Sex-specific genetic dissection of diabetes in a rodent model identifies Ica1 and Ndufa4 as major candidate genes

2010 ◽  
Vol 42 (3) ◽  
pp. 445-455 ◽  
Author(s):  
Ronit Barkalifa ◽  
Yoram Yagil ◽  
Chana Yagil
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed ◽  
Diabetic Rat ◽  
Genetic Dissection ◽  
Promoter Regions ◽  
F2 Population ◽  
Trait Locus ◽  
Functional Relevance ◽  
Consomic Strain ◽  
Major Qtl

The aim of the study was to initiate a sex-specific investigation of the molecular basis of diabetes, using a genomic approach in the Cohen Diabetic rat model of diet-induced Type 2 diabetes. We used an F2 population resulting from a cross between Cohen Diabetic susceptible (CDs) and resistant (CDr) and consisting of 132 males and 159 females to detect relevant QTLs by linkage and cosegregation analyses. To confirm the functional relevance of the QTL, we applied the “chromosome substitution” strategy. We identified candidate genes within the quantitative trait locus (QTL) and studied their differential expression. We sequenced the differentially expressed candidate genes to account for differences in their expression. We confirmed in this new cross in males a previously detected major QTL on rat chromosome 4 (RNO4); we identified in females this major QTL as well. We found three additional diabetes-related QTLs on RNO11, 13, and 20 in females only. We pursued the investigation of the QTL on RNO4 and generated a CDs.4CDr consomic strain, which provided us with functional confirmation for the contribution of the QTL to the diabetic phenotype in both sexes. We successfully narrowed the QTL span to 2.6 cM and identified within it six candidate genes, but only two of which, Ica1 (islet cell autoantigen 1) and Ndufa4 (NADH dehydrogenase ubiquinone) were differentially expressed between CDs and CDr. We sequenced the exons and promoter regions of Ica1 and Ndufa4 but did not identify sequence variations between the strains. The detection of the QTL on RNO4 in both sexes suggests involvement of Ica1, Ndufa4, the Golgi apparatus, the mitochondria and genetic susceptibility to dietary-environmental factors in the pathophysiology of diabetes in our model. The additional sex-specific QTLs are likely to account for differences in the diabetic phenotype between the sexes.

scholarly journals Identification of candidate genes for self-compatibility in perennial ryegrass (Lolium perenne L.)

2021 ◽  
Author(s):  
Claudio Cropano ◽  
Chloé Manzanares ◽  
Steven Yates ◽  
Dario Copetti ◽  
Javier Do Canto ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Lolium Multiflorum ◽  
Italian Ryegrass ◽  
Forage Grasses ◽  
Lolium Perenne L ◽  
F2 Population ◽  
Self Compatibility ◽  
Trait Locus

Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in approximately 40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in a F2 population segregating for SC. Using a subset of the same population (n=73), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 cM using additional 2,056 plants and 23 novel sequence-based markers. Using an Italian ryegrass (Lolium multiflorum Lam.) genome assembly as reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our work is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.

scholarly journals Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper

HortScience ◽  
2019 ◽  
Vol 54 (7) ◽  
pp. 1143-1148
Author(s):  
Jareerat Chunthawodtiporn ◽  
Theresa Hill ◽  
Kevin Stoffel ◽  
Allen Van Deynze
Keyword(s):  
Candidate Genes ◽  
Gene Annotation ◽  
Phytophthora Capsici ◽  
Genetic Resistance ◽  
Bell Pepper ◽  
Chromosome 5 ◽  
Horticultural Traits ◽  
Trait Locus ◽  
High Level ◽  
Major Qtl

Phytophthora capsici is one of the major pathogens found in pepper production, especially in bell pepper. Due to the high level of genetic diversity of the pathogen, bell pepper varieties with broad genetic resistance are essential for disease management. Criollo de Morelos – 334 (CM334), a landrace that has a high level of genetic resistance to P. capsici, has been used as the resistant source for P. capsici to generate a recombinant inbred line (RIL) population with the susceptible bell pepper cultivar Maor. From the resulting population, quantitative trait locus (QTL) models explaining resistance to each of four isolates of P. capsici were derived from QTL regions on three chromosomes using stepwiseqtl in R/qtl. A single region of chromosome 5 contained major QTL for resistance to each of the four isolates. Two isolate-specific QTL conferring resistance to isolates PWB53 and PWB106 were located on chromosomes 10 and 11, respectively. Both isolate-specific QTL had epistatic interactions with a major QTL on chromosome 5. Using the pepper reference genome and gene annotation, candidate genes for P. capsici resistance within 1.5-logarithm of odds (LOD) interval were identified. Based on functional annotations derived from Arabidopsis thaliana and solanaceous crop databases, multiple candidate genes related to resistance (R) gene complexes or to plant immune system were found under the QTL on all three chromosomes. A comparison of the locations of resistance QTL and previously identified horticultural QTL using the same population revealed tight linkage between resistance to P. capsici and a stem pubescence QTL o chromosome 10. Both candidate genes for P. capsici resistance and the linkages between resistance and horticultural traits could be applied for selection to broad resistance to P. capsici in bell pepper–breeding programs.

scholarly journals Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

2021 ◽  
Author(s):  
Rajanikanth Govindarajulu ◽  
Ashley N Hostetler ◽  
Yuguo Xiao ◽  
Srinivasa R Chaluvadi ◽  
Margarita Mauro-Herrera ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interspecific Cross ◽  
Crop Improvement ◽  
Differentially Expressed ◽  
Plant Domestication ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Locus ◽  
Genomic Regions ◽  
Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

scholarly journals Genetic Mechanisms Underlying Apimaysin and Maysin Synthesis and Corn Earworm Antibiosis in Maize (Zea mays L.)

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1997-2006
Author(s):  
E A Lee ◽  
P F Byrne ◽  
M D McMullen ◽  
M E Snook ◽  
B R Wiseman ◽  
...  
Keyword(s):  
Helicoverpa Zea ◽  
Larval Growth ◽  
Corn Earworm ◽  
Phenotypic Variance ◽  
Significant Qtls ◽  
F2 Population ◽  
Genetic Mechanisms ◽  
Trait Locus ◽  
Maize Silks ◽  
Related Compounds

Abstract C-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14.1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.

scholarly journals Genetic Dissection of an Elite Rice Hybrid Revealed That Heterozygotes Are Not Always Advantageous for Performance

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1885-1895
Author(s):  
J P Hua ◽  
Y Z Xing ◽  
C G Xu ◽  
X L Sun ◽  
S B Yu ◽  
...  
Keyword(s):  
Field Trials ◽  
Genetic Dissection ◽  
F2 Population ◽  
Genetic Components ◽  
Large Numbers ◽  
Marker Loci ◽  
Component Traits ◽  
Single Locus Analysis ◽  
Immortalized F2 ◽  
Heterotic Hybrid

Abstract We introduced an experimental design that produced an “immortalized F2” population allowing for complete dissection of genetic components underlying quantitative traits. Data for yield and three component traits of the immortalized F2 were collected from replicated field trials over 2 years. Using 231 marker loci, we resolved the genetic effects into individual components and assessed relative performance of all the genotypes at both single- and two-locus levels. Single-locus analysis detected 40 QTL for the four traits. Dominance effects for about one-half of the QTL were negative, resulting in little “net” positive dominance effect. Correlation between genotype heterozygosity and trait performance was low. Large numbers of digenic interactions, including AA, AD, and DD, were detected for all the traits, with AA as the most prevalent interaction. Complementary two-locus homozygotes frequently performed the best among the nine genotypes of many two-locus combinations. While cumulative small advantages over two-locus combinations may partly explain the genetic basis of heterosis of the hybrid as double heterozygotes frequently demonstrated marginal advantages, double heterozygotes were never the best genotypes in any of the two-locus combinations. It was concluded that heterozygotes were not necessarily advantageous for trait performance even among genotypes derived from such a highly heterotic hybrid.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 224-234 ◽  
Author(s):  
C E Durel ◽  
L Parisi ◽  
F Laurens ◽  
W E Van de Weg ◽  
R Liebhard ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Malus Domestica ◽  
Quantitative Trait ◽  
Partial Resistance ◽  
Venturia Inaequalis ◽  
Genetic Dissection ◽  
Resistance Breakdown ◽  
Trait Locus ◽  
New Races ◽  
Genomic Regions

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus × domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has been inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.Key words: Malus × domestica, partial resistance, Venturia inaequalis, resistance breakdown, quantitative trait locus.

scholarly journals Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats

2005 ◽  
Vol 23 (2) ◽  
pp. 192-205 ◽  
Author(s):  
Chris J. Sullivan ◽  
Thomas H. Teal ◽  
Ian P. Luttrell ◽  
Khoa B. Tran ◽  
Mette A. Peters ◽  
...  
Keyword(s):  
Gene Expression ◽  
Smooth Muscle ◽  
Erectile Dysfunction ◽  
Splice Variants ◽  
Full Range ◽  
Diabetic Rats ◽  
Differentially Expressed ◽  
Diabetic Rat ◽  
Literature Mining ◽  
Mrna Levels

To investigate the full range of molecular changes associated with erectile dysfunction (ED) in Type 1 diabetes, we examined alterations in penile gene expression in streptozotocin-induced diabetic rats and littermate controls. With the use of Affymetrix GeneChip arrays and statistical filtering, 529 genes/transcripts were considered to be differentially expressed in the diabetic rat cavernosum compared with control. Gene Ontology (GO) classification indicated that there was a decrease in numerous extracellular matrix genes (e.g., collagen and elastin related) and an increase in oxidative stress-associated genes in the diabetic rat cavernosum. In addition, PubMatrix literature mining identified differentially expressed genes previously shown to mediate vascular dysfunction [e.g., ceruloplasmin ( Cp), lipoprotein lipase, and Cd36] as well as genes involved in the modulation of the smooth muscle phenotype (e.g., Kruppel-like factor 5 and chemokine C-X3-C motif ligand 1). Real-time PCR was used to confirm changes in expression for 23 relevant genes. Further validation of Cp expression in the diabetic rat cavernosum demonstrated increased mRNA levels of the secreted and anchored splice variants of Cp. CP protein levels showed a 1.9-fold increase in tissues from diabetic rats versus controls. Immunohistochemistry demonstrated localization of CP protein in cavernosal sinusoids of control and diabetic animals, including endothelial and smooth muscle layers. Overall, this study broadens the scope of candidate genes and pathways that may be relevant to the pathophysiology of diabetes-induced ED as well as highlights the potential complexity of this disorder.

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