scholarly journals Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11707
Author(s):  
Yinchao Zhang ◽  
Peng Liu ◽  
Chen Wang ◽  
Na Zhang ◽  
Yuxiao Zhu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Seed Germination ◽  
Association Study ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Chilling Stress ◽  
Nucleotide Polymorphisms ◽  
Plant Tolerance ◽  
Multiple Traits

As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 ×  10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.

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 towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Y. Tilahun ◽  
T. A. Gipson ◽  
T. Alexander ◽  
M. L. McCallum ◽  
P. R. Hoyt
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Predictive Power ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

Genome-wide association study of physical and microstructure-related traits in peanut shell

2021 ◽  
pp. 1-11
Author(s):  
Kailu Cui ◽  
Feiyan Qi ◽  
Ziqi Sun ◽  
Jingjing Feng ◽  
Bingyan Huang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Potential Contribution ◽  
Peanut Shell ◽  
Nucleotide Polymorphisms ◽  
B Genome ◽  
Genome Wide

Abstract Peanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var. hypogaea, var. vulgaris, var. fastigiata and var. hirsuta was used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var. hypogaea, var. hirsuta, var. vulgaris and var. fastigiata for mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P < 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.

scholarly journals Genome wide association study of plant height and tiller number in hulless barley

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260723
Author(s):  
Yixiong Bai ◽  
Xiaohong Zhao ◽  
Xiaohua Yao ◽  
Youhua Yao ◽  
Likun An ◽  
...  
Keyword(s):  
Association Study ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Hulless Barley ◽  
Genome Wide ◽  
A Genome

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.

scholarly journals Genome-wide Association Study Reveals Novel Quantitative Trait Loci and Candidate Genes of Lint Percentage in Upland Cotton Based on the CottonSNP80K Array

2021 ◽  
Author(s):  
Yu Chen ◽  
Yang Gao ◽  
Pengyun Chen ◽  
Juan Zhou ◽  
Chuanyun Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Cotton Production ◽  
Lint Percentage ◽  
Genome Wide

Abstract Cotton (Gossypium spp.) is an important natural textile fiber and oilseed crop widely cultivated in the world. Lint percentage (LP, %) is one of the important yield factor, thus increasing lint percentage is a core goal of cotton breeding improvement. However, the underlying genetic and molecular mechanisms that control lint percentage in upland cotton remain largely unknown. Here, we performed a Genome-wide association study (GWAS) for LP based on phenotypic tests of 254 upland cotton accessions in four environments and BLUPs using the high-density CottonSNP80K array. A total of 41,413 high-quality single-nucleotide polymorphisms (SNPs) were screened and 34 SNPs within 22 QTLs were identified as significantly associated with lint percentage trait in different environments. In total, 175 candidate genes were identified from two major genomic loci (GR1 and GR2) of upland cotton and 50 hub genes were identified through GO enrichment and WGCNA analysis. Furthermore, two candidate/causal genes, Gh_D01G0162 and Gh_D07G0463, which pleiotropically increased lint percentage were identified and further verified its function through LD blocks, haplotypes and qRT-PCR analysis. Co-expression network analysis showed that the candidate/causal and hub gene, Gh_D07G0463, was significantly related to another candidate gene, Gh_D01G0162, and the simultaneous pyramid of the two genes lays the foundation for a more efficient increase in cotton production. Our study provides crucial insights into the genetic and molecular mechanisms underlying variations of yield traits and serves as an important foundation for lint percentage improvement via marker-assisted breeding.

scholarly journals Genome-wide association study (GWAS) with productivity in Romanov sheep breed

2021 ◽  
Vol 59 (1) ◽  
pp. 71-80
Author(s):  
A. Y. Krivoruchko ◽  
O. A. Yatsyk ◽  
T. Y. Saprikina ◽  
D. D. Petukhova
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Elite Group ◽  
Genome Wide ◽  
Productive Traits

Genetic technologies used in breeding of small ruminants requires searching for new molecular markers of productive traits. The most effective for this is genome-wide association study (GWAS) of single nucleotide polymorphisms (SNP) with economically valuable traits. The paper presents results of study of associations of the frequency of single nucleotide polymorphisms with a rank assessment according to complex of productive traits (super-elite) in Romanov sheep using DNA biochips Ovine Infinium HD BeadChip 600K. Eleven SNPs have been found having significant correlation with the animals belonging to the “super-elite” group. Five substitutions are located in the genes introns, six are related to intergenic polymorphisms. The highest reliability of association with productivity was observed in substitution rs410516628 (р = 3,14 · 10-9) located on the 3rd chromosome. Substitution rs422028000 on 2nd chromosome differs with the fact that in the “super-elite” group it was found in 90 % of haplotypes. Polymorphisms rs411162754 (1st chromosome) and rs417281100 (10th chromosome) in our study turned out to be the rarest – only in “super-elite” group and only in a quarter of haplotypes. The genes located near the identified SNPs are mainly associated with metabolic and regulatory processes. Our study has identified several new candidate genes with polymorphism probably associated with the ranking in terms of productivity in Romanov sheep: LTBP1, KCNH8, LMX1B, ZBTB43, MSRA, CHPF, PID1 and DNER. The results obtained create a theoretical basis for further study of candidate genes affecting implementation of phenotypic traits in Romanov sheep. The revealed polymorphisms associated with the productive traits of sheep can be used in practical breeding as molecular and genetic markers for selection of parental pairs.

scholarly journals Genome-wide association study (GWAS) of seed germination-related traits in rice and identification of candidate genes

2021 ◽  
Author(s):  
Rahele Panhabadi ◽  
Asadollah Ahmadikhah ◽  
Naser Farokhi ◽  
Nadali Bagheri
Keyword(s):  
Seed Germination ◽  
Association Study ◽  
Candidate Genes ◽  
Gene Cluster ◽  
Genome Wide Association Study ◽  
Hydrolytic Enzyme ◽  
Seed Vigor ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Germination Traits

Abstract Background Genome-wide association study (GWAS) has become an accepted and powerful method for understanding the associations between phenotypes and genotypes. In agricultural production, uniform and rapid germination is an important prerequisite in crop production. Here, a rice (Oryza sativa L.) GWAS with 33,934 SNPs (MAF > 0.05) for eight germination traits including germination percentage (GP), shoot (SL) and root length (RL), root (RFW) and shoot fresh weight (SFW), root (RDW) and shoot (SDW) dry weight, and number of days to germinate (NDG) was performed to define genomic regions influencing seed germination. Results Loci (43) with 70 significant germination-associated markers were detected across all rice chromosomes. Some of novel candidate associated genes were: LOC_Os01g26210 (OsWAK6) co-located with qGR-1 that is seed vigor QTL, LOC_Os07g23944 (GH31) with an α-glucosidases /starch lyase activity; id7000519 marker that corresponds to a gene cluster containing glutathione S-transferase and glucan endo-1,3-β-glucosidase co-located with qAG3 germination-related marker, LOC_Os06g47640 (calmodulin-related calcium sensor protein 29) involved in the inhibition of ABA during seed germination, and id4006430 marker that corresponds to a gene cluster containing three GH17 hydrolytic enzyme that are co-located with qHD4 and qGI1 markers. Conclusion The germination process is an initial and important step in the production of agricultural products, especially for rice, which is a crop plant that is grown in flooded lands. Here, the genetic diversity of rice genotypes was put under scrutiny for germination. Our GWAS results identified several likely candidate genes for germination traits that will greatly contribute to our understanding of the genetic complexity underlying the corresponding traits. The associated genes with the germination traits can be generally classified as hydrolytic enzymes and regulatory proteins that can directly or indirectly influence germination.

scholarly journals Genetic risk of clozapine-induced leukopenia and neutropenia: a genome-wide association study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jianhua Chen ◽  
Ping Yang ◽  
Qian Zhang ◽  
Ruirui Chen ◽  
Peng Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Significance Level ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Significance

Abstract Background Clozapine is considered to be the most effective antipsychotic medication for schizophrenia. However, it is associated with several adverse effects such as leukopenia, and the underlying mechanism has not yet been fully elucidated. The authors performed a genome-wide association study (GWAS) in a Chinese population to identify genetic markers for clozapine-induced leukopenia (CIL) and clozapine-induced neutropenia (CIN). Methods A total of 1879 patients (225 CIL cases, including 43 CIN cases, and 1,654 controls) of Chinese descent were included. Data from common and rare single nucleotide polymorphisms (SNPs) were tested for association. The authors also performed a trans-ancestry meta-analysis with GWAS results of European individuals from the Clozapine-Induced Agranulocytosis Consortium (CIAC). Results The authors identified several novel loci reaching the threshold of genome-wide significance level (P < 5 × 10−8). Three novel loci were associated with CIL while six were associated with CIN, and two T cell related genes (TRAC and TRAT1) were implicated. The authors also observed that one locus with evidence close to genome-wide significance (P = 5.08 × 10−8) was near the HLA-B gene in the major histocompatibility complex region in the trans-ancestry meta-analysis. Conclusions The associations provide novel and valuable understanding of the genetic and immune causes of CIL and CIN, which is useful for improving clinical management of clozapine related treatment for schizophrenia. Causal variants and related underlying molecular mechanisms need to be understood in future developments.

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