scholarly journals Genome-wide association study (GWAS) of leaf wax components of apple

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Fuguo Cao ◽  
Zhongxing Li ◽  
Lijuan Jiang ◽  
Chen Liu ◽  
Qian Qian ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Wax Ester ◽  
Nucleotide Polymorphisms ◽  
Lipid Transfer ◽  
Apple Leaves ◽  
Genome Wide ◽  
A Genome ◽  
Wax Synthesis

AbstractThe wax layer of apple leaves plays an important role in improving stress resistance, but relatively little is known about the mechanisms of wax synthesis and transport in apple leaves. In this study, 17 wax components, including alcohols, alkanes, fatty acids and terpenes, were analyzed by gas chromatography-tandem mass spectrometry (GC-MS) from the leaves of 123 apple germplasms. Whole-genome sequencing of these apple accessions yielded 5.9 million high-quality single nucleotide polymorphisms (SNPs). We performed a genome-wide association study (GWAS) on 17 wax components and identified several genes related to wax synthesis and transport, including MdSHN1 (SHINE1), MdLTP4 (LIPID TRANSFER PROTEIN4), MdWSD1 (WAX ESTER SYNTHASE/ACYL-COA DIAC-YLGLYCEROL ACYLTRANSFERASE1), MdRDR1 (RNA-DEPENDENT RNA POLYMERASE1), MdACBP6 (ACYL-COA-BINDING PROTEIN6), MdNLE (NOTCHLESS) and MdABCG21 (ATP-BINDING CASSETTE G21). Moreover, we identified some prominent SNPs that may affect gene expression and protein function. These results provide insights into mechanisms of wax synthesis and transport in apple leaves and broaden the genetic resources and basis for facilitating resistance breeding.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

Abstract 4437: Genome-Wide Association Study for the Response to Antihypertensive Medication: HOMED-BP-GENE Study

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Tomohiro Katsuya ◽  
Kei Asayama ◽  
Ryusuke Inoue ◽  
Ken Sugimoto ◽  
Takayoshi Ohkubo ◽  
...  
Keyword(s):  
Association Study ◽  
Antihypertensive Medication ◽  
Genome Wide Association Study ◽  
Early Morning ◽  
Home Blood Pressure ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome ◽  
Drug Responsiveness

AAntihypertensive therapy is a powerful approach to prevent the cardiovascular disease. However, the responsiveness of the therapy is highly individual due to the variability of genetic or environmental factors. To elucidate the genetic background underlying antihypertensive drug responsiveness, we carried out a genome-wide association study (GWAS). The subjects studied were recruited from the participants of HOMED-BP study (UMIN Registered ID C000000137, http://www.cpt.med.tohoku.ac.jp/HOMED-BP/) after obtaining the informed consent for the genetic analysis. After DNA extraction from peripheral blood, about half million single nucleotide polymorphisms (SNPs) were examined using GeneChip Genome-Wide Human SNP5.0 Array (Affymetrix). Home blood pressure (HBP) was measured every day within 1 hour after wake-up and before going to bed using HEM747-IC-N (Omron). The study protocol was approved by the ethical committee of Osaka University. SNP5.0 Array analysis was demonstrated for 300 participants. Antihypertensive therapy for 4weeks decreased their average HBP from 149.9/88.8mmHg to 137.7/82.2mmHg in early morning and 142.6/82.3mmHg to 129.1/74.7mmHg before going to bed. We excluded the SNPs data that showed low call rate, lack of Hardy-Weinberg’s equilibrium and minor allele frequency less than 0.05. Eight SNPs were significantly (p<0.001) associated with mean HBP reduction both in the early morning and at bedtime. Nine SNPs were more significantly (p<0.0001) associated with morning HBP reduction and 3 SNPs were associated with bedtime HBP reduction. In conclusion, GWAS of antihypertensive medication revealed several candidate loci responsible for a month therapy with the difference between morning and evening.

scholarly journals Genome-wide Association Study and Possible Candidate Genes for Root Color and Carotenoid Contents in Japanese Orange Carrot F2 Populations

2021 ◽  
Author(s):  
Taeko Shibaya ◽  
Chika Kuroda ◽  
Hisano Tsuruoka ◽  
Chiharu Minami ◽  
Akiko Obara ◽  
...  
Keyword(s):  
Amino Acid ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Carotenoid Biosynthesis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Visual Evaluation ◽  
Genome Wide ◽  
A Genome

Abstract Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed a genome-wide association study (GWAS) using genome-wide single-nucleotide polymorphisms (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred by a Japanese seed company. The GWAS revealed 21 significant associations, and the physical position of some associations suggested two possible candidate genes. An Orange (Or) gene was a possible candidate for visual color evaluation and the α- and β-carotene contents. Sanger sequencing detected a new allele of Or with an SNP which caused a non-synonymous amino acid substitution. Genotypes of this SNP corresponded to the visual evaluation of root color in another breeding line. A chromoplast-specific lycopene β-cyclase (CYC-B) gene was a possible candidate for the β/α carotene ratio. On CYC-B, five amino acid substitutions were detected between parental plants of the F2 population. The detected associations and SNPs on the possible candidate genes will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

Genome-wide association study for buffalo mammary gland morphology

2020 ◽  
Vol 87 (1) ◽  
pp. 27-31
Author(s):  
Jun Li ◽  
Jiajia Liu ◽  
Shenhe Liu ◽  
Giuseppe Campanile ◽  
Angela Salzano ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Chromosome 10 ◽  
Genome Wide ◽  
A Genome ◽  
Mammary Gland Morphology

AbstractThis research communication describes a genome-wide association study for Italian buffalo mammary gland morphology. Three single nucleotide polymorphisms (AX-85117983, AX-8509475 and AX-85117518) were identified to be significantly associated with buffalo anterior teat length, posterior teat length and distance between anterior and posterior teat, respectively. Two significant signals for buffalo mammary gland morphology were observed in two genomic regions on the chromosome 10, and chromosome 20. One of the regions located on the chromosome 10 has the most likely candidate genes ACTC1 and GJD2, both of which have putative roles in the regulation of mammary gland development. This study provides new insights into the genetic variants of buffalo mammary gland morphology and may be beneficial for understanding of the genetic regulation of mammary growth.

scholarly journals Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation

2016 ◽  
Vol 30 (3) ◽  
pp. 382-398 ◽  
Author(s):  
Ming-Fen Ho ◽  
Tim Bongartz ◽  
Mohan Liu ◽  
Krishna R. Kalari ◽  
Paul E. Goss ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Aromatase Inhibitor ◽  
Association Study ◽  
Proinflammatory Cytokines ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Musculoskeletal Symptoms ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Abstract We previously reported, on the basis of a genome-wide association study for aromatase inhibitor-induced musculoskeletal symptoms, that single-nucleotide polymorphisms (SNPs) near the T-cell leukemia/lymphoma 1A (TCL1A) gene were associated with aromatase inhibitor-induced musculoskeletal pain and with estradiol (E2)-induced TCL1A expression. Furthermore, variation in TCL1A expression influenced the downstream expression of proinflammatory cytokines and cytokine receptors. Specifically, the top hit genome-wide association study SNP, rs11849538, created a functional estrogen response element (ERE) that displayed estrogen receptor (ER) binding and increased E2 induction of TCL1A expression only for the variant SNP genotype. In the present study, we pursued mechanisms underlying the E2-SNP-dependent regulation of TCL1A expression and, in parallel, our subsequent observations that SNPs at a distance from EREs can regulate ERα binding and that ER antagonists can reverse phenotypes associated with those SNPs. Specifically, we performed a series of functional genomic studies using a large panel of lymphoblastoid cell lines with dense genomic data that demonstrated that TCL1A SNPs at a distance from EREs can modulate ERα binding and expression of TCL1A as well as the expression of downstream immune mediators. Furthermore, 4-hydroxytamoxifen or fulvestrant could reverse these SNP-genotype effects. Similar results were found for SNPs in the IL17A cytokine and CCR6 chemokine receptor genes. These observations greatly expand our previous results and support the existence of a novel molecular mechanism that contributes to the complex interplay between estrogens and immune systems. They also raise the possibility of the pharmacological manipulation of the expression of proinflammatory cytokines and chemokines in a SNP genotype-dependent fashion.

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