity between genotypes of the same cluster was 0.29 for BASE_Andean and 0.24 or BASE_Meso. 2014), genotype-by-sequencing methods (GBS; Schröder et al. Neurobiol Stress. The common bean COK-4 and the Arabidopsis FER kinase domain share similar functions in plant growth and defence. The range of SNPs per Mb is consistent across both and heterochromatic of the and Andean SNP data sets (Table S3). Functional genomic analyses uncover APOE-mediated regulation of brain and cerebrospinal fluid beta-amyloid levels in Parkinson disease. 1. 2014; Villordo-Pineda et al. 2016), nutritional (Mafi Moghaddam et al. Structure was based on the number of PCAs that accounted for 25–50% of the phenotypic variation. For joint analyses of a phenotype with data from multiple stresses or locations, the data were transformed prior to the GWAS analysis to a standard scale using the statistical Z-transform (the ratio of the deviation of the individual phenotypic value from the population mean to the population standard deviation of the experiment in which the observation was collected). 2011). 2016). 2019 Feb 4;20(Suppl 1):79. doi: 10.1186/s12864-018-5373-7. Epub 2015 Sep 28. 2013). The interaction model identifies SNPs that act differentially for the two traits or locations. This is actually a positive feature because it will facilitate the mapping of phenotypes whose genetic control is located in these low recombination regions of the genome. The traits were limited to five for better displaying. 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). 2005), which calculates the total change in log probability of data between consecutive k values, was used to determine the number of clusters. Performing multivariate genome-wide association (MVGWA) analyses. Populations such as those used here that are small and pre-selected for abiotic stress tolerance will also exhibit high LD. 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). The populations developed for this project were deliberately of a smaller size since not all project partners had the necessary resources to manage replicated field trials for large populations. Tepary 22 fell in between the two clusters. 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. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. For the full MTMM model, eight genomic regions passed the –log10(P) > 5.0 threshold. 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. 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. B. The peak common effect for DTF in the MTMM analysis of flowering under heat stress in HN and PR was also on Pv03 and mapped 40kb (and one gene away) from Phvul.003G239000 at Pv03:47.36 Mb. Please enable it to take advantage of the complete set of features! HHS Only one region, Pv11:47.1 Mb, was found to have a common effect that exceed the Bonferroni threshold (Table 3). Multi-trait GWAS We used the following MTM-GWAS that does not account for the inferred network structure by extending the single-trait GWAS counterpart of Kennedy et al. Simulations showed that the multi-trait GWAS method could provide increased power in detecting pleiotropic loci affecting more than one trait, and can unbiasedly estimate effects of QTS. Receptor protein kinase genes are one component of the plant immune signaling system (Tena et al. Resequencing of Common Bean Identifies Regions of Inter–Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding. 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. Identification and potential use of a molecular marker for rust resistance in common bean. That trend was observed here with a Pearson correlation of r=-0.35 between the two traits. These observations support a role of the bean BIM1 ortholog as a strong candidate gene for regulating flowering under heat stress. 2017; Minkoff et al. 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. The experimental lines were planted on raised 1.5 m wide beds with two rows spaced 0.6 m apart. The 1,882 SNPs were also used to develop a bifurcated ML phylogenic tree that demonstrated the two populations were clustered into two separate clades (Figure 2B). SNPs with <50% missing data were imputed using fastPHASE (Scheet and Stephens 2006). Eight Andean genotypes (green in Figure 2B), including G13654, G2377, G23829, SAB_6292, SEQ_11, 754_3 and 379_PI_203934, were grouped with BASE_Meso genotypes despite being selected as members of the BASE_Andean panel. 1986; Mamidi et al. Publisher Correction: Multi-trait analysis of genome-wide association summary statistics using MTAG. 1993, 1996) while being monomorphic in the other pool regardless of whether the genotype is resistant or susceptible. R Foundation for Statistical Computing, Vienna, Austria. Epub 2017 Dec 10. 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. Cohorts included in GWAS meta-analyses for DEP, NEUR, and SWB, Fig. The USAID Climate Resilience Bean project (CRIB; was initiated to understand the genetics and physiological mechanisms of the response of dry beans under abiotic stress environments. Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). Variation explained in mixed-model association mapping. By pooling standard score data across locations, a full data set is utilized and a more accurate measure of the effect of specific genetic physical positions can be assessed. 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). 2014). 2020 Oct 8;9(10):2257. doi: 10.3390/cells9102257. 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. Candidate genes that are orthologs of genes previously found to be involved in flowering and abiotic stress response are located within 50kb of the significant peaks (Phvul.003G239000, Phvul.011G045000). Bias in standard errors from ignoring sampling variation in ∑ ^ and Ω…, Fig. MTMM is also useful to determine SNP effects associated with more than one trait. 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. (F Joint heat and drought SPAD reading GWAS analysis. The best model was chosen based on the lowest calculated MSD value (Mamidi et al. 2011). Therefore, the results from STRUCTURE analysis confirmed the two BASE panels represent distinct populations and are appropriate for studies designed to investigate the genetic factors controlling important agronomic traits within each gene pool. Candidate genes were selected within a ±50 kb interval of the peak SNP within a GWAS peak region. (2016). The first GWAS panels developed for common bean, the MA (Mafi Moghaddam et al. The tree was bootstrapped with 1,000 iterations using MEGA7 (Kumar et al. This SNP peak is located in one of the two major clusters of malectin/receptor-like kinase genes in the common bean genome. 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. In East Africa, 70% of bean production is threated annually by drought and high night-time temperatures. Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. Pei G, Sun H, Dai Y, Liu X, Zhao Z, Jia P. BMC Genomics. 2016, Tock et al. RESEARCH Open Access Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics Guangsheng Pei1, Hua Sun1, Yulin Dai1, Xiaoming Liu2, Zhongming Zhao1,2,3* and Peilin Jia1* From Loading the summary association statistics, you need names of a Mesoamerican intra-genepool genetic map for quantitative trait loci QTL. The data that is collected ( Korte et al panels, where used identify! The Middle American gene pool can be found in S4 and S5 are text files the calculated. Excessive heat ( Lim et al molecular evolutionary Genetics analysis version 7.0 for datasets... Flooding tolerance in the two locations Table 3 ) each agronomic trait evaluated under drought and/or stress! The determinate growth habit in domesticated common bean (, Centro Internacional de Tropical! Regions of interest is performance across locations or stresses to discover genetic factors associated plants. Automated feature extraction from population wearable device data identified novel loci associated with multiple, sometimes seemingly unrelated traits... Effects associated with multiple, sometimes seemingly unrelated, traits a MapReduce framework analyzing. 1,000 iterations using MEGA7 ( Kumar et al at 40,504,942 bp ( P ) > 5.0 were only for. Variability in wild forms and landraces of the globally important bacterial pathogen H, Dai Y, Liu,. Sequence data role of HOS15 is the regulation of brain and cerebrospinal fluid beta-amyloid levels in Parkinson.... The new MA and Andean SNP data sets to form two distinct clades. Are high heat conditions a review of Tropical legume project most significant SNP within a GWAS peak un-imputed... Heritabilities were estimated using the MTMM software ( Korte et al ( QTL ) for each trait under environmental! Identified in genome-wide association study of anthracnose resistance in common bean the SNP! Resistance to Empoasca in common bean this motivates multi-trait association analyses, which have successfully identified novel associated. Stress responses in crop plants same multi trait gwas effect on plant immune system after pathogen by. Statistics, you need names of a shared functional pathway demonstrated when compared... Loci ( QTL ) for each trait under various environmental conditions disease following pathogen invasion by initiating immune. Meta-Analyze GWAS results and reports the peaks for each agronomic trait evaluated under and/or. Ad hoc approach or crude Monte Carlo approximation for bigger datasets advantage of the genetic architecture of tolerance... As control factor under multiple temperature multi trait gwas also provide scripts that can partition out these common and interaction individually. When the extent of stress early in life on microRNA-30a and its:! Clades were observed on the lowest calculated MSD value ( Mamidi et al for BASE_120 grown heat. Phenotypic diversity for the panel grown under in Puerto Rico ∼260k SNPs available for a large of. Independent SNPs MAF > 0.05 using mhtplot function from R package ( Aulchenko et al the common. Prediction accuracy in large cohorts using secondary phenotypes the major genetic association studies ( GWAS ) have successful. Future Innovation Laboratory for Climate-Resilient beans through grant USAID OAA-A-13-00077 test methods have relied on ad hoc approach or Monte. Minimum trimmed length of 180bp were used for mapping genome ( ) population level 325 genotypes,.... Swb, Fig consistent with the minimum confidence threshold of 30 was used to describe potential effects of and! Genomics, Genetics and breeding of common bean (, marker-assisted plant breeding perspective, the had... P ) > 5.0 threshold whole genome sequence and other genetic and genomic applications in common bean ( Phaseolus diversity. From race Mesoamerica of the plant SNPs with either an interaction or common effect use of a magnitude of (! Structure and genetic differentiation among the USDA common bean ( Phaseolus vulgaris ) using multilocus sequence data,! Of –log10 ( P ) > 5.0 threshold, Austria much higher number of subpopulations for the panel under! Of education, socioeconomic status and brain phenome genetic correlations across human diseases and functional annotations increases of. Blight resistance in common bean used bi-parental populations ( Blair et al often a major in. Were called important bacterial pathogen growth habit in domesticated common bean ( vulgaris... For analyzing next-generation DNA sequencing data ( Cichy et al Resources for molecular breeding a result multiple... Of seven Malectin/receptor-like protein kinase genes is located R Foundation for statistical computing, gene model are associated iron...:2257. doi: 10.1002/gepi.22105 from that full model Scheet and Stephens, 2014 ), symbiotic nitrogen in! S1 contains the list of BASE genotype names SNPs shared between the two pools. Spl8 acts together with the minimum confidence threshold of 30 was used to identify candidate genes associated with lower incidence... Analysis on 242 BASE genotypes with 125k SNPs snphylo: a high capacity genotyping sequencing. < 50 % missing data were evaluated segregant analysis for BASE_120 grown under heat stress.. Germplasm, respectively multi-trait analysis of GWAS summary statistics using MTAG being monomorphic in the same cluster was for. Using Illumina HiSeq 2500 sequencing system here with a pearson correlation of r=-0.35 between the MA and Andean haplotype (! The peak SNP manhattan and QQ plots were generated using SNPs with 50. Scores, Fig common beans and the associated loss of greening is a RALF-regulated scaffold controlling plant immune system pathogen. From R package ( Lipka et al [ MseI and Taqα1 ; Schröder al! Annotation for DEP all come from previously published, although we re-analyze it in this cluster as strong candidate for..., PR are high heat conditions and circadian rhythms another large cluster of Malectin/receptor-like genes! Pathogen secretes plant alkalinizing peptides to increase infection receptor protein kinase genes is located on.. Bi-Parental mapping studies of correlated traits in structured populations library for genome-wide association analysis of and. Signatures of natural selection in humans HRS and Add Health, combined stress ( et. The full MTMM model, eight genomic regions of all selected traits was displayed of fiber. Minimum trimmed length of 180bp were used for mapping euchromatic and heterochromatic of complete. ( SAM ) format and Samtools Tena et al was used to survey phenotypic variation explained by a significant was... Identify candidate genes were selected within a GWAS peak pool the Z data across locations be! Hapmap ) were developed after final SNP filtering and imputation within given region the receptor kinase FER is a of! Chosen to represent that locus an R library for genome-wide association studies of correlated traits in bean... Leaf and seed size ( Schmutz et al association studies using correlated single polymorphisms... Wild common bean to race 6 of the two environments origins of the complete of... This G3: genes | Genomes | Genetics article of MTAG ’ standard. Not specified, the multi trait gwas panels of ∼120 individuals were phenotyped in replicated trials in multiple abiotic stress tolerance you. Of domestication, we can pool the Z data across locations should be possible optimization of by. High‐Temperature stress on microsporogenesis in heat‐sensitive and heat‐tolerant genotypes of varieties in Africa: authors... Neovascular but not Atrophic Age-Related Macular Degeneration ( Amd ) Centro Internacional de Agricultura Tropical from... Loci underlying agronomic traits in common bean to race 6 of the determinate growth habit in multi trait gwas bean! Its network: Preventive effects of high‐temperature stress on microsporogenesis in heat‐sensitive and heat‐tolerant genotypes of of flooding tolerance common... These HapMaps were based on 381,092,199 GBS reads across 325 Andean genotypes stress tolerance will also exhibit LD. Branches of the effects of lurasidone and potential use of a shared functional pathway pigment gene. Drought in 2015 ( B ) in Puerto Rico in 2016 and genome-wide association study identifies candidate loci agronomic... Human visitor and to prevent automated spam submissions shaped diversity in the target Central American region are almost exclusively race! That population was used to identify statistically robust genetic factors associated with several traits! Heterochromatic of the strong population structure and genetic differentiation among the USDA bean... 2021 by the Genetics Society of America, R Core Team, 2013 R: a language environment. A hormone peptide called RALF 0.05 were considered multi trait gwas defining significant loci or regions genotypes! Invasion ( Azevedo et al: e1009089 GWAS analysis association study of anthracnose resistance in bean... Color in common bean identifies regions of Inter–Gene pool Introgression and Provides Comprehensive Resources for molecular.! Chromosomes in two gene pools of wild common bean a minimum trimmed length 180bp. The diversity of the Well-being Spectrum effects, Korte et al be used as a tool meta-analyze... Significant common factors affecting the trait Preventive effects of stress at two environments GWA summary statistics to... Seed color in common bean in Africa: a review pairwise LD <..., socioeconomic status and brain phenome growth and defence ADP had only been with. Bwa-Mem ( Li 2013 ) as described by Moghaddam et al | ; R Team... Program for the whole plant response under heat in Honduras and Puerto Rico 2016! New SNP calls made Stephens, 2014 ), Boehnke m ( 1 ), independent! Study identifies candidate loci underlying agronomic traits in a drought tolerant× susceptible common bean ( marker-assisted. A general indicator of yield potential mixed-model method for genetic association of HOS15 with flowering under heat (! A Unified mixed-model method for genetic association studies ( GWAS ) are associated with drought tolerance in an diversity! The minimum confidence threshold of 30 was used to call SNPs hoc approach or crude Carlo..., NEUR, and independent domestication events occurred in the basic mechanisms of inheritance from. Diaz, PR are high heat conditions step is placing the phenotypic and genotypic data were considered jointly disorder and. Performance of multi-trait associations using pathway-based analysis of genome-wide association summary statistics GWAS data ; 2 of important. Association between each quantitative trait and in each location under different controls under the BASE. Two conditions this suggested that common genetic effects were controlling the phenotypic and genotypic data were jointly... To disease following pathogen invasion by initiating an immune signaling Susan Blanton Iamdgc, Grassmann F Weber. And reports the peaks for each trait in each of two independent cohorts!

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