scholarly journals A multi-locus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild-collected Arabidopsis thaliana

2017 ◽  
Author(s):  
Yanjun Zan ◽  
Örjan Carlborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Association Analysis ◽  
Natural Populations ◽  
Biological Information ◽  
Phenotypic Variance ◽  
Novel Approach ◽  
Genome Wide ◽  
Public Data ◽  
Candidate Loci

AbstractWhen a species adapts to a new habitat, selection for the fitness traits often result in a confounding between genome-wide genotype and adaptive alleles. It is a major statistical challenge to detect such adaptive polymorphisms if the confounding is strong, or the effects of the adaptive alleles are weak. Here, we describe a novel approach to dissect polygenic traits in natural populations. First, candidate adaptive loci are identified by screening for loci that are directly associated to the trait or control the expression of genes known to affect it. Then, the multi-locus genetic architecture is inferred using a backward elimination association analysis across all the candidate loci using an adaptive false-discovery rate based threshold. Effects of population stratification are controlled by corrections for population structure in the pre-screening step and by simultaneously testing all candidate loci in the multi-locus model. We illustrate the method by exploring the polygenic basis of an important adaptive trait, flowering time in Arabidopsis thaliana, using public data from the 1,001 genomes project. Our method revealed associations between 33 (29) loci and flowering time at 10 (16)°C in this collection of natural accessions, where standard genome wide association analysis methods detected 5 (3) loci. The 33 (29) loci explained approximately 55 (48)% of the total phenotypic variance of the respective traits. Our work illustrates how the genetic basis of highly polygenic adaptive traits in natural populations can be explored in much greater detail by using new multi-locus mapping approaches taking advantage of prior biological information as well as genome and transcriptome data.

scholarly journals Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata [L.] Walp)

2021 ◽  
Author(s):  
Dev Paudel ◽  
Rocheteau Dareus ◽  
Julia Rosenwald ◽  
Maria Munoz-Amatriain ◽  
Esteban Rios
Keyword(s):  
Flowering Time ◽  
Candidate Genes ◽  
Vigna Unguiculata ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genome Wide

Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

scholarly journals Genome-wide association analysis of opioid use disorder: A novel approach using clinical data

2020 ◽  
Vol 217 ◽  
pp. 108276
Author(s):  
Wenyu Song ◽  
Joe Kossowsky ◽  
John Torous ◽  
Chia-Yen Chen ◽  
Hailiang Huang ◽  
...  
Keyword(s):  
Association Analysis ◽  
Clinical Data ◽  
Opioid Use Disorder ◽  
Genome Wide Association ◽  
Opioid Use ◽  
Genome Wide Association Analysis ◽  
Novel Approach ◽  
Genome Wide

scholarly journals Genome-wide association analysis with selective genotyping identifies candidate loci for adult height at 8q21.13 and 15q22.33-q23 in Mongolians

2008 ◽  
Vol 123 (6) ◽  
pp. 655-660 ◽  
Author(s):  
Tetsuaki Kimura ◽  
Terukazu Kobayashi ◽  
Batmunkh Munkhbat ◽  
Ganjuur Oyungerel ◽  
Tsolmon Bilegtsaikhan ◽  
...  
Keyword(s):  
Association Analysis ◽  
Adult Height ◽  
Selective Genotyping ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Candidate Loci

scholarly journals Genome wide Association Analysis of Flowering Time in Brassica campestris

2020 ◽  
Author(s):  
Jianxia Jiang ◽  
Yanli Li ◽  
Meiyan Jiang ◽  
Jifeng Zhu ◽  
Xirong Zhou ◽  
...  
Keyword(s):  
Flowering Time ◽  
Association Analysis ◽  
Brassica Campestris ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana

2019 ◽  
Vol 116 (36) ◽  
pp. 17890-17899 ◽  
Author(s):  
Mark A. Taylor ◽  
Amity M. Wilczek ◽  
Judith L. Roe ◽  
Stephen M. Welch ◽  
Daniel E. Runcie ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Environmental Conditions ◽  
Regulatory Networks ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Fitness Landscapes ◽  
Natural Environments ◽  
Multiple Phenotypes ◽  
Mutant Phenotypes

Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.

scholarly journals Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 30 ◽  
Author(s):  
Gwen Iris Descalsota-Empleo ◽  
Abd Aziz Shamsudin Noraziyah ◽  
Ian Paul Navea ◽  
Chongtae Chung ◽  
Maria Stefanie Dwiyanti ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Analysis ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Anthocyanin Content ◽  
Phenotypic Variance ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Colored Rice ◽  
Resistance Traits

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

scholarly journals Assortment of flowering time and immunity alleles in natural Arabidopsis thaliana populations suggests immunity and vegetative lifespan strategies coevolve

2017 ◽  
Author(s):  
Shirin Glander ◽  
Fei He ◽  
Gregor Schmitz ◽  
Anika Witten ◽  
Arndt Telschow ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Optimal Investment ◽  
Host Immunity ◽  
Host Defenses ◽  
Immunity Genes ◽  
Pleiotropic Action ◽  
The Impact

ABSTRACTThe selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host immunity, however, has seldom been documented. Optimal investment into immunity is expected to decrease with shortening lifespan, because a shorter life decreases the probability to encounter pathogens or enemies. Here, we document that in natural populations of Arabidopsis thaliana, the expression levels of immunity genes correlate positively with flowering time, which in annual species is a proxy for lifespan. Using a novel genetic strategy based on bulk-segregants, we partitioned flowering time-dependent from – independent immunity genes and could demonstrate that this positive co-variation can be genetically separated. It is therefore not explained by the pleiotropic action of some major regulatory genes controlling both immunity and lifespan. Moreover, we find that immunity genes containing variants reported to impact fitness in natural field conditions are among the genes whose expression co-varies most strongly with flowering time. Taken together, these analyses reveal that natural selection has likely assorted alleles promoting lower expression of immunity genes with alleles that decrease the duration of vegetative lifespan in A. thaliana and vice versa. This is the first study documenting a pattern of variation consistent with the impact that selection on flowering time is predicted to have on diversity in host immunity.

Sign in / Sign up

Export Citation Format

Share Document