Genetic diversity of Striga hermonthica and Striga asiatica populations in Kenya

The parasitic angiosperms, Striga hermonthica and Striga asiatica, severely constrain cereal production in sub-Saharan Africa by causing huge losses in grain yield. Understanding the diversity of Striga populations is important because it allows identification of races or biotypes thus improving chances of breeding success. Amplified fragment length polymorphism (AFLP) analysis was used to study genetic diversity among 17 populations of S. asiatica and 24 populations of S. hermonthica from Kenya. A total of 349 DNA fragments ranging from 51 to 500 bp were obtained from four EcoRI and MseI primer combinations. Genetic distances for S. asiatica populations ranged from 0.009 to 0.116 with a mean of 0.032. S. hermonthica populations had a genetic distance that ranged from 0.007 to 0.025 with a mean of 0.015. Only two clusters were found in S. asiatica populations whereas no apparent structure was evident in S. hermonthica populations. There was no evidence of isolation by distance for the two species. Although the low genetic diversity suggests Striga is relatively uniform across the populations studied, it is possible that pathogenicity and virulence genes may be located in genomic regions that were not sampled. The data, however, does not provide evidence to support diversification of both Striga species in the region where the study was conducted.     

Long-term management of Striga hermonthica: strategy evaluation with a spatio-temporal population model

The parasitic weed Striga hermonthica poses a serious threat to cereal production in sub-Saharan Africa. Striga hermonthica seedbanks are long-lived; therefore, long-term effects of control strategies on the seedbank only emerge after several years. We developed a spatially explicit, stochastic model to study the effectiveness of control strategies in preventing invasion of S. hermonthica into previously uninfested fields and in reducing established infestations. Spatial expansion of S. hermonthica and decrease in millet yield in a field was slower, on average, when stochasticity of attachment of seedlings to the host was included and compared to the deterministic model. The spatial patterns of emerged S. hermonthica plants 4–7 years after point inoculation (e.g. seeds in a dung patch) in the spatial-stochastic model resembled the distribution typically observed in farmers' fields. Sensitivity analysis showed that only three out of eight life cycle parameters were of minor importance for seedbank dynamics and millet yield. Weeding and intercropping millet with sesame or cowpea reduced the seedbank in the long term, but rotations of millet with trap crops did not. High seedbank replenishment during years of millet monoculture was not sufficiently offset by seedbank depletion in years of trap crop cultivation. Insight from simulations can be employed in a participatory learning context with farmers to have an impact on S. hermonthica control in practice.     

Genetic diversity and population structure of Lasiodiplodia theobromae from different hosts in northeastern Brazil and Mexico

Lasiodiplodia theobromae is one of the most frequent fungal pathogens associated with dieback, gummosis, leaf spot, stem-end rot and fruit rot symptoms in cashew, mango, papaya and grapevine. In this study, the variation in the genetic diversity of 117 L. theobromae isolates from northeastern Brazil (n = 100) and Mexico (n = 17), which were collected from these four crops, was analysed using microsatellite markers. The results revealed low genetic diversity among L. theobromae populations and the existence of two genetic groups. All Mexican isolates were grouped with Brazilian isolates, suggesting a low level of differentiation between these populations. Furthermore, no evident host or climate-based population differentiation was observed for L. theobromae in Brazil. The populations studied were mostly clonal, but additional studies are needed to better understand the mode of reproduction of the pathogen. The low genetic diversity of L. theobromae populations in northeastern Brazil suggests that resistant cultivars could be used as a durable management strategy to reduce the impact of the diseases caused by this pathogen.     

Ecological determinants and risk areas of Striga hermonthica infestation in western Kenya under changing climate

Striga hermonthica (Del.) Benth is a parasitic weed that is damaging major cereal crops in sub-Saharan Africa (SSA). Although Striga is recognised as an agricultural scourge, there is limited information available indicating the extent of its growth and spread as impacted by the changing climate in Kenya. This study investigated the impact of current climate conditions and projected future (2050) climate change on the infestation of Striga hermonthica in the western Kenya region. Specifically, the study aimed to predict Striga hermonthica habitat suitability in five counties in the western Kenya region through using the maximum entropy (MaxEnt) model and bioclimatic, soil, topographic and land use, and land cover (LULC) variables. Striga hermonthica geolocations were collected and collated and ecological niche models were developed to determine the habitat suitability. The results showed that approximately 1767 km² (10% of the total study area) is currently highly suitable for Striga hermonthica occurrence. The future projections showed a range between 2106 km² (19% of the total study area) and 2712 km² (53% of the total study area) at the minimum carbon (RCP 2.6) and the maximum carbon emission scenarios (RCP 8.5) respectively. Elevation, annual precipitation, LULC, temperature seasonality and soil type were determined to be the most influential ecological predictor variables for Striga hermonthica establishment. The study revealed the importance of using climate, soil, topographic and LULC variables when evaluating agricultural production constraints such as Striga's prevalence. The methodology used in this study should be tested in other Striga affected areas.     

Genetic diversity and structure of Hemileia vastatrix populations on Coffea spp.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms (AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity (h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance (r = ?0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy.     

Genetic diversity of East and West African Striga hermonthica populations and virulence effects on a contrasting set of sorghum cultivars

The root hemiparasite Striga hermonthica causes very significant yield loss in its dryland staple cereal host, Sorghum bicolor. Striga‐resistant sorghum cultivars could be an important part of integrated S. hermonthica control. For effective resistance breeding, knowledge about the diversity of the parasite is essential. This study aimed (i) to determine the genetic diversity within and between seven S. hermonthica populations from East and West Africa using 15 microsatellite markers and (ii) to assess the virulence and host–parasite interactions of these Striga populations grown on 16 diverse sorghum genotypes in a glasshouse trial. Most of the genetic variance (91%) assessed with microsatellite markers occurred within S. hermonthica populations. Only a small portion (8%) occurred between regions of origin of the populations. A positive correlation (R² = 0.14) between pairwise geographic and genetic distances reflected the slightly increasing differentiation of S. hermonthica populations with increasing geographic distance. East African S. hermonthica populations, especially those from Sudan, had significantly greater average infestation success across all sorghum genotypes than West African populations. Some specific host–parasite interaction effects were observed. The high genetic variation among individuals of each S. hermonthica population underlines the high potential adaptability to different hosts and changing environments. This points to the need to manage sorghum resistance alleles in space and time and to employ resistant varieties as part of integrated S. hermonthica control, so as to hinder the parasite overcoming resistance.     

Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean

Simple sequence repeat (SSR) markers were used to classify 116 isolates of Phakopsora pachyrhizi, the cause of soyabean rust, collected from infected soyabean leaves in four agroecological zones in Nigeria. A high degree of genetic variation was observed within the sampled populations of P. pachyrhizi. Eighty‐four distinct genotypes were identified among three of the four agroecological zones. Nei’s average genetic diversity across geographical regions was 0·22. Hierarchical analysis of molecular variance showed low genetic differentiation among all populations of P. pachyrhizi. The majority (> 90%) of the genetic diversity was distributed within each soyabean field, while approximately 6% of the genetic diversity was distributed among fields within geographic regions. Low population differentiation was indicated by the low F_ST values among populations, suggesting a wide dispersal of identical genotypes on a regional scale. Phylogenetic analysis indicated a strictly clonal structure of the populations and five main groups were observed, with group II accounting for 30% of the entire population. Because of the asexual reproduction of P. pachyrhizi, single‐step mutations in SSR genotypes are likely to account for the genetic differences within each group.     

Nei's gene diversity and the index of average differences are identical measures of diversity within populations

It has been established that Nei's measure of the average genetic diversity per locus, H _S , and the measure of average differences between isolates with respect to simple mismatch dissimilarity, are identical measures of diversity within populations. The Müller index of diversity can be considered as the correction of Nei's measure for small samples.     

Genetic diversity and interfertility among highly differentiated populations of Ceratocystis fimbriata in Brazil

Mating studies showed that isolates of the insect‐associated wilt pathogen Ceratocystis fimbriata from Eucalyptus spp., mango, fig, inhame (Colocasia esculenta), Gmelina arborea and sweet potato were interfertile, and progeny from those crosses showed normal segregation for microsatellite markers. Genetic diversity was compared among 13 populations of C. fimbriata collected from six states in Brazil using 15 highly polymorphic microsatellite markers. The gene diversity values of most eucalyptus and mango populations from Minas Gerais, Bahia, Rio de Janeiro and São Paulo states were similar to putatively native populations of Ceratocystis platani and C. cacaofunesta, two other species in the C. fimbriata complex that are homothallic. Index of association values indicated substantial asexual reproduction or selfing in populations on mango and eucalyptus. Most of these eucalyptus and mango populations were not highly differentiated from each other, and these populations and genotypes appeared to be more closely related to each other than to other populations by upgma analyses. By contrast, the G. arborea population from Pará and the fig and inhame populations from São Paulo had relatively low levels of diversity and were highly differentiated from each other and all other studied populations, suggesting that they were from different origins and had gone through genetic bottlenecks. One of the eucalyptus populations in Bahia consisted of a single genotype and may have been introduced to the site in infected cuttings from another Bahia location. Similarly, a mango population from Mato Grosso do Sul consisted of a single genotype, which was identical to one of the genotypes found on mango in São Paulo. Aside from introductions by humans, mating studies and genetic analyses suggest that limited dispersal distance and a high degree of selfing or asexual reproduction lead to local populations of C. fimbriata that have limited diversity but are highly differentiated from other populations.     

Farmers' perspectives on the biotic constraint of Striga hermonthica and its control in western Kenya

Witchweed, Striga hermonthica (hereafter, referred to as “Striga”), is a major biotic constraint to cereal production in sub‐Saharan Africa. The parasitic plant is a socioeconomic problem that has forced some resource‐poor farmers to abandon their farms due to high infestation. This study was designed in order to elucidate farmers' perceptions of Striga control measures and to determine their potential adoption in two villages in western Kenya. Participatory rural appraisals and individual interviews were conducted in 2009 and 2010 in a sample of 128 and 120 households in Kaura and Kogweno‐Oriang villages in Homabay and Rachuonyo districts, respectively. The results revealed that crop production was the main occupation in most households. The farmers identified Striga as one of the major constraints to maize, sorghum, and finger millet production. According to the farmers, the most popular control measures were hand‐pulling, crop rotation, and intercropping, even though rotational systems might need a longer timeframe to reduce the soil seed bank of Striga. Although the level of Striga infestation and damage were increasing in the farmers' fields, the adoption of the control options was limited. The reason for the low adoption level of the control methods by the farmers is because they are “too risky” as there is no guarantee of a direct pay‐off in increased crop yield. Farmer‐led evaluation and adaptation of the various Striga control technologies in real‐life situations will facilitate the choice of appropriate options and facilitate their uptake.     

Low genetic diversity and strong geographic structure in introduced populations of the Eucalyptus foliar pathogen Teratosphaeria destructans

The aggressive Eucalyptus leaf pathogen, Teratosphaeria destructans, causes widespread damage in tropical and subtropical Eucalyptus-growing regions of Indonesia, China, Thailand, East Timor, Vietnam, Lao, and South Africa. Little is known regarding the origin, pathways of dispersal, or reproductive biology of this pathogen. The aim of this study was to investigate the genetic structure of a global collection of T. destructans isolates. This was achieved by developing and using polymorphic microsatellite markers. Low genotypic diversity and a limited number of private alleles were found in all investigated populations, with the highest maximum diversity of 10.7% in isolates from South Sumatra. This supports the hypothesis that T. destructans was introduced to these regions. High levels of clonality were common in all populations, especially in isolates sampled from the recent disease outbreak in South Africa, which were all identical. The global collection of isolates grouped into three distinct clusters, corresponding largely to their sampled regions. Low levels of genotypic diversity, high levels of clonality, and strong geographic structure suggest independent introductions into all the sampled areas from an unknown source. The results imply that strict biosecurity measures are needed to avoid introductions of additional genotypes in these areas.     

Effect of phosphate‐based seed priming on strigolactone production and Striga hermonthica infection in cereals

Strigolactones, plant‐secreted underground signalling molecules, play an important role in agricultural ecosystems, because they mediate the interaction of crops with symbiotic AM fungi and parasitic weeds like Striga hermonthica. Cereal host plants secret these signalling molecules particularly under nutrient‐deficient conditions and especially when phosphate (P) is limiting. The objective of the present study was to see the potential of P seed priming for S. hermonthica management in cereals in relation to strigolactone production. It has been demonstrated that P fertiliser application down‐regulates the production of these signalling molecules in the rhizosphere, which results in lower S. hermonthica infection of cereals. The laboratory study showed maximum production of strigolactones from dry and water‐soaked seeds, while seed soaking in P solution reduced their production. Similarly, maximum S. hermonthica infection was observed under control treatments with dry sowing or water soaking, while P seed soaking decreased S. hermonthica germination, emergence and dry biomass in all cereal crops. Our study shows that P seed priming resulted in lower exudation of strigolactones, which induced less S. hermonthica seeds germination and hence may lead to lower S. hermonthica infection. P‐based seed priming could prove to be an effective and affordable strategy to reduce S. hermonthica infection in cereals. Further research for practical field application is needed.     

Genetic diversity in populations of the fungi Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on grapevine in France

Isolates of Phaeomoniella chlamydospora ( Phc ) and Phaeoacremonium aleophilum ( Pha ), two haploid, deuteromycetous fungi, were obtained from vines showing symptoms of esca disease in different localities in two French regions, and within a single vineyard in one of these regions. The population genetic structure was determined in both fungi using random amplified polymorphic DNA (RAPD) analysis. Populations of Phc showed similar levels of diversity at local and regional levels. The most frequent Phc haplotypes were found in every population, and the frequencies of positive alleles of markers were similar across populations. The hypothesis that recombination had occurred was rejected for the full set of samples, but not for the samples reduced to haplotypes, indicating that Phc may be a recombining species. Different features were identified in Pha populations. First, the southern population of Pha appeared more diverse than the south-western populations. Second, genetic differentiation was identified between Pha populations from southern and south-western regions for several RAPDs. Finally, in the southern population of Pha no evidence for recombination was obtained, even by reducing the sample to haplotypes. Within the single vineyard surveyed, several haplotypes of both fungi were recovered and randomly distributed. Thus different infection events appeared to have occurred on a low spatial scale. Data from this study showed that haplotypes of both fungi were distributed over long distances geographically, and that most of the vineyards surveyed were infested by more than one haplotype of Phc and Pha .     

Genetic diversity and population structure of Acidovorax avenae subsp. avenae isolated from sugarcane in Argentina

A significant increase in the occurrence of red stripe (caused by Acidovorax avenae subsp. avenae) has been observed in the last decade in Argentina. Considering that no extensive sampling of the main sugarcane-producing area in the country has been conducted to characterize the diversity and population structure of A. avenae subsp. avenae, molecular markers were employed to analyse 112 isolates from Tucumán. By using repetitive element polymorphism-based polymerase chain reaction (rep-PCR) almost all isolates were differentiated and grouped into 10 clusters, revealing a high genetic diversity. Using the amplified fragment length polymorphism (AFLP) technique, five pairs of isolates were discriminated that could not be distinguished with rep-PCR. Cluster analysis showed no clear association between isolate clustering, sugarcane host genotype, crop age, type of tissue sampled, fertilization, or year of sampling. Linkage equilibrium analysis by using rep-PCR data indicated that the population has some degree of clonality. Three housekeeping genes were also sequenced: ugpB and pilT sequences were highly similar to A. avenae subsp. avenae sequences from other Argentinian isolates, whereas the lepA sequence did not reveal significant similarity. An additional four housekeeping genes could not be amplified, suggesting the existence of differences in those regions. Subsequently, virulence of 14 A. avenae subsp. avenae isolates was evaluated under controlled conditions. Results showed a differential level of aggressiveness among the isolates on a resistant sugarcane variety. This study confirmed that rep-PCR is an adequate tool for genetic analysis and population structure characterization in bacteria, and revealed both high genetic diversity and clonal population structure of A. avenae subsp. avenae in Tucumán, Argentina.     

Genetic variation among populations of Pythium irregulare in southern Australia

Isolates of Pythium irregulare were sampled from seven cereal crops throughout South Australia to determine the extent of genetic diversity within this pathogen and the scale of genetic differentiation among populations. Data derived from 29 individual restriction fragment length polymorphism (RFLP) loci differentiated 54 DNA fingerprints among the 92 isolates analysed. Some isolates had two alleles at several RFLP loci and were scored as heterozygous. One such isolate was selfed in vitro and segregation ratios in the progeny were not significantly different from those expected for allelic variation in a diploid. These data provided evidence that outcrossing occurs within P. irregulare and may contribute to the high level of genetic variation within the species ( D _T = 0·502). Allelic frequencies were significantly different among all seven populations and G _ST values showed significant genetic differentiation between populations. The average genetic identity among populations was low and hierarchical cluster analysis provided no clear evidence that populations formed geographically related groups. These analyses indicate low levels of interpopulation gene flow within P. irregulare and imply that population differentiation results from genetic drift.     

Genetic structure of Fusarium oxysporum f. sp. cubense in different regions from Brazil

Panama disease, caused by Fusarium oxysporum f. sp. cubense (Foc), is ranked among the most destructive diseases of banana. The use of resistant varieties is the most desirable and effective control measure. Information on the pathogen population structure is essential, as durability of the resistance and effective cultivar deployment are strongly linked to this structure. In this study, 214 Foc isolates from different banana producing states in three regions of Brazil (northeastern, southeastern and southern) were analysed. Initially, nine microsatellite markers (SSR) were tested, which revealed 52 distinct haplotypes distributed in the different geographical regions and cultivars. While amova analysis showed that 68·01% of the total variation occurred within states, correlation between genetic and geographical distances was only found in the southern region. Results indicated that isolates from different states comprise a single population, which is predominantly clonal. When isolates representing different haplotypes were inoculated in four banana cultivars, differences in severity were found, with the high severity values being caused by isolates from haplotypes H7, H31 and H41. The diversity found here points to the need for additional studies, as this characteristic may be related to Foc's evolutionary potential and possibly to its ability to overcome the resistance from breeding programme‐generated cultivars. This is the most comprehensive study on population biology of Foc in Brazil.     

Genetic analysis of Grapevine leafroll‐associated virus 3 population from Galicia,Spain

Grapevine leafroll‐associated virus 3 (GLRaV‐3; Ampelovirus, Closteroviridae) isolates from Galicia in northwestern Spain were selected to characterize their genetic diversity according to different factors (age, origin, location, variety, etc.). The vines belonged either to local white and red varieties autochthonous to Galicia or to varieties from other Spanish regions but widely used in Galicia. These GLRaV‐3 isolates came from different vineyards in Galicia located in coastal or inner areas. Multiplex RT‐PCR allowed the detection of isolates belonging to groups I, II, III–V and VI. Two genomic regions were studied in the isolates, the HSP70h and the capsid protein, using specific primers that allow the detection of variants from groups I to V. Some possible recombinants could be detected; however, multiple infections with different variants indicated that they were not genuine recombinants. No differences were found in the population structure considering variety or geographical factors. Isolates belonging to four groups were found in the distinct areas surveyed: groups I and II were the most common, followed by groups VI and III, as is the case in the rest of the world. In the same surveys, the presence of insect vectors for GLRaV‐3 was investigated and found lacking in inland areas but present in those with milder climate. Genetic analysis did not support isolation of the GLRaV‐3 isolates in Galicia, suggesting that the uncontrolled exchange of infected vines and/or rootstocks has been a major agent of virus spread.     

Subdivision and genetic structure of four populations of Venturia inaequalis in Switzerland

Analyses of four populations of Venturia inaequalis in Switzerland were performed to obtain information about migration and to predict the probable speed of the spread of new pathotypes able to overcome resistance, e.g. Vf-resistance, of new cultivars.Genetic and haplotype diversity was calculated based on allele frequencies of random amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS)-region of ribosomal DNA, which are regarded to be neutral, and the -tubulin locus which may be under selection pressure. Within-population diversity was found to be quite similar over all four populations. Normalised haplotype diversity based on RAPD and ITS data was very high with a mean of 0.95. Diversity among populations (G_ST) was consistent over all neutral loci with a low mean of 0.04, but reached the high value of 0.26 for the selected -tubulin locus. Low G_ST based on neutral loci may suggest a high level of gene flow.Considering these results, new pathotypes would be expected soon outside their place of identification. But actual gene flow is easily overestimated because of effects of gene flow in the past. However, naturally occurring gene flow could be increased by human activity. Therefore, it is very difficult to predict durability of the Vf-resitance in Switzerland.     

基于SRAP标记的黄瓜霜霉菌遗传多样性分析

本研究对来自黑龙江、辽宁、河北、山东、江苏5个省12个黄瓜主产区的77个黄瓜霜霉菌菌株,采用SRAP分子标记进行了遗传多样性分析。从35对SRAP引物中筛选出10对引物,共产生9 554条扩增条带,其中9 132条表现多态性,占95.6%。基于SRAP分子标记,77个黄瓜霜霉菌菌株的遗传距离为0.60~1.00,表明黄瓜霜霉菌具有丰富的遗传多样性。通过聚类分析,77个黄瓜霜霉菌菌株聚类为8个类群,并且来自相同地区的菌株大多数聚集于同一类群中,表明黄瓜霜霉菌群体的遗传多样性与其地理来源密切相关。