scholarly journals Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kaixuan Zhang ◽  
Ming He ◽  
Yu Fan ◽  
Hui Zhao ◽  
Bin Gao ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Association Studies ◽  
Northern China ◽  
Genomic Variation ◽  
Tartary Buckwheat ◽  
Genome Wide Association Studies ◽  
Fagopyrum Tataricum ◽  
Genome Wide ◽  
History Of ◽  
Whole Genome Resequencing

Abstract Background Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. Results Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. Conclusions We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.

Genome-wide association studies of 14 agronomic traits in rice landraces

2010 ◽  
Vol 42 (11) ◽  
pp. 961-967 ◽  
Author(s):  
Xuehui Huang ◽  
Xinghua Wei ◽  
Tao Sang ◽  
Qiang Zhao ◽  
Qi Feng ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Rice Landraces ◽  
Genome Wide

scholarly journals Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yousef Rahimi ◽  
Mohammad Reza Bihamta ◽  
Alireza Taleei ◽  
Hadi Alipour ◽  
Pär K. Ingvarsson
Keyword(s):  
Bread Wheat ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Wheat Varieties ◽  
Data Set ◽  
Protein Coding ◽  
Genome Wide

Abstract Background Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles. Results GWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively. Conclusions Our finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

scholarly journals Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation

2019 ◽  
Vol 48 (D1) ◽  
pp. D659-D667 ◽  
Author(s):  
Wenqian Yang ◽  
Yanbo Yang ◽  
Cecheng Zhao ◽  
Kun Yang ◽  
Dongyang Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Missing Genotypes

Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.

Alzheimer's disease genetics: lessons to improve disease modelling

2011 ◽  
Vol 39 (4) ◽  
pp. 910-916 ◽  
Author(s):  
Rita J. Guerreiro ◽  
John Hardy
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Current Knowledge ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Biological Processes ◽  
Complete Understanding ◽  
Genome Wide ◽  
History Of ◽  
Ad Alzheimer’S Disease

In the present review, we look back at the recent history of GWAS (genome-wide association studies) in AD (Alzheimer's disease) and integrate the major findings with current knowledge of biological processes and pathways. These topics are essential for the development of animal models, which will be fundamental to our complete understanding of AD.

scholarly journals The impact of transposable elements on tomato diversity

2020 ◽  
Author(s):  
Marisol Domínguez ◽  
Elise Dugas ◽  
Médine Benchouaia ◽  
Basile Leduque ◽  
José Jimenez-Gomez ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Agronomic Traits ◽  
Association Studies ◽  
Low Frequency ◽  
Genome Wide Association Studies ◽  
Environmental Response ◽  
Whole Genome Resequencing ◽  
Wild Accessions ◽  
Genetic Pool ◽  
The Impact

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

scholarly journals Genome-wide Identification of Powdery Mildew Resistance in Common Bean

2020 ◽  
Author(s):  
Papias Hongera Binagwa ◽  
Sy M. Traore ◽  
Marceline Egnin ◽  
Gregory C. Bernard ◽  
Inocent Ritte ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Resistance Genes ◽  
Agronomic Traits ◽  
Association Studies ◽  
Significant Snps ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Disease Resistance Protein ◽  
Resistance Protein

Abstract Background: Genome-wide association studies (GWAS) was utilized to detect genetic variations related to the powdery mildew (PM) resistance and several agronomic traits in common bean. However, its application in common bean and the PM interactions to identify genes and their location in the common bean genome has not been fully addressed. Results: Genome-wide association studies (GWAS) through marker-trait association are useful molecular tools for the identification of disease resistance and other agronomic traits. SNP genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to resistance to PM disease in a panel of 206 genotypes grown under field conditions for two consecutive years. Significant SNPs identified on chromosomes 4 and 10 (Pv04 and Pv10) were repeatable, confirming the reliability of the phenotypic data scored from the genotypes grown in two locations within two years. A cluster of resistance genes was revealed on the chromosome 4 of common bean genome among which CNL and TNL like resistance genes were identified. Furthermore, two resistance genes Phavu_010G1320001g and Phavu_010G136800g were also identified on Pv10; further sequence analysis showed that these genes were homologs to the Arabidopsis disease resistance protein (RLM1A-like) and the putative disease resistance protein (At4g11170.1), respectively. Two LRR receptor-like kinases (RLK) were also identified on Pv11 in samples collected in 2018 only. Many genes encoding auxin-responsive protein, TIFY10A protein, growth-regulating factor 5-like, ubiquitin-like protein, cell wall protein RBR3-like protein related to PM resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed and may generate several layers of defense barriers or inducible reactions.Conclusion: Our results provide new insights into common bean and PM interactions, and revealed putative resistance genes as well as their location on common bean genome that could be used for marker-assisted selection, functional genomic study approaches to confirm the role of these putative genes; hence, developing common bean resistance lines to the PM disease.

scholarly journals Precision Mapping of a Maize MAGIC Population Identified a Candidate Gene for the Senescence-Associated Physiological Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Marlon Caicedo ◽  
Eduardo D. Munaiz ◽  
Rosa A. Malvar ◽  
José C. Jiménez ◽  
Bernardo Ordas
Keyword(s):  
Candidate Gene ◽  
Defense Mechanism ◽  
Agronomic Traits ◽  
Association Studies ◽  
Recombinant Inbred Lines ◽  
Sugar Transport ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Important Trait

Senescence is an important trait in maize (Zea mais L.), a key crop that provides nutrition values and a renewable source of bioenergy worldwide. Genome-wide association studies (GWAS) can be used to identify causative genetic variants that influence the major physiological measures of senescence, which is used by plants as a defense mechanism against abiotic and biotic stresses affecting its performance. We measured four physiological and two agronomic traits that affect senescence. Six hundred seventy-two recombinant inbred lines (RILs) were evaluated in two consecutive years. Thirty-six candidate genes were identified by genome-wide association study (GWAS), and 11 of them were supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport, and sink activity. We identified a candidate gene, Zm00001d043586, significantly associated with chlorophyll, and independently studied its transcription expression in an independent panel. Our results showed that Zm00001d043586 affects chlorophyl rate degradation, a key determinant of senescence, at late plant development stages. These results contribute to better understand the genetic relationship of the important trait senescence with physiology related parameters in maize and provide new putative molecular markers that can be used in marker assisted selection for line development.

scholarly journals Genetic loci of the R. anatipestifer serotype discovered by Pan-GWAS and its application for the development of a multiplex PCR serotyping method

2021 ◽  
Author(s):  
Zhishuang Yang ◽  
Xueqin Yang ◽  
Mingshu Wang ◽  
Renyong Jia ◽  
Shun Chen ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Capsular Polysaccharide ◽  
Association Studies ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Economic Losses ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Genome Wide ◽  
Pcr Method

The disease caused by Riemerella anatipestifer (R. anatipestifer) causes large economic losses to the global duck industry every year. Serotype-related genomic variation (such as in O-antigen and capsular polysaccharide gene clusters) has been widely used for the serotyping in many gram-negative bacteria. To date, there have been few studies focused on genetic basis of serotypes in R. anatipestifer. Here, we used pan-genome-wide association studies (Pan-GWAS) to identify the serotype-specific genetic loci of 38 R. anatipestifers strain. Analyses of the loci of 11 serotypes showed that the loci could be well mapped with the serotypes of the corresponding strains. We constructed the knockout strain for the wzy gene at the locus, and the results showed that the mutant lost the agglutination characteristics to positive antisera. Based on the of Pan-GWAS results, we developed a multiple PCR method to identify serotypes 1, 2, and 11 of R. anatipestifer. Our study provides a precedent for systematically analysing the genetic basis of the R anatipestifer serotypes and establishing a complete serotyping system in the future.

scholarly journals Host genetics and microbiome associations from the lens of genome wide association studies

2018 ◽  
Author(s):  
Omer Weissbrod ◽  
Daphna Rothschild ◽  
Elad Barkan ◽  
Eran Segal
Keyword(s):  
Gut Microbiome ◽  
Complex Traits ◽  
Association Studies ◽  
Meta Analysis ◽  
Lessons Learned ◽  
Host Genome ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
History Of

Recent studies indicate that the gut microbiome is partially heritable, motivating the need to investigate microbiome-host genome associations via microbial genome-wide association studies (mGWAS). Existing mGWAS demonstrate that microbiome-host genotypes associations are typically weak and are spread across multiple variants, similar to associations often observed in genome-wide association studies (GWAS) of complex traits. Here we reconsider mGWAS by viewing them through the lens of GWAS, and demonstrate that there are striking similarities between the challenges and pitfalls faced by the two study designs. We further advocate the mGWAS community to adopt three key lessons learned over the history of GWAS: (a) Adopting uniform data and reporting formats to facilitate replication and meta-analysis efforts; (b) enforcing stringent statistical criteria to reduce the number of false positive findings; and (c) considering the microbiome and the host genome as distinct entities, rather than studying different taxa and single nucleotide polymorphism (SNPs) separately. Finally, we anticipate that mGWAS sample sizes will have to increase by orders of magnitude to reproducibly associate the host genome with the gut microbiome.

scholarly journals Detecting polygenic adaptation in admixture graphs

2017 ◽  
Author(s):  
Fernando Racimo ◽  
Jeremy J. Berg ◽  
Joseph K. Pickrell
Keyword(s):  
Human Evolution ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Mcmc Algorithm ◽  
Genome Wide ◽  
Polygenic Adaptation ◽  
History Of ◽  
Different Populations ◽  
The Mean ◽  
Open Question

AbstractAn open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred. To address this, we created a method to detect polygenic adaptation in an admixture graph, which is a representation of the historical divergences and admixture events relating different populations through time. We developed a Markov chain Monte Carlo (MCMC) algorithm to infer branch-specific parameters reflecting the strength of selection in each branch of a graph. Additionally, we developed a set of summary statistics that are fast to compute and can indicate which branches are most likely to have experienced polygenic adaptation. We show via simulations that this method - which we call PolyGraph - has good power to detect polygenic adaptation, and applied it to human population genomic data from around the world. We also provide evidence that variants associated with several traits, including height, educational attainment, and self-reported unibrow, have been influenced by polygenic adaptation in different populations during human evolution.

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