scholarly journals Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1174
Author(s):  
San Mar Lar ◽  
Jeonghwan Seo ◽  
Seong-Gyu Jang ◽  
Hongjia Zhang ◽  
Ah-Rim Lee ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Phenotypic Variation ◽  
Evaluation System ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Total Phenotypic Variation ◽  
Genome Wide

Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(P) threshold of ≥3.66. The QTL of qSIS2, showed −log10(P) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4, showed −log10(P) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10(P) = 3.78 and the lead SNP explained 7.83% of total phenotypic variation. Among the annotated genes located in these three QTL regions, five genes were selected as candidates (Os04g0481600, Os04g0485300, Os04g0493000, Os04g0493300, and Os08g0390200) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions.

scholarly journals Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1005
Author(s):  
Jie Wang ◽  
Bo Zhu ◽  
Jie Wen ◽  
Qinghe Li ◽  
Guiping Zhao
Keyword(s):  
Association Study ◽  
Pathway Analysis ◽  
Phenotypic Variation ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Genetic Selection ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Disease control and prevention have been critical factors in the dramatic growth of the poultry industry. Disease resistance in chickens can be improved through genetic selection for immunocompetence. The heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. Our objective was to conduct a genome-wide association study (GWAS) and pathway analysis to identify possible biological mechanisms involved in H/L traits. In this study, GWAS for H/L was performed in 1317 Cobb broilers to identify significant single-nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (p < 1/8068) reached a significant level of association. The significant SNP on GGA 19 (chicken chromosome 19) was in the gene for complement C1q binding protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five identified SNPs (p < 0.05). According to the results of pathway analysis, nine associated pathways (p < 0.05) were identified. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L, and 52 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

scholarly journals Genome-wide Association Study for Number of Vertebrae in an F2 Large White × Minzhu Population of Pigs

2015 ◽  
Author(s):  
Longchao Zhang ◽  
Xin Liu ◽  
Jing Liang ◽  
Kebin Zhao ◽  
Hua Yan ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Mammalian Embryos ◽  
Strong Candidate

Porcine carcass that is approximately 800 mm long may be expected to have one additional vertebra. Therefore, the number of vertebrae in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 593 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study identified 39 significant single-nucleotide polymorphisms (SNPs) on the chromosomes SSC1 and SSC7. An 8.82-Mb region that contained all 21 significant SNPs on SSC1 harbored the gene NR6A1, previously reported to influence the number of vertebrae in pigs. The remaining 18 significant SNPs on SSC7 were concentrated in a 4.56-Mb region, which was within the quantitative trait loci interval for number of vertebrae. A haplotype sharing analysis refined the locus to a segment of ~637 Kb. The most significant SNP, SIRI0001067, was contained in this refined region on SSC7 and located in one of the introns of TGFB3. As TGFB3 influences the development of vertebrae in mammalian embryos, the gene may be another strong candidate for the number of vertebrae in pigs.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P &lt; 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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.

scholarly journals A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

2020 ◽  
Vol 10 (5) ◽  
pp. 1685-1696
Author(s):  
Lorenzo Stagnati ◽  
Vahid Rahjoo ◽  
Luis F. Samayoa ◽  
James B. Holland ◽  
Virginia M. G. Borrelli ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Germination Rate ◽  
Fusarium Verticillioides ◽  
Screening Method ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Seedling Length ◽  
A Genome

Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

scholarly journals A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

2018 ◽  
Vol 19 (10) ◽  
pp. 3145 ◽  
Author(s):  
Jie Yu ◽  
Weiguo Zhao ◽  
Wei Tong ◽  
Qiang He ◽  
Min-Young Yoon ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Phenotypic Correlation ◽  
Genome Wide ◽  
A Genome ◽  
Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

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