multi trait gwas

Two peaks were observed on the distal end of Pv03 at ∼40Mb that were located 135.2 kb apart. doi: 10.1371/journal.pgen.1009089. Data from the UKB for all three traits has been previously published, although we re-analyze it in this paper with slightly different protocols. 2016), and available database resources (http://phaseolusgenes.bioinformatics.ucdavis.edu/) are enabling the discovery of genetic factors associated with the abiotic stress response. 2011a). 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. The first MTMM analysis evaluated DTF measured in HN and PR under heat stress conditions in 2016 (Figure 5A). GWAS were performed for each trait in each location under different stress conditions using untransformed data. Days to flower in Honduras, (Trait 1) and Puerto Rico (Trait 2) grown in 2016. 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. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Methods for meta-analysis of multiple traits using GWAS summary statistics. 1. 2016 and Kessler et al. It has been subsequently extended for many other analyses to better understand the genetic architecture of complex traits. Identification and potential use of a molecular marker for rust resistance in common bean. The interaction model identifies SNPs that act differentially for the two traits or locations. The peak SNP was located at 40,504,942 bp (P = 9.02E-06) and accounted for 9.9% of the variation. It can also be used as a tool to meta-analyze GWAS results. Green are the BASE_Meso genotypes and purple and the BASE_Anjdean genotypes. 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. For Juana Diaz, the panels were grown in separate drought and heat experiments, using a lattice design with three replications in 2014, an RCBD design with three replications in 2015, and an RCBD design with six replications under drought and four replications under heat in 2016. Pooling data across different experiments to extract factors that affect a phenotype across those experiments normally assumes the population parameters across the two experiments are equal. 2010). Three SNPs are located in this gene model, and these SNPs are in high LD relative to the peak SNP located 36kb distal to Phvul.003G181900. http://biorxiv.org/content/early/2017/03/11/115915.abstract, G1001799/MRC_/Medical Research Council/United Kingdom, P01 HD031921/HD/NICHD NIH HHS/United States, MR/N01104X/2/MRC_/Medical Research Council/United Kingdom, R01 HD060726/HD/NICHD NIH HHS/United States, MC_QA137853/MRC_/Medical Research Council/United Kingdom, R01 HD073342/HD/NICHD NIH HHS/United States, R01 MH107649/MH/NIMH NIH HHS/United States, U01 MH109539/MH/NIMH NIH HHS/United States, 647648/ERC_/European Research Council/International, P30 AG034532/AG/NIA NIH HHS/United States, R01 MH101244/MH/NIMH NIH HHS/United States, P01 AG005842/AG/NIA NIH HHS/United States, P30 AG012810/AG/NIA NIH HHS/United States, R01 AG042568/AG/NIA NIH HHS/United States, T32 AG000186/AG/NIA NIH HHS/United States, eScholarship, California Digital Library, University of California, Galesloot TE, Van Steen K, Kiemeney LALM, Janss LL, Vermeulen SH. For each trait and in each of two independent replication cohorts (HRS and Add Health, combined. A flexible system for the evaluation of these lines under different abiotic environments is designated here as the Bean Abiotic Stress Evaluation (BASE) approach. This phenotype data were then coupled with a robust SNP data set built with reads from a much larger set of individuals from a diverse pool of genotypes that represented the genetic diversity of the two bean gene pools. Importantly for small population sizes, the power of the MTMM approach is greater than the marginal GWAS tests typical of mixed model statistical methods because of the additional power obtained when data for the two traits (or environments) are considered jointly (Korte et al. 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. Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris). 2015 and Li et al. 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. 2013; Schmutz et al. 2014; Bello et al. Conserved molecular components for pollen tube reception and fungal invasion. An example is DTF and DTM, two traits often found to be correlated. Epub 2015 Sep 28. ROS regulation during abiotic stress responses in crop plants. 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. Automated feature extraction from population wearable device data identified novel loci associated with sleep and circadian rhythms. File S4 and S5 are text files containing un-imputed HapMap genetic data for Andean and MA genotypes respectively. 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). 2017; Minkoff et al. 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. 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. Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project. None of the effects acted differentially between DTF and DTM. GCTA currently supports the following analyses. Nat Genet. 2015). DISTRUCT: a program for the graphical display of population structure. Principal component analysis (PCA) was performed using the Prcom function in R, and relatedness was measured using the EMMA algorithm implemented in GAPIT. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. For all GWAS analyses, the SNP with the lowest P-value was chosen to represent that locus. This corresponded to a FDR of 0.9 and 0.1%2). 2012; R Core Team 2013) as described by Moghaddam et al. The experiment with the BASE_Meso in PR in 2016 population found 1) a significant genetic correlation between the two traits, 2) the environmental effects were not significant, and 3) both traits were heritable. -, Maier R, et al. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0469-9. Supplemental material available at Figshare: https://doi.org/10.25387/g3.7965305. A general linear model with fixed effect, and a univariate unified mixed linear model with random effect, and both fixed and random effects were tested for GWAS analysis for each trait. The tree was bootstrapped with 1,000 iterations using MEGA7 (Kumar et al. So, when data from multiple locations or stresses were merged, Z transformed data were used to provide a common relative estimate of the phenotype (Figure S1). The major SNP peak under heat (Figure 4D) was located at Pv09:17,981,113 (P = 1.08E-6) and accounted for 12.7% of the phenotypic variation (Table S2). 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. GAPIT: genome association and prediction integrated tool. 2011a; Schmutz et al. The BASE_Meso panel consists of 119 genotypes primarily from Race Mesoamerica within the Middle American gene pool. 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. Author Correction: Multi-trait analysis of genome-wide association summary statistics using MTAG. 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. 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. bioRxiv. Only recently did these gene pools undergo independent domestications about ∼7k years ago (Mamidi et al. 2017; Masachis et al. Population structure, as estimated by PCA, was considered a fixed effect, and relatedness, as estimated by EMMA, was considered a random effect. 2012; Mukeshimana et al. Please enable it to take advantage of the complete set of features! 2015a), flooding tolerance (Soltani et al., 2018), and agronomic traits such as phenology, aboveground biomass, and seed yield (Kamfwa et al. The primary role of HOS15 is the regulation of flowering under cold stress. We will perform single and multi Out of the 102,878 SNPs shared by the two gene pools, a reduced set of 1,882 SNPs with pairwise LD values less than 0.1 were chosen for a Bayesian structure analysis with genotypes used for the BASE populations. Previously, the ADP had only been genotyped with the ∼6k SNPs from the BARCBean 6K_3 BeadChip (Song et al. Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant× susceptible common bean (. These SNP data sets can also serve as a base to build much larger SNP sets such as those developed for maize (Glaubitz et al. The data were standardized using the Z transformation. This SNP was annotated as a missense variant. The usefulness of this approach was demonstrated when we compared standard DTF data pooled across locations and Macrophomina data pooled across stresses. 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. This result suggests that genetic factors that are common or show an interaction effect of significance between the two heat stress environments may be discovered. Pearson phenotypic, genetic and environmental correlations and joint heritability estimates for environmental DTF HN 2016 & DF PR 2016 and DTF PR 2016 & DTM PR 2016 combinations, Significant associations for days to flower measured in heat conditions in Nacaome, Hondouras (HN) and Juana Dias, PR (PR) on the BASE_Meso panel in 2016. Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris). MLM GWAS analysis for BASE panels. 2012). 2016) and Andean (Cichy et al. This makes it now possible for groups of bean researchers with modest resources to use the panels and SNP data sets developed here to search for genetic factors and polymorphisms that would be useful for improvement in their breeding programs. 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. We do not retain these email addresses. 2015a) Diversity Panels, where used to survey phenotypic variation in U.S. commercial and African landrace germplasm, respectively. 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, 2020 Dec 21. doi: 10.1038/s41562-020-00980-y. The range of SNPs per Mb is consistent across both and heterochromatic of the and Andean SNP data sets (Table S3). 2011b). Genetic analysis of flooding tolerance in an Andean Diversity Panel of dry bean (Phaseolus vulgaris L.). 2017;13:e1006836. Populations such as those used here that are small and pre-selected for abiotic stress tolerance will also exhibit high LD. The genotypes forming these panels were obtained from breeding programs at CIAT, Colorado State University, USA; Zamorano University, Honduras; USDA-ARS, Prosser, Washington; USDA-ARS, Puerto Rico; and the University of Puerto Rico. Days to flower GWAS results for the panel grown under heat in Honduras and Puerto Rico in 2016. Am J Hum Genet. Phenotypic diversity for seed mineral concentration in North American dry bean germplasm of MA ancestry. Bi-parental population studies are important to discover rare alleles with large effects (Singh and Singh 2015). Orthologs of this gene model are associated with plants response to heat stress (Li et al. Social Science Genetic Association Consortium. 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 â¦ Pei G, Sun H, Dai Y, Liu X, Zhao Z, Jia P. BMC Genomics. 2018 Mar;42(2):134-145. doi: 10.1002/gepi.22105. This was expected because beans grown in the target Central American region are almost exclusively from race Mesoamerica of the MA gene pool. 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. Thank you for sharing this G3: Genes | Genomes | Genetics article. The density of SNPs is essentially equal across the full genome of the two gene pools with an enrichment of SNPs in the heterochromatic regions. COMPETING FINANCIAL INTERESTS: The authors declare no competing financial interests. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. It is predicted these effects would be components of a shared functional pathway. 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 genotypes used to develop the HapMaps represent many of genotypes used for production purposes over the last 50 years in the USA and elsewhere. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. The CRIB project designed new MA and Andean germplasm panels that are specifically adapted to the climate challenged regions of Central America and Africa. 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 GWA analyses can be done on individual level data or on single-trait GWA summary statistics only. Table S2 contains a summary of MLM GWAS results and reports the peaks for each trait under various environmental conditions. SSGAC results, GPC results, GERA results, and 23andMe results for DEP all come from previously published work. Only processed reads with a quality score ≥ 20 and a minimum trimmed length of 180bp were used for mapping. Pearson phenotypic, genetic, and environmental correlations and heritabilities were estimated using the MTMM software (Korte et al. In the latter case, this interaction reflects the genotype x environment interaction effect that is important in the context of breeding for multiple environments. By contrast, association panels can sample variation across a larger number of genotypes and be used to discover both large or small effect genetic factors that are associated with the plant’s response to abiotic stress conditions (Risch 2000; Mamidi et al. 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. While appealing, most existing methods focus on analyzing a relatively small number of traits, and may yield â¦ These two are significant common factors and had the same positive effect at both locations (Figure 5A). The SPAD rating under heat stress is one indicator of variation in the response to heat stress. 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. For DTF at the same location and years, the major QTL peak from the joint MLM analysis was located in the Pv03:40.46-40.50 Mb interval (Figure 3B). Genome-wide association study of agronomic traits in common bean. 7. A Phaseolus vulgaris diversity panel for Andean bean improvement. The advantages and limitations of trait analysis with GWAS: a review. 2010). Phylogenetic relatedness of the full set of 807 genotypes, from the panels from which SNP reads were obtained, was investigated by calculating a maximum likelihood (ML) phylogenic tree using the SNPhylo pipeline (Lee et al. Ray D(1), Boehnke M(1). 2012) GWAS approaches to discover genetic factors associated with several phenotypic traits. In Arabidopsis, BIM1 functions in the brassinosteroid pathway to regulate flowering through its interaction with SPL8 to promote anthesis (Xing et al. For ease of presentation, it is Consistent with the individual trials, the peak SNP accounted for 8.4% of the variation (Table S2). This procedure considers the effects of population structure and/or relatedness in the calculation. If not specified, the most significant region of all selected traits was displayed. 1991; Schmutz et al. Compare GWAS locus for multiple traits within given region. Maximum likelihood phylogenic tree of 769 genotypes from Andean and Middle American gene pools using 5,637 loci with LD < 0.1. 2012). 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. Individual MA and Andean haplotype maps (HapMap) were developed after final SNP filtering and imputation. Table S1 contains the list of BASE genotype names. Recently, an Andean Diversity Panel (ADP; n∼350) was developed (Cichy 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. 2015b), disease resistance (Zuiderveen et al. 2012). Structure was based on the number of PCAs that accounted for 25–50% of the phenotypic variation. 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). Manhattan plots of GWAS and MTAG results, Fig. 2019 Jul;51(7):1190. doi: 10.1038/s41588-019-0444-5. PLoS One. Online ahead of print. 2016) protocol were pooled, and new SNP calls made. This peak QTL region is located in a cluster of chitinase genes. Epub 2018 Jun 16. This suggested that common genetic effects were controlling the phenotypic response in the two environments. 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. For both traits, the pooled data identified the same significant peak SNP regions that were observed in the individual analyses with the untransformed data. Of these significant factors, none of them exhibited an interaction effect, rather many were found to be common between the two environments. (F Joint heat and drought SPAD reading GWAS analysis. Sequencing barcodes were removed and low-quality sequences were trimmed. 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). 2016). We introduce multi-trait analysis of GWAS (MTAG), a method for joint analysis of summary statistics from genome-wide association studies (GWAS) of different traits, possibly from overlapping samples. (2016)] of were remapped, and SNPs were called. 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. 2014) in distinct locations to form two distinct domesticated clades. 2014). Therefore, selection on these markers can have positive effects in the same direction for both traits. 5. | GWAS are typically based on using linear mixed models to fit one SNP at a time to a single trait (Hackinger and Zeggini 2017). Copyright © 2021 by the Genetics Society of America, R Core Team, 2013 R: A language and environment for statistical computing. Quantitative trait loci associated with drought tolerance in common bean. Turley P, Walters RK, Maghzian O, Okbay A, Lee JJ, Fontana MA, Nguyen-Viet TA, Wedow R, Zacher M, Furlotte NA; 23andMe Research Team; Social Science Genetic Association Consortium, Magnusson P, Oskarsson S, Johannesson M, Visscher PM, Laibson D, Cesarini D, Neale BM, Benjamin DJ. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. The MTMM statistical method and scripts (, Centro Internacional de Agricultura Tropical. In gene regions harboring â¦ SPAD-related QTL can point to important genetic factors associated with one aspect of the heat stress response. GWAS analysis for SPAD rating for BASE_Meso grown under heat (D) and drought (E) in Puerto Rico in separate trials in 2016. 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. 2018). 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 variation explained by a significant marker was described as a likelihood-ratio-based R2 (R2LR; Sun et al. Results: Many existing GWAS summary data-based association test methods have relied on ad hoc approach or crude Monte Carlo approximation. (Rosenberg 2004). 1993, 1996) while being monomorphic in the other pool regardless of whether the genotype is resistant or susceptible. 2005), which calculates the total change in log probability of data between consecutive k values, was used to determine the number of clusters. 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. Resequencing of Common Bean Identifies Regions of Inter–Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding. 2017 at <. NIH We apply MTAG to summary statistics for depressive symptoms (Neff= 354,862), neuroticism (N= â¦ The experimental lines were planted on raised 1.5 m wide beds with two rows spaced 0.6 m apart. Tepary 22 fell in between the two clusters. Three other SNPs (Pv08:9,135,122 bp, Pv11: 41,873,950 bp; Pv11: 47,305,350 bp) defined other individual loci, and each accounted for more than 7% of the variation, and along with the peak SNP, these four SNPs collectively accounted for 20.2% of the variation in yield under heat stress (Table S2). 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. 1990; where 1 = no visible symptoms and 9 = completely susceptible and dead plants), SPAD index measured using a Konica Minolta SPAD 502 Chlorophyll meter device for each individual plot, and days to maturity (DTM) representing the duration from planting to physiological maturity. Recent advancements such as a reference bean genome sequence (Schmutz et al. 2018; Stegmann et al. The BASE_Andean panel contained 124 genotypes. As mentioned above, both Nacome, HN and Juana Diaz, PR are high heat stress environments. Evaluation of MTAG’s standard errors…, Fig. Variation explained in mixed-model association mapping. The MA HapMap contained 205,293SNPs, and the Andean HapMap consisted of 260,670 SNPs. 2007) to estimate the amount of variation explained by the most significant SNP within a GWAS peak. Multivariate genome-wide analysis of education, socioeconomic status and brain phenome. Herein we focus on climate change conditions in Central America using the new MA panel. 6. 3. A comparison of multivariate genome-wide association methods. 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. 1986; Mamidi et al. Effects of high‐temperature stress on microsporogenesis in heat‐sensitive and heat‐tolerant genotypes of. In addition, MTMM testing can uncover interaction genetic effects that act in the opposite direction between two traits or for a single trait in two environments. Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). 2016), nutritional (Mafi Moghaddam et al. Domestication within each of the clades involved between 748 (Andean) and 1748 (MA) genes, but only 59 of genes were shared (Schmutz et al. 7. 2008) to calculate that number of markers which in turn was used to determine our P-value cutoff of -log10(P) = 4.1. 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. Phaseolin‐protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. 2014; Lobaton et al; 2018). 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. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Given the large number of genotypes in each of the two HapMaps, researchers can now design experiments to capture phenotypic data from all or a subset of the genotypes in the HapMap populations and then perform GWAS analyses with a very large SNP dataset to discover important genetic factors controlling traits of interest. A reference genome for common bean and genome-wide analysis of dual domestications. [] and Yu et al. Clipboard, Search History, and several other advanced features are temporarily unavailable. 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). Each gene pool has specific agronomic, morphological, physiological and molecular characteristics, and allele frequencies differ between the two gene pools for genetic factors controlling a trait (Singh et al. The un-imputed HapMap data for each gene pool can be found in S4 and S5 text files. 2018). 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 2009) were used to align the data against reference genome Phaseolus vulgaris v2.1, and to index, and sort the aligned reads (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris). USA.gov. 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. From a plant breeding perspective, the most significant SNP within a cluster of protein! Multiple origins of the plant cell membrane MTMM software ( Korte et al wild common gene. And 0.24 or BASE_Meso multi trait gwas marker for rust resistance in common bean used bi-parental populations ( Blair et.... Time in dry bean ( Phaseolus vulgaris ) using multilocus sequence data and MTAG-based polygenic scores, Fig grm estimating. To Empoasca in common bean > 0.05 using mhtplot function from R package Aulchenko... Located on Pv08 ; 51 ( 7 ):1190. doi: 10.1038/s41467-019-08535-0 and reproduction ( et... Under multiple temperature stresses genetic effects, Korte et al ; 20 ( Suppl 1 ):569.:. Hapmap consisted of 260,670 SNPs population genotype data: applications to inferring genotypes! Pleiotropic locus 15q24.1 Reveals a Gender-Specific association with Neovascular but not Atrophic Age-Related Macular Degeneration ( Amd.! > 0.05 using mhtplot function from R package gap ( Zhao 2007 ) to estimate the amount of variation the. R: a program for the panel grown under heat stress being monomorphic in two. 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Reading GWAS analysis ( Korte et al with GWAS: a MapReduce framework for analyzing next-generation DNA sequencing data survey.: Body traits are generally controlled by several genes in vertebrates ( i.e applied the simpleM algorithm ( Gao al.

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