Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis

Abstract The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.

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Identification, Characterization and Functional Analysis of C-Class Genes Associated with Double Flower Trait in Carnation (Dianthus caryphyllus L.)

Plants ◽

10.3390/plants9010087 ◽

2020 ◽

Vol 9 (1) ◽

pp. 87 ◽

Cited By ~ 2

Author(s):

Qijian Wang ◽

Naizhen Dan ◽

Xiaoni Zhang ◽

Shengnan Lin ◽

Manzhu Bao ◽

...

Keyword(s):

Spinacia Oleracea ◽

Chenopodium Quinoa ◽

Floral Organ ◽

Pcr Analysis ◽

Flower Formation ◽

Double Flower ◽

Flower Bud ◽

Precocious Flowering ◽

Organ Identity ◽

Significant Difference

Flowers with more petals are of more ornamental value. It is well known that AGAMOUS (AG) is the core member of the C-class gene which plays an essential role in double flower formation and identification of stamens and carpels in Arabidopsis thaliana. We searched C-class genes in the genome of the carnation, and found two AG orthologs (DcaAGa, DcaAGb). Phylogenetic analysis showed that the two genes were closely related to the euAG subclade. Then we searched the genomes of other Caryophyllales plants (Beta vulgaris, Spinacia oleracea, Chenopodium quinoa) for C-class genes, and found that their C-class genes all belonged to the euAG subclade. Semi-quantitative PCR (sq-PCR) analysis indicated that the expression of DcaAG genes in the single flower phenotype was higher than that in the double flower phenotype. Quantitative real-time RT-PCR (qRT-PCR) analysis showed that the expressions of DcaAG genes in the flower bud were significantly different from those in the root, stem, and leaf between the single and double flower phenotype carnations, and that DcaAG genes were specifically expressed in the stamen and carpel of carnation. Moreover, the expression of other floral organ identity genes (AP1 and AP2, PI and AP3, SEP1 and SEP3 corresponding to the A-, B-, and E-class of genes, respectively) showed no significant difference in all floral organs between the single and double flower phenotype carnations, suggesting that C-class (DcaAG) genes might play an important role in the double flower phenotype in carnation. Petal loss or decrease, precocious flowering, silique shortening, and seed sterility were observed in 35S::DcaAGa and 35S::DcaAGb transgenic Arabidopsis plants. All these results show that DcaAG genes might affect the petal number negatively and have a specific function in stamen and carpel development in carnation.

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QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize

Scientific Reports ◽

10.1038/s41598-019-50853-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Delphine Van Inghelandt ◽

Felix P. Frey ◽

David Ries ◽

Benjamin Stich

Keyword(s):

Qtl Mapping ◽

Heat Tolerance ◽

Prediction Models ◽

Genotypic Diversity ◽

Phenotypic Variance ◽

Nucleotide Polymorphisms ◽

Prediction Ability ◽

Specific Pcr ◽

Genome Wide ◽

Trait Locus

Abstract Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.

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Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

Genetics Research ◽

10.1017/s0016672307008634 ◽

2007 ◽

Vol 89 (1) ◽

pp. 1-6 ◽

Cited By ~ 52

Author(s):

H. ZHAO ◽

D. NETTLETON ◽

J. C. M. DEKKERS

Keyword(s):

Linkage Disequilibrium ◽

Single Nucleotide Polymorphisms ◽

Qtl Mapping ◽

Marker Assisted Selection ◽

Nucleotide Polymorphisms ◽

Chi Square ◽

Single Nucleotide ◽

Standardized Measures ◽

Trait Locus ◽

Standardized Measure

Effectiveness of marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTLs depends on the extent of LD and how it declines with distance between markers and QTLs in a population. Marker–QTL LD can be predicted from LD between markers. Our previous work evaluated LD measures between multi-allelic markers as predictors of usable LD of multi-allelic markers with QTLs. Since single nucleotide polymorphisms (SNPs) are the current marker of choice for high-density genotyping and LD-mapping of QTLs, the objective of this study was to use LD between multi-allelic markers to predict LD among biallelic SNPs or between SNPs and QTLs. Observable LD between multi-allelic markers was evaluated using nine measures. These included two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy–Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. The standardized chi-square measure that best predicted usable LD between multi-allelic markers and QTLs, based on our previous work, overestimated usable SNP–SNP or SNP–QTL LD. Instead, three other measures were found to be good predictors of usable SNP–SNP or SNP–QTL LD when LD is generated by drift. Therefore, the LD measure between multi-allelic markers that is best for predicting usable LD in a population depends on the type of markers (i.e. multi-allelic or biallelic) that will eventually be used for QTL mapping or MAS.

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

BMC Plant Biology ◽

10.1186/s12870-021-02824-x ◽

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.

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Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content

Genetics ◽

10.1534/genetics.109.106591 ◽

2009 ◽

Vol 183 (3) ◽

pp. 1153-1164 ◽

Cited By ~ 68

Author(s):

Bala R. Thumma ◽

Bronwyn A. Matheson ◽

Deqiang Zhang ◽

Christian Meeske ◽

Roger Meder ◽

...

Keyword(s):

Quantitative Traits ◽

Association Studies ◽

Allelic Expression ◽

Cellulose Content ◽

Nucleotide Polymorphisms ◽

Cis Acting ◽

Functional Polymorphisms ◽

Functional Variants ◽

Regulatory Polymorphism ◽

Trait Locus

Populations with low linkage disequilibrium (LD) offer unique opportunities to study functional variants influencing quantitative traits. We exploited the low LD in forest trees to identify functional polymorphisms in a Eucalyptus nitens COBRA-like gene (EniCOBL4A), whose Arabidopsis homolog has been implicated in cellulose deposition. Linkage analysis in a full-sib family revealed that EniCOBL4A is the most strongly associated marker in a quantitative trait locus (QTL) region for cellulose content. Analysis of LD by genotyping 11 common single-nucleotide polymorphisms (SNPs) and a simple sequence repeat (SSR) in an association population revealed that LD declines within the length of the gene. Using association studies we fine mapped the effect of the gene to SNP7, a synonymous SNP in exon 5, which occurs between two small haplotype blocks. We observed patterns of allelic expression imbalance (AEI) and differential binding of nuclear proteins to the SNP7 region that indicate that SNP7 is a cis-acting regulatory polymorphism affecting allelic expression. We also observed AEI in SNP7 heterozygotes in a full-sib family that is linked to heritable allele-specific methylation near SNP7. This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations.

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Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽

10.1093/genetics/159.2.581 ◽

2001 ◽

Vol 159 (2) ◽

pp. 581-588

Author(s):

Mohamed A F Noor ◽

Aimee L Cunningham ◽

John C Larkin

Keyword(s):

Quantitative Trait Locus ◽

Drosophila Melanogaster ◽

Qtl Mapping ◽

Quantitative Trait ◽

Recombination Rate ◽

Genome Project ◽

Gene Density ◽

Rate Variation ◽

Trait Locus ◽

Recombination Rate Variation

Abstract We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the “small X-effect” that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

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Dw2, a New Dwarfing Locus in Apple Rootstocks and Its Relationship to Induction of Early Bearing in Apple Scions

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.2.87 ◽

2014 ◽

Vol 139 (2) ◽

pp. 87-98 ◽

Cited By ~ 33

Author(s):

Gennaro Fazio ◽

Yizhen Wan ◽

Dariusz Kviklys ◽

Leticia Romero ◽

Richard Adams ◽

...

Keyword(s):

Genetic Map ◽

Production Systems ◽

Breeding Population ◽

Breeding Strategy ◽

Nucleotide Polymorphisms ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Yield Data ◽

Trait Locus ◽

Rootstock Breeding

The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.

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Quantitative trait loci associated with susceptibility to therapy-related acute murine promyelocytic leukemia in hCG-PML/RARA transgenic mice

Blood ◽

10.1182/blood-2008-01-132084 ◽

2008 ◽

Vol 112 (4) ◽

pp. 1434-1442 ◽

Cited By ~ 10

Author(s):

Ryan K. Funk ◽

Taylor J. Maxwell ◽

Masayo Izumi ◽

Deepa Edwin ◽

Friederike Kreisel ◽

...

Keyword(s):

Quantitative Trait ◽

Complex Trait ◽

Myelogenous Leukemia ◽

Mouse Strains ◽

Spleen Weight ◽

Nucleotide Polymorphisms ◽

Treatment Regimens ◽

Multiple Loci ◽

Acute Myelogenous ◽

Trait Locus

Abstract Therapy-related acute myelogenous leukemia (t-AML) is an important late adverse effect of alkylator chemotherapy. Susceptibility to t-AML has a genetic component, yet specific genetic variants that influence susceptibility are poorly understood. We analyzed an F2 intercross (n = 282 mice) between mouse strains resistant or susceptible to t-AML induced by the alkylator ethyl-N-nitrosourea (ENU) to identify genes that regulate t-AML susceptibility. Each mouse carried the hCG-PML/RARA transgene, a well-characterized initiator of myeloid leukemia. In the absence of ENU treatment, transgenic F2 mice developed leukemia with higher incidence (79.4% vs 12.5%) and at earlier time points (108 days vs 234 days) than mice in the resistant background. ENU treatment of F2 mice further increased incidence (90.4%) and shortened median survival (171 vs 254 days). We genotyped F2 mice at 384 informative single nucleotide polymorphisms across the genome and performed quantitative trait locus (QTL) analysis. Thirteen QTLs significantly associated with leukemia-free survival, spleen weight, or white blood cell count were identified on 8 chromosomes. These results suggest that susceptibility to ENU-induced leukemia in mice is a complex trait governed by genes at multiple loci. Improved understanding of genetic risk factors should lead to tailored treatment regimens that reduce risk for patients predisposed to t-AML.

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Abstract 3666: Common Polymorphisms in Familial Vascular Malformation Genes do not Show Association with Sporadic Brain Arteriovenous Malformation

Stroke ◽

10.1161/str.43.suppl_1.a3666 ◽

2012 ◽

Vol 43 (suppl_1) ◽

Author(s):

Shantel Weinsheimer ◽

Nasrine Bendjilali ◽

Ludmila Pawlikowska ◽

Pui-Yan Kwok ◽

Michael T Lawton ◽

...

Keyword(s):

Arteriovenous Malformation ◽

Vascular Malformation ◽

Multiple Testing ◽

Nucleotide Polymorphisms ◽

Brain Arteriovenous Malformation ◽

Inherited Disorders ◽

Venous Circulation ◽

Snp Association ◽

Number Variation ◽

Genome Wide Data

Background: The genetic basis of brain arteriovenous malformation (BAVM), a tangle of abnormal vessels directly shunting blood from the arterial to venous circulation, is unknown. However, there are two rare vascular disorders with known familial mutations in which a subset of patients display a BAVM phenotype: hereditary hemorrhagic telangiectasia ( ACVRL1 , ENG , and SMAD4 mutations) and capillary malformation-arteriovenous malformation ( RASA1 mutations). To investigate whether variants in these four vascular malformation genes are associated with sporadic BAVM, we performed a case-control study, evaluating both single nucleotide polymorphisms (SNPs) and copy number variation (CNV). Methods: We used genome-wide data (Affymetrix SNP 6.0) from 319 cases and 496 healthy controls. There were 27 unlinked SNPs (r 2 <0.8) on the array with minor allele frequency >1% and in Hardy-Weinberg equilibrium (p>0.01) mapping within 20kb of the four genes: ACVRL1 (n=16), ENG (n=6), SMAD4 (n=2), and RASA1 (n=3). Single SNP association was tested using multivariate logistic regression in PLINK, adjusting for age, gender, and top 3 principal components of ancestry (to control for population stratification). The Bonferroni method (p<0.0019) was used to correct for multiple comparisons. CNVs in these genes were called using the PennCNV algorithm. Results: Two SNPs located upstream and downstream of ACVRL1 were associated with BAVM at nominal p<0.05: rs10783480 (OR=0.69, 95% CI=0.50 - 0.96, p=0.029,) and rs11169956 (OR=0.69, 95% CI=0.48 - 0.99, p=0.046). However, these SNPs were not associated with BAVM after correction for multiple testing of all SNPs. Polymorphisms in the RASA1 , ENG , and SMAD4 genes were not significantly associated with BAVM (p>0.05). We observed one CNV, a duplication that mapped to the ACVRL1 gene, in one control. We did not observe any CNVs mapping to RASA1 , ENG , or SMAD4 . Conclusions: Common SNPs and CNVs in four vascular malformation genes associated with inherited disorders displaying BAVM were not significantly associated with sporadic BAVM. A previously reported ACVRL1 intronic SNP (rs2071219) was not on the Affymetrix array and none of the existing ACVRL1 SNPs tagged this SNP. Further, rare polymorphisms in these genes were not genotyped and may contribute to BAVM risk.

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Patterns of hybridization and cryptic introgression among one- and four-needled pinyon pines

Annals of Botany ◽

10.1093/aob/mcaa045 ◽

2020 ◽

Vol 126 (3) ◽

pp. 401-411

Author(s):

Ryan Buck ◽

Sandra Hyasat ◽

Alice Hossfeld ◽

Lluvia Flores-Rentería

Keyword(s):

Distinct Species ◽

Hybrid Origin ◽

Interspecific Mating ◽

Nucleotide Polymorphisms ◽

Intermediate Morphology ◽

The Status ◽

Number Variation ◽

Genetic Clusters ◽

Variable Morphology ◽

Genetic Contributions

Abstract Background and Aims Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex. Methods We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves. Key Results We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression. Conclusions Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

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