scholarly journals Genomics of sorghum local adaptation to a parasitic plant

2019 ◽  
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.

scholarly journals Genomics of sorghum local adaptation to a parasitic plant

2020 ◽  
Vol 117 (8) ◽  
pp. 4243-4251 ◽  
Author(s):  
Emily S. Bellis ◽  
Elizabeth A. Kelly ◽  
Claire M. Lorts ◽  
Huirong Gao ◽  
Victoria L. DeLeo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Species Interactions ◽  
Balancing Selection ◽  
Control Plant ◽  
Farming Systems ◽  
Striga Hermonthica ◽  
Loss Of Function ◽  
Trade Offs ◽  
Genome Wide

Host–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 trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, 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 that 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.

Long-term management of the parasitic weed Striga hermonthica: Strategy evaluation with a population model

2007 ◽  
Vol 26 (3) ◽  
pp. 219-227 ◽  
Author(s):  
P.R. Westerman ◽  
A. van Ast ◽  
T.J. Stomph ◽  
W. van der Werf
Keyword(s):  
Population Model ◽  
Striga Hermonthica ◽  
Parasitic Weed ◽  
Strategy Evaluation ◽  
Term Management

Molecular evidence of genetic diversity changes in pea (Pisum sativum L.) germplasm after long-term maintenance

2010 ◽  
Vol 58 (3) ◽  
pp. 439-451 ◽  
Author(s):  
Jaroslava Cieslarová ◽  
Petr Smýkal ◽  
Zuzana Dočkalová ◽  
Pavel Hanáček ◽  
Stanislav Procházka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pisum Sativum ◽  
Molecular Evidence ◽  
Pisum Sativum L ◽  
Term Maintenance

scholarly journals Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

2020 ◽  
Author(s):  
Chloé Schmidt ◽  
Stéphane Dray ◽  
Colin J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Species Richness ◽  
Gene Diversity ◽  
Spatial Scales ◽  
Ecological Opportunity ◽  
Biogeographic Patterns ◽  
Genome Wide ◽  
Diversity Gradients ◽  
Low Levels

AbstractSpecies richness and genetic diversity are the two most fundamental products of evolution. Both are important conservation targets—species richness contributes to ecosystem functioning and human wellbeing, while genetic diversity allows those species to respond to changes in their environment and persist in the long-term. Biogeographic patterns of species richness are well-described, but we know little about patterns of genome-wide genetic diversity at similar spatial scales. Further, despite considerable attention to latitudinal trends in species richness, we still do not have a solid empirical understanding of the various processes that produce them, how they interact, or how they affect genetic diversity. Here we show that genome-wide genetic diversity and species richness share spatial structure, however, species richness hotspots tend to harbor low levels of within-species genetic variation. A single model encompassing eco-evolutionary processes related to environmental energy availability, niche availability, and proximity to humans explained 75% of variation in gene diversity and 90% of the variation in species richness. Our empirical model of both levels of biodiversity supports theory and demonstrates the importance of carrying capacity and ecological opportunity at individual and species levels for generating continent-wide genetic and species diversity gradients.

scholarly journals Founding Events and the Maintenance of Genetic Diversity in Reintroduced Populations

2021 ◽  
Author(s):  
◽  
Kimberly Anne Miller
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Loss Of Heterozygosity ◽  
Genetic Drift ◽  
Reproductive Output ◽  
Introduced Predators ◽  
Reintroduced Population ◽  
Loss Of Genetic Diversity ◽  
Term Maintenance

<p>As habitat loss, introduced predators, and disease epidemics threaten species worldwide, translocation provides one of the most powerful tools for species conservation. However, reintroduced populations of threatened species are often founded by a small number of individuals (typically 30 in New Zealand) and generally have low success rates. The loss of genetic diversity combined with inbreeding depression in a small reintroduced population could reduce the probability of establishment and persistence. Effective management of genetic diversity is therefore central to the success of reintroduced populations in both the short- and long-term. Using population modelling and empirical data from source and reintroduced populations of skinks and tuatara, I examined factors that influence inbreeding dynamics and the long-term maintenance of genetic diversity in translocated populations. The translocation of gravid females aided in increasing the effective population size after reintroduction. Models showed that supplementation of reintroduced populations reduced the loss of heterozygosity over 10 generations in species with low reproductive output, but not for species with higher output. Harvesting from a reintroduced population for a second-order translocation accelerated the loss of heterozygosity in species with low intrinsic rates of population growth. Male reproductive skew also accelerated the loss of genetic diversity over 10 generations, but the effect was only significant when the population size was small. Further, when populations at opposite ends of a species' historic range are disproportionately vulnerable to extinction and background inbreeding is high, genetic differentiation among populations may be an artefact of an historic genetic gradient coupled with rapid genetic drift. In these situations, marked genetic differences should not preclude hybridising populations to mitigate the risks of inbreeding after reintroduction. These results improve translocation planning for many species by offering guidelines for maximising genetic diversity in founder groups and managing populations to improve the long-term maintenance of diversity. For example, founder groups should be larger than 30 for  reintroductions of species with low reproductive output, high mortality rates after release, highly polygynous mating systems, and high levels of background inbreeding. This study also provides a basis for the development of more complex models of losses of genetic diversity after translocation and how genetic drift may affect the long-term persistence of these valuable  populations.</p>

Changes in the sensitivity of parasitic weed seeds to germination stimulants

2004 ◽  
Vol 14 (4) ◽  
pp. 335-344 ◽  
Author(s):  
Radoslava Matusova ◽  
Tom van Mourik ◽  
Harro J. Bouwmeester
Keyword(s):  
Rapid Change ◽  
Field Conditions ◽  
Striga Hermonthica ◽  
Wild Plant ◽  
Parasitic Weed ◽  
Germination Stimulant ◽  
Secondary Dormancy ◽  
Short Period ◽  
Weed Seeds ◽  
Germination Stimulants

The effects of preconditioning temperature and preconditioning period on the sensitivity of parasitic weed seeds to the synthetic germination stimulant GR24 were studied under laboratory and field conditions. The temperature during preconditioning ofOrobanche cumanaandStriga hermonthicaseeds strongly affected the responsiveness of the seeds to the applied germination stimulant. Preconditioning at an optimal temperature (21°C forO. cumanaand 30°C forS. hermonthica) rapidly released dormancy and increased the sensitivity to GR24 by several orders of magnitude. After reaching maximum sensitivity, prolonged preconditioning rapidly induced secondary dormancy, i.e. decreased sensitivity ofO. cumanaandS. hermonthicato GR24. The rapid change in sensitivity of preconditioned seeds to germination stimulants during prolonged preconditioning was particularly visible at low concentrations of GR24. GR24 at higher concentrations (0.1 and 1 mg l1) usually induced high germination of both species, regardless of the preconditioning period. The striking similarities between the response of parasitic weed seeds to GR24, described here, and results in the literature on non-parasitic wild plant seeds are discussed. Our results show that parasitic weed seeds are highly sensitive to the germination stimulant for a short period of time only, and then enter into secondary dormancy relatively quickly. The similar germination pattern ofS. hermonthicaseeds preconditioned for prolonged periods of time under laboratory and field conditions suggests that the mechanism observed is of ecological significance.

scholarly journals Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

2019 ◽  
Vol 110 (6) ◽  
pp. 707-719 ◽  
Author(s):  
Jared J Homola ◽  
Cynthia S Loftin ◽  
Kristina M Cammen ◽  
Caren C Helbing ◽  
Inanc Birol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Parallel Evolution ◽  
Urban Environments ◽  
Wood Frogs ◽  
Urban Populations ◽  
Genome Wide ◽  
Outlier Loci ◽  
Selection Factors ◽  
Fst Outlier

Abstract Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

The interplay of population dynamics and the evolutionary process

1990 ◽  
Vol 330 (1257) ◽  
pp. 253-259 ◽  
Keyword(s):  
Genetic Diversity ◽  
Interspecific Interactions ◽  
Genotypic Variation ◽  
Evolutionary Process ◽  
Interactive System ◽  
Population Fluctuations ◽  
Genetic Changes ◽  
Local Extinctions ◽  
Term Maintenance

Long-term maintenance of genetic diversity is affected by ecological forces that are driven in turn by current levels of genetic variation. The strength of population regulation and the consequent patterns of population fluctuations determine the likelihood of genetic changes considered pivotal for rapid speciation. However, genetic diversity in the susceptibility to regulatory forces can reduce the magnitude of such fluctuations and minimize the likelihood of genetic revolutions. A group of populations that experiences local extinctions and recolonizations may hold lower levels of genetic diversity than in the absence of such extinctions, but local adaption, which provides enhanced genetic diversity, can reduce the likelihood of local extinctions. Tightly regulated populations experience different selection pressures than poorly regulated populations, although tighter regulation itself can evolve. When genotypic variation affects the outcome of interspecific interactions on a local scale, this effect, coupled with appropriate spatial variation, can enhance the resilience of the interactive system.

scholarly journals Genetic effects of long-term captive breeding on the endangered pygmy hog

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12212
Author(s):  
Deepanwita Purohit ◽  
Shivakumara Manu ◽  
Muthuvarmadam Subramanian Ram ◽  
Shradha Sharma ◽  
Harika Chinchilam Patnaik ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Mitochondrial Genomes ◽  
Captive Population ◽  
Genetic Changes ◽  
Captive Populations ◽  
Genome Wide ◽  
Pygmy Hog ◽  
Conservation Breeding

Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.

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

2021 ◽  
Author(s):  
Farah Bendaoud ◽  
Gunjune Kim ◽  
Hailey Larose ◽  
James Westwood ◽  
Nadjia Zermane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Principal Components ◽  
Faba Bean ◽  
Isolation By Distance ◽  
Host Specialization ◽  
Nucleotide Polymorphisms ◽  
Vegetable Crops ◽  
Orobanche Crenata ◽  
Parasitic Weed

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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