Genetic Diversity In Response Research Articles

Evaluation of Spring-type and Winter-type Brassica napus Germplasm for Genetic Diversity in Response to Flea Beetle Herbivory in Typical and Atypical Planting Windows

Current practices of flea beetle [Phyllotreta spp.] control in Brassica napus L. rely heavily on seed treatments and due to growing concerns regarding the safety of such treatments on non-target and beneficial insect populations, genetic resistance would be beneficial for a more balanced integrated pest management strategy. However, none of the registered B. napus. canola varieties exhibit measurable resistance to flea beetle injury. To this end, an evaluation of 14 winter-type B. napus breeding lines and 15 spring-type B. napus breeding lines for resistance to flea beetle feedings was conducted, as it was found that at least one line in each family exhibited noticeably reduced flea beetle damage compared to sister lines in a breeding nursery. The study revealed natural genetic variation within B. napus for flea beetle antixenosis which could be used by dedicated breeders to develop canola varieties with higher levels of flea beetle resistance. Data indicated that host plant resistance did not vary between feeding by newly emerged adult flea beetles in the fall and the overwintered adults in the spring in either winter-type or spring-type canola, as well as for adult feeding preferences. This indicates that favourable genes identified in in either habitat-type could be used interchangeably to confer resistance even though the flea beetle life cycle is different for each planting period, while either overwintered adults or newly emerged adults can be used to evaluate feeding damage.

Identification and Genome-Wide Association Analysis for Fusarium Crown Rot Resistance in Wheat.

Fusarium crown rot (FCR) is a fungal disease and severely decreases wheat production worldwide. Tibetan semiwild wheat, Yunnan hulled wheat, Xinjiang rice wheat, and Sichuan white wheat are four subspecies landraces endemic to western China and have rich genetic diversity in response to biotic and abiotic stresses. Here, a natural population, including 209 wheat accessions of four subspecies, was evaluated for FCR resistance. he genome-wide association study was performed using the wheat 55K single-nucleotide polymorphisms (SNPs). The results showed that the disease index (DI) ranged from 16.88 to 85.00, while six accessions showed moderate to high resistance (DI ≤ 30). Genome-wide association analysis identified 10 stable loci for FCR resistance on chromosomes 1B, 2A (5), 5A, 7A, 7B, and 7D. Four major loci-Qfcr.sicau.2A-1, Qfcr.sicau.2A-3, Qfcr.sicau.5A, and Qfcr.sicau.7D-explained 6.01 to 14.48, 9.76 to 13.11, 8.19 to 10.29, and 5.76 to 12.21% phenotypic variation, respectively. Quantitative trait loci (QTL) pyramiding analysis of these four major loci revealed that accessions with four resistance haplotypes could significantly decrease FCR severity by 9.35 to 31.61% compared with those without or with one to three resistance haplotypes. One kompetitive allele-specific PCR (KASP) marker each was successfully developed for Qfcr.sicau.2A-1 and Qfcr.sicau.7D. The KASP marker of Qfcr.sicau.2A-1 was used to genotype in an F6 recombinant inbred line population. The result showed that the lines carrying the resistance allele reduced FCR severity by 17.78%, demonstrating the importance of Qfcr.sicau.2A-1 in resistance breeding programs. Our findings provide valuable QTL and breeder-friendly PCR-based markers for applications in FCR resistance breeding programs. Our study also proved that gene pyramiding of major loci could enhance FCR resistance.

Genetic variability, heritability and genetic gain of common bean (Phaseolus vulgaris L.) genotypes in response to Mexican bean weevil (Zabrotes subfasciatus Boheman) infestation

The aims of the study were to determine expected genetic gains from selection and the extent and pattern of genetic diversity of common bean genotypes to Mexican bean weevil. Three hundred bean genotypes were artificially infested with the Mexican bean weevil. The experiment was laid out in a randomized complete block design with three replications. Data on thirteen insect and seed related traits were recorded and subjected to statistical analysis. The broad-sense heritability values ranged from 68.5%–93.9% for the traits studied. The expected genetic gains from selection ranged from 5.9%-67.1% for insect related traits and from 0.2%-82.2% for seed related traits. Seed weight loss showed significant positive phenotypic and genotypic correlation with number of eggs, number of adults emerged, percent adult emergence, index of susceptibility, number of holes and first and second progeny damage. Cluster analysis classified the 300 genotypes into two major clusters and seven sub-clusters. Mahalanobis’s D2 value calculated among the sub clusters ranged from 5.6 to 191.6. There was no defined relationship between geographic origins and the pattern of genetic diversity in response to Mexican been weevil infestation. Therefore, parental selection should be made based on genetic diversity and other special merits of the genotype for the resistance attributes. The introgression of the resistance gene into the adapted improved varieties and landraces, and increasing the frequency of resistance genes through selection could be used as a strategy to improve bruchid resistance in the future

Temporal evolution of sulfadoxine-pyrimethamine resistance genotypes and genetic diversity in response to a decade of increased interventions against Plasmodium falciparum in northern Ghana

BackgroundAnti-malarial drug resistance remains a key concern for the global fight against malaria. In Ghana sulfadoxine-pyrimethamine (SP) is used for intermittent preventive treatment of malaria in pregnancy and combined with amodiaquine for Seasonal Malaria Chemoprevention (SMC) during the high malaria season. Thus, surveillance of molecular markers of SP resistance is important to guide decision-making for these interventions in Ghana.MethodsA total of 4469 samples from uncomplicated malaria patients collected from 2009 to 2018 was submitted to the Wellcome Trust Sanger Institute, UK for DNA sequencing using MiSeq. Genotypes were successfully translated into haplotypes in 2694 and 846 mono infections respectively for pfdhfr and pfdhps genes and the combined pfhdfr/pfdhps genes across all years.ResultsAt the pfdhfr locus, a consistently high (> 60%) prevalence of parasites carrying triple mutants (IRNI) were detected from 2009 to 2018. Two double mutant haplotypes (NRNI and ICNI) were found, with haplotype NRNI having a much higher prevalence (average 13.8%) than ICNI (average 3.2%) across all years. Six pfdhps haplotypes were detected. Of these, prevalence of five fluctuated in a downward trend over time from 2009 to 2018, except a pfdhps double mutant (AGKAA), which increased consistently from 2.5% in 2009 to 78.2% in 2018. Across both genes, pfdhfr/pfdhps combined triple (NRNI + AAKAA) mutants were only detected in 2009, 2014, 2015 and 2018, prevalence of which fluctuated between 3.5 and 5.5%. The combined quadruple (IRNI + AAKAA) genotype increased in prevalence from 19.3% in 2009 to 87.5% in 2011 before fluctuating downwards to 19.6% in 2018 with an average prevalence of 37.4% within the nine years. Prevalence of parasites carrying the quintuple (IRNI + AGKAA or SGEAA) mutant haplotypes, which are highly refractory to SP increased over time from 14.0% in 2009 to 89.0% in 2016 before decreasing to 78.9 and 76.6% in 2017 and 2018 respectively. Though quintuple mutants are rising in prevalence in both malaria seasons, together these combined genotypes vary significantly within season but not between seasons.ConclusionsDespite high prevalence of pfdhfr triple mutants and combined pfdhfr/pfdhps quadruple and quintuple mutants in this setting SP may still be efficacious. These findings are significant as they highlight the need to continuously monitor SP resistance, particularly using deep targeted sequencing to ascertain changing resistance patterns.

Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation

Comparative landscape genetic studies provide insights into whether relationships between landscape features and patterns of spatial genetic structure differ among populations, species, habitat types, and regions. For species with fragmented distributions, especially when management practices contribute to fragmentation, tests of the factors structuring population connectivity are particularly important for understanding continued risks. We determined levels of genetic diversity and tested the relationships of landscape-scale vegetative, geographic, and climate variables with genetic distance in two congeneric, endemic salamander species with status of concern. Using microsatellite data for 326 Rhyacotriton kezeri and 557 Rhyacotriton variegatus individuals collected from 17 to 29 localities, respectively, we implemented a model of landscape resistance based on circuit theory. The northernmost portions of each species’ range is more fragmented than areas to the south, leading to the prediction that these areas would have relatively lower genetic diversity in response. Due to reliance of both species upon cold-water habitats, we predicted that landscape variables maintaining cool, moist microhabitats would be correlated with gene flow. Genetic structure was high overall and trended toward increasing with the proportion of the forested landscape. Based on maximum likelihood population effects models across genetic clusters and species, land cover and roads were the best predictors of genetic distance, even though the degree of fragmentation differed across each species’ geographic range. Our results suggest that forest cover is essential for dispersal in these salamanders, indicating negative effects of fragmentation resulting from timber harvest and other forest disturbances.

Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence.

Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ecological niche modeling, coalescent simulation and direct spatio-temporal reconstruction of lineage diffusion using a relaxed random walk model. This multi-model inference framework is particularly useful to investigate the complex dynamics and current patterns in genetic diversity in response to processes operating on multiple taxonomic levels in comparative phylogeography. In addition, because of the lack, or incompleteness of fossil record, the understanding of the role of biogeographical events (vicariance and dispersal routes) in most regions worldwide is barely known. Thus, we believe that the expansion of that framework for multiple species under a comparative approach may give clues on genetic legacies in response to Quaternary climate changes and other biogeographical processes.

Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change.

Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangered due to excessive and illegal harvesting for use in Chinese medicine. Here, we test a general computational method for the prediction of priority conservation areas (PCAs) by measuring the genetic diversity of P. amurense across the entirety of northeast China using a single strand repeat analysis of twenty microsatellite markers. Using computational modeling, we evaluated the geographical distribution of the species, both now and in different future climate change scenarios. Different populations were analyzed according to genetic diversity, and PCAs were identified using a spatial conservation prioritization framework. These conservation areas were optimized to account for the geographical distribution of P. amurense both now and in the future, to effectively promote gene flow, and to have a long period of validity. In situ and ex situ conservation, strategies for vulnerable populations were proposed. Three populations with low genetic diversity are predicted to be negatively affected by climate change, making conservation of genetic diversity challenging due to decreasing habitat suitability. Habitat suitability was important for the assessment of genetic variability in existing nature reserves, which were found to be much smaller than the proposed PCAs. Finally, a simple set of conservation measures was established through modeling. This combined molecular and computational ecology approach provides a framework for planning the protection of species endangered by climate change.

Dual Threats of Imperiled Native Agroecosystems and Climate Change to World Food Security: Genomic Perspectives

All of our crop plants originated in the Vavilovian centers of plant genetic diversity. Following domestication, crop plants went through a period of reduced diversity caused by a domestication bottleneck. The cultivation of crop plants in native habitats where crop plants and their wild relatives grew in close contact created native agroecosystems, which facilitated frequent genetic exchange between crop plants and their wild ancestors, thereby enriching the crop gene pool. These native agroecosystems even produced new crop plants, such as bread wheat. Humans traveled with their crop plants spanning the globe, and the enriched crop gene pools were adapted to diverse habitats, creating landraces that nourished preindustrial agriculture and human civilizations. Genomic research has shown that many of the genes that were exploited in the Green Revolution evolved recently by the active evolutionary processes made possible by functioning native agroecosystems and the selection pressure imposed by various abiotic and biotic stresses. With the dawn of the scientific method of breeding, the genetic diversity in the landraces of crop plants and wild relatives was exploited to develop highly productive crop cultivars. Population pressure, habitat destruction, and the spread of modern industrialization are destroying the very native agroecosystems that are our lifeline. We need functioning native agroecosystems as well as springs of new genetic diversity in response to changing climate. Although the genetic diversity conserved in crop genebanks is, and will be, useful in the long run, they may not contain the new genes that we may need as an insurance policy against the vagaries of drastic climate change. A plan of action is suggested for the conservation of native agroecosystems.

Genetic control of susceptibility to infection with Plasmodium chabaudi chabaudi AS in inbred mouse strains

To identify genetic effects modulating blood stage replication of the malarial parasite, we phenotyped a group of 25 inbred mouse strains for susceptibility to Plasmodium chabaudi chabaudi AS infection (peak parasitemia, survival). A broad spectrum of responses was observed, with strains such as C57BL/6J being the most resistant (low parasitemia, 100% survival), and strains such as NZW/LacJ and C3HeB/FeJ being extremely susceptible (very high parasitemia and uniform lethality). A number of strains showed intermediate phenotypes and gender specific effects, suggestive of rich genetic diversity in response to malaria in inbred strains. An F2 progeny were generated from SM/J (susceptible) and C57BL/6J (resistant) parental strains, and was phenotyped for susceptibility to P. chabaudi chabaudi AS. A whole genome scan in these animals identified the Char1 locus (LOD=7.40) on chromosome 9 as a key regulator of parasite density and pointed to a conserved 0.4Mb haplotype at Char1 that segregates with susceptibility/resistance to infection. In addition, a second locus was detected in [SM/J x C57BL/6J] F2 mice on the X chromosome (LOD=4.26), which was given the temporary designation Char11. These studies identify a conserved role of Char1 in regulating response to malaria in inbred mouse strains, and provide a prioritized 0.4Mb interval for the search of positional candidates.

Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans

ABSTRACTGenetic diversity is often generated during adaptation to stress, and in eukaryotes some of this diversity is thought to arise via recombination and reassortment of alleles during meiosis. Candida albicans, the most prevalent pathogen of humans, has no known meiotic cycle, and yet it is a heterozygous diploid that undergoes mitotic recombination during somatic growth. It has been shown that clinical isolates as well as strains passaged once through a mammalian host undergo increased levels of recombination. Here, we tested the hypothesis that stress conditions increase rates of mitotic recombination in C. albicans, which is measured as loss of heterozygosity (LOH) at specific loci. We show that LOH rates are elevated during in vitro exposure to oxidative stress, heat stress, and antifungal drugs. In addition, an increase in stress severity correlated well with increased LOH rates. LOH events can arise through local recombination, through homozygosis of longer tracts of chromosome arms, or by whole-chromosome homozygosis. Chromosome arm homozygosis was most prevalent in cultures grown under conventional lab conditions. Importantly, exposure to different stress conditions affected the levels of different types of LOH events, with oxidative stress causing increased recombination, while fluconazole and high temperature caused increases in events involving whole chromosomes. Thus, C. albicans generates increased amounts and different types of genetic diversity in response to a range of stress conditions, a process that we term “stress-induced LOH” that arises either by elevating rates of recombination and/or by increasing rates of chromosome missegregation.

Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis)

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations. Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential “rescue effect” of immigration. Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3 years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations. Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bottleneck events based on one technique.

New phenotyping methods for screening wheat and barley for beneficial responses to water deficit

This review considers stomatal conductance as an indicator of genotypic differences in the growth response to water stress. The benefits of using stomatal conductance are compared with photosynthetic rate and other indicators of genetic variation in water stress tolerance, along with the use of modern phenomics technologies. Various treatments for screening for genetic diversity in response to water deficit in controlled environments are considered. There is no perfect medium: there are pitfalls in using soil in pots, and in using hydroponics with ionic and non-ionic osmotica. Use of mixed salts or NaCl is recommended over non-ionic osmotica. Developments in infrared thermography provide new and feasible screening methods for detecting genetic variation in the stomatal response to water deficit in controlled environments and in the field.

Population genetic responses of wild forage species to grazing along a rainfall gradient in the Sahel: A study combining phenotypic and molecular analyses

Genetic diversity was studied in wild forage species subjected to grazing along a rainfall gradient in West Niger, within the Sahel with aim of identifying adapted genotypes, which could be used to reclaim degraded land. Two legumes (Alysicarpus ovalifolius and Zornia glochidiata) and two grasses (Brachiaria xantholeuca and Cenchrus biflorus) were selected to relate phenotypic adaptation to genetic diversity in response to grazing and rainfall. Populations of each species were sampled from both heavily grazed and ungrazed sites along a rainfall gradient, approximating 200 mm yr−1 to 800 mm yr−1 rainfall isohyets. The adaptative phenotypic expressions to aridity and grazing of the populations from each of the species were characterised by morphological measures performed on the plants sampled in the field. These analyses were then compared with the results from genetic analyses using the PCR-based techniques of amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD). Analyses of molecular data using cluster analysis (UPGMA), principal co-ordinates analysis (PCO), Mantel tests and an Analysis of Molecular Variance (AMOVA), revealed genotypic distinction between populations subjected to both differing aridity and grazing. The majority of the total genotypic variation sampled in all species occurred among individuals within a population. The significant morphological differentiation found among populations subjected to varying grazing and aridity stresses, determined through linear regression analyses, did not correlate significantly with the genotypic differentiation, as revealed by Mantel tests. The results suggest that grazing does not cause a loss of genetic diversity in the wild forage species studied, although with increasing aridity the impact of grazing on the genetic diversity of populations may increase.

Screening of kenaf ( Hibiscus cannabinus L.) genotypes for low temperature requirements during germination and evaluation of feasibility of seed production in Italy

Kenaf ( Hibiscus cannabinus L.), an annual plant of the family Malvaceae, with potential use as a non-wood fiber source is a relatively new crop in Italy where it can be used in the manufacture of paper and pulp products. Cultivars differ markedly in their response to daylength, but stem growth generally declines rapidly following the onset of flowering such that under Italian conditions sowing for fiber production has to be carried out early to allow maximum growth before floral initiation. Sowing is generally delayed until soil temperature exceeds 12°C (approximately the middle of May), and therefore it is important to evaluate genetic diversity in response to low temperature during the germination stage to determine which kenaf cultivars are suited to early sowing. These trials screened various lines to identify those able to germinate at low temperature and therefore suitable for early sowing. The lines were also grown to evaluate photoperiodic requirements and seed yield in the trial environment (Experimental Centre of Rottaia, Pisa, central Italy, 43°40′N latitude;10°19′E longitude). In addition, the germination characteristics of seed obtained here were tested at low constant temperature (8°C) and at alternating 20–30°C temperature. Seed belonging to 15 lines – produced in Australia and selected for tolerance to low temperature – showed high germination percentage at 8°C in comparison with Tainung 2, a cultivar sensitive to low temperature and produced in USA (75 and 12% as overall mean of lines and Tainung 2, respectively). Lines differed significantly in their response to temperature both in germination percentage and mean germination time. Lines showed a wide range of duration of vegetative period. Flowering took place from 31 July to 23 August in most lines, and they are therefore considered early-maturing-types. Lines differed in duration of the period from emergence to seed maturity (from 134 to 187 days), in seed yield per plant (from 0.9 to 27.7 g plant −1), and harvest index (from 0.3 to 16.6%). In some lines, flowering occurred in mid-August and seed filling was then not completed due to low air temperature and unfavourable moisture conditions. Seed produced in central Italy had low quality due to more rapid deterioration and susceptibility to fungal pathogens. Sensitivity to low temperature during germination was greater in most lines and germination percentages were considerably lower than for seed produced in north-eastern Australia. Environmental conditions in central Italy appear inadequate for seed production.

Genetic Response of Inbred Lines of Chickens to Rous Sarcoma Virus

This study demonstrates the genetic variation among families of White Leghorn chickens, representing 5 different and unrelated inbred lines, when they were inoculated intracerebrally at 1 day of age with Rous sarcoma virus. The differences in response to inoculation of chickens with Rous sarcoma virus, both within and between lines, were marked. The progeny from line 10 representing 4 different sire matings, each mated to different groups of females, were completely susceptible and all died from the effects of the disease induced by inoculation. In contrast the progeny from line 7, representing 3 different sire matings, were highly resistant and only 2 chickens of 327 died. Progeny from lines 6, 9, and 15 showed considerable genetic diversity in response to Rous sarcoma virus. Within lines the progeny from certain males showed considerable resistance, while the progeny of other males in these same lines all died before 25 days of age. Likewise, progeny from dams, within sires and lines, showed similar genetic diversity in response to Rous sarcoma virus, some being completely resistant and others completely susceptible.