Clubroot Symptoms and Resting Spore Production in a Doubled Haploid Population of Oilseed Rape (Brassica napus) Are Controlled by Four Main QTLs

Impact of Susceptibility on Plant Hormonal Composition during Clubroot Disease Development in Canola (Brassica napus)

Clubroot, caused by Plasmodiophora brassicae, is a soilborne disease of crucifers associated with the formation of large root galls. This root enlargement suggests modulation of plant hormonal networks by the pathogen, stimulating cell division and elongation and influencing host defense. We studied physiological changes in two Brassica napus cultivars, including plant hormone profiles-salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), the auxin indole-3-acetic acid (IAA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC)-along with their selected derivatives following inoculation with virulent and avirulent P. brassicae pathotypes. In susceptible plants, water uptake declined from the initial appearance of root galls by 21 days after inoculation, but did not have a significant effect on photosynthetic rate, stomatal conductance, or leaf chlorophyll levels. Nonetheless, a strong increase in ABA levels indicated that hormonal mechanisms were triggered to cope with water stress due to the declining water uptake. The free SA level in the roots increased strongly in resistant interactions, compared with a relatively minor increase during susceptible interactions. The ratio of conjugated SA to free SA was higher in susceptible interactions, indicating that resistant interactions are linked to the plant's ability to maintain higher levels of bioactive free SA. In contrast, JA and its biologically active form JA-Ile declined up to 7-fold in susceptible interactions, while they were maintained during resistant interactions. The ACC level increased in the roots of inoculated plants by 21 days, irrespective of clubroot susceptibility, indicating a role of ethylene in response to pathogen interactions that is independent of disease severity. IAA levels at early and later infection stages were lower only in susceptible plants, suggesting a modulation of auxin homeostasis by the pathogen relative to the host defense system.

A Comparison of Methods to Estimate Additive-by-Additive-by-Additive of QTL×QTL×QTL Interaction Effects by Monte Carlo Simulation Studies

The goal of the breeding process is to obtain new genotypes with traits improved over the parental forms. Parameters related to the additive effect of genes as well as their interactions (such as epistasis of gene-by-gene interaction effect and additive-by-additive-by-additive of gene-by-gene-by-gene interaction effect) can influence decisions on the suitability of breeding material for this purpose. Understanding the genetic architecture of complex traits is a major challenge in the post-genomic era, especially for quantitative trait locus (QTL) effects, QTL-by-QTL interactions and QTL-by-QTL-by-QTL interactions. With regards to the comparing methods for estimating additive-by-additive-by-additive of QTL×QTL×QTL interaction effects by Monte Carlo simulation studies, there are no publications in the open literature. The parameter combinations assumed in the presented simulation studies represented 84 different experimental situations. The use of weighted regression may be the preferred method for estimating additive-by-additive-by-additive of QTL-QTL-QTL triples interaction effects, as it provides results closer to the true values of total additive-by-additive-by-additive interaction effects than using unweighted regression. This is also indicated by the obtained values of the determination coefficients of the proposed models.

Fine mapping and candidate gene analysis of proportion of four-seed pods by soybean CSSLs

Soybean yield, as one of the most important and consistent breeding goals, can be greatly affected by the proportion of four-seed pods (PoFSP). In this study, QTL mapping was performed by PoFSP data and BLUE (Best Linear Unbiased Estimator) value of the chromosome segment substitution line population (CSSLs) constructed previously by the laboratory from 2016 to 2018, and phenotype-based bulked segregant analysis (BSA) was performed using the plant lines with PoFSP extreme phenotype. Totally, 5 ICIM QTLs were repeatedly detected, and 6 BSA QTLs were identified in CSSLs. For QTL (qPoFSP13-1) repeated in ICIM and BSA results, the secondary segregation populations were constructed for fine mapping and the interval was reduced to 100Kb. The mapping results showed that the QTL had an additive effect of gain from wild parents. A total of 14 genes were annotated in the delimited interval by fine mapping. Sequence analysis showed that all 14 genes had genetic variation in promoter region or CDS region. The qRT-PCR results showed that a total of 5 candidate genes were differentially expressed between the plant lines having antagonistic extreme phenotype (High PoFSP > 35.92%, low PoFSP< 17.56%). The results of haplotype analysis showed that all five genes had two or more major haplotypes in the resource population. Significant analysis of phenotypic differences between major haplotypes showed all five candidate genes had haplotype differences. And the genotypes of the major haplotypes with relatively high PoFSP of each gene were similar to those of wild soybean. The results of this study were of great significance to the study of candidate genes affecting soybean PoFSP, and provided a basis for the study of molecular marker-assisted selection (MAS) breeding and four-seed pods domestication.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L

Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean

Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.

Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01

Plasmodiophora brassicae causes clubroot disease in brassica crops worldwide. Brassica rapa, a progenitor of Brassica napus (canola), possesses important sources for resistance to clubroot. A doubled haploid (DH) population consisting of 84 DH lines were developed from a Backcross2 (BC₂) plant through an interspecific cross of B. rapa turnip cv. ECD01 (resistant, R) with canola line DH16516 (susceptible, S) and then backcrossed with DH16516 as the recurrent parent. The DH lines and their parental lines were tested for resistance to four major pathotypes (3A, 3D, 3H, and 5X) of P. brassicae identified from canola. The R:S segregation ratio for pathotype 3A was 1:3, and 3:1 for pathotypes 3D, 3H, and 5X. From genotyping by sequencing (GBS), a total of 355.3 M short reads were obtained from the 84 DH lines, ranging from 0.81 to 11.67 M sequences per line. The short reads were aligned into the A-genome of B. napus "Darmor-bzh" version 4.1 with a total of 260 non-redundant single-nucleotide polymorphism (SNP) sites. Two quantitative trait loci (QTLs), Rcr10 ^ECD01 and Rcr9 ^ECD01 , were detected for the pathotypes in chromosomes A03 and A08, respectively. Rcr10 ^ECD01 and Rcr9 ^ECD01 were responsible for resistance to 3A, 3D, and 3H, while only one QTL, Rcr9 ^ECD01 , was responsible for resistance to pathotype 5X. The logarithm of the odds (LOD) values, phenotypic variation explained (PVE), additive (Add) values, and confidence interval (CI) from the estimated QTL position varied with QTL, with a range of 5.2-12.2 for LOD, 16.2-43.3% for PVE, 14.3-25.4 for Add, and 1.5-12.0 cM for CI. The presence of the QTLs on the chromosomes was confirmed through the identification of the percentage of polymorphic variants using bulked-segregant analysis. There was one gene encoding a disease resistance protein and 24 genes encoding proteins with function related to plant defense response in the Rcr10 ^ECD01 target region. In the Rcr9 ^ECD01 region, two genes encoded disease resistance proteins and 10 genes encoded with defense-related function. The target regions for Rcr10 ^ECD01 and Rcr9 ^ECD01 in B. napus were homologous to the 11.0-16.0 Mb interval of chromosome A03 and the 12.0-14.5 Mb interval of A08 in B. rapa "Chiifu" reference genome, respectively.