Genomic regions affecting fitness of the sweet corn mutant sugary1

2012 ◽  
Vol 151 (3) ◽  
pp. 396-406 ◽  
Author(s):  
A. DJEMEL ◽  
M. C. ROMAY ◽  
P. REVILLA ◽  
L. KHELIFI ◽  
A. ORDÁS ◽  
...  
Keyword(s):  
Inbred Line ◽  
Sweet Corn ◽  
Recombinant Inbred Lines ◽  
Genetic Regulation ◽  
Theoretical Point ◽  
Nucleotide Polymorphisms ◽  
Multiple Traits ◽  
Wild Allele ◽  
Major Interest ◽  
Genomic Regions

SUMMARYMutants often reduce fitness when incorporated into some genotypes, as is the case of the mutant gene sugary1 (su1) in maize (Zea mays L.). Understanding the genetic factors affecting variation in the fitness of a mutant is of major interest from a theoretical point of view and also from a breeder's perspective. The genetic regulation of su1 behaviour was examined in two independent materials. First, populations of two recombinant inbred lines (RIL) were used, belonging to the Nested Association Mapping (NAM) design produced from crosses between the maize inbred B73 and two sweet corn lines (P39 and Il14h) that were genotyped with 1106 single nucleotide polymorphisms (SNPs). These RILs had a group of lines with the su1 allele and another group with the wild allele. At each marker, the allele frequencies of both groups of RILs were compared. Second, an F2 population derived from the cross between A619 (a field maize inbred line) and P39 (a sweet corn inbred line) was characterized with 295 simple sequence repeats (SSRs). In addition, the population was phenotyped for several traits related to viability. A large linkage block was detected around su1 in the RILs belonging to the NAM. Furthermore, significant genomic regions associated with su1 fitness were detected along the 10 maize chromosomes, although the detected effects were small. Quantitative trait loci (QTLs) with effects in multiple traits related to su1 fitness were detected in the F2 population, for example at bin 5·04. Therefore, the present results suggest that the su1 fitness depends on many genes of small effect distributed along the genome, with pleiotropic effects on multiple traits.

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 Genetic Variants in Smoking-Related Genes in Two Smoking Cessation Programs: A Cross-Sectional Study

2021 ◽  
Vol 18 (12) ◽  
pp. 6597
Author(s):  
Gloria Pérez-Rubio ◽  
Luis Alberto López-Flores ◽  
Ana Paula Cupertino ◽  
Francisco Cartujano-Barrera ◽  
Luz Myriam Reynales-Shigematsu ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Sectional Study ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Quitting Smoking ◽  
Genes Encoding ◽  
Genomic Regions

Previous studies have identified variants in genes encoding proteins associated with the degree of addiction, smoking onset, and cessation. We aimed to describe thirty-one single nucleotide polymorphisms (SNPs) in seven candidate genomic regions spanning six genes associated with tobacco-smoking in a cross-sectional study from two different interventions for quitting smoking: (1) thirty-eight smokers were recruited via multimedia to participate in e-Decídete! program (e-Dec) and (2) ninety-four attended an institutional smoking cessation program on-site. SNPs genotyping was done by real-time PCR using TaqMan probes. The analysis of alleles and genotypes was carried out using the EpiInfo v7. on-site subjects had more years smoking and tobacco index than e-Dec smokers (p < 0.05, both); in CYP2A6 we found differences in the rs28399433 (p < 0.01), the e-Dec group had a higher frequency of TT genotype (0.78 vs. 0.35), and TG genotype frequency was higher in the on-site group (0.63 vs. 0.18), same as GG genotype (0.03 vs. 0.02). Moreover, three SNPs in NRXN1, two in CHRNA3, and two in CHRNA5 had differences in genotype frequencies (p < 0.01). Cigarettes per day were different (p < 0.05) in the metabolizer classification by CYP2A6 alleles. In conclusion, subjects attending a mobile smoking cessation intervention smoked fewer cigarettes per day, by fewer years, and by fewer cumulative pack-years. There were differences in the genotype frequencies of SNPs in genes related to nicotine metabolism and nicotine dependence. Slow metabolizers smoked more cigarettes per day than intermediate and normal metabolizers.

scholarly journals L2,1-norm regularized multivariate regression model with applications to genomic prediction

2021 ◽  
Author(s):  
Alain J Mbebi ◽  
Hao Tong ◽  
Zoran Nikoloski
Keyword(s):  
Variable Selection ◽  
Regression Model ◽  
Multivariate Regression ◽  
Statistical Testing ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Multiple Traits ◽  
Multivariate Regression Model ◽  
Proposed Model ◽  
Iterative Optimization Algorithm

AbstractMotivationGenomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP).ResultsHere, we propose a L2,1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L2,1-joint, applicable in multi-trait GS. The usage of the L2,1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.Availability and implementation: The model is implemented using R programming language and the code is freely available from https://github.com/alainmbebi/L21-norm-GS.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals A NOTE ON PHASING LONG GENOMIC REGIONS USING LOCAL HAPLOTYPE PREDICTIONS

2006 ◽  
Vol 04 (03) ◽  
pp. 639-647 ◽  
Author(s):  
ELEAZAR ESKIN ◽  
RODED SHARAN ◽  
ERAN HALPERIN
Keyword(s):  
Large Scale ◽  
Computational Cost ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Maximum Likelihood Criterion ◽  
The Common ◽  
Genomic Regions ◽  
High Computational Cost ◽  
Combining Information

The common approaches for haplotype inference from genotype data are targeted toward phasing short genomic regions. Longer regions are often tackled in a heuristic manner, due to the high computational cost. Here, we describe a novel approach for phasing genotypes over long regions, which is based on combining information from local predictions on short, overlapping regions. The phasing is done in a way, which maximizes a natural maximum likelihood criterion. Among other things, this criterion takes into account the physical length between neighboring single nucleotide polymorphisms. The approach is very efficient and is applied to several large scale datasets and is shown to be successful in two recent benchmarking studies (Zaitlen et al., in press; Marchini et al., in preparation). Our method is publicly available via a webserver at .

scholarly journals Carbohydrate and Enzymic Characterization of a High Sucrose Sugary Inbred Line of Sweet Corn

1976 ◽  
Vol 58 (1) ◽  
pp. 28-32 ◽  
Author(s):  
Jorge W. Gonzales ◽  
Ashby M. Rhodes ◽  
David B. Dickinson
Keyword(s):  
Inbred Line ◽  
Sweet Corn ◽  
High Sucrose

scholarly journals Selección de líneas para formar híbridos de maíz dulce ricos en Lisina l. Probadores.

2016 ◽  
Vol 9 (2) ◽  
pp. 57
Author(s):  
María Cristina Vega ◽  
Enrique Navarro ◽  
José Espinoza ◽  
José Luis Guerrero ◽  
Gustavo A. Burciaga
Keyword(s):  
Inbred Line ◽  
Sweet Corn ◽  
Agronomic Traits ◽  
Average Response ◽  
Performance Factors ◽  
Grain Color ◽  
Color Uniformity ◽  
Ear Height ◽  
And Performance ◽  
Selection Of

Twenty S5 sweet corn lines containing the opaque-2 gene that increases Iysine  contents as well as the sugary-2 gene were evaluated. The lines were crossed with three testers: one unrelated inbred line, and two related synthetic varieties. Six commercial and three experimental hybrids were used during the trials. Test crosses were evaluated in two locations of Mexico during 1994 using a randomized complete block designo The experiment's goal was to compare lines' performance in combination with three testers, taking into account yield, soundness, uniformity, and corn quality. The average response of lines combined with testers was superior than that of commercial hybrids for traits such as flowering time and plant and ear height. Performance factors analyzed (ear length, grain color, uniformity, soundness, and number of marketable ears) in trial crosses were superior or equal in average to those in experimental hybrids, but this was not the case with sugar percentage. The best results were observed with the unrelated LD tester inbred line for agronomic traits and performance factors. This study made possible the selection of lines for future breeding based on the above mentioned traits, as well as the general combining ability for ear length and number of green flag leaves.

scholarly journals Identification of Genetic Loci and Candidate Genes Related to Grain Zinc and Iron Concentration Using a Zinc-Enriched Wheat ‘Zinc-Shakti’

2021 ◽  
Vol 12 ◽  
Author(s):  
Nagenahalli Dharmegowda Rathan ◽  
Deepmala Sehgal ◽  
Karthikeyan Thiyagarajan ◽  
Ravi Singh ◽  
Anju-Mahendru Singh ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Iron Concentration ◽  
Small Peptides ◽  
Growing Seasons ◽  
Grain Zinc ◽  
Pleiotropic Qtl ◽  
Genomic Regions ◽  
Yield Trials

The development of nutritionally enhanced wheat (Triticum aestivum L.) with higher levels of grain iron (Fe) and zinc (Zn) offers a sustainable solution to micronutrient deficiency among resource-poor wheat consumers. One hundred and ninety recombinant inbred lines (RILs) from ‘Kachu’ × ‘Zinc-Shakti’ cross were phenotyped for grain Fe and Zn concentrations and phenological and agronomically important traits at Ciudad Obregon, Mexico in the 2017–2018, 2018–2019, and 2019–2020 growing seasons and Diversity Arrays Technology (DArT) molecular marker data were used to determine genomic regions controlling grain micronutrients and agronomic traits. We identified seven new pleiotropic quantitative trait loci (QTL) for grain Zn and Fe on chromosomes 1B, 1D, 2B, 6A, and 7D. The stable pleiotropic QTL identified have expanded the diversity of QTL that could be used in breeding for wheat biofortification. Nine RILs with the best combination of pleiotropic QTL for Zn and Fe have been identified to be used in future crossing programs and to be screened in elite yield trials before releasing as biofortified varieties. In silico analysis revealed several candidate genes underlying QTL, including those belonging to the families of the transporters and kinases known to transport small peptides and minerals (thus assisting mineral uptake) and catalyzing phosphorylation processes, respectively.

scholarly journals Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1786
Author(s):  
Soumeya Rida ◽  
Oula Maafi ◽  
Ana López-Malvar ◽  
Pedro Revilla ◽  
Meriem Riache ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Seedling Traits ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

scholarly journals Longitudinal Phenotypes Improve Genotype Association for Hyperketonemia in Dairy Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1059 ◽  
Author(s):  
Francisco A. Leal Yepes ◽  
Daryl V. Nydam ◽  
Sabine Mann ◽  
Luciano Caixeta ◽  
Jessica A. A. McArt ◽  
...  
Keyword(s):  
Linear Models ◽  
Association Studies ◽  
Genetic Selection ◽  
Area Under The Curve ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Mixed Linear Models ◽  
Biological Insight ◽  
Group 2 ◽  
Genomic Regions

The objective of our study was to identify genomic regions associated with varying concentrations of non-esterified fatty acid (NEFA), β-hydroxybutyrate (BHB), and the development of hyperketonemia (HYK) in longitudinally sampled Holstein dairy cows. Our study population consisted of 147 multiparous cows intensively characterized by serial NEFA and BHB concentrations. To identify individuals with contrasting combinations in longitudinal BHB and NEFA concentrations, phenotypes were established using incremental area under the curve (AUC) and categorized as follows: Group (1) high NEFA and high BHB, group (2) low NEFA and high BHB), group (3) low NEFA and low BHB, and group (4) high NEFA and low BHB. Cows were genotyped on the Illumina Bovine High-density (777 K) beadchip. Genome-wide association studies using mixed linear models with the least-related animals were performed to establish a genetic association with HYK, BHB-AUC, NEFA-AUC, and the comparisons of the 4 AUC phenotypic groups using Golden Helix software. Nine single-nucleotide polymorphisms were associated with high longitudinal concentrations of BHB and further investigated. Five candidate genes related to energy metabolism and homeostasis were identified. These results provide biological insight and help identify susceptible animals thus improving genetic selection criteria thereby decreasing the incidence of HYK.

scholarly journals Molecular mapping of QTLs for resistance to early and late Fusarium wilt in chickpea

2014 ◽  
Vol 50 (No. 2) ◽  
pp. 171-176 ◽  
Author(s):  
B.S. Patil ◽  
R.L. Ravikumar ◽  
J.S. Bhat ◽  
C.D. Soregaon
Keyword(s):  
Fusarium Wilt ◽  
Recombinant Inbred ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Reference Map ◽  
Genomic Regions ◽  
Marker Distance

A molecular map of chickpea was constructed using F<sub>9</sub>:F<sub>10</sub> recombinant inbred lines from an intraspecific cross between Fusarium wilt susceptible (JG 62) and resistant (WR 315) genotypes. A total of 23 markers with LOD scores of &gt; 3.0 were mapped on the recombinant inbred lines (RILs). Twenty sequence tagged microsatellites (STMSs) and three amplified fragment length polymorphisms (AFLPs) covered 300.2 cM in five linkage groups at an average inter-marker distance of 13 cM. Early and late wilting due to Fusarium infection was recorded in RILs at 30&nbsp;and 60 DAS, respectively. There was a significant variation among RILs for wilt resistance for both early and late wilting. QTLs associated with early (30 days after sowing (DAS)) and late (60&nbsp;DAS) wilting are located on LG II. The flanking markers for these QTLs were the same as those of previous reports. Five STMS markers located on LG II of reference map (interspecific) were mapped on LG II of the present map (intraspecific) with minor changes in the order of markers indicating the conservation of these genomic regions across the Cicer species.

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