GBS analysis of Orobanche crenata populations in Algeria supports local adaptation and host-specialization

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 Algerian O. crenata populations with different geographical origins and host species (faba bean, pea, chickpea, carrot and tomato). In total, 8,004 high-quality single-nucleotide polymorphisms 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 (FST) 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 hosts with more evident structuring among hosts than strictly along a geographic gradient. In the most striking example, O. crenata growing on pea had a distinct SNP profile from those growing on faba bean or other crops. These results illustrate the potential of GBS to reveal the dynamics of parasitic weed dispersal and adaptation.

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Genetic Diversity of Orobanche crenata Populations in Ethiopia Using Microsatellite Markers

International Journal of Genomics ◽

10.1155/2020/3202037 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8

Author(s):

Gashaw Belay ◽

Kassahun Tesfaye ◽

Aladdin Hamwieh ◽

Seid Ahmed ◽

Tiegist Dejene ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Distance ◽

Faba Bean ◽

Polymorphic Information Content ◽

Hot Spot ◽

Molecular Techniques ◽

Orobanche Crenata ◽

Parasitic Weed ◽

South Gondar

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.

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Genomics of sorghum local adaptation to a parasitic plant

10.1101/633529 ◽

2019 ◽

Cited By ~ 1

Author(s):

Emily S. Bellis ◽

Elizabeth A. Kelly ◽

Claire M. Lorts ◽

Huirong Gao ◽

Victoria L. DeLeo ◽

...

Keyword(s):

Genetic Diversity ◽

Local Adaptation ◽

Striga Hermonthica ◽

Wild Plant ◽

Parasitic Weed ◽

Genome Wide ◽

Staple Crop ◽

Term Maintenance ◽

Maintenance Of Diversity

ABSTRACTHost-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential tradeoffs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and belowground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with tradeoffs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9 edited sorghum further indicate the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.SIGNIFICANCE STATEMENTUnderstanding co-evolution in crop-parasite systems is critical to management of myriad pests and pathogens confronting modern agriculture. In contrast to wild plant communities, parasites in agricultural ecosystems are usually expected to gain the upper hand in co-evolutionary ‘arms races’ due to limited genetic diversity of host crops in cultivation. Here, we develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. We find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for co-evolutionary dynamics in smallholder agroecosystems.

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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

10.1101/500041 ◽

2018 ◽

Author(s):

Marco A. Escalante ◽

Charles Perrier ◽

Francisco J. García-De León ◽

Arturo Ruiz-Luna ◽

Enrique Ortega-Abboud ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Genetic Variation ◽

Local Adaptation ◽

Population Genomics ◽

Landscape Heterogeneity ◽

Genotyping By Sequencing ◽

Anthropogenic Factors ◽

Nucleotide Polymorphisms ◽

Evolutionary Potential

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

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Effects of environment and sowing date on the competition between faba bean (Vicia faba) and the parasitic weed Orobanche crenata

Field Crops Research ◽

10.1016/j.fcr.2004.11.001 ◽

2005 ◽

Vol 93 (2-3) ◽

pp. 300-313 ◽

Cited By ~ 38

Author(s):

J.H Grenz ◽

A.M Manschadi ◽

F.N Uygur ◽

J Sauerborn

Keyword(s):

Vicia Faba ◽

Faba Bean ◽

Sowing Date ◽

Orobanche Crenata ◽

Parasitic Weed

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Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq

Frontiers in Plant Science ◽

10.3389/fpls.2021.618245 ◽

2021 ◽

Vol 12 ◽

Author(s):

Amal Boukteb ◽

Shota Sakaguchi ◽

Yasunori Ichihashi ◽

Mohamed Kharrat ◽

Atsushi J. Nagano ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Faba Bean ◽

Isolation By Distance ◽

Distance Effect ◽

Wild Plant ◽

Clustering Methods ◽

North West ◽

North East ◽

The North

Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.

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Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽

10.3390/genes10100822 ◽

2019 ◽

Vol 10 (10) ◽

pp. 822 ◽

Cited By ~ 2

Author(s):

Kyung Jun Lee ◽

Jung-Ro Lee ◽

Raveendar Sebastin ◽

Myoung-Jae Shin ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Discriminant Analysis ◽

Single Nucleotide Polymorphisms ◽

Genetic Differentiation ◽

Principal Components ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

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Genetic diversity in global chicken breeds in relation to their genetic distances to wild populations

Genetics Selection Evolution ◽

10.1186/s12711-021-00628-z ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Dorcus Kholofelo Malomane ◽

Steffen Weigend ◽

Armin Otto Schmitt ◽

Annett Weigend ◽

Christian Reimer ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Protein Transport ◽

Isolation By Distance ◽

Genetic Distances ◽

Nucleotide Polymorphisms ◽

Founder Population ◽

Wild Populations ◽

Evolutionary Patterns ◽

The One

Abstract Background Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted by the theory of genetic isolation by distance. Consistent with that theory, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be explained well by their geographic expansion from their founders, which is correlated with genetic differentiation. Methods To investigate this in chicken, we estimated the relationship between the genetic diversity of 160 domesticated chicken populations and their genetic distances to wild chicken populations. Results Our results show a strong inverse relationship, i.e. 88.6% of the variation in the overall genetic diversity of domesticated chicken populations was explained by their genetic distance to the wild populations. We also investigated whether the patterns of genetic diversity of different types of single nucleotide polymorphisms (SNPs) and genes are similar to that of the overall genome. Among the SNP classes, the non-synonymous SNPs deviated most from the overall genome. However, genetic distance to the wild chicken still explained more variation in domesticated chicken diversity across all SNP classes, which ranged from 83.0 to 89.3%. Conclusions Genetic distance between domesticated chicken populations and their wild relatives can predict the genetic diversity of the domesticated populations. On the one hand, genes with little genetic variation across populations, regardless of the genetic distance to the wild population, are associated with major functions such as brain development. Changes in such genes may be detrimental to the species. On the other hand, genetic diversity seems to change at a faster rate within genes that are associated with e.g. protein transport and protein and lipid metabolic processes. In general, such genes may be flexible to changes according to the populations’ needs. These results contribute to the knowledge of the evolutionary patterns of different functional genomic regions in the chicken.

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Genetic Diversity of Moroccan Orobanche crenata Populations Revealed by Sequence-Related Amplified Polymorphism Markers

Journal of Agricultural Science ◽

10.5539/jas.v9n4p164 ◽

2017 ◽

Vol 9 (4) ◽

pp. 164 ◽

Cited By ~ 3

Author(s):

Mounia Ennami ◽

Fatima Zahra Briache ◽

Joseph Mbasani Mansi ◽

Fatima Gaboun ◽

Lamiae Ghaouti ◽

...

Keyword(s):

Genetic Diversity ◽

Faba Bean ◽

Population Level ◽

Epidemiological Studies ◽

Orobanche Crenata ◽

Breeding Programs ◽

Prerequisite Knowledge ◽

Clear Differentiation ◽

Amova Analysis ◽

Efficient Selection

Orobanche crenata Forsk. is a root holoparasitic plant that affects legume species in Mediterranean basin especially in Northern Africa. This parasitic weed is particularly problematic in faba bean (Vicia faba L.) and lentil (Lens culinaris Medik.) fields. In Morocco, development of legume resistant/tolerant genotypes is considered the most economical and ecological control strategy against O. crenata. Efficient selection of resistant/tolerant cultivars requires prerequisite knowledge of the genetic diversity of the parasite. Thus, the present study focused on the assessment of the genetic diversity among and within Moroccan O. crenata populations, growing in faba bean fields, using Sequence-Related Amplified Polymorphism markers (SRAP). This marker system proved to be a powerful and an efficient tool for the evaluation of the genetic diversity among O. crenata populations. In fact, a total of 101 markers were identified and used for the Analysis of Molecular Variance (AMOVA), among which 98 bands were polymorphic (97.02%), indicating considerable genetic variation of these O. crenata populations. However, at population level, low level of polymorphic loci was observed with a percentage ranging between 41.58% and 67.33%. The Jaccard’s similarity coefficient and Principal Coordinate Analysis (PCoA) showed a clear differentiation among O. crenata samples according to the geographical origin of each population. AMOVA analysis revealed also a large extent of variation among O. crenata populations (60%; p < 0.010). Our outputs on molecular genetics of O. crenata combined with future epidemiological studies of these populations should clarify occurrence of O. crenata pathotypes and thereby validate the relevance of using multisite screening trials during breeding programs.

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