scholarly journals Genetic Architecture of Novel Sources for Reproductive Cold Tolerance in Sorghum

2021 ◽  
Vol 12 ◽  
Author(s):  
Subhadra Chakrabarty ◽  
Natalja Kravcov ◽  
André Schaffasz ◽  
Rod J. Snowdon ◽  
Benjamin Wittkop ◽  
...  
Keyword(s):  
High Altitude ◽  
Cold Tolerance ◽  
High Latitude ◽  
Genetic Architecture ◽  
Association Studies ◽  
Field Trials ◽  
Genome Wide Association Studies ◽  
Multiple Trait ◽  
Genomic Regions ◽  
High Degree

Enhancements in reproductive cold tolerance of sorghum are essential to expand growing areas into both high-latitude temperate areas and tropical high-altitude environments. Here we present first insights into the genetic architecture of this trait via genome-wide association studies in a broad genetic diversity set (n = 330) phenotyped in multi-location field trials including high-altitude tropical (Mexico) and high-latitude temperate (Germany) environments. We observed a high degree of phenotypic variation and identified several novel, temperate-adapted accessions with superior and environmentally stable cold tolerance. Good heritability indicates strong potential for implementation of reproductive cold tolerance in breeding. Although the trait was found to be strongly quantitative, promising genomic regions with multiple-trait associations were found, including hotspots on chromosomes 3 and 10 which contain candidate genes implicated in different developmental and survival processes under abiotic stress conditions.

Genome-Wide Association Studies (GWAS) for Traits Related to Fodder Quality and Biofuel in Sorghum: Progress and Prospects

2021 ◽  
Vol 28 ◽  
Author(s):  
Vinutha Kanuganahalli Somegowda ◽  
Laavanya Rayaprolu ◽  
Abhishek Rathore ◽  
Santosh Pandurang Deshpande ◽  
Rajeev Gupta
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Current Status ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Crop Species ◽  
Fodder Quality ◽  
Genome Wide ◽  
Genomic Regions ◽  
Model Crop

: The main focus of this review is to discuss the current status of the use of GWAS for fodder quality and biofuel owing to its similarity of traits. Sorghum is a potential multipurpose crop, popularly cultivated for various uses as food, feed fodder, and biomass for ethanol. Production of a huge quantity of biomass and genetic variation for complex sugars are the main motivation not only to use sorghum as fodder for livestock nutritionists but also a potential candidate for biofuel generation. Few studies have been reported on the knowledge transfer that can be used from the development of biofuel technologies to complement improved fodder quality and vice versa. With recent advances in genotyping technologies, GWAS became one of the primary tools used to identify the genes/genomic regions associated with the phenotype. These modern tools and technologies accelerate the genomic assisted breeding process to enhance the rate of genetic gains. Hence, this mini-review focuses on GWAS studies on genetic architecture and dissection of traits underpinning fodder quality and biofuel traits and their limited comparison with other related model crop species.

scholarly journals A global overview of pleiotropy and genetic architecture in complex traits

2018 ◽  
Author(s):  
Kyoko Watanabe ◽  
Sven Stringer ◽  
Oleksandr Frei ◽  
Maša Umićević Mirkov ◽  
Tinca J.C. Polderman ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Human Genetics ◽  
Association Studies ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Multiple Trait ◽  
Current Availability ◽  
Flanking Regions

ABSTRACTAfter a decade of genome-wide association studies (GWASs), fundamental questions in human genetics are still unanswered, such as the extent of pleiotropy across the genome, the nature of trait-associated genetic variants and the disparate genetic architecture across human traits. The current availability of hundreds of GWAS results provide the unique opportunity to gain insight into these questions. In this study, we harmonized and systematically analysed 4,155 publicly available GWASs. For a subset of well-powered GWAS on 558 unique traits, we provide an extensive overview of pleiotropy and genetic architecture. We show that trait associated loci cover more than half of the genome, and 90% of those loci are associated with multiple trait domains. We further show that potential causal genetic variants are enriched in coding and flanking regions, as well as in regulatory elements, and how trait-polygenicity is related to an estimate of the required sample size to detect 90% of causal genetic variants. Our results provide novel insights into how genetic variation contributes to trait variation. All GWAS results can be queried and visualized at the GWAS ATLAS resource (http://atlas.ctglab.nl).

scholarly journals Genetic Mapping Reveals Complex Architecture and Candidate Genes Involved in Common Bean Response to Meloidogyne Incognita Infection

2021 ◽  
Author(s):  
Willian Giordani ◽  
Henrique Castro Gama ◽  
Alisson Fernando Chiorato ◽  
João Paulo Rodrigues Marques ◽  
Luis Eduardo Aranha Camargo ◽  
...  
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Resistance Genes ◽  
Meloidogyne Incognita ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Crop Species ◽  
Egg Masses ◽  
Genomic Regions

Abstract Root-knot nematodes (RKN), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crop species, including common bean. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging since little has been done to discover resistance genes or find markers to assist selection. In this study, we performed genome-wide association studies and QTL mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and root-galling index were evaluated 30 days after inoculation. Complex genetic architecture and independent genomic regions were associated with each trait according to the Fixed and random model Circulating Probability Unification. SNPs located on chromosomes Pv06, Pv07, Pv08 and Pv11 were associated with the number of egg masses, and on Pv01, Pv02, Pv05 and Pv10 with root-galling. A total of 215 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA-seq analysis. The histochemical analysis indicated that the reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance in common bean, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

scholarly journals Phenome-wide search for pleiotropic loci highlights key genes and molecular pathways for human complex traits

2019 ◽  
Author(s):  
Anton E. Shikov ◽  
Alexander V. Predeus ◽  
Yury A. Barbitoff
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Human Genetics ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Statistical Framework ◽  
Genome Wide ◽  
Mhc Locus ◽  
High Degree ◽  
Human Complex

AbstractOver recent decades, genome-wide association studies (GWAS) have dramatically changed the understanding of human genetics. A recent genetic data release by UK Biobank has allowed many researchers worldwide to have comprehensive look into the genetic architecture of thousands of human phenotypes. In this study, we developed a novel statistical framework to assess phenome-wide significance and genetic pleiotropy across the human phenome based on GWAS summary statistics. We demonstrate widespread sharing of genetic architecture components between distinct groups of traits. Apart from known multiple associations inside the MHC locus, we discover high degree of pleiotropy for genes involved in immune system function, apoptosis, hemostasis cascades, as well as lipid and xenobiotic metabolism. We find several notable examples of novel pleiotropic loci (e.g., the MIR2113 microRNA broadly associated with cognition), and provide several possible mechanisms for these association signals. Our results allow for a functional phenome-wide look into the shared components of genetic architecture of human complex traits, and highlight crucial genes and pathways for their development.

The genetic architecture and breeding towards cold tolerance in maize: review.

2021 ◽  
pp. 282-294
Author(s):  
Hai-xiao Dong ◽  
Zhao Li ◽  
Guang-hui Hu ◽  
Ya-ping Yuan ◽  
Zhi-wu Zhang
Keyword(s):  
Cold Tolerance ◽  
Expression Profiling ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Cold Response ◽  
Genome Wide ◽  
Maize Varieties ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract This chapter reviews the global adaptation of maize, the effect of cold stress, existing cold-tolerant or cold-sensitive maize varieties or mutants, research on linkage analysis, and genome-wide association studies and gene expression profiling in maize cold response. In addition, the potential usage of genomic selection to accelerate the breeding process is explored. The objectives are to integrate knowledge for the benefit of geneticists to understand the genetic architecture of cold tolerance and for breeders to select 'hyper-tolerant' maize varieties adapted to broader and changeable environments.

scholarly journals Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xuechun Bai ◽  
Tianfu Yang ◽  
Austin M. Putz ◽  
Zhiquan Wang ◽  
Changxi Li ◽  
...  
Keyword(s):  
Blood Cell ◽  
Genetic Architecture ◽  
Blood Count ◽  
Complete Blood Count ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Before And After ◽  
Genomic Regions

Abstract Background Genetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of performance in the face of infection. However, multiple biological functions are known to be involved in disease resilience and this complexity means that the genetic architecture of disease resilience remains largely unknown. Here, we conducted genome-wide association studies (GWAS) of 465,910 autosomal SNPs for complete blood count (CBC) traits that are important in an animal’s disease response. The aim was to identify the genetic control of disease resilience. Results Univariate and multivariate single-step GWAS were performed on 15 CBC traits measured from the blood samples of 2743 crossbred (Landrace × Yorkshire) barrows drawn at 2-weeks before, and at 2 and 6-weeks after exposure to a polymicrobial infectious challenge. Overall, at a genome-wise false discovery rate of 0.05, five genomic regions located on Sus scrofa chromosome (SSC) 2, SSC4, SSC9, SSC10, and SSC12, were significantly associated with white blood cell traits in response to the polymicrobial challenge, and nine genomic regions on multiple chromosomes (SSC1, SSC4, SSC5, SSC6, SSC8, SSC9, SSC11, SSC12, SSC17) were significantly associated with red blood cell and platelet traits collected before and after exposure to the challenge. By functional enrichment analyses using Ingenuity Pathway Analysis (IPA) and literature review of previous CBC studies, candidate genes located nearby significant single-nucleotide polymorphisms were found to be involved in immune response, hematopoiesis, red blood cell morphology, and platelet aggregation. Conclusions This study helps to improve our understanding of the genetic basis of CBC traits collected before and after exposure to a polymicrobial infectious challenge and provides a step forward to improve disease resilience.

scholarly journals Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

2020 ◽  
Author(s):  
Xuechun Bai ◽  
Tianfu Yang ◽  
Austin Putz ◽  
Zhiquan Wang ◽  
Changxi Li ◽  
...  
Keyword(s):  
Blood Cell ◽  
Genetic Architecture ◽  
Blood Count ◽  
Complete Blood Count ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Before And After ◽  
Genomic Regions

Abstract BackgroundGenetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of performance in the face of infection. However, multiple biological functions are known to be involved in disease resilience and this complexity means that the genetic architecture of disease resilience remains largely unknown. Here, we conducted genome-wide association studies (GWAS) of 465,910 autosomal SNPs for complete blood count (CBC) traits that are important in an animal’s disease response. The aim was to identify the genetic control of disease resilience.ResultsUnivariate and multivariate single-step GWAS were performed on fifteen CBC traits measured from the blood samples of 2743 crossbred (Landrace × Yorkshire) barrows drawn at 2-weeks before, and at 2 and 6-weeks after exposure to a polymicrobial infectious challenge. Overall, at a genome-wise false discovery rate of 0.05, five genomic regions located on Sus scrofa chromosome (SSC) 2, SSC4, SSC9, SSC10, and SSC12, were significantly associated with white blood cell traits in response to the polymicrobial challenge, and nine genomic regions on multiple chromosomes (SSC1, SSC4, SSC5, SSC6, SSC8, SSC9, SSC11, SSC12, SSC17) were significantly associated with red blood cell and platelet traits collected before and after exposure to the challenge. By functional enrichment analyses using Ingenuity Pathway Analysis (IPA) and literature review of previous CBC studies, candidate genes located nearby significant single-nucleotide polymorphisms were found to be involved in immune response, hematopoiesis, red blood cell morphology, and platelet aggregation.ConclusionsThis study helps to improve our understanding of the genetic basis of CBC traits collected before and after exposure to a polymicrobial infectious challenge and provides a step forward to improve disease resilience.

scholarly journals Genetic architecture of schizophrenia: a review of major advancements

2021 ◽  
pp. 1-10
Author(s):  
Sophie E. Legge ◽  
Marcos L. Santoro ◽  
Sathish Periyasamy ◽  
Adeniran Okewole ◽  
Arsalan Arsalan ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Copy Number Variants ◽  
Risk Scores ◽  
Genome Wide Association Studies ◽  
Loss Of Function ◽  
Genetic Loci ◽  
Significant Enrichment ◽  
High Heritability ◽  
Coding Variants

Abstract Schizophrenia is a severe psychiatric disorder with high heritability. Consortia efforts and technological advancements have led to a substantial increase in knowledge of the genetic architecture of schizophrenia over the past decade. In this article, we provide an overview of the current understanding of the genetics of schizophrenia, outline remaining challenges, and summarise future directions of research. World-wide collaborations have resulted in genome-wide association studies (GWAS) in over 56 000 schizophrenia cases and 78 000 controls, which identified 176 distinct genetic loci. The latest GWAS from the Psychiatric Genetics Consortium, available as a pre-print, indicates that 270 distinct common genetic loci have now been associated with schizophrenia. Polygenic risk scores can currently explain around 7.7% of the variance in schizophrenia case-control status. Rare variant studies have implicated eight rare copy-number variants, and an increased burden of loss-of-function variants in SETD1A, as increasing the risk of schizophrenia. The latest exome sequencing study, available as a pre-print, implicates a burden of rare coding variants in a further nine genes. Gene-set analyses have demonstrated significant enrichment of both common and rare genetic variants associated with schizophrenia in synaptic pathways. To address current challenges, future genetic studies of schizophrenia need increased sample sizes from more diverse populations. Continued expansion of international collaboration will likely identify new genetic regions, improve fine-mapping to identify causal variants, and increase our understanding of the biology and mechanisms of schizophrenia.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nadav Brandes ◽  
Nathan Linial ◽  
Michal Linial
Keyword(s):  
Cancer Risk ◽  
Protein Function ◽  
Association Studies ◽  
Genetic Effects ◽  
Cancer Predisposition ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Functional Interpretation ◽  
Gene Damage ◽  
Genomic Regions

AbstractThe characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Studies of genetic cancer predisposition typically identify significant genomic regions based on family-based cohorts or genome-wide association studies (GWAS). However, the results of such studies rarely provide biological insight or functional interpretation. In this study, we conducted a comprehensive analysis of cancer predisposition in the UK Biobank cohort using a new gene-based method for detecting protein-coding genes that are functionally interpretable. Specifically, we conducted proteome-wide association studies (PWAS) to identify genetic associations mediated by alterations to protein function. With PWAS, we identified 110 significant gene-cancer associations in 70 unique genomic regions across nine cancer types and pan-cancer. In 48 of the 110 PWAS associations (44%), estimated gene damage is associated with reduced rather than elevated cancer risk, suggesting a protective effect. Together with standard GWAS, we implicated 145 unique genomic loci with cancer risk. While most of these genomic regions are supported by external evidence, our results also highlight many novel loci. Based on the capacity of PWAS to detect non-additive genetic effects, we found that 46% of the PWAS-significant cancer regions exhibited exclusive recessive inheritance. These results highlight the importance of recessive genetic effects, without relying on familial studies. Finally, we show that many of the detected genes exert substantial cancer risk in the studied cohort determined by a quantitative functional description, suggesting their relevance for diagnosis and genetic consulting.

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