Variation Among and Within Populations of the Parasitic Weed Orobanche crenata from Spain and Israel Revealed by Inter Simple Sequence Repeat Markers

Genotyping‐by‐sequencing analysis of Orobanche crenata populations in Algeria reveals genetic differentiation

Crenate broomrape (Orobanche crenata Forsk.) is a serious long‐standing parasitic weed problem in Algeria, mainly affecting legumes but also vegetable crops. Unresolved questions for parasitic weeds revolve around the extent to which these plants undergo local adaptation, especially with respect to host specialization, which would be expected to be a strong selective factor for obligate parasitic plants. In the present study, the genotyping‐by‐sequencing (GBS) approach was used to analyze genetic diversity and population structure of 10 Northern Algerian O. crenata populations with different geographical origins and host species (faba bean, pea, chickpea, carrot, and tomato). In total, 8004 high‐quality single‐nucleotide polymorphisms (5% missingness) were obtained and used across the study. Genetic diversity and relationships of 95 individuals from 10 populations were studied using model‐based ancestry analysis, principal components analysis, discriminant analysis of principal components, and phylogeny approaches. The genetic differentiation (F_ST) between pairs of populations was lower between adjacent populations and higher between geographically separated ones, but no support was found for isolation by distance. Further analyses identified four genetic clusters and revealed evidence of structuring among populations and, although confounded with location, among hosts. In the clearest example, O. crenata growing on pea had a SNP profile that was distinct from other host/location combinations. These results illustrate the importance and potential of GBS to reveal the dynamics of parasitic weed dispersal and population structure.

Population genetic structure and marker-trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy-2 and FK3

To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, F_ST  = 0.012, P < 0.05), but intermediate genetic differentiation (F_ST  = 0.143, P < 0.01) underlies the S. hermonthica groups that are differentiated by their phenotypic responses to Fos isolates. An expressed sequence tag SSR (EST-SSR) marker Y53 (P < 0.01) and a genomic SSR marker E1009 (P < 0.05) were associated with the S. hermonthica class susceptible to Foxy-2 and FK3 (group A). A divergent S. hermonthica class, consisting of groups with intermediate susceptibility to Foxy-2 (group B) and susceptibility to either FK3 (group C) or Foxy-2 (group D), showed no marker-trait association, instead demonstrated linkage disequilibrium decay. Owing to point substitutions and insertion-deletion mutations, the unique, protein-coding nucleotide sequence at the E1009 locus in group A was partly dissimilar to group B, but was totally distinct from groups C and D. These findings implied that the inconsistent effectiveness of a Fos isolate is better explained by genomic variation in S. hermonthica, rather than by S. hermonthica sampling zones.

Genetic Diversity of Orobanche crenata Populations in Ethiopia Using Microsatellite Markers

Orobanche crenata is a parasitic weed that causes considerable yield losses on food legumes in Ethiopia and the Mediterranean region. Understanding the genetic diversity of Orobanche crenata using molecular techniques generate useful information in managing the weed through resistance breeding. This study aimed at assessing the genetic diversity of O. crenata populations collected from major faba bean growing areas of Ethiopia. A total of 96 samples were collected from the Orobanche-infested faba bean farmer field. The genetic diversity of the population was studied using 30 O. cumana SSR markers. The results showed that 11 SSRs were functional and transferable markers to study the diversity of O. crenata populations. The average number of alleles, gene diversity, heterozygosity, and polymorphic information content values for the SSR loci were 9.6, 0.82, 0.38, and 0.80, respectively. The pairwise genetic similarity analysis showed the lowest genetic distance between samples collected from South Gondar and South Wollo (0.12) while the highest genetic distance (0.48) was found between South Gondar and North Wollo. The analysis of molecular variance result indicated that the variation among individuals was a major source of genetic variation (55%) followed by within individuals (43%) and among populations (2%) variation. The output of population genetic structure analysis indicated the presence of two major groups irrespective of the area of collection or region of origin. Besides, the outcome of the spatial autocorrelation computation indicated a significant and positive genetic correlation between samples collected under a 28 km radius. In general, the absence of geographic region based genetic structure presumably demonstrates the expansion of the parasitic weed between farming sites upon its recent introduction to the country. Thus, the clear absence of population differentiation warrants screening faba bean population in hot spot area.

Host differentiation and variability of Orobanche crenata populations from legume species in Morocco as revealed by cross-infestation and molecular analysis

BACKGROUND

Orobanche crenata represents a major biotic constraint to production of faba bean and lentil in Morocco. While this parasitic plant attacks both of these crops, the extent to which Orobanche biotypes specialise in parasitising specific crops is unknown. To address this question, we studied O. crenata that grew on different hosts and quantified their host specificity to faba bean and lentil. The virulence of O. crenata populations on each host was investigated through field trials, pot and Petri dishes assays. Genetic diversity of the parasite populations was also assessed through molecular analyses.

RESULTS

The two legume species showed distinct patterns of specificity. Faba bean was more susceptible to both O. crenata populations, while the specificity for lentil by lentil-grown O. crenata was evident at the final stage of the parasite life cycle as shown by correspondence factorial analyses. Considerable internal variation (81%) within O. crenata populations parasitising both legume species was observed by molecular analyses, but significant divergence (19%; Ø = 0.189; P = 0.010) among the populations was detected.

CONCLUSION

These results indicate that O. crenata can adapt to specific host species, which is important knowledge when developing integrated pest management practices for parasitic weed control. © 2017 Society of Chemical Industry.

Molecular Characterization of Broomrape Populations from Republic of Moldova using SSR Markers

The genetic diversity study of 39 broomrape populations from the Republic of Moldova was performed using 12 highly polymorphic SSR primer pairs, which shown the high level of polymorphism (average PIC value 0.57). We found that some of the SSR primers (Ocum-59 and Ocum-108) produced polymorphic bands suitable for discrimination between the studied populations. The diversity analysis within broomrape populations revealed a higher number of detected alleles and heterozygous loci in the accessions from the Southern region when compared to the Northern and Central ones. The average PIC values for the Northern, Central and Southern accessions ranged from 0.43, 0.48 to 0.56, respectively. Some populations from the Southern region (especially, Carabetovca, Alexanderfeld, Stefan-Voda and Slobozia Mare) have shown the major differences in the profiles obtained and presented the high level of genetic variability. The dendrogram based on genetic distance divided the 39 broomrape accessions into twelve clusters. High variability of

Temperature and water stress during conditioning and incubation phase affecting Orobanche crenata seed germination and radicle growth

Orobanche crenata is a holoparasitic plant that is potentially devastating to crop yield of legume species. Soil temperature and humidity are known to affect seed germination, however, the extent of their influence on germination and radicle growth of those of O. crenata is largely unknown. In this work, we studied the effects of temperature, water potential (Ψt) and the type of water stress (matric or osmotic) on O. crenata seeds during conditioning and incubation periods. We found that seeds germinated between 5 and 30°C during both periods, with a maximum around 20°C. Germination increased with increasing Ψt from -1.2 to 0 MPa during conditioning and incubation periods. Likewise, seed germination increased logarithmically with length of conditioning period until 40 days. The impact of the type of water stress on seed germination was similar, although the radicle growth of seeds under osmotic stress was lower than under matric stress, what could explain the lowest infestation of Orobanche sp. in regions characterized by saline soil. The data in this study will be useful to forecast infection of host roots by O. crenata.

Plant resistance to parasitic plants: molecular approaches to an old foe

Parasitic weeds pose severe constraint on major agricultural crops. Varying levels of resistance have been identified and exploited in the breeding programmes of several crops. However, the level of protection achieved to date is either incomplete or ephemeral. Resistance is mainly determined by the coexistence of several mechanisms controlled by multigenic and quantitative systems. Efficient control of the parasite requires a better understanding of the interaction and their associated resistance mechanisms at the histological, genetic and molecular levels. Application of postgenomic technologies and the use of model plants should improve the understanding of the plant-parasitic plant interaction and drive not only breeding programmes through either marker-assisted selection (MAS) or transgenesis but also the development of alternative methods to control the parasite. This review presents the current approaches targeting the characterization of resistance mechanisms and explores their potentiality to control parasitic plants.

Population genetic structure of Carchesium polypinum (Ciliophora: Peritrichia) in four Chinese lakes inferred from ISSR fingerprinting: high diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.