Systems genetics: A paradigm to improve discovery of candidate genes and mechanisms underlying complex traits

Plant Science ◽  
2014 ◽  
Vol 223 ◽  
pp. 45-48 ◽  
Author(s):  
F. Alex Feltus
Keyword(s):  
Candidate Genes ◽  
Complex Traits ◽  
Systems Genetics

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Tifeng Yang ◽  
Lian Zhou ◽  
Junliang Zhao ◽  
Jingfang Dong ◽  
Qing Liu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Differential Expression ◽  
Candidate Genes ◽  
Complex Traits ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Sequence Comparisons ◽  
Cold Environments ◽  
Promising Source

Abstract Background Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. Results In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines. Conclusion Among the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

149 Integration of Selection Signatures Analyses and Weighted Single-step GWAS to Prioritize Candidate Genes for Body Conformation Traits in Pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-77
Author(s):  
Seyed Milad Vahedi ◽  
Siavash Salek Ardestani ◽  
Duy Ngoc Do ◽  
Karim Karimi ◽  
Younes Miar
Keyword(s):  
Candidate Genes ◽  
Complex Traits ◽  
Body Height ◽  
Single Step ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Selection Signatures ◽  
Body Conformation ◽  
Yorkshire Pigs ◽  
Estimated Breeding Values

Abstract Body conformation traits such as body height (BH) and body length (BL) have been included in the swine industry’s selection criteria. The objective of this study was to identify the quantitative trait loci (QTLs) and candidate genes for pig conformation traits using an integration of selection signatures analyses and weighted single-step GWAS (WssGWAS). Body measurement records of 5,593 Yorkshire pigs of which 598 animals were genotyped with Illumina 50K panel were used. Estimated breeding values (EBVs) for BH and BL were computed using univariate animal models. Genotyped animals were grouped into top 5% and bottom 5% based on their EBVs, and selection signatures analyses were performed using fixation index (Fst), FLK, hapFLK, and Rsb statistics, which were then combined as a Mahalanobis distance (Md) framework. The WssGWAS was conducted to detect the single nucleotide polymorphisms (SNPs) associated with the studied traits. The top 1% SNPs (n=530) from Md distribution that overlapped with the top 1% SNPs from WssGWAS (n = 530) were used to detect the candidate genes. A total of 31 and six overlapped SNPs were found to be associated with BH and BL, respectively. Several candidate genes were identified for BH (PARVA, DCDC1, SYT1, CASTOR2, RGSL1, RGS8, RBMS3, TGFBR2, and HS6ST1) and BL (SNTB1, AK7, PAPOLA, KSR1, CHODL, and BMP2), explaining 2.58% and 0.42% of the trait’s genetic variation, respectively. Our results indicated that integrating data from the signatures of selection tests with WssGWAS could help elucidate genomic regions underlying complex traits.

scholarly journals The association between the serotonin and dopamine neurotransmitters and personality traits

2016 ◽  
Vol 25 (2) ◽  
pp. 109-112 ◽  
Author(s):  
G. Delvecchio ◽  
M. Bellani ◽  
A. C. Altamura ◽  
P. Brambilla
Keyword(s):  
Personality Traits ◽  
Psychiatric Disorders ◽  
Candidate Genes ◽  
Genetic Polymorphisms ◽  
Complex Traits ◽  
Healthy Subjects ◽  
Mental Illnesses ◽  
Biological Mechanisms ◽  
Normal Personality ◽  
The Impact

Evidence from previous studies has reported that complex traits, including psychiatric disorders, are moderately to highly heritable. Moreover, it has also been shown that specific personality traits may increase the risk to develop mental illnesses. Therefore the focus of the research shifted towards the identification of the biological mechanisms underpinning these traits by exploring the effects of a constellation of genetic polymorphisms in healthy subjects. Indeed, studying the effect of genetic variants in normal personality provides a unique means for identifying candidate genes which may increase the risk for psychiatric disorders. In this review, we discuss the impact of two of the most frequently studied genetic polymorphisms on personality in healthy subjects, the 5-HTT polymorphism of the serotonin transporter and the DRD2/DRD4 polymorphisms of the D2/D4 dopamine's receptors. The main aims are: (a) to highlight that the study of candidate genes provides a fruitful ground for the identification of the biological underpinnings of personality without, though, reaching a general consensus about the strength of this relationship; and (b) to outline that the research in personality genetics should be expanded to provide a clearer picture of the heritability of personality traits.

scholarly journals Systems Genetics for Mechanistic Discovery in Heart Diseases

2020 ◽  
Vol 126 (12) ◽  
pp. 1795-1815 ◽  
Author(s):  
Christoph D. Rau ◽  
Aldons J. Lusis ◽  
Yibin Wang
Keyword(s):  
Heart Failure ◽  
Cardiovascular Diseases ◽  
Complex Traits ◽  
Heart Diseases ◽  
Association Studies ◽  
Systems Genetics ◽  
Genome Wide Association Studies ◽  
Large Populations ◽  
Genetic Landscape ◽  
Important Approach

Cardiovascular diseases are the leading cause of death worldwide. Complex diseases with highly heterogenous disease progression among patient populations, cardiovascular diseases feature multifactorial contributions from both genetic and environmental stressors. Despite significant effort utilizing multiple approaches from molecular biology to genome-wide association studies, the genetic landscape of cardiovascular diseases, particularly for the nonfamilial forms of heart failure, is still poorly understood. In the past decade, systems-level approaches based on omics technologies have become an important approach for the study of complex traits in large populations. These advances create opportunities to integrate genetic variation with other biological layers to identify and prioritize candidate genes, understand pathogenic pathways, and elucidate gene-gene and gene-environment interactions. In this review, we will highlight some of the recent progress made using systems genetics approaches to uncover novel mechanisms and molecular bases of cardiovascular pathophysiological manifestations. The key technology and data analysis platforms necessary to implement systems genetics will be described, and the current major challenges and future directions will also be discussed. For complex cardiovascular diseases, such as heart failure, systems genetics represents a powerful strategy to obtain mechanistic insights and to develop individualized diagnostic and therapeutic regiments, paving the way for precision cardiovascular medicine.

scholarly journals Recent advances in genetic predisposition to clinical acute lung injury

2009 ◽  
Vol 296 (5) ◽  
pp. L713-L725 ◽  
Author(s):  
Li Gao ◽  
Kathleen C. Barnes
Keyword(s):  
Acute Lung Injury ◽  
Lung Injury ◽  
Candidate Genes ◽  
Genetic Variants ◽  
Complex Traits ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Special Focus ◽  
Disease Manifestation ◽  
The Impact

It has been well established that acute lung injury (ALI), and the more severe presentation of acute respiratory distress syndrome (ARDS), constitute complex traits characterized by a multigenic and multifactorial etiology. Identification and validation of genetic variants contributing to disease susceptibility and severity has been hampered by the profound heterogeneity of the clinical phenotype and the role of environmental factors, which includes treatment, on outcome. The critical nature of ALI and ARDS, compounded by the impact of phenotypic heterogeneity, has rendered the amassing of sufficiently powered studies especially challenging. Nevertheless, progress has been made in the identification of genetic variants in select candidate genes, which has enhanced our understanding of the specific pathways involved in disease manifestation. Identification of novel candidate genes for which genetic association studies have confirmed a role in disease has been greatly aided by the powerful tool of high-throughput expression profiling. This article will review these studies to date, summarizing candidate genes associated with ALI and ARDS, acknowledging those that have been replicated in independent populations, with a special focus on the specific pathways for which candidate genes identified so far can be clustered.

Modelling effects of candidate genes on complex traits as variables over time

2014 ◽  
Vol 45 (3) ◽  
pp. 322-328 ◽  
Author(s):  
J. Szyda ◽  
J. Komisarek ◽  
I. Antkowiak
Keyword(s):  
Candidate Genes ◽  
Complex Traits ◽  
Over Time

scholarly journals Genomic basis underlying the metabolome-mediated drought adaptation of maize

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fei Zhang ◽  
Jinfeng Wu ◽  
Nir Sade ◽  
Si Wu ◽  
Aiman Egbaria ◽  
...  
Keyword(s):  
Environmental Stress ◽  
Candidate Genes ◽  
Genetic Control ◽  
Stress Responses ◽  
Complex Traits ◽  
Inbred Lines ◽  
Drought Response ◽  
Eqtl Analysis ◽  
Drought Adaptation ◽  
Hub Genes

Abstract Background Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive. Results Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance. Conclusion Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits.

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