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Reliable estimates of genetic diversity among the accessions in a breeding population is important knowledge for use in breeding. Among the different types of molecular markers, single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) are largely used by breeders; however, our knowledge of the reliability of the estimates of genetic diversity based on these two types of markers in multiple populations is limited. In this study, a doubled haploid (DH) and an inbred population developed from Brassica napus × Brassica oleracea interspecific crosses were used for comparative analysis of these two types of markers. The estimates based on SNP and SSR markers showed a stronger correlation in the inbred population which was expected to carry greater genetic diversity as compared to the DH population. This inference was also evident from the analysis of different diversity groups (least, intermediate, and most similar) of these two populations for significant difference between the groups for six agronomic and seed quality traits, where this analysis failed to differentiate the diversity groups of the DH population for any of the traits. However, both marker types could differentiate the diversity groups of the inbred population for several traits. Furthermore, the six sub-populations of the inbred population could also be differentiated by both marker types. Thus, the results demonstrate the greater utility of the SSR and SNP markers in a genetically diverse population. This knowledge can be used while grouping a breeding population for diversity groups; however, caution needs to be taken while using the markers in a genetically narrow population.

Gene expression profiling offers a means of understanding pathogenesis in clubroot of crucifers caused by the biotrophic pathogen Plasmodiophora brassicae. In this study, a canola (Brassica napus) cultivar 45H29 was inoculated with P. brassicae pathotypes 5I (P5I) and 5X (P5X), and the pathogen:plant DNA biomass ratio in roots was determined at 7, 14, and 21 days after inoculation (dai) by quantitative PCR (qPCR) analysis. The P5X:plant biomass ratio increased across the time course, while the P5I:plant biomass ratio decreased. To investigate genes differentially expressed during the infection process, the expression of 205 P. brassicae genes encoding putative secreted proteins was analysed from the inoculated samples at 14 dai. One of the 205 genes was expressed at a higher level in P5X than in P5I, while 15 genes were expressed at a higher level in P5I than in P5X. Of these 16, 13 genes encoded proteins with high cysteine content, while three genes encoded proteins with an RXLR motif. The expression of the 16 genes was analysed further in the 7‐ and 21‐dai samples. No transcripts of the 16 genes were detected from either pathotype at 7 dai. In contrast, 11 genes were differentially expressed between the two pathotypes at 21 dai, with nine being more highly expressed in P5X and two in P5I. One gene showed homology to PbSUNK2 found in P. brassicae‐infected Arabidopsis thaliana root tissues. These 16 genes may offer important information to improve the current understanding of canola–P. brassicae interactions.

Genetic mapping for faba bean lags far behind other major crops. Density enhancement of the faba bean genetic linkage map was carried out by screening 5,325 genomic SSR primers and 2033 expressed sequence tag (EST)‐SSR primers on the parental cultivars '91825' and 'K1563'. Two hundred and fifteen genomic SSR and 133 EST‐SSR primer pairs that detected polymorphisms in the parents were used to screen 129 F₂ individuals. This study added 337 more SSR markers and extended the previous linkage map by 2928.45 cM to a total of 4516.75 cM. The number of SSR markers in the linkage groups varied from 12 to 136 while the length of each linkage group ranged from 129.35 to 1180.21 cM. The average distance between adjacent loci in the enhanced genetic linkage map was 9.71 cM, which is 2.79 cM shorter than the first linkage map of faba bean. The density‐enhanced genetic map of faba bean will be useful for marker‐assisted selection and breeding in this important legume crop.

This study was conducted with the objective of finding genetic marker(s) to differentiate pathotypes of the clubroot pathogen Plasmodiophora brassicae. Ideally, such markers should be used as a diagnostic tool to identify or predict certain pathotypes. By using PCR with gene-specific primers, 117 non-housekeeping P. brassicae genes were investigated for their presence/absence in isolates representing pathotypes 2, 3, 5, 6 or 8 (Williams’ system), and in new strains of the pathogen recently identified from Alberta, Canada, which are highly virulent on clubroot resistant canola (Brassica napus) cultivars. One gene, named Cr811, was present in isolates of pathotype 5 and in a new strain of P. brassicae that also is classified as pathotype 5 on the system of Williams, but causes severe clubroot on resistant canola. Three additional newly identified virulent populations, similar to pathotype 3, also were tested and found to carry Cr811. In contrast, the Cr811 gene was absent in all isolates representing the original pathotypes 2, 3, 6 and 8. Quantitative real-time PCR analysis indicated greater copy numbers of Cr811 in the new virulent pathotype 3-like and pathotype 5-like populations versus the original pathotype 5, indicating a potential method to identify new pathotypes of P. brassicae before the breakdown of resistance could be detected in a canola crop. The association of Cr811 with infection by P. brassicae of previously resistant canola cultivars, as revealed by qPCR analysis, suggests that Cr811 plays an important role in the interaction between host resistance and P. brassicae pathogenicity.

Simple sequence repeat (SSR) markers have previously been applied to linkage mapping of the pea (Pisum sativum L.) genome. However, the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited. A novel set of pea SSR markers was accordingly developed. Together with existing SSR sequences, the genome of the G0003973 (winter hardy) × G0005527 (cold sensitive) cross was mapped using 190 F2 individuals. In total, 157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM. The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.

Simple sequence repeat (SSR) marker is a powerful tool for construction of genetic linkage map which can be applied for quantitative trait loci (QTL) and marker-assisted selection (MAS). In this study, a genetic map of faba bean was constructed with SSR markers using a 129 F2 individuals population derived from the cross of Chinese native variety 91825 (large seed) and K1563 (small seed). By screening 11 551 SSR primers between two parents, 149 primer pairs were detected polymorphic and used for F2 population analysis. This SSR-based genetic linkage map consisted of 15 linkage groups with 128 SSR. The map encompassed 1587 cM with an average genetic distance of 12.4 cM. The genetic map generated in this study will be beneficial for genetic studies of faba bean for identification of marker-locus-trait associations as well as comparative mapping among faba bean, pea and grasspea.

Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.

Background Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required. Results A library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology. Conclusions Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts.

UNLABELLED PREMISE OF THE STUDY Expressed sequence tag (ESTs)-derived microsatellite markers were developed in Lathyrus sativus by screening the National Center for Biotechnology Information (NCBI) database. The usefulness of these novel markers was validated for size polymorphism among grasspea accessions. • METHODS AND RESULTS Three hundred EST-simple sequence repeat (SSR) primer pairs were identified and loci characterized for size polymorphism among 24 grasspea accessions from worldwide sources. Among them 139 SSR loci produced no PCR product, 117 SSR loci were monomorphic, and 44 SSR loci were polymorphic. The mean number of alleles per locus ranged from two to 11. The observed heterozygosity and expected heterozygosity ranged from 0.000 to 1.000 and 0.042 to 0.836, respectively. • CONCLUSIONS These novel markers will be useful and convenient to study genetic mapping and molecular breeding in grasspea.