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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). The analysis was performed with the genABLE R package (Aulchenko et al. Regression-based test of replicability of MTAG-identified loci, Fig. 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). 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. These observations support a role of the bean BIM1 ortholog as a strong candidate gene for regulating flowering under heat stress. 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. At this position, three SNPs are located in Phvul.003G181900, an ortholog of the Arabidopsis BIM1 gene. 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. We tested that premise on two data sets. With these considerations in mind, the three panels of ∼120 individuals were phenotyped in replicated trials in multiple abiotic stress conditions. Again, because the trials were under two stress conditions, Z transform data were evaluated. Clipboard, Search History, and several other advanced features are temporarily unavailable. Phenotypic diversity for seed mineral concentration in North American dry bean germplasm of MA ancestry. al. (2018). 2008) to calculate that number of markers which in turn was used to determine our P-value cutoff of -log10(P) = 4.1. 2014; Villordo-Pineda et al. 5. 2020 Dec 21. doi: 10.1038/s41562-020-00980-y. This suggested that common genetic effects were controlling the phenotypic response in the two environments.  |  The peak MLM QTL for SPAD rating under heat stress is located at Pv09:17.99 Mb, and this QTL is located within a cluster of basic chitinase genes. 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. Resequencing of Common Bean Identifies Regions of Inter–Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding. 2017, 2018). 2014). 2017;13:e1006836. A Phaseolus vulgaris diversity panel for Andean bean improvement. Regression-based test of replicability of…, Fig. Manhattan plots of GWAS and MTAG results, Fig. The MA HapMap contained 205,293SNPs, and the Andean HapMap consisted of 260,670 SNPs. The multi-trait GWAS was conducted using GEMMA (Zhou and Stephens, 2014). Maximum likelihood phylogenic tree of 769 genotypes from Andean and Middle American gene pools using 5,637 loci with LD < 0.1. 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. The critical P -value for significant QTNs in the GEMMA and EMMAX methods was determined by Bonferroni correction: α =1/54 294 = 1.84×10 –5 ( Xu et al ., 2018 b ; Zhang et al ., 2019 b ). Orthologs of this gene model are associated with plants response to heat stress (Li et al. 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). Genetic analysis of flooding tolerance in an Andean Diversity Panel of dry bean (Phaseolus vulgaris L.). Biological annotation for DEP using…, Fig. The first MTMM analysis evaluated DTF measured in HN and PR under heat stress conditions in 2016 (Figure 5A). The expected heterozygosity between genotypes of the same cluster was 0.29 for BASE_Andean and 0.24 or BASE_Meso. 2015) and discovered several quantitative trait loci (QTL) for each agronomic trait evaluated under drought and/or heat stress. Table S2 contains a summary of MLM GWAS results and reports the peaks for each trait under various environmental conditions. 2012; McClean 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). The USAID Climate Resilience Bean project (CRIB; https://plantscience.psu.edu/research/labs/roots/projects/usaid-crb) was initiated to understand the genetics and physiological mechanisms of the response of dry beans under abiotic stress environments. GAPIT: genome association and prediction integrated tool. GCTA (Genome-wide Complex Trait Analysis) was initially designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (i.e., the GREML method). MTMM is also useful to determine SNP effects associated with more than one trait. bioRxiv. MTMM methods are another way of maximizing the data that is collected (Korte 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. See this image and copyright information in PMC. Development and delivery of bean varieties in Africa: the Pan-Africa Bean Research Alliance (PABRA) model. []. Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. Macrophomina infection rating GWAS for BASE_120 grown under heat in 2014 (A) and drought in 2015 (B) in Puerto Rico. The BASE_120 panel consists of 93 genotypes from the MA gene pool, 22 genotypes from the Andean gene pool, and four tepary bean (Phaseolus acutifolius) genotypes. Nat Genet. Recombination-facilitated RAPD marker-assisted selection for disease resistance in common bean. 2014;9:e95923. Two distinct clades were observed that separated the MA and Andean genotypes. Inference of population structure using multilocus genotype data. At the proximal end of this interval, gene model Phvul.003G181900 is located. 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). 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. In East Africa, 70% of bean production is threated annually by drought and high night-time temperatures. Another large cluster of Malectin/receptor-like protein kinase genes is located on Pv08. Genome-wide association analysis identifies candidate genes associated with iron deficiency chlorosis in soybean. This peak QTL region is located in a cluster of chitinase genes. For the full MTMM model, eight genomic regions passed the –log10(P) > 5.0 threshold. 2013; Schmutz et al. [ 38 ] [] and Yu et al. 2005), which calculates the total change in log probability of data between consecutive k values, was used to determine the number of clusters. (2016). This will not be the case when the extent of stress at two environments cannot be controlled. Publisher Correction: Multi-trait analysis of genome-wide association summary statistics using MTAG. URL. 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). MultiABEL does NOT require different single-trait GWAS having been performed in exactly the same individuals. The genetic architecture of dietary fiber and olidosaccharide content in a MA panel of edible dry bean (. Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection. Methods Mol Biol. The Sequence alignment/map (SAM) format and SAMtools. Genome-wide association study of anthracnose resistance in Andean beans (Phaseolus vulgaris). 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). SPAD readings are a general indicator of greenness of the plant. 2018; Stegmann et al. 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). This supports other observations that the diversity of the Mesoamerican race is greater than that found within Andean genotypes. Conserved molecular components for pollen tube reception and fungal invasion. The peak SNP was located at 40,504,942 bp (P = 9.02E-06) and accounted for 9.9% of the variation. PDF | Background: Body traits are generally controlled by several genes in vertebrates (i.e. 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. 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. 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. Cells. BASEMeso = green; BASEAndean = blue. 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. We will perform single and multi Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris). Supplemental material available at Figshare: https://doi.org/10.25387/g3.7965305. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Multi-trait GWAS Simulator User Manual Heather F. Porter & Paul F. O’Reilly multitraitgwas@gmail.com MRC Social, Genetic and Developmental Psychiatry Centre, Contents 1 Background 3 2 Software program 4 3 R packages 4 4 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). While the full MTMM model uncovers both common and interaction genetic effects, Korte et al. Curr Opin Genet Dev. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. -, Porter HF, O’Reilly PF. (F Joint heat and drought SPAD reading GWAS analysis. Yield GWAS results for the panel grown under heat in Honduras and Puerto Rico in 2016. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. The critical step is placing the phenotypic data on a standard scale. 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. However, recent GBS methods generated a much higher number of SNPs per population for fine-mapping genomic regions of interest (Moghaddam et al. It is predicted these effects would be components of a shared functional pathway. Bean productivity on these farms is reduced by high ambient temperatures and drought that affect development and reproduction (Buruchara et al. doi: 10.1371/journal.pgen.1009089. We apply MTAG to summary statistics for depressive symptoms (N eff = 354,862), neuroticism (N = 168,105), and subjective well-being (N = 388,538). This research was supported by USAID Feed the Future Innovation Laboratory for Climate-Resilient Beans through grant USAID OAA-A-13-00077. 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). 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. 2012) GWAS approaches to discover genetic factors associated with several phenotypic traits. Relationship among the BASE_Meso and BASE_Andean diversity panels. 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). In this way, we can pool the Z data across locations or stresses to discover common factors affecting the trait. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Author Correction: Multi-trait analysis of genome-wide association summary statistics using MTAG. 2017; Minkoff et al. We apply MTAG to summary statistics for depressive symptoms (N eff= 354,862), neuroticism (N = 168,105), and subjective well-being (N = 388,538). 2018). DISTRUCT: a program for the graphical display of population structure. 2013; Schmutz et al. 2012; Mukeshimana et al. 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). On Pv11, significant peaks were observed at 4.0 Mb and 45.3 Mb. Functional genomic analyses uncover APOE-mediated regulation of brain and cerebrospinal fluid beta-amyloid levels in Parkinson disease. 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. 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. GWAS experiments are also revealing that adaptation to environmental stress conditions evolved differentially in the two gene pools as exemplified by the discovery that distinct genetic factors are associated with the response to flooding in the two gene pools (Soltani et al. 2015;96:283–94. 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. 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. -, Baselmans BML, et al. 1986; Mamidi et al. Repeated studies have shown genetic diversity is greater among domesticated MA beans than domesticated Andean beans (Velasquez and Gepts 1994; Mamidi et al. Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean. Structure was based on the number of PCAs that accounted for 25–50% of the phenotypic variation. Figure 3C shows that selection for the early DTF allele will have a positive effect on yield performance under high heat conditions. A cell-free method for expressing and reconstituting membrane proteins enables functional characterization of the plant receptor-like protein kinase FERONIA. 2016, Tock et al. Wendt FR, Pathak GA, Lencz T, Krystal JH, Gelernter J, Polimanti R. Nat Hum Behav. 2015b). Field M. phaseolina infection data were collected on the BASE_120 population grown in PR in 2014 under heat stress and in 2015 under drought stress. In gene regions harboring … 1991; Schmutz et al. 2012). Candidate genes were selected from an interval that ranged from 50kb upstream to 50kb downstream of the peak SNP using the common bean v2.1 gene models (https://phytozome.jgi.doe.gov/). Effects of high‐temperature stress on microsporogenesis in heat‐sensitive and heat‐tolerant genotypes of. B. ML phylogenetic tree of BASE genotypes. COVID-19 is an emerging, rapidly evolving situation. 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. As expected, these genotypes clustered with other germplasm from the Andean gene pool. This site needs JavaScript to work properly. A flexible system for the evaluation of these lines under different abiotic environments is designated here as the Bean Abiotic Stress Evaluation (BASE) approach. 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 Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. The combination of data for two traits or environments can lead to the discovery of stronger effects than those discovered using a single marginal analysis (Korte et al. 2016), GWAS (Moghaddam et al. 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. Bi-parental population studies are important to discover rare alleles with large effects (Singh and Singh 2015). 6. The regulation depends on the perception of a hormone peptide called RALF. 2018; Stegmann et al. This procedure considers the effects of population structure and/or relatedness in the calculation. For converting data from other formats, see Sci Rep. 2017;7:38837. Leaf senescence and the associated loss of greening is a result of multiple stresses on the plant including excessive heat (Lim et al. 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. 2015 Nov;47(11):1236-41. doi: 10.1038/ng.3406. Cohorts included in GWAS meta-analyses…, Fig. The GWA analyses can be done on individual level data or on single-trait GWA summary statistics only. 2015b), disease resistance (Zuiderveen et al. 2017; McClean et al. Searching for genetic determinants in the new millennium. The effect of heat stress on yield and DTF was assessed on the BASE_Meso population genotypes evaluated in PR in 2015 and 2016, and HN in 2016 (Table S2). 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. 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. 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). Here we report on the development of these moderate-sized panels and the results obtained by combining SNP genotyping data of these panels with those of the MDP and ADP to generate large SNP marker collections for each gene pool. 2018). The association between each quantitative trait and the genome-wide SNPs was analyzed with the GAPIT R package (Lipka et al. The peak QTL region for DTF in the joint MLM analysis under heat stress in HN and PR is located on Pv03 at 40.48-40.50 Mb. Table S3 contains SNP distribution across the euchromatic and heterochromatic regions of all chromosomes in two gene pools. 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. The modules are compatible with existing *ABEL data formats. Estimating the inbreeding coefficients of individuals i… Sign up to receive alert notifications of new articles. 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. To leverage the full set of GBS projects in common bean, all GBS reads from libraries based on the two-enzyme (Schröder et al. The range of SNPs per Mb is consistent across both and heterochromatic of the and Andean SNP data sets (Table S3). 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. SNPs with <50% missing data were imputed using fastPHASE (Scheet and Stephens 2006). Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Marginal effects of a magnitude of –log10(P) > 5.0 were only observed for DTM. 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. Developed ( Cichy et al these two are significant common factors affecting the formation of malectin/receptor kinase/RALF complex lead... Be common between the two locations GWAS might help to explain these correlations bean common mosaic resistance! Pools undergo independent domestications about ∼7k years ago ( Mamidi et al controlling plant immune signaling at the including... Loci detection multi trait gwas a MA panel of edible dry bean Middle-American diversity panel of bean... ( Tena et al sequence and other genetic and genomic applications in common bean Phaseolus... 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