Lack Of Genetic Variation Research Articles

Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis.

Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), is known to exhibit host specialization. The virulence of different isolates of the pathogen can be classified into pathotypes based on their compatibility with a differential set composed of specific cucurbit host types. However, the genetic basis of host specialization within P. cubensis is not yet known. Total genomic DNA extracted from nine isolates of P. cubensis collected from 2008 to 2013 from diverse cucurbit host types (Cucumis sativus, C. melo var. reticulatus, Cucurbita maxima, C. moschata, C. pepo, and Citrullus lanatus) in the United States were subjected to whole‐genome sequencing. Comparative analysis of these nine genomes confirmed the presence of two distinct evolutionary lineages (lineages I and II) of P. cubensis. Many fixed polymorphisms separated lineage I comprising isolates from Cucurbita pepo, C. moschata, and Citrullus lanatus from lineage II comprising isolates from Cucumis spp. and Cucurbita maxima. Phenotypic characterization showed that lineage II isolates were of the A1 mating type and belonged to pathotypes 1 and 3 that were not known to be present in the United States prior to the resurgence of CDM in 2004. The association of lineage II isolates with the new pathotypes and a lack of genetic diversity among these isolates suggest that lineage II of P. cubensis is associated with the resurgence of CDM on cucumber in the United States.

Transcriptional mechanisms underlying life-history responses to climate change in the three-spined stickleback.

Phenotypic plasticity, the ability of an organism to express different phenotypes depending on the environment, provides an important mechanism by which an animal population can persist under rapid climate change. We experimentally tested both life‐history and transcriptional responses of an ecological model species, the three‐spined stickleback, to warm acclimation at the southern edge of its European range. We explored cross‐environment genetic correlations of key life‐history traits in male sticklebacks exposed to long‐term temperature changes to examine whether the plasticity pattern was variable among genotypes by using a character‐state approach. We also studied gene expression plasticity by analysing both whole‐transcriptome and candidate gene expression in brain and liver. Male sticklebacks that developed under warmer conditions during winter were smaller in size and invested less in nuptial coloration at the beginning of the breeding season, showing similar responses across different genotypes. The lack of genetic variation in life‐history responses may limit any future evolution of the thermal reaction norm in the study population. After long‐term exposure to increased winter temperatures, genes responsible for several metabolic and oxidation–reduction processes were upregulated, and some hormone genes involved in growth and reproduction were downregulated in the brain. In the liver, there was no significantly represented gene ontology by the differentially expressed genes. Since a higher temperature leads to a higher resting metabolic rate, living in warmer environments may incur higher energetic costs for ectotherms to maintain cellular homoeostasis, resulting in negative consequences for life‐history traits. The expression of genes related to metabolism, cellular homoeostasis and regulatory signalling may underlie temperature‐induced changes in life history.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA.

Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n=116231 SNPs) to describe signatures of fine-scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST =0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean=236 SNPs), 18 environmental variables (mean=99 SNPs), and those detected through genetic differentiation (n=110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P.albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine-scale adaptation.

RAPD assisted selection of black gram (Vigna mungo L. Hepper) towards the development of multiple disease resistant germplasm

Black gram (Vigna mungo L. Hepper), is an extensively studied food crop which is affected by many abiotic and biotic factors, especially diseases. The yield potential of Black gram is shallow due to lack of genetic variability and biotic stress susceptibility. Core biotic stress factors include mung bean yellow mosaic virus (MYMV), urdbean leaf crinkle virus (UCLV), wilt (Fusarium oxysporum) and powdery mildew (Erysiphe polygoni DC). Although many studies determine resistant varieties to a particular disease, however, it is often complimented by low yield and susceptibility to other diseases. Hence, this study focuses on investigating the genetic relationships among three varieties and nine accessions of black gram having disease resistance to previously described diseases and susceptibility using random amplified polymorphic deoxyribonucleic acid (RAPD) markers. A total of 33 RAPD primers were used for diversity analysis and yielded 206 fragments. Number of amplified fragments ranged from two (OPN-1) to 13 (OPF-1). The highest similarity coefficient was observed between IC-145202 and IC-164118 (0.921), while lowest similarity was between PU-31 and IC-145202 (0.572). The genetic diversity obtained in this study along with disease analysis suggests PU31as a useful variety for the development of markers linked to MYMV, UCLV, wilt and powdery mildew resistance by marker-assisted back cross breeding and facilitates the production of crosses with multiple disease resistance.

Tubastraea micranthus, comments on the population genetics of a new invasive coral in the western Atlantic and a possible secondary invasion

The Indo-Pacific azooxanthellate coral Tubastraea micranthus (Cairns and Zibrowius, 1997) has successfully invaded offshore oil/gas production platforms in the Gulf of Mexico. The genetic structure of these populations has been unknown. A question has arisen regarding whether there have been multiple invasions of this species. Five platforms were surveyed; only two were found to possess populations large enough to sample – GI-93C and MC-280A. Tissue samples were collected and analyzed via Amplified Fragment Length Polymorphisms (AFLPs). STRUCTURE analysis identified four genetically distinct clusters or groups among the two platforms. The MC-280A population exhibited an overwhelming association with only one genetic group. Although the three other groups were represented, they were present in small proportions – 1–5%. By contrast, the GI-93C population showed high genetic diversity, with colonies exhibiting association with all four groups in widely varying proportions. The lack of genetic variability on MC-280A most likely resulted from a single recruitment event on this more isolated platform. It is possible that this event could have been derived from a second invasion of this species. In that case, treatment of the invasive would best be focused on the species at the vector point (e.g., treating the hull or ballast water of a ship prior to reaching its destination) rather than in the already infected environment, to avoid repeated replacement invasions. On GI-93-C, the genetic variability was most likely the result of multiple recruitment events. Other possible factors causing the observed pattern could include recruitment from genetically diverse populations in the region and sampling from an older age population where reproduction could result in admixture.

Genetic variation in wild and hatchery population of Catla catla (Hamilton, 1822) analyzed through mtDNA cytochrome b region

Catla (Catla catla) is a one of the most harvested Indian major carps and is widely cultured fish species in Indian subcontinent. In the present study, genetic variability between hatchery and wild stocks of Catla was surveyed using sequence data of mitochondrial DNA of partial 307 bp of cytochrome b region. A total of 174 Catla individuals were examined from three different river basins and hatcheries. Significant genetic heterogeneity was observed for the sequence data (FST = 0.308, p ≤ 0.001). However, analysis of molecular variance (AMOVA) resulted in insignificant genetic differentiation among the samples of three rivers and culture zones (FCT = −0.10, p = 0.44). The result suggested a significant genetic variation within different riverine system, low genetic differentiation among samples from river basins and a lack of genetic variation in hatchery populations.

High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives.

A lack of genetic diversity between wheat breeding lines has been recognized as a significant block to future yield increases. Wheat breeding and prebreeding strategies are increasingly using material from wheat ancestors or wild relatives to reintroduce diversity. Where molecular markers are polymorphic between the host and introgressed material, they may be used to track the size and location of the introgressed material through generations of backcrossing. To generate markers for this purpose, sequence capture targeted resequencing was carried out for a range of wheat varieties, wheat relatives, and wheat progenitors. From these sequences, putative SNPs were identified and used to generate the Axiom® Wheat HD array. A selection of varieties representing a selection of elite wheat breeding material, progenitor species, and wild relatives were used to validate the array. The procedures used are described here in detail.

Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

SummaryTargeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism‐based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high‐density Affymetrix Axiom® genotyping array (the Wheat Breeders’ Array), in a high‐throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders’ Array is also suitable for generating high‐density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site ‘CerealsDB’.

Soybean Resistance to the Soybean Cyst Nematode Heterodera glycines: An Update.

The soybean cyst nematode (SCN), Heterodera glycines, remains a serious threat to soybean production throughout the world. A lack of genetic diversity in resistant soybean cultivars has led to a widespread shift toward virulence in SCN populations, leaving farmers with few proven options other than nonhost rotation to manage this nematode. Recent advances in our understanding of the genes controlling resistance to the nematode have led to improved molecular markers, which are, in turn, increasing the efficiency and precision of the breeding pipeline. A better understanding of the molecular and biochemical basis of SCN resistance and nematode virulence will provide information useful for the development of a long-term strategic plan for diversification and the deployment of cultivars that protect current sources of natural resistance while identifying new targets for engineering novel resistance.

Establishment ofNasutitermes corniger(Isoptera: Termitidae: Nasutitermitinae) on Abaco Island, The Bahamas

Summary Ten years after its discovery, a survey of the exotic termite Nasutitermes corniger (Motschulsky) (Isoptera: Termitidae) on Abaco Island, The Bahamas, revealed an infested area of about 40 ha. The age and spread of the Abaco infestation is remarkably similar to the introduced N. corniger population in Dania Beach, Florida. Survey evidence corroborated that both dispersal at the Abaco location and lack of genetic variation (from its subsequent spread) of this established population point to a single introduction event fostered through a maritime introduction.

Heritability and evolvability of fitness and nonfitness traits: Lessons from livestock.

Data from natural populations have suggested a disconnection between trait heritability (variance standardized additive genetic variance, VA ) and evolvability (mean standardized VA ) and emphasized the importance of environmental variation as a determinant of trait heritability but not evolvability. However, these inferences are based on heterogeneous and often small datasets across species from different environments. We surveyed the relationship between evolvability and heritability in >100 traits in farmed cattle, taking advantage of large sample sizes and consistent genetic approaches. Heritability and evolvability estimates were positively correlated (r = 0.37/0.54 on untransformed/log scales) reflecting a substantial impact of VA on both measures. Furthermore, heritabilities and residual variances were uncorrelated. The differences between this and previously described patterns may reflect lower environmental variation experienced in farmed systems, but also low and heterogeneous quality of data from natural populations. Similar to studies on wild populations, heritabilities for life-history and behavioral traits were lower than for other traits. Traits having extremely low heritabilities and evolvabilities (17% of the studied traits) were almost exclusively life-history or behavioral traits, suggesting that evolutionary constraints stemming from lack of genetic variability are likely to be most common for classical "fitness" (cf. life-history) rather than for "nonfitness" (cf. morphological) traits.

ESTIMATING CONTACT RATES OF HAWAIIAN MONK SEALS (NEOMONACHUS SCHAUINSLANDI) USING SOCIAL NETWORK ANALYSIS

Understanding disease transmission dynamics, which are in part mediated by rates and patterns of social contact, is fundamental to predicting the likelihood, rate of spread, impacts, and mitigation of disease outbreaks in wildlife populations. Contact rates, which are important parameters required for epidemiologic models, are difficult to estimate. The endangered Hawaiian monk seal (Neomonachus schauinslandi) may be particularly vulnerable to morbillivirus outbreaks, due to its low abundance, lack of genetic diversity, and history of isolation from mammalian diseases. Morbillivirus epizootics have had devastating effects on other seal populations. We constructed social networks based on visual observations of individually identifiable monk seals associating onshore to estimate contact rates, assuming random mixing, and also to investigate contact patterns of different age and sex classes. Contact rates estimated from two island populations in 4 yr were remarkably similar, indicating any two individuals have about a one in 1,000 chance of making contact on any given day. Further, contact patterns within and among age and sex classes were statistically different from random. The methods we used could be broadly applied to empirically derive contact rates using association data. These rates are critical for epidemiologic modelling to simulate wildlife disease outbreaks and to inform science-based prevention and mitigation programs.

Phenotypic diversity and relationships among Chilean Choclero maize (Zea mays L. mays) landraces

AbstractChoclero is a Chilean traditional floury maize, consumed as a vegetable, with large economic and cultural value due to its culinary properties that give unique characteristics to the traditional local cuisine. Market diversification demands new materials with different ear and kernel characteristics, which are at present not fulfilled by breeders due to lack of genetic diversity. At present, the Instituto de Investigaciones Agropecuarias has a Choclero germplasm collection composed of 96 accessions, which can supply this lack of diversity, or increase the gene pool. In the present study, 34 selected Chilean Choclero landraces were characterized for 41 agromorphological traits. Phenotypic evaluation in three environments representative of the core production area revealed significant genetic variability for most of the evaluated traits, leading to the identification of several promising accessions. The greater contribution of genotype in most phenological plant, ear and kernel traits suggest their potential usefulness for breeding purposes. Principal component analysis explained over 75% of the total variation for 29 quantitative agromorphological traits. Cluster analysis separated accessions into four major groups, differentiated mainly by plant phenology and ear trait. These findings indicate a number of useful traits at an intra-racial level and a wide range of phenotypic variation that provides a good source of diversity for use in the development of new Choclero varieties.

Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifoliumRamat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.

Lack of genetic variation in the response of a trematode parasite to ocean acidification

Ocean acidification is already having measurable impacts on marine ecosystems. Intraspecific variation in the responses of marine organisms to ocean acidification can reveal genetic differences in tolerance to low pH conditions and determine the potential for a species to adapt to a changing environment. This study tests for the existence of genetic variation in both the transmission success of the trematode Maritrema novaezealandense to its second intermediate amphipod host, Paracalliope novizealandiae, and the extent of parasite-induced mortality in that host, in response to decreasing pH. Eight parasite genotypes were tested in a custom-built ocean acidification simulation system, at 8.1 pH (current ocean conditions) and under conditions of 7.4 pH (worst-case scenario future prediction). The parasites had significantly higher infection success in the more acidic treatment, but there was no significant difference among genotypes in how infection success was affected by pH. In contrast, some parasite genotypes induced higher mortality in amphipods than other genotypes, but this genetic effect was also independent of pH. Overall, our results reveal no significant intergenotype variation in how the parasite responds to ocean acidification with respect to two key traits, infection success and parasite-induced host mortality, suggesting limited potential for adaptation in the face of acidifying conditions.

MORPHO-PHYSIOLOGICAL AND BIOCHEMICAL TRAIT BASED SELECTION OF WHEAT GENOTYPES FOR DROUGHT TOLERANCE

Drought stress is now become the most important abiotic stress for wheat in Bangladesh. Rabi season often compromised wheat production by imposing drought stress. Therefore, it has been a priority to develop drought tolerant wheat variety for Bangladesh. However, the lack of genetic variability for drought tolerance in wheat has been a major bottleneck for developing drought tolerance wheat variety. The present investigation was carried out in an aim to evaluate several exotic and locally cultivated wheat genotypes for drought tolerance based on morpho-physiological and biochemical traits. Experiment was carried out at the net house of Field Laboratory of Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh with seven replications in a RCBD design. Ten locally cultivated and exotic wheat genotypes were grown under control (100% field capacity) and drought (30% field capacity) conditions. Genotypes used in the study were identified with different types of drought tolerance mechanisms, viz., Berkut for earliness, Shatabdi for grain weight, BARI Gom 26 for spike and grain number, along with Vorobey, Berkut for enhanced biosynthesis of proline, Sokoll for undamaged leaf Chlorophyll content and relative water content, Sakha8, Gaurav, Sonalika and Shatabdi for membrane thermostability; Sakha8 and Sourav for improved stress tolerance index. The genotypes screened out with different traits related to drought tolerance can be utilized as gene source for future breeding programs.

Microsatellite and chloroplast DNA diversity of the invasive aquatic weed Hygrophila polysperma in native and invasive ranges

As part of an ongoing effort on biocontrol of hygrophila, Hygrophila polysperma, a combination of microsatellite and chloroplast DNA sequences were used to examine the genetic variation of exotic and native populations of this invasive weed and to understand its invasion history. In the US, hygrophila is well established in Florida and Texas and also is found in Alabama, Kentucky, South Carolina and Virginia. This weed is also invasive in Australia, Germany and Mexico. Plant samples were collected from all regions that hygrophila is known to have invaded as well as its native range in India (West Bengal and Assam) and Mymensingh, Bangladesh. Results showed that hygrophila genotypes across the invasive regions are nearly identical and appear to be from a similar clonal lineage. In contrast, native genotypes were highly variable and consisted of 49 multi-locus genotypes (MLGs). The lack of genetic variation and available historical information suggest that hygrophila was first introduced to the US and this population acted as a source for secondary introduction to Mexico and Australia. The German population may be the result of an independent introduction from the same source population.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

SummaryIn wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Distribution of crop wild relatives of conservation priority in the UK landscape

Many crop species suffer from a lack of genetic diversity which reduces the ability of cultivars to withstand new pests or environmental stresses. The wild relatives of crop plants are an important source of genetic variation and can be used to introduce new traits into existing crops. Identification and conservation of crop wild relatives (CWR) is, therefore, an important step to safeguard future food security. Recent efforts have identified geographical hotspots of CWR diversity in several countries but, as yet, there have been no surveys to identify the habitats and landscape features within these areas that might be most suitable for conservation efforts. Here, we use a UK-wide vegetation survey covering a range of both habitats and landscape features (e.g. fields, hedgerows, waterways and roadsides) to identify the habitats and features with the highest proportion of CWR identified as priority taxa for conservation. Priority CWR were most abundant in grassland habitats, although this was most striking in CWR related to forage and fodder crops. CWR related to food crops were most common in cropped and weedy areas, fertile grassland and lowland woodland. Within habitats, CWR occurrence was significantly associated with linear features including hedgerows, roadsides, field boundaries and field margins. Our findings indicate that CWR of conservation interest are often associated with disturbed habitats and landscape features that are not considered as priorities under site-based conservation measures. We suggest that efforts to maintain linear features in hotspots of CWR diversity would be most effective at conserving the UK's CWR resource.

Resilience in a concentrated and consolidated food system

The focus of this article is to articulate the risks of a consolidated, industrialized agrifood system for our planet’s ecology and our ability to guarantee a future food supply, while also considering how the food system might become more resilient. A relatively small number of agribusiness firms, operating globally, have powerfully shaped who produces food, what is produced, how and where it is produced, and by whom it is eaten. To examine food system resilience, one must see that ecological risks of agriculture (e.g., monoculture, overuse of fertilizer and chemicals, and lack of genetic diversity) are intertwined with its social and economic organization, that relationships between people and between people and their particular places are critical to situate food decisions within ecology, and that issues of scale in a global food system are keenly important and challenging to resolve. Our highly concentrated global food system has resulted from horizontal and vertical integration in food system sectors and globalization of agricultural and food markets. This system constrains farmers (and others) in making choices that can fend off likely ecological and social disruptions while limiting their ability to accommodate change. It has eliminated smaller farms and businesses that provided a redundancy of role and function, resulting in few fail-safe mechanisms for the food system. A focus on efficiency, standardization, and specialization has decreased the diversity of scale, form, and organization across the food system. Finally, the dominant food system’s inability to solve food insecurity and hunger within both rich and poor countries, coupled with an industrial diet that uses up a great many natural resources, makes the system precarious. While there is no single approach at any given scale that will accomplish food system resilience, a combination of actions, strategies, and policies at multiple levels that are rooted in ecology, democracy, and economic and social equality is necessary to move forward.