Association Study
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2021 ◽  
Author(s):  
Piyi Xing ◽  
Xia Zhang ◽  
Dandan Li ◽  
Honggang Wang ◽  
Yinguang Bao ◽  
...  

Abstract Nitrogen is an important nutrient for crop growth and development. Plant height-related traits can be affected by nitrogen supplementation. In this study, we performed a genome-wide association study (GWAS) on plant height, spike length, length of different internodes, and lodging resistance strength at the grain-filling stage based on a natural wheat population subjected to low nitrogen and normal (CK) treatments. GWAS analysis showed that a total of 86 quantitative trait locus (QTLs) were detected, including 13 QTLs for plant height, 10 QTLs for spike length, 19 QTLs for the length of the first internode from the top of the plant, 6 QTLs for the second internode length, 11 QTLs for the third internode length, 13 QTLs for the fourth internode length, and 14 QTLs for the fifth internode length. Compared to the CK treatment, the plant height, spike length, and fourth and fifth internode lengths were significantly affected by the low nitrogen treatment. A total of 18 QTLs responding to low nitrogen stress were detected, including three QTLs for the fourth internode length detected on 3A, 6A, and 6D chromosomes, eleven QTLs for the fifth internode length on 1A, 1B, 1D, 2A, 2B, 3A, 3B, 4A, 5B and 7B chromosomes, one QTL for spike length on 3A chromosome, and one QTL for plant height on 5B chromosome. These QTLs will enhance our understanding of the genetic basis of plant height responses to nitrogen deficiency and will benefit genetic reactions to nitrogen fertilization.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jie Zhang ◽  
Stephanie C. Dulawa

Anorexia nervosa (AN) is a severe eating disorder that primarily affects young women and girls, and is characterized by abnormal restrictive feeding and a dangerously low body-mass index. AN has one of the highest mortality rates of any psychiatric disorder, and no approved pharmacological treatments exist. Current psychological and behavioral treatments are largely ineffective, and relapse is common. Relatively little basic research has examined biological mechanisms that underlie AN compared to other major neuropsychiatric disorders. A recent large-scale genome-wide association study (GWAS) revealed that the genetic architecture of AN has strong metabolic as well as psychiatric origins, suggesting that AN should be reconceptualized as a metabo-psychiatric disorder. Therefore, identifying the metabo-psychiatric mechanisms that contribute to AN may be essential for developing effective treatments. This review focuses on animal models for studying the metabo-psychiatric mechanisms that may contribute to AN, with a focus on the activity-based anorexia (ABA) paradigm. We also highlight recent work using modern circuit-dissecting neuroscience techniques to uncover metabolic mechanisms that regulate ABA, and encourage further work to ultimately identify novel treatment strategies for AN.


2021 ◽  
Author(s):  
Muktar Ahmed ◽  
Ville-Petteri Mäkinen ◽  
Anwar Mulugeta ◽  
Jisu Shin ◽  
Terry Boyle ◽  
...  

Abstract Hormone-related cancers, including cancers of the breast, prostate, ovaries, uterine, and thyroid, globally contribute to the majority of cancer incidence. We hypothesize that hormone-sensitive cancers share common genetic risk factors that have rarely been investigated by previous genomic studies of site-specific cancers. To test this hypothesis, we analysed five hormone-sensitive cancers in the UK Biobank as a single disease. We observed that a significant proportion of variance in disease liability was explained by the genome-wide single nucleotide polymorphisms (SNPs), i.e., SNP-based heritability on the liability scale was estimated as 10.06% (SE 0.70%) for the disease. Moreover, we found 55 genome-wide significant SNPs for the disease, using a genome-wide association study. Our finding suggests that heritable genetic factors may be a key driver in the mechanism of carcinogenesis shared by hormone-sensitive cancers.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chenguang Shen ◽  
Yi Xu ◽  
Jingkai Ji ◽  
Jinli Wei ◽  
Yujin Jiang ◽  
...  

Abstract Background The incidence of hand foot and mouth disease (HFMD) has increased in recent years, making it a very common childhood illness worldwide. The relationship between different enterovirus genotypes and disease severity is not clearly understood. Given that enteroviruses are transmitted through the gastrointestinal tract, we hypothesized that variation in intestinal microorganisms of the host might play a role in the prognosis of HFMD. Methods We carried out a meta-transcriptomic-wide association study of fecal samples obtained from a cohort of children (254 patients, 227 tested positive for enterovirus, including 16 patients co-infectied with 2 kinds of enterovirus) with mild and severe HFMD and healthy controls. Results We found there was no significant difference in the amount of each virus type between the mild and severe cases. Genes of enterovirus 71 (EV71) and coxsackievirus A (CV-A) from the severe and mild cases did not show significant clustering. Clostridium sp. L2-50 and Bacteroides stercoris ATCC 43183 were enriched in the guts of children with severe HFMD and KEGG enrichment was found between mild and severe cases. Conclusions Intestinal microorganisms appear to interact with enterovirus to determine the progression of HFMD. Genes of Bacteroides and Clostridium may be used as predictive markers for a more efficient prognosis and intervention. The enrichment of intestinal bacteria genes with functions may facilitate the development of severe symptoms for HFMD patients.


Author(s):  
Kotomi Tanida ◽  
Mihoko Shimada ◽  
Seik-Soon Khor ◽  
Hiromi Toyoda ◽  
Kayoko Kato ◽  
...  

2021 ◽  
Author(s):  
Wayne Xu ◽  
Andriy Bilichak ◽  
Raman Dhariwal ◽  
Maria Henriquez ◽  
Harpinder Randhawa

Background: Fusarium head blight (FHB) is one of the most devastating diseases of wheat worldwide and artificial intelligence can assist with understanding resistance to the disease. Considering different sample populations, marker types, reference maps, and statistical methods, we developed a Deep Learning Genome-wide Linkage Association Study (dpGLAS) of FHB resistance in wheat. Results: The dpGLAS was first applied to two bi-parental population datasets in which the cultivar AC Barrie was a common parent for FHB resistance. Eight candidate gene markers were discovered in the one AC Barrie population and 10 in the other associated with FHB resistance. Eight of these markers were also supported by the conventional QTL mapping. Most of these candidate marker genes were found associated with the Reactive Oxygen Species (ROS) and Abscisic acid (ABA) axes. These ROS and ABA pathways were further supported by RNA-seq transcriptome data of FHB resistant cv. AAC Tenacious, a parent of the third bi-parental population. In this dataset, the ROS-centered Panther protein families were significantly enriched in those genes that had most different response to FHB when compared the resistance Tenacious and the susceptible Roblin. Conclusions: This study developed the framework of dpGLAS and identified candidate genes for FHB resistance in the Canadian spring wheat cultivars AC Barrie and AAC Tenacious.


2021 ◽  
Author(s):  
Veronika Odintsova ◽  
Matthew Sudermann ◽  
Fiona Hagenbeek ◽  
Doretta Caramaschi ◽  
Jouke-Jan Hottenga ◽  
...  

Abstract Handedness has low heritability and epigenetic mechanisms have been proposed as an etiological mechanism. To examine this hypothesis, we performed an epigenome-wide association study (EWAS) of left-handedness. In a meta-analysis of 3,914 adults of whole-blood DNA methylation, we observed that CpG sites located in proximity of handedness-associated genetic variants were more strongly associated with left-handedness than other CpG sites (P = 0.04), but did not identify any differentially methylated positions. We identified differentially methylated regions at 20q11.23 (P = 0.00004) and 2p25.1 (P = 0.03), which were less methylated in left-handed adults. In longitudinal analyses of DNA methylation in peripheral blood and buccal cells from children (N = 1,737), we observed moderately stable associations across age (correlation range [0.355–0.578]) but inconsistent across tissues (correlation range [-0.384-0.318]). We conclude that DNA methylation in peripheral tissues captures little of the variance in handedness. Future investigations should consider other more targeted sources of tissue, such as the brain.


2021 ◽  
Author(s):  
Gui-Juan Feng ◽  
Qian Xu ◽  
Jing-Jing Ni ◽  
Shan-Shan Yang ◽  
Bai-Xue Han ◽  
...  

Abstract Age at menarche (AAM) is a sign of puberty of females. It is a heritable trait associated with various adult diseases. However, the genetic mechanism that determines AAM and links it to disease risk is poorly understood. Aiming to uncover the genetic basis for AAM, we conducted a joint association study in up to 438,089 participants from 3 genome-wide association studies of European and East Asian ancestries. Twenty-one novel genomic loci were identified at the genome-wide significance level. Besides, we observed significant genetic correlations between AAM and 67 complex traits, and the highest genetic correlation was observed between AAM and body mass index (rg=-0.19, P=6.11×10−31). Latent causal variable analyses demonstrate that there is a genetically causal effect of AAM on high blood pressure (GCP=0.47, P=0.02), forced vital capacity (GCP=0.63, P=0.02), age at first live birth (GCP=0.51, P=0.03), impedance of right arm (GCP=0.41, P<1×10-7) and right leg fat percentage (GCP=-0.10, P=0.02), etc. Enrichment analysis identified 5 enriched tissues and 51 enriched gene sets. Four of the five enriched tissues were related to the nervous system, including the hypothalamus middle, hypothalamo hypophyseal system, neurosecretory systems and hypothalamus. The fifth tissue was the retina in the sensory organ. The most significant gene set was the ‘decreased circulating luteinizing hormone level’ (P=2.45×10-6). Our findings may provide useful insights that elucidate the mechanisms determining AAM and the genetic interplay between AAM and some traits of women.


2021 ◽  
Vol 27 (11) ◽  
pp. 1425-1428
Author(s):  
Wei Zhou ◽  
Luan Chen ◽  
Bixuan Jiang ◽  
Yidan Sun ◽  
Mo Li ◽  
...  

2021 ◽  
Author(s):  
Daqiu Sun ◽  
Sibo Chen ◽  
Zhenhai Cui ◽  
Jingwei Lin ◽  
Meiling Liu ◽  
...  

Abstract Background:Brace roots are an important part of the maize root system. Among brace root traits, brace root angle (BRA) and brace root diameter (BRD) are important components that affect plant growth and development. However, there are no reports on the genetic basis of maize BRA and BRD. Results:Here, a genome-wide association study (GWAS) was conducted using 508 associated populations with extensive natural variation. The broad heritability of BRA and BRD reached 0.91 and 0.82, respectively. The analysis of different subgroups showed that there were significant differences in BRA traits in different subgroups, whereas there was no significant difference in BRD. Evaluation of phenotypic diversity in three different environments showed that BRA and BRD exhibit a wide range of natural variability. In the GWAS, the BRA and BRD were combined with 55,8629 single nucleotide polymorphisms, and four candidate genes were found for BRA within the threshold of P < 1.78×10-6 that were significantly related to BRD). These genes may (1) participate in maize brace root cell wall synthesis through cell transport (GRMZM2G479243); (2) involve hormone signaling pathways in the horizontal expansion of brace root cells (GRMZM2G101928 and GRMZM2G174736); or (3) involve the PLETHORA (PLT1/2) gene (GRMZM2G151934) to promote stem cells and transport expanded cells to affect the growth of root meristems.Conclusions:These results provide theoretical information for understanding the genetic basis of brace root development. Further research on candidate genes will help clarify the molecular pathways regulating BRA and BRD in maize.


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