scholarly journals Trade-offs and selection conflicts in hybrid poplars indicate the stomatal ratio as an important trait regulating disease resistance

2019 ◽  
Author(s):  
Karl C. Fetter ◽  
David M. Nelson ◽  
Stephen R. Keller
Keyword(s):  
Disease Resistance ◽  
Common Garden ◽  
Phenotypic Variance ◽  
Populus Balsamifera ◽  
Rust Disease ◽  
Stomata Density ◽  
Hybrid Poplars ◽  
Intermediate Phenotypes ◽  
Trade Offs ◽  
A Genome

ABSTRACTNatural selection can remove maladaptive genotypic variance from populations, leaving reduced phenotypic variation as a signal of its action. Hybrid populations offer a unique opportunity to study phenotypic variance before selection purifies it, as these populations can have increased genotypic and phenotypic variance than can reveal trade-offs and selection conflicts not visible, or visible to a lesser extent, in unadmixed populations. Here, we study the interactions between a fungal leaf rust disease (Melampsora medusae) and stomata and ecophysiology traits in a set of hybrid and unadmixed individuals formed by natural matings between Populus balsamifera, P. trichocarpa, P. angustifolia, and P. deltoides. Phenotypes were measured on cloned genotypes grown in a common garden and genotyped at 227K SNPs with GBS. Our analyses indicate hybridization decreases disease resistance and increases the variance of stomatal ratio (SR), or the ratio of upper leaf surface stomata density to total stomata density. Heritability of SR was high in admixed populations (H2 = 0.72) and covaries strongly with the proportion of P. balsamifera ancestry in a genome; thus, selection could effectively reduce disease by selecting for low values of stomatal ratio. However, selection conflicts present in some admixed populations may prevent adaptation to pathogens as a result of these populations being unable to occupy adaptive trait space along the growth-defense spectrum. These results suggest an important role for SR and stomatal patterning traits as a target of pathogen induced selection to achieve local fitness optima. Additionally, we demonstrate that hybridization is capable of generating, or magnifying maladaptive intermediate phenotypes to reveal trade-offs and selection conflicts.

Sex ratio and life history traits at reaching sexual maturity in the dioecious shrub Fuchsia parviflora: field and common garden experiments

2021 ◽  
pp. 1-6
Author(s):  
Jessica S. Ambriz ◽  
Clementina González ◽  
Eduardo Cuevas
Keyword(s):  
Natural Population ◽  
Sexual Maturity ◽  
Sex Ratios ◽  
Natural Populations ◽  
Common Garden ◽  
Common Garden Experiment ◽  
Trade Offs ◽  
Reproductive Biomass ◽  
Common Garden Experiments ◽  
Growth And Reproduction

Abstract Fuchsia parviflora is a dioecious shrub that depends on biotic pollination for reproduction. Previous studies suggest that the male plants produce more flowers, and male-biased sex ratios have been found in some natural populations. To assess whether the biased sex ratios found between genders in natural populations are present at the point at which plants reach sexual maturity, and to identify possible trade-offs between growth and reproduction, we performed a common garden experiment. Finally, to complement the information of the common garden experiment, we estimated the reproductive biomass allocation between genders in one natural population. Sex ratios at reaching sexual maturity in F. parviflora did not differ from 0.5, except in one population, which was the smallest seedling population. We found no differences between genders in terms of the probability of germination or flowering. When flowering began, female plants were taller than males and the tallest plants of both genders required more time to reach sexual maturity. Males produced significantly more flowers than females, and the number of flowers increased with plant height in both genders. Finally, in the natural population studied, the investment in reproductive biomass was seven-fold greater in female plants than in male plants. Our results showed no evidence of possible trade-offs between growth and reproduction. Despite the fact that female plants invest more in reproductive biomass, they were taller than the males after flowering, possibly at the expense of herbivory defence.

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

scholarly journals Genetically Raised Circulating Bilirubin Levels and Risk of Ten Cancers: A Mendelian Randomization Study

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 394
Author(s):  
Nazlisadat Seyed Seyed Khoei ◽  
Robert Carreras-Torres ◽  
Neil Murphy ◽  
Marc J. Gunter ◽  
Paul Brennan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lung Cancer ◽  
Squamous Cell ◽  
Cell Lung Cancer ◽  
Hodgkin’S Lymphoma ◽  
Mendelian Randomization ◽  
Hodgkin's Lymphoma ◽  
Squamous Cell Lung Cancer ◽  
Phenotypic Variance ◽  
A Genome

Bilirubin, an endogenous antioxidant, may play a protective role in cancer development. We applied two-sample Mendelian randomization to investigate whether genetically raised bilirubin levels are causally associated with the risk of ten cancers (pancreas, kidney, endometrium, ovary, breast, prostate, lung, Hodgkin’s lymphoma, melanoma, and neuroblastoma). The number of cases and their matched controls of European descent ranged from 122,977 and 105,974 for breast cancer to 1200 and 6417 for Hodgkin’s lymphoma, respectively. A total of 115 single-nucleotide polymorphisms (SNPs) associated (p < 5 × 10−8) with circulating total bilirubin, extracted from a genome-wide association study in the UK Biobank, were used as instrumental variables. One SNP (rs6431625) in the promoter region of the uridine-diphosphoglucuronate glucuronosyltransferase1A1 (UGT1A1) gene explained 16.9% and the remaining 114 SNPs (non-UGT1A1 SNPs) explained 3.1% of phenotypic variance in circulating bilirubin levels. A one-standarddeviation increment in circulating bilirubin (≈ 4.4 µmol/L), predicted by non-UGT1A1 SNPs, was inversely associated with risk of squamous cell lung cancer and Hodgkin’s lymphoma (odds ratio (OR) 0.85, 95% confidence interval (CI) 0.73–0.99, P 0.04 and OR 0.64, 95% CI 0.42–0.99, p 0.04, respectively), which was confirmed after removing potential pleiotropic SNPs. In contrast, a positive association was observed with the risk of breast cancer after removing potential pleiotropic SNPs (OR 1.12, 95% CI 1.04–1.20, p 0.002). There was little evidence for robust associations with the other seven cancers investigated. Genetically raised bilirubin levels were inversely associated with risk of squamous cell lung cancer as well as Hodgkin’s lymphoma and positively associated with risk of breast cancer. Further studies are required to investigate the utility of bilirubin as a low-cost clinical marker to improve risk prediction for certain cancers.

Protocol for screening rust disease resistance in Dalbergia sissoo

2006 ◽  
Vol 36 (3) ◽  
pp. 176-182 ◽  
Author(s):  
N. S. K. Harsh ◽  
K. Uniyal ◽  
D. S. Bhandari
Keyword(s):  
Disease Resistance ◽  
Dalbergia Sissoo ◽  
Rust Disease

scholarly journals Identification and fine-mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and production markers validation in breeding lines

2021 ◽  
Author(s):  
Jiaojiao Ren ◽  
Penghao Wu ◽  
Gordon M. Huestis ◽  
Ao Zhang ◽  
Jingtao Qu ◽  
...  
Keyword(s):  
Latin American ◽  
Fine Mapping ◽  
Genome Wide Association Study ◽  
Selective Genotyping ◽  
Doubled Haploid Population ◽  
Phenotypic Variance ◽  
Breeding Lines ◽  
A Genome ◽  
Tar Spot ◽  
Major Qtl

Abstract Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively. A total of 115 SNPs in bin 8.03 were detected by GWAS and three QTL in bins 6.05, 6.07, and 8.03 were detected by selective genotyping. The major QTL qRtsc8-1 located in bin 8.03 was detected by both analyses, it explained 14.97% of the phenotypic variance. To fine-map qRtsc8-1, the recombinant-derived progeny test was implemented. Recombinations in each generation were backcrossed, and the backcross progenies were genotyped with Kompetitive Allele Specific PCR (KASP) markers and phenotyped for TSC resistance individually. The significant tests for comparing the TSC resistance between the two classes of progenies with and without resistant alleles were used for fine-mapping. In BC5 generation, qRtsc8-1 was fine mapped in an interval of ~721 kb flanked by markers of KASP81160138 and KASP81881276. In this interval, the candidate genes GRMZM2G063511 and GRMZM2G073884 were identified, which encode an integral membrane protein-like and a leucine-rich repeat receptor-like protein kinase, respectively. Both genes are involved in maize disease resistance responses. Two production markers KASP81160138 and KASP81160155 were verified in 471 breeding lines. This study provides valuable information for cloning the resistance gene, it will also facilitate the routine implementation of marker-assisted selection in the breeding pipeline for improving TSC resistance.

scholarly journals Straightening the crooked: intraspecific divergence of stem posture control and associated trade-offs in a model conifer

2021 ◽  
Author(s):  
R Sierra-de-Grado ◽  
V Pando ◽  
J Voltas ◽  
R Zas ◽  
J Majada ◽  
...  
Keyword(s):  
Mechanical Stability ◽  
Common Garden ◽  
Shoot Elongation ◽  
Reaction Wood ◽  
Forest Trees ◽  
Manipulative Experiment ◽  
Intraspecific Divergence ◽  
Trade Offs ◽  
Adaptive Phenotypic Plasticity ◽  
Light Capture

Abstract Although the straightening capacity of the stem is key for light capture and mechanical stability in forest trees, little is known about its adaptive implications. Assuming that stem straightening is costly, trade-offs are expected with competing processes such as growth, maintenance and defences. We established a manipulative experiment in a common garden of Pinus pinaster including provenances typically showing either straight-stemmed or crooked-stemmed phenotypes. We imposed a bending up to 35º on plants aged nine years of both provenance groups and followed the straightening kinetics and shoot elongation after releasing. Eight months later, we destructively assessed biomass partitioning, reaction wood, wood microdensity, xylem reserve carbohydrates and phloem secondary metabolites. The experimental bending and release caused significant, complex changes with a marked difference between straight- and crooked-type plants. The straight-type recovered verticality faster and to a higher degree and developed more compression wood, while displaying a transitory delay in shoot elongation, reducing resource allocation to defences and maintaining the levels of non-structural carbohydrates compared to the crooked type. This combination of responses indicates the existence of intraspecific divergence in the reaction to mechanical stresses which may be related to different adaptive phenotypic plasticity.

scholarly journals Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 33 ◽  
Author(s):  
Md. Islam ◽  
John Ontoy ◽  
Prasanta Subudhi
Keyword(s):  
Quantitative Trait Loci ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Oryza Sativa L ◽  
Meta Analysis ◽  
Seedling Stage ◽  
Phenotypic Variance ◽  
A Genome ◽  
Trait Loci

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

scholarly journals Non-parametric interval mapping in half-sib designs: use of midranks to account for ties

2003 ◽  
Vol 81 (3) ◽  
pp. 221-228 ◽  
Author(s):  
P. TILQUIN ◽  
I. VAN KEILEGOM ◽  
W. COPPIETERS ◽  
E. LE BOULENGÉ ◽  
P. V. BARET
Keyword(s):  
Disease Resistance ◽  
Infectious Diseases ◽  
Qtl Analysis ◽  
Statistical Power ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Total Phenotypic Variance ◽  
Non Parametric ◽  
Normally Distributed

In QTL analysis of non-normally distributed phenotypes, non-parametric approaches have been proposed as an alternative to the use of parametric tests on mathematically transformed data. The non-parametric interval mapping test uses random ranking to deal with ties. Another approach is to assign to each tied individual the average of the tied ranks (midranks). This approach is implemented and compared to the random ranking approach in terms of statistical power and accuracy of the QTL position. Non-normal phenotypes such as bacteria counts showing high numbers of zeros are simulated (0–80% zeros). We show that, for low proportions of zeros, the power estimates are similar but, for high proportions of zeros, the midrank approach is superior to the random ranking approach. For example, with a QTL accounting for 8% of the total phenotypic variance, a gain from 8% to 11% of power can be obtained. Furthermore, the accuracy of the estimated QTL location is increased when using midranks. Therefore, if non-parametric interval mapping is chosen, the midrank approach should be preferred. This test might be especially relevant for the analysis of disease resistance phenotypes such as those observed when mapping QTLs for resistance to infectious diseases.

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