scholarly journals QTL Analysis for Downy Mildew Resistance in Cucumber Inbred Line PI 197088

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1240-1245 ◽  
Author(s):  
Lixia Li ◽  
Huiqiang He ◽  
Zhirong Zou ◽  
Yuhong Li
Keyword(s):  
Qtl Mapping ◽  
Downy Mildew ◽  
Genetic Architecture ◽  
Plant Introduction ◽  
Minor Effect ◽  
Phenotypic Variance ◽  
Chromosome 4 ◽  
Phenotypic Data ◽  
Trait Locus ◽  
Simple Sequence

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the major foliar diseases prevailing in cucumber-growing areas. The mechanism of DM resistance in cucumber, particularly the plant introduction (PI) 197088 from India, is presently unclear. Quantitative trait locus (QTL) mapping is an efficient approach to studying DM resistance genes in cucumber. In this study, we performed QTL mapping for DM resistance in PI 197088 with 183 F2-derived F3 (F2:3) families from the cross between PI 197088 (DM resistant) and Changchunmici (DM susceptible). A linkage map was constructed using 141 simple sequence repeat markers. Phenotypic data were collected from seven independent experiments. In total, five QTL were detected on chromosomes 1, 3, 4, and 5 with DM resistance contributed by PI 197088. The QTL on chromosome 4, dm4.1, was reproducibly detected in all indoor experiments, which could explain 27% of the phenotypic variance detected. Additionally, dm1.1 and dm5.2 showed moderate effects, while dm3.1 and dm5.1 were minor-effect QTL. This study revealed the unique genetic architecture of DM resistance in PI 197088, which may provide important guidance for efficient use in cucumber breeding for DM resistance.

scholarly journals Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan Brassac ◽  
Quddoos H. Muqaddasi ◽  
Jörg Plieske ◽  
Martin W. Ganal ◽  
Marion S. Röder
Keyword(s):  
Flowering Time ◽  
Aspartic Acid ◽  
Synonymous Substitution ◽  
Minor Effect ◽  
Phenotypic Variance ◽  
Spikelet Number ◽  
Wheat Varieties ◽  
Trait Locus ◽  
A Minor ◽  
Spikelet Number Per Spike

AbstractTotal spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

scholarly journals Resistance to Downy Mildew in Lettuce ‘La Brillante’ is Conferred by Dm50 Gene and Multiple QTL

2015 ◽  
Vol 105 (9) ◽  
pp. 1220-1228 ◽  
Author(s):  
Ivan Simko ◽  
Oswaldo E. Ochoa ◽  
Mathieu A. Pel ◽  
Cayla Tsuchida ◽  
Carolina Font i Forcada ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Field Experiments ◽  
Field Resistance ◽  
Phenotypic Variance ◽  
Lactuca Sativa L ◽  
Trait Locus ◽  
Group 2 ◽  
High Level ◽  
Harvest Maturity ◽  
Multiple Field

Many cultivars of lettuce (Lactuca sativa L.) are susceptible to downy mildew, a nearly globally ubiquitous disease caused by Bremia lactucae. We previously determined that Batavia type cultivar ‘La Brillante’ has a high level of field resistance to the disease in California. Testing of a mapping population developed from a cross between ‘Salinas 88’ and La Brillante in multiple field and laboratory experiments revealed that at least five loci conferred resistance in La Brillante. The presence of a new dominant resistance gene (designated Dm50) that confers complete resistance to specific isolates was detected in laboratory tests of seedlings inoculated with multiple diverse isolates. Dm50 is located in the major resistance cluster on linkage group 2 that contains at least eight major, dominant Dm genes conferring resistance to downy mildew. However, this Dm gene is ineffective against the isolates of B. lactucae prevalent in the field in California and the Netherlands. A quantitative trait locus (QTL) located at the Dm50 chromosomal region (qDM2.2) was detected, though, when the amount of disease was evaluated a month before plants reached harvest maturity. Four additional QTL for resistance to B. lactucae were identified on linkage groups 4 (qDM4.1 and qDM4.2), 7 (qDM7.1), and 9 (qDM9.2). The largest effect was associated with qDM7.1 (up to 32.9% of the total phenotypic variance) that determined resistance in multiple field experiments. Markers identified in the present study will facilitate introduction of these resistance loci into commercial cultivars of lettuce.

scholarly journals Further mapping of quantitative trait loci for female sterility in wheat (Triticum aestivum L.)

2010 ◽  
Vol 92 (1) ◽  
pp. 63-70 ◽  
Author(s):  
BINGDE DOU ◽  
BEIWEI HOU ◽  
FANG WANG ◽  
JINBIN YANG ◽  
ZHONGFU NI ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Triticum Aestivum L ◽  
Female Sterility ◽  
Phenotypic Variance ◽  
Crop Breeding ◽  
Main Effect ◽  
Sterile Mutant ◽  
Likelihood Approach ◽  
Trait Locus ◽  
Simple Sequence

SummaryEpistasis underlying fertility plays an important role in crop breeding. Although a new female sterile mutant in wheat, XND126, has been identified and a major quantitative trait locus (QTL), taf1, for the female sterility has been mapped, the genetic architecture of the female sterility needs to be further addressed. To identify the interaction involving the gene(s) controlling the female sterility, an investigation was carried out for the seed setting ratio in an F2 population derived from the cross between XND126 and Gaocheng 8901. Among 1250 simple sequence repeat (SSR) primer pairs in the whole genome, a total of 21 markers, obtained by recessive class approach, along with other ten tightly linked markers on reference maps in wheat, were used to survey 243 F2 individuals. As a result, 28 markers were mapped into five genetic linkage groups. The performance for female sterility for each F2 individual was evaluated simultaneously at the Urumqi and Huai'an experimental stations in 2006–2007. The two phenotypic datasets along with marker information were jointly analysed in the detection of QTL using penalized maximum likelihood approach. A total of six QTLs, including two main-effect QTLs, three epistatic QTLs and one environmental interaction and accounting for 0·67–24·55% of the total phenotypic variance, were identified. All estimated effects accounted for 53·26% of the total phenotypic variation. The taf1 detected in previous study was also located on the same marker interval on chromosome 2DS. These results enrich our understanding of the genetic basis of the female sterility.

scholarly journals High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

2021 ◽  
pp. PHYTO-12-19-048
Author(s):  
Kai Su ◽  
Yinshan Guo ◽  
Weihao Zhong ◽  
Hong Lin ◽  
Zhendong Liu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Dna Sequencing ◽  
Quantitative Trait ◽  
Restriction Site ◽  
Genetic Distances ◽  
Snp Markers ◽  
High Density ◽  
White Rot ◽  
Phenotypic Variance ◽  
Trait Locus

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca ‘Zhuosexiang’) and white rot-susceptible cultivar (V. vinifera ‘Victoria’). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

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

2019 ◽  
Vol 9 (1) ◽  
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.

scholarly journals High resolution genetic dissection of the major QTL for tipburn resistance in lettuce, Lactuca sativa

2021 ◽  
Author(s):  
Miguel Macias-González ◽  
Maria Jose Truco ◽  
Rongkui Han ◽  
Sylvie Jenni ◽  
Richard W Michelmore
Keyword(s):  
Quantitative Trait Locus ◽  
Lactuca Sativa ◽  
Quantitative Trait ◽  
Calcium Deficiency ◽  
Phenotypic Variance ◽  
Physiological Disorder ◽  
Phenotypic Data ◽  
Resistant Parent ◽  
Trait Locus ◽  
Calcium Transporter

Abstract Tipburn is an important physiological disorder of lettuce, Lactuca sativa L., related to calcium deficiency that can result in leaf necrosis and unmarketable crops. The major quantitative trait locus, qTPB5.2, can account for up to 70% of the phenotypic variance for tipburn incidence in the field. This quantitative trait locus was genetically dissected to identify candidate genes for tipburn by creating lines with recombination events within the quantitative trait locus and assessing their resistance to tipburn. By comparing lines with contrasting haplotypes, the genetic region was narrowed down to ∼877 Kb that was associated with a reduction of tipburn by ∼60%. Analysis of the lettuce reference genome sequence revealed 12 genes in this region, one of which is a calcium transporter with a single nucleotide polymorphism in an exon between haplotypes with contrasting phenotypes. RNA-seq analysis of recombinants revealed two genes that were differentially expressed between contrasting haplotypes consistent with the tipburn phenotype. One encodes a Teosinte branched1/Cycloidea/Proliferating Cell factor transcription factor; however, differential expression of the calcium transporter was not detected. The phenotypic data indicated that there is a second region outside of the ∼877 Kb region but within the quantitative trait locus, at which a haplotype from the susceptible parent decreased tipburn by 10 to 20%. A recombinant line was identified with beneficial haplotypes in each region from both parents that showed greater tipburn resistance than the resistant parent; this line could be used as the foundation for breeding cultivars with more resistance than is currently available.

scholarly journals Quantitative Trait Loci Differentiating the Outbreeding Mimulus guttatus From the Inbreeding M. platycalyx

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1115-1121 ◽  
Author(s):  
Jing-Zhong Lin ◽  
Kermit Ritland
Keyword(s):  
Mating System ◽  
Quantitative Trait ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Random Amplified Polymorphic Dna ◽  
Phenotypic Variance ◽  
Mimulus Guttatus ◽  
Theoretical Predictions ◽  
Trait Locus ◽  
Plant Mating System

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6–28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect.

scholarly journals Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data

2019 ◽  
Vol 20 (24) ◽  
pp. 6114 ◽  
Author(s):  
Pei Sun ◽  
Huixia Jia ◽  
Yahong Zhang ◽  
Jianbo Li ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Adventitious Root ◽  
Adventitious Roots ◽  
Genetic Architecture ◽  
Populus Deltoides ◽  
Transmembrane Domain ◽  
Root Traits ◽  
Rna Seq ◽  
Correlation Relationship ◽  
Trait Locus

Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F1 genotypes originating from Populus deltoides ‘Danhong’ × Populus simonii ‘Tongliao1’ and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1–6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1–19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that PtAAAP19 (Potri.004G111400) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with ‘Danhong’, 153 bp deletion in the coding sequence of PtAAAP19 in ‘Tongliao1’ gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.

scholarly journals The Evolution of Larger Size in High Altitude Drosophila melanogaster has a Polymorphic Genetic Architecture

2021 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Justin B Lack ◽  
Dylan T Braun ◽  
Matthew J Monette ◽  
John E. Pool
Keyword(s):  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Genetic Architecture ◽  
Natural Populations ◽  
Enrichment Analysis ◽  
Thorax Length ◽  
Adaptive Trait ◽  
Polygenic Adaptation ◽  
Trait Locus ◽  
Population Genetic Analyses

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus (QTL) mapping approach to four unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of QTLs for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of QTL regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures our QTL mapping results for size traits mirror those from similar experiments on other recently-evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

scholarly journals Funmap2: an R package for QTL mapping using longitudinal phenotypes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7008
Author(s):  
Nating Wang ◽  
Tinyi Chu ◽  
Jiangtao Luo ◽  
Rongling Wu ◽  
Zhong Wang
Keyword(s):  
Qtl Mapping ◽  
Covariance Matrix ◽  
Complex Traits ◽  
Genetic Architecture ◽  
R Package ◽  
Information Criteria ◽  
Functional Mapping ◽  
Biological Knowledge ◽  
Phenotypic Traits ◽  
Trait Locus

Quantitative trait locus (QTL) mapping has been used as a powerful tool for inferring the complexity of the genetic architecture that underlies phenotypic traits. This approach has shown its unique power to map the developmental genetic architecture of complex traits by implementing longitudinal data analysis. Here, we introduce the R package Funmap2 based on the functional mapping framework, which integrates prior biological knowledge into the statistical model. Specifically, the functional mapping framework is engineered to include longitudinal curves that describe the genetic effects and the covariance matrix of the trait of interest. Funmap2 chooses the type of longitudinal curve and covariance matrix automatically using information criteria. Funmap2 is available for download at https://github.com/wzhy2000/Funmap2.

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