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 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 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 The genetic architecture of gene expression levels in wild baboons

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Jenny Tung ◽  
Xiang Zhou ◽  
Susan C Alberts ◽  
Matthew Stephens ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Genetic Architecture ◽  
Eqtl Mapping ◽  
Rna Seq ◽  
Specific Expression ◽  
Data Set ◽  
Expression Levels ◽  
Trait Locus ◽  
Eqtl Data ◽  
Gene Expression Levels

Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

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.

Molecular Dissection of a Genomic Region Governing Root Traits Associated with Drought Tolerance Employing a Combinatorial Approach of QTL Mapping and RNA-seq in Rice

2017 ◽  
Vol 35 (4) ◽  
pp. 457-468 ◽  
Author(s):  
Santosh Patil ◽  
A Srividhya ◽  
Roja Veeraghattapu ◽  
D A K Deborah ◽  
Gopalakrishna Murty Kadambari ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Qtl Mapping ◽  
Root Traits ◽  
Genomic Region ◽  
Combinatorial Approach ◽  
Rna Seq ◽  
Molecular Dissection

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

2022 ◽  
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

Abstract 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 QTL mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat (Triticum aestivum L.)

2021 ◽  
Vol 20 (5) ◽  
pp. 1180-1192
Author(s):  
Meng-jiao YANG ◽  
Cai-rong WANG ◽  
Muhammad Adeel HASSAN ◽  
Yu-ying WU ◽  
Xian-chun XIA ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Qtl Mapping ◽  
Bread Wheat ◽  
Root Traits ◽  
Triticum Aestivum L ◽  
Seedling Biomass ◽  
Nitrogen Conditions

EFFECTS OF ALUMINIUM ON THE ADVENTITIOUS ROOT SYSTEM, AERIAL BIOMASS AND GRAIN YIELD OF MAIZE GROWN IN THE FIELD AND IN A RHIZOTRON

2006 ◽  
Vol 42 (3) ◽  
pp. 351-366 ◽  
Author(s):  
J. J. COMIN ◽  
J. BARLOY ◽  
V. HALLAIRE ◽  
F. ZANETTE ◽  
P. R. M. MILLER
Keyword(s):  
Grain Yield ◽  
Root System ◽  
Soil Solution ◽  
Root Length ◽  
Adventitious Root ◽  
Adventitious Roots ◽  
Total Root Length ◽  
Al Tolerance ◽  
Root Branching ◽  
Four Levels

The aim of this work was to study the effects of soluble aluminium on the morphology and growth of the adventitious root system, aerial biomass and grain yield of maize (Zea mays). The analysis focuses on two hybrid cultivars (Al-sensitive HS7777 and Al-tolerant C525M). Experiments were carried out in the field and in a rhizotron in Curitiba, Paraná, Brazil. In the field, four levels of lime application were used: T0 = 0 t ha−1, T1 = 3.5 t ha−1, T2 = 7.0 t ha−1, and T3 = 10.5 t ha−1. Two levels were used in a rhizotron: T0 and T3. In the surface horizon (0–15 cm), the Al concentrations of the soil solution were: T0 = 15, T1 = 5.1, T2 = 4.4, and T3 = 3.1 μM. In the field, neither Al concentration in the soil solution nor cultivar affected the number of primary adventitious roots per internode or the total number of primary adventitious roots. However, root diameter, plant population and grain yield of the two cultivars confirmed the differences in Al tolerance between them. Al was observed to have an adverse effect on the grain yield from C525M, while low yields from HS7777, at all levels of Al, precluded any response to liming. In the rhizotron studies, Al concentration and cultivar affected the root branching and total root length. Cultivar C525M had more branches and total root length than HS7777, mainly at low concentrations of soil Al solution, leading to greater spatial colonization of the soil down to 0.9 m depth.

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

Genetics ◽  
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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