scholarly journals Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

2020 ◽  
Vol 10 (5) ◽  
pp. 1713-1725 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Jhon A. Berdugo-Cely ◽  
Roberto A. Coronado-Silva ◽  
Eliana Baez ◽  
Yeirme Jaimes ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Theobroma Cacao ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Moniliophthora Perniciosa ◽  
Genome Wide ◽  
A Genome ◽  
Frosty Pod Rot

Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

scholarly journals Genome wide association study reveals novel candidate genes associated with productivity and disease resistance to Moniliophthora spp. in cacao (Theobroma cacao L.)

2019 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Jhon A. Berdugo-Cely ◽  
Roberto A. Coronado-Silva ◽  
Eliana Baez ◽  
Yeirme Jaimes ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Theobroma Cacao ◽  
Genome Wide Association Study ◽  
Economic Benefits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Moniliophthora Perniciosa ◽  
Genome Wide ◽  
A Genome

ABSTRACTCacao (Theobroma cacao L.), the source of chocolate, is one the most important commodity products for farmers to improve their economic benefits. However, diseases such as frosty pod rot (FPRD) caused by Moniliophthora roreri and witches’ broom (WBD) caused by Moniliophthora perniciosa, limits the increase in yields. Molecular tools can help to develop more rapidly cacao varieties with disease resistance. In the present study, we sequenced by genotyping-by-sequencing (GBS), 229 cacao accessions to examine their genetic diversity and population structure. From those accessions, 102 have been evaluated for disease resistance and productivity to conduct a genome-wide association study (GWAS) based on 9,003 and 8,131 SNPs recovered by mapping against to the annotated cacao genomes (Criollo and Matina). Three promissory accessions for productivity and 10 accessions showing good tolerance to the evaluated diseases were found in the phenotypic evaluation. The work presented herein provides the first association mapping study in cacao using SNP markers based on GBS data. The GWAS identified two genes associated to productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated to important traits in cacao that can have significant implications for conservation and breeding strategies such as marker-assisted selection (MAS).

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.

scholarly journals Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 260 ◽  
Author(s):  
Bo Zhu ◽  
Qinghe Li ◽  
Ranran Liu ◽  
Maiqing Zheng ◽  
Jie Wen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Immune Defense ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

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.

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