Rapa Populations Research Articles

Biochemical and genetic mechanisms in Pieris rapae (Lepidoptera: Pieridae) resistance under emamectin benzoate stress

Pieris rapae (Lepidoptera: Pieridae) poses a significant threat to Brassicaceae crops, leading to substantial losses annually. Repeated insecticide applications are widely used to protect crops and increase the resistance of P. rapae. Exploring the biochemical and molecular basis of insecticide tolerance in P. rapae is crucial for achieving effective insect suppuration and implementing resistance control strategies. In our research, emamectin benzoate (EBZ) resistance was developed in P. rapae strain through selective pressure over 15 generations. Moreover, the biochemical mechanisms underlying resistance to EBZ and its potential cross-resistance to other insecticides were studied. Additionally, the expression levels of cytochrome P450 (CYP450) and glutathione-s-transferase (GST) genes in P. rapae were quantitatively assessed upon exposure to EBZ using real-time PCR. Our data exhibited that the LC50 value of susceptible strain (Sus) and EBZ resistance strain (EBZ-R) were 0.009 and 8.09 mg/L, with a resistance ratio (RR) reaching 898.8-fold. The EBZ-R stain displayed notably low cross-resistance to lambda-cyhalothrin, spinetoram, and cypermethrin. However, it demonstrated a moderate level of cross-resistance to deltamethrin. Conversely, no cross-resistance was noted to chlorantraniliprole and indoxacarb. Notably, enzyme inhibitors of detoxification enzymes revealed that piperonyl butoxide (PBO) and diethyl maleate (DEM) enhanced the EBZ toxicity to the resistant strain, indicating the potential involvement of CYP450 and GST in avermectin resistance. A remarkable enhancement in CYP450 and GST activity was observed in the EBZ-R stain. CYP450 and GST genes are upregulated in the EBZ-R stain compared to the Sus strain, which serves as a basis for comprehending the mechanism behind P. rapae resistance to EBZ. The molecular docking analysis demonstrated that EBZ has a high binding affinity with CYP6AE120 and PrGSTS1 with docking energy values of −20.19 and −22.57 kcal/mol, respectively. Our findings offer valuable insights into crafting efficient strategies to monitor and manage resistance in P. rapae populations in Egypt.

Combined cytogenetic and molecular methods for taxonomic verification and description of Brassica populations deriving from different origins

Agriculture faces great challenges to overcome global warming and improve system sustainability, requiring access to novel genetic diversity. So far, wild populations and local landraces remain poorly explored. This is notably the case for the two diploid species, Brassica oleracea L. (CC, 2n=2x=18) and B. rapa L. (AA, 2n=2x=20). In order to explore the genetic diversity in both species, we have collected populations in their centre of origin, the Mediterranean basin, on a large contrasting climatic and soil gradient from northern Europe to southern sub-Saharan regions. In these areas, we also collected 14 populations belonging to five B. oleracea closely related species. Our objective was to ensure the absence of species misidentification at the seedling stage among the populations collected and to describe thereafter their origins. We combined flow cytometry, sequencing of a species-specific chloroplast genomic region, as well as cytogenetic analyses in case of unexpected results for taxonomic verification. Out of the 112 B. oleracea and 154 B. rapa populations collected, 103 and 146, respectively, presented a good germination rate and eighteen populations were misidentified. The most frequent mistake was the confusion of these diploid species with B. napus. Additionally for B. rapa, two autotetraploid populations were observed. Habitats of the collected and confirmed wild populations and landraces are described in this study. The unique plant material described here will serve to investigate the genomic regions involved in adaptation to climate and microbiota within the framework of the H2020 Prima project ‘BrasExplor’.

No fitness cost in Brassica rapa L. (wild turnip) populations associated with transgenic glyphosate and non-transgenic AHAS-inhibiting herbicides resistance

The adoption of genetically modified (GM) and non-GM Brassica napus herbicide-resistant cultivars, along with the possibility of introgression with B. rapa, has led to the emergence of new weedy biotypes. In Argentina, in 2012, natural populations of transgenic (GM) glyphosate-resistant and non-GM AHAS-inhibiting resistant B. rapa were detected. The investigation of the pleiotropic effects between herbicide resistance and fitness in these biotypes can help determine the potential persistence of these resistances in agricultural fields. The aim of this study was to assess the effect of the glyphosate transgene (GT73) and AHAS Trp574Leu mutation on B. rapa vegetative and reproductive traits. Fitness components were compared between susceptible (S) and resistant (R) populations in two trials in a common garden experiment. Each assay was performed in the spring and winter season. One trial was carried out using populations with homogeneous genetic background, and the other using populations with different genetic backgrounds. Plants grown during the winter season exhibited superior performance compared to those grown in spring. No differences were found between R and S biotypes in the parameters evaluated in populations with homogeneous genetic background, except for siliques per main inflorescence where the S biotype produced more siliques than the R, although this later compensated with more seeds per silique. When comparing R and S biotypes with different genetic backgrounds, no significant differences were found in the evaluated parameters. Therefore, glyphosate and AHAS-inhibiting resistances are likely to persist in Brassica rapa populations, even in the absence of herbicide selection pressure.

Convergent Adaptation of Multiple Herbicide Resistance to Auxin Mimics and ALS- and EPSPS-Inhibitors in Brassica rapa from North and South America.

Herbicide-resistant weeds have been identified and recorded on every continent where croplands are available. Despite the diversity of weed communities, it is of interest how selection has led to the same consequences in distant regions. Brassica rapa is a widespread naturalized weed that is found throughout temperate North and South America, and it is a frequent weed among winter cereal crops in Argentina and in Mexico. Broadleaf weed control is based on glyphosate that is used prior to sowing and sulfonylureas or mimic auxin herbicides that are used once the weeds have already emerged. This study was aimed at determining whether a convergent phenotypic adaptation to multiple herbicides had occurred in B. rapa populations from Mexico and Argentina by comparing the herbicide sensitivity to inhibitors of the acetolactate synthase (ALS), 5-enolpyruvylshikimate-3-phosphate (EPSPS), and auxin mimics. Five B. rapa populations were analyzed from seeds collected in wheat fields in Argentina (Ar1 and Ar2) and barley fields in Mexico (Mx1, Mx2 and MxS). Mx1, Mx2, and Ar1 populations presented multiple resistance to ALS- and EPSPS-inhibitors and to auxin mimics (2,4-D, MCPA, and fluroxypyr), while the Ar2 population showed resistance only to ALS-inhibitors and glyphosate. Resistance factors ranged from 947 to 4069 for tribenuron-methyl, from 1.5 to 9.4 for 2,4-D, and from 2.7 to 42 for glyphosate. These were consistent with ALS activity, ethylene production, and shikimate accumulation analyses in response to tribenuron-methyl, 2,4-D, and glyphosate, respectively. These results fully support the evolution of the multiple- and cross-herbicide resistance to glyphosate, ALS-inhibitors, and auxinic herbicides in B. rapa populations from Mexico and Argentina.

A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

BackgroundAllotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.ResultsBased on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.ConclusionsThe phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.

Seasonal Abundance of the White Butterfly Pieris rapae L. in the old and reclaimed areas with reference to its relative susceptibility and damage to certain cabbage cultivars

The main goal of this study was to determine the seasonal abundance of the white butterfly Pieris rapae L. (Lepidoptera: Pieridae) on several local and imported cabbage cultivars in old and reclaimed lands. The impact of certain cabbage metabolites on P. rapae populations was examined, as well as the relative susceptibility of different cabbage cultivars. Damage caused by P. rapae Varies. During the first two months following transplantation, P. rapae can cause economic damage to cabbage plants in both areas. One month later, its population had multiplied several times in the old land. Three of the six tested cabbage cultivars were appeared as susceptible (S) cultivars and harbored high numbers of the pest with an average of 0.63, 0.60 and 0.53 Kenz, Crossina and Ganzory cultivars, respectively. However, the imported white cabbage hybrids, 728, 730 and 747 showed sort of resistance and appeared as low resistant (LR) hybrids and harbored 0.40, 0.41 and 0.45 individuals/plant, respectively. Chlorophyll only showed highly significant negative correlation with P. rapae populations. However, the remaining metabolites showed non-significant positive correlation. In a comparison between P. rapae populations in Assiut (the old area) and El-Fath province (the reclaimed area), it can be note that the pest populations, the damaged (infested and unmarketable) plants were multiplied several times in the later. It can be noted that the general mean of the pest numbers recorded in the reclaimed area (2.14 individuals/plant) was found to equal 4.28 folds more than that recorded in the old area (0.50 individuals/plant).

Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population

BackgroundPathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought.ResultsPreviously, we combined a resurrection experiment with genome-wide sequencing of 124 pooled ancestral and descendant plants. Here, using these previously generated sequence data (Franks et al. in Mol Ecol 25(15):3622–3631, 2016), we show that well-characterized necrotrophic fungal pathogen response (NFPR) genes have evolved, as indicated by changes in allele frequency, between ancestors and descendants, with several of them identified as extreme FST outliers. The jasmonic acid (JA) signaling pathway in particular seems to underlie the evolution of disease susceptibility, in addition to its well characterized role in plastic disease response. We identify a list of 260 genes that are both NFPR genes and are differentially expressed in response to drought, based on publicly available data. We present evidence that five of these genes evolved between ancestors and descendants, suggesting that the drought acted as the evolutionary driver, and that the accompanying increase in disease susceptibility may have been a consequence of genetic pleiotropy.ConclusionsOur study provides evidence that for this population, standing variation in NFPR genes is affected by natural selection related to climate change. Our results reveal potentially important candidates that may underlie trait evolution in both crops and natural systems. Additionally, this trade-off between adaptation to biotic and abiotic stresses is an example of how climate change can have diverse and unexpected consequences.

Changes in arthropod community but not plant quality benefit a specialist herbivore on plants under reduced water availability.

Plants growing under reduced water availability can affect insect herbivores differently, in some instances benefitting them. However, the forces mediating these positive impacts remain mostly unclear. To identify how water availability impacts plant quality and multi-trophic interactions, we conducted manipulative field studies with two populations of the specialist herbivore Pieris rapae, and its host plant, Rorippa indica. We found that P. rapae larvae experienced higher survival on R. indica growing under low water availability compared with plants grown under high water availability. Higher survival of eggs and larvae was related to the reduced abundance of other herbivores and natural enemies. Water availability had differential impacts on other members of the herbivore community by altering plant quality. Low water availability decreased the quality of R. indica to most herbivores, as indicated by reduced abundance in the field and decreased relative growth rate in laboratory feeding assays. In contrast, P. rapae larval performance was not affected by sympatric R. indica grown under different water availability. These results indicate that local P. rapae populations possess physiological adaptations to overcome fluctuations in host quality. Our findings illustrate that reduced water availability is beneficial to a specialist herbivore but detrimental to most other herbivores. Our work highlights the complex effects of the arthropod communities associated with plants in determining the impacts of water availability on insect herbivores.

Molecular characterization of imidazolinone-resistant Brassica rapa × B. napus hybrids.

Herbicide-resistant oilseed rape (Brassica napus) cultivation in our country entails the risk of gene transfer to related wild species. One of these species is the wild turnip (B. rapa), an important weed of winter crops widely distributed in the Pampas region. Despite hybridization risks, Clearfield ® oilseed rape is available in Argentina. In 2008, a B. rapa population, which was sympatric to an imidazolinone-resistant and a conventional oilseed rape cultivar, was located on a farm in the main cropping area of the country. Herbicide-resistant individuals were found in the progeny of this population in a herbicide screening test. Therefore, a molecular characterization using cleaved amplified polymorphic sequence (CAPS) and simple sequence repeat (SSR) markers was conducted on these plants to determine their hybrid nature and to establish the origin of the imidazolinone resistance trait. The results of this study, along with information of field records, confirmed that the resistant plants were first generation interspecific hybrids. Imidazolinone resistance had been effectively transferred from the herbicide-resistant oilseed rape, even in the particular situation of pollen competition. Oilseed rape resistant cultivars are becoming more common in the country. So, considering that seed loss and crop volunteers are common in these species, it is crucial to avoid the dispersion of new resistant weed biotypes as they reduce the effectiveness of chemical control technologies.

Mapping and identification of potential target genes from short–RNA seq for the control of Pieris rapae larvae

Pieris rapae is a serious pest of brassicas worldwide. We performed de novo assembly of P. rapae transcriptome by next-generation sequencing and assembled approximately 65,727,422 clean paired-end reads into 32,118 unigenes, of which 13,585 were mapped to 255 pathways in the KEGG database. A total of 6173 novel transcripts were identified from reads directly mapped to P. rapae genome. Additionally, 1490 SSRs, 301,377 SNPs, and 29,284 InDels were identified as potential molecular markers to explore polymorphism within P. rapae populations. We screened and mapped 36 transcripts related to OBP, CSP, SNMP, PBAN, and OR. We analyzed the expression profiles of 7 selected genes involved in pheromone transport and degradation by quantitative real-time PCR; these genes are sex-specific and differentially expressed in the developmental stages. Overall, the comprehensive transcriptome resources described in this study could help understand and identify molecular targets particularly reproduction-related genes for developing effective P. rapae management tools.

Transgene escape and persistence in an agroecosystem: the case of glyphosate-resistant Brassica rapa L. in central Argentina.

Brassica rapa L. is an annual Brassicaceae species cultivated for oil and food production, whose wild form is a weed of crops worldwide. In temperate regions of South America and especially in the Argentine Pampas region, this species is widely distributed. During 2014, wild B. rapa populations that escaped control with glyphosate applications by farmers were found in this area. These plants were characterized by morphology and seed acidic profile, and all the characters agreed with B. rapa description. The dose-response assays showed that the biotypes were highly resistant to glyphosate. It was also shown that they had multiple resistance to AHAS-inhibiting herbicides. The transgenic origin of the glyphosate resistance in B. rapa biotypes was verified by an immunological test which confirmed the presence of the CP4 EPSPS protein and by an event-specific GT73molecular marker. The persistence of the transgene in nature was confirmed for at least 4years, in ruderal and agrestal habitats. This finding suggests that glyphosate resistance might come from GM oilseed rape crops illegally cultivated in the country or as a seed contaminant, and it implies gene flow and introgression between feral populations of GM B. napus and wild B. rapa. The persistence and spread of the resistance in agricultural environments was promoted by the high selection pressure imposed by intensive herbicide usage in the prevalent no-till farming systems.

Ecological specialization in Diaeretiella rapae (Hymenoptera: Braconidae: Aphidiinae) on aphid species from wild and cultivated plants.

Diaeretiella rapae is an aphid parasitoid with potential for use in biological control strategies. However, several recent genetic studies have challenged the long held view that it is a generalist parasitoid. We investigated its ecological specialization and ability to use resources in cultivated and uncultivated areas. Ecological specialization would reduce its ability to exploit the diversity of aphid species, particularly in uncultivated areas, and to control pest aphids. Four D. rapae strains were studied, three reared on pest aphids on Brassicaceae and one strain on a non-pest aphid on Chenopodiaceae. For each strain, we performed host-switching experiments, with a total of six aphid species, five of which D. rapae parasitizes in France. We tested cross-breeding ability between strains to detect potential reproductive isolation linked to aphid host species in D. rapae. The strain reared on non-pest aphids was able to develop on aphid species from both cultivated and uncultivated plants. The strains reared on pest aphids, however, exclusively parasitized aphid species on cultivated Brassicaceae. In addition, reproductive isolation was detected between strains from uncultivated and cultivated plants. Thus, the D. rapae populations examined here appear to be showing ecological specialization or they may even be composed of a complex of cryptic species related to the aphid hosts. The role of Chenopodium album as a reservoir for D. rapae, by providing a habitat for non-pest aphids on which it can feed, appears to be severely limited, and thus its efficiency to maintain local populations of D. rapae in the vicinity of crops is questionable.

IMI resistance associated to crop-weed hybridization in a natural Brassica rapa population: characterization and fate.

Wild turnip (Brassica rapa) is a common weed and a close relative to oilseed rape (Brassica napus). The Clearfield® production system is a highly adopted tool which provides an alternative solution for weed management, but its efficiency is threatened by gene transfer from crop to weed relatives. Crop-weed hybrids with herbicide resistance were found in the progeny of a B. rapa population gathered from a weedy stand on the borders of an oilseed rape (B. napus) imidazolinone (IMI)-resistant crop. Interspecific hybrids were confirmed by morphological traits in the greenhouse and experimental field, survival after imazethapyr applications, DNA content through flow cytometry, and pollen viability. The transference of herbicide resistance was demonstrated even in a particular situation of pollen competition between both an herbicide-resistant crop and a non-resistant crop. However, IMI resistance was not found in further generations collected at the same location. These results verify gene transmission from oilseed rape to B. rapa in the main crop area in Argentina where resistant and susceptible varieties are found and seed loss and crop volunteers are common. Hybridization, introgression, and herbicide selection would be associated with the loss of effectiveness of IMI technology.

Factors Affecting the Disease Severity of Alternaria Blackspot In Natural Brassica rapa Populations On the California and Oregon Coasts

Abstract Fungal disease has important effects in natural and agricultural plant populations; however, we are still uncovering factors that influence severity in these systems. Understanding these factors is especially important because it has been predicted that climate change will increase fungal disease widely as a result of changes in precipitation. Here, we investigate the role of water availability and other ecological variables in determining disease severity of a foliar fungal disease. For this study, we focused on natural populations of an important annual, herbaceous plant, Brassica rapa and its fungal disease, Alternaria blackspot. We explored three hypotheses: (1) The factors that drive disease severity differ early in the growing season compared to late in the growing season. (2) Disease severity patterns for this fungus are driven by water availability to a greater extent than other ecological variables. (3) Disease severity increases with plant density. To address these hypotheses, data were...

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome‐wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late‐season drought in California. These ancestor‐descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (F ST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome‐wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.

A Geometric Morphometric Study of the Wing Shapes ofPieris rapae(Lepidoptera: Pieridae) from the Qinling Mountains and Adjacent Regions: An Environmental and Distance-Based Consideration

Butterflies possess attributes that are sensitive to gradual environmental changes. Recently, the effects of environmental factors on the shapes of organisms, as well as the interactions of these elements, have been extensively examined, i.e., effects of seasonal changes on the colors of butterfly wings, and effects of landscape structure on butterfly distribution and morphology. However, few studies have dealt with variations in butterfly shapes in response to varying environmental conditions. Here we aimed to determine how body size and shape variations in butterflies are correlated to environmental heterogeneity. We used geometric morphometrics to quantify Pieris rapae wing shape variations. Results showed that forewing and hind wing sizes were significantly different among the 15 populations. P. rapae individuals with larger wing sizes were mainly distributed in mountainous areas, whereas those with smaller-sized wings were found on the plains. Canonical variate analysis was employed to examine the patterns of variation in wing shapes among and within the populations. Significant differences in shape were revealed in the forewings and the hind wings of P. rapae populations. All populations were divided into 2 groups on the first canonical variate axis (CV1), which followed the Qinling Mountains as an important boundary between the Palearctic and Oriental Realms in zoogeographical division of the world. The unweighted pair group method with arithmetic mean (UPGMA) clustered the 15 populations into 4 groups by forewing and hind wing shape in response to the 4 environment types in Qinling Mountains. We suggest that wing shapes of P.rapae are sensitive to environmental heterogeneity. The isolating effect of the Qinling Mountains on P. rapae population interactions was apparent.

Selection against hybrids in mixed populations of Brassica rapa and Brassica napus: model and synthesis

Pollen of the crop oilseed rape (Brassica napus, AACC) can cross-fertilize ovules of Brassica rapa (AA), which leads to an influx of unpaired C-chromosomes into wild B. rapa populations. The presence of such extra chromosomes is thought to be an indicator of introgression. Backcrosses and F(1) hybrids were found in Danish populations but, surprisingly, only F(1) hybrids were found in the UK and the Netherlands. Here, a model tests how the level of selection and biased vs unbiased transmission affect the population frequency of C-chromosomes. In the biased-transmission scenario the experimental results of the first backcross are extrapolated to estimate survival of gametes with different numbers of C-chromosomes from all crosses in the population. With biased transmission, the frequency of C-chromosomes always rapidly declines to zero. With unbiased transmission, the continued presence of plants with extra C-chromosomes depends on selection in the adult stage and we argue that this is the most realistic option for modeling populations. We suggest that selection in the field against plants with unpaired C-chromosomes is strong in Dutch and UK populations. The model highlights what we do not know and makes suggestions for further research on introgression.

Association of sequence variation in Brassica GLABRA1 orthologs with leaf hairiness

A 5-bp deletion in exon 3 of a Brassica rapa ortholog of GLABRA1 (BrGL1) was previously thought to be responsible for the hairless trait of a doubled haploid line. In this study, the sequence variation of Brassica GL1 was characterized. The DNA-binding domain of GL1 in Arabidopsis thaliana was found to be highly conserved in Brassica species, while in hairless B. oleracea lines, frameshifts and nonsynonymous substitutions were detected in the coding sequences of BoGL1. Phylogenetic analysis showed that BnGL1 in hairless B. napus lines is closely related to BiGL1 in a hairy B. incana line. In 11 lines of B. rapa germplasm, nucleotide polymorphisms were only detected in exon 3 of BrGL1. Regarding the nucleotide polymorphisms in the DNA-binding domain of BrGL1, four alleles were identified, and corresponding dot-blot single nucleotide polymorphism (SNP) markers were developed and used for genotyping of 63 lines of B. rapa. The genotyping results showed that nucleotide polymorphisms in the DNA-binding domain of BrGL1 are associated with leaf hairiness. Reverse-transcription PCR analysis indicated that different BrGL1 alleles are all expressed normally. These findings reveal the key nucleotide polymorphisms of BrGL1 affecting leaf hairiness in the natural B. rapa population.

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

BackgroundThe amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species.ResultsThree chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained.ConclusionsThe distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes.

Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea

Publicly available genomic tools help researchers integrate information and make new discoveries. In this paper, we describe the development of immortal mapping populations of rapid cycling, self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea and make the data and germplasm available to the Brassica research community. The B. rapa population consists of 160 recombinant inbred (RI) lines derived from the cross of highly inbred lines of rapid cycling and yellow sarson B. rapa. The B. oleracea population consists of 155 double haploid (DH) lines derived from an F1 cross between two DH lines, rapid cycling and broccoli. A total of 120 RFLP probes, 146 SSR markers, and one phenotypic trait (flower color) were used to construct genetic linkage maps for both species. The B. rapa map consists of 224 molecular markers distributed along 10 linkage groups (A1-A10) with a total distance of 1125.3 cM and a marker density of 5.7 cM/marker. The B. oleracea genetic map consists of 279 molecular markers and one phenotypic marker distributed along nine linkage groups (C1-C9) with a total distance of 891.4 cM and a marker density of 3.2 cM/marker. A syntenic analysis with Arabidopsis thaliana identified collinear genomic blocks that are in agreement with previous studies, reinforcing the idea of conserved chromosomal regions across the Brassicaceae.