Source Of Genetic Variation Research Articles

Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Mutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15-fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.

Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.

Copy number variation is an important source of genetic variation, yet data are often lacking due to technical limitations for detection given the current genome assemblies. Our goal is to demonstrate the extent to which an array-based platform (aCGH) can identify genomic loci that are collapsed in genome assemblies that were built with short-read technology. Taking advantage of two cichlid species for which genome assemblies based on Illumina and PacBio are available, we show that inter-species aCGH log2 hybridization ratios correlate more strongly with inferred copy number differences based on PacBio-built genome assemblies than based on Illumina-built genome assemblies. With regard to inter-species copy number differences of specific genes identified by each platform, the set identified by aCGH intersects to a greater extent with the set identified by PacBio than with the set identified by Illumina. Gene function, according to Gene Ontology analysis, did not substantially differ among platforms, and platforms converged on functions associated with adaptive phenotypes. The results of the current study further demonstrate that aCGH is an effective platform for identifying copy number variable sequences, particularly those collapsed in short read genome assemblies.

Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem

BackgroundStructural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exact genomic position. Breakpoint uncertainty is a characteristic issue of structural variants detected via short-read sequencing methods and complicates subsequent population analyses. The commonly used heuristic strategy reduces this issue by clustering/merging nearby structural variants of the same type before the data from individual samples are merged.ResultsWe compared the two most used dissimilarity measures for SV clustering in terms of Mendelian inheritance errors (MIE), kinship prediction, and deviation from Hardy–Weinberg equilibrium. We analyzed the occurrence of Mendelian-inconsistent SV clusters that can be collapsed into one Mendelian-consistent SV as a new measure of dataset consistency. We also developed a new method based on constrained clustering that explicitly identifies these types of clusters.ConclusionsWe found that the dissimilarity measure based on the distance between SVs breakpoints produces slightly better results than the measure based on SVs overlap. This difference is evident in trivial and corrected clustering strategy, but not in constrained clustering strategy. However, constrained clustering strategy provided the best results in all aspects, regardless of the dissimilarity measure used.

Genome-wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations.

Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome-wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (Hordeum vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley—P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here, we provide the first genome-wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and 10 against P. teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.

Genetic Structure, Differentiation and Originality of Pinus sylvestris L. Populations in the East of the East European Plain

In order to carry out activities aimed at conservation and rational use of forest resources; it is necessary to study the main forest-forming plant species in detail. Scots pine (Pinus sylvestris L., Pinaceae) is mainly found in the boreal forests of Eurasia and is not so often encountered in the east of the East European Plain. The aim of the study was to study the genetic diversity, structure and differentiation of Scots pine populations in the east of the East European Plain. We studied ten populations of P. sylvestris using the Inter Simple Sequence Repeats (ISSR)-based DNA polymorphism detection method. Natural populations are demonstrated by relatively high rates of genetic diversity (He = 0.167; ne = 1.279; I = 0.253). At the same time, there is a tendency for a decrease in the genetic diversity of the studied populations of P. sylvestris from west to east. Analysis of the genetic structure shows that the studied populations are highly differentiated (GST = 0.439), the intrapopulation component accounts for about 56% of the genetic diversity. Using various algorithms for determining the spatial genetic structure, it is found that the studied populations form two groups of populations in accordance with geographic location. With the help of a genetic originality coefficient, populations with specific and typical gene pools are identified. They are recommended as sources of genetic diversity and reserves for the conservation of genetic resources of the species.

Temperature dependence of spontaneous mutation rates.

Mutation is the source of genetic variation and the fundament of evolution. Temperature has long been suggested to have a direct impact on realized spontaneous mutation rates. If mutation rates vary in response to environmental conditions, such as the variation of the ambient temperature through space and time, they should no longer be described as species-specific constants. By combining mutation accumulation with whole-genome sequencing in a multicellular organism, we provide empirical support to reject the null hypothesis of a constant, temperature-independent mutation rate. Instead, mutation rates depended on temperature in a U-shaped manner with increasing rates toward both temperature extremes. This relation has important implications for mutation-dependent processes in molecular evolution, processes shaping the evolution of mutation rates, and even the evolution of biodiversity as such.

Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates

In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.

Assessing effects of chronic heavy metal exposure through a multibiomarker approach: the case of Liomys irroratus (Rodentia: Heteromyidae)

Wild animals that inhabit inside mine tailings which contain heavy metals are an excellent study model to conduct ecotoxicological studies that analyze chronic metal exposures at low doses (realistic exposures). This study was conducted in Huautla, Morelos, Mexico, in a mining district where 780,000 tons of wastes were deposited in open air. Liomys irroratus is a small mammal species that lives inside these mine tailings. A multibiomarker approach study was performed to analyze metal bioaccumulation levels (biomarker of exposure) by inductively coupled plasma mass spectrometry, DNA damage levels (biomarker of early effects) through the alkaline comet assay, and population genetic structure and diversity (biomarker of permanent effects), using seven microsatellite loci, in 75 L. irroratus individuals, from two mine tailings and one reference site. Concentrations of aluminum, copper, iron, nickel, lead, and zinc were statistically higher in the liver of exposed individuals. Significant DNA damage levels were registered in the mine tailings groups. Aluminum, lead, and nickel had the highest contribution to the genetic damage levels observed, while aluminum and nickel had the highest contribution to genetic diversity effects. A positive and significant relationship was detected between individual genetic diversity (internal relatedness) and genetic damage (DNA single-strand breaks). Genetic structure of L. irroratus populations revealed that the main source of genetic variation was located within populations. We consider that multibiomarker studies in environmental settings using sentinel species are valuable for environmental risk assessment and ecological responses in chronic exposed populations.

Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds.

Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of22 other European cattle breeds were included in the study for comparison. A total of 28562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (U HE =0.341, HO =0.368), and the highest heterozygote excess (U FIS =-0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.

Amplification dynamics of miniature inverted‐repeat transposable elements and their impact on rice trait variability

Transposable elements (TEs) are a rich source of genetic variability. Among TEs, Miniature Inverted-repeat Transposable Elements (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103,109 Transposon Insertion Polymorphisms (TIPs) in 738 O. sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-GWAS to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than SNPs on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidences of the replicative amplification of MITEs.

The UCR Minicore: a resource for cowpea research and breeding

AbstractIncorporation of new sources of genetic diversity into plant breeding programs is crucial for continuing to improve yield and quality, as well as tolerance to abiotic and biotic stresses. A minicore (the “University of California, Riverside (UCR) Minicore”) composed of 368 worldwide accessions of cultivated cowpea has been assembled, having been derived from the UCR cowpea collection. High‐density genotyping with 51,128 SNPs followed by principal component and genetic assignment analyses identified six subpopulations in the UCR Minicore, mainly differentiated by cultivar group and geographic origin. All six subpopulations were present to some extent in West African material, suggesting that West Africa is a center of diversity for cultivated cowpea. Additionally, population structure analyses supported two routes of introduction of cowpea into the U.S.: (1) from Spain to the southwest U.S. through Northern Mexico and (2) from Africa to the southeast U.S. via the Caribbean. Genome‐wide association studies (GWAS) narrowed several traits to regions containing strong candidate genes. For example, orthologs of the Arabidopsis FLOWERING LOCUS T lie within a major QTL for flowering time. In summary, this diverse, yet compact cowpea collection constitutes a suitable resource to identify loci controlling complex traits, consequently providing markers to assist with breeding to improve this crop of high relevance to global food and nutritional security.

Comparison of anthocyanins, polyphenols, and antioxidant capacities among raspberry, blackberry, and Japanese wild Rubus species

The breeding of raspberries (Rubus idaeus L.) and blackberries (R. fruticosus Agg.) has shifted in focus toward traits associated with the sensory qualities and potential health benefits of the fruit, and Rubus wild species have attracted a great deal of attention as new sources of genetic diversity. In this study, the anthocyanin and polyphenol contents and compositions, and three types of antioxidant capacities were compared in mature fruits including raspberries, blackberries, and Japanese wild Rubus species. ‘Blackcap’ black raspberry showed the significantly highest values of total anthocyanin content and total polyphenol content among 12 Rubus species or cultivars. Cyanidin-3-xylosyl-rutinoside was contained only in black raspberries, and was characteristic anthocyanin in Rubus species. R. croceacanthus H. Lév., a Japanese wild species that is adapted to warm regions, had a deep red fruit color, and had the highest total anthocyanin and total polyphenol contents among the four Japanese wild species examined. As for the antioxidant capacities, the highest values were observed in ‘Blackcap’ among 12 Rubus species. Furthermore, a high positive correlation was shown between total anthocyanin or total polyphenol content and antioxidant capacities. In particular, black raspberries and blackberries contained high concentrations of rutin. Thus, rutin might contribute to the high antioxidant capacities in these cultivars.

Recent extinctions among Little Spotted Kiwi (Apteryx owenii) and the origin of extant populations

ABSTRACT Little Spotted Kiwi (LSK; Apteryx owenii) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D’Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (n = 31 mtDNA, 97 nDNA) than recently extinct (n = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (FST = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.

The Proteomic Expression of Nuclear Apoptosis-Inducing Factor1 (NAIF1) in Colorectal Tissues

The neogenic recombinases are potentially a source of genetic variability possibly implicated in themechanisms of genetic instability involved in the processes of carcinogenesis. One of these neogenicrecombinases is the nuclear apoptosis-inducing factor 1(NAIF1), which codes the protein NAIF1 thatinduces apoptosis in various human cancers.The aim of this work is to study the expression of NAIF1 neogene in cancerous and non-cancerous colorectaltissues.The protein expression of NAIF1gene has been studied by western blot method in the samples of proteinextracted from 29 patients with colorectal cancer.The result of this study showed that the protein expression of NAIF1 was found in both cancerous andnon-cancerous colorectal tissues, but it is highly expressed in non-cancerous tissues adjacent to cancerousone. Its expression is higher in non-metastatic cancerous tissues compared with metastatic one. Also thisexpression is higher in microsatellite instable (MSI) group of cancer compared with microsatellite stable(MSS) group.It can be concluded that NAIF1 protein expression inversely related with more advanced stage or grade ofcolorectal cancer and it may have a role in inhibition of proliferation, migration and invasion of colorectalcancer by inducing apoptosis.

Analysis of reproductive seasonality in Entrepelado and Retinto Iberian pig varieties under intensive management

ABSTRACT Seasonal patterns in the farrowing distribution of two Iberian pig varieties (Retinto and Entrepelado) and its environmental and genetic sources of variation were analyzed within the context of a von Mises circular mixed model solved through Bayesian inference. Estimates about the dispersion parameter supported a low seasonal pattern for both Entrepelado and Retinto varieties with the farrowing peak located between March and April. Nevertheless, seasonality was corroborated by the deviance information criterion when comparing against a uniform circular model by the deviance information criterion (DIC); the uniform model increased more than 100 DIC units in both Iberian pig varieties. Regarding systematic effects, only the parity number of the sow had a relevant impact on farrowing distribution, advancing the farrowing peak in gilts and old sows. Genetic variability was only suggested in the Retinto population although with a small estimate, which would indicate little chance to modify farrowing distribution by genetic selection in the Iberian pig.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BackgroundNative cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.ResultsThe population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6).ConclusionWe provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks.

Cancer is one of the leading causes of death and chromosomal instability (CIN) is a hallmark feature of cancer. CIN, a source of genetic variation in either altered chromosome number or structure contributes to tumor heterogeneity and has become a hot topic in recent years prominently for its role in therapeutic responses. Synthetic lethality and synthetic rescue based approaches, for example, advancing CRISPR-Cas9 platform, are emerging as a powerful strategy to identify new potential targets to selectively eradicate cancer cells. Unfortunately, only few of them are further explored therapeutically due to the difficulty in linking these targets to small molecules for pharmacological intervention. This, however, can be alleviated by the efforts to bring chemical, bioactivity, and genomic data together, as well as established computational approaches. In this chapter, we will discuss some of these advances, including established databases and in silico target-ligand prediction, with the aim to navigate through the synthetically available chemical space to the biologically targetable landscape, and eventually, to the chemical modeling of synthetic lethality and synthetic rescue interactions, that are of great clinical and pharmaceutical relevance and significance.

Assessment of Somaclonal Variations in Embryo-derived Axillary Shoots of Chickpea using Molecular Markers

Background: Somaclonal variation is considered as a source of genetic variation for crop improvement. It has been investigated using cytological, biochemical and molecular techniques.Methods: Genetic stability in the embryo-derived axillary shoots of 4 chickpea genotypes was assessed using eight inter-simple sequence repeat (ISSR) and 19 random amplified polymorphic DNA (RAPD) primers. Result: RAPD primers produced 94 and ISSR primers produced 38 distinct and scorable alleles, with an average of 4.9 alleles for RAPD and 4.75 for ISSR primers. The polymorphic information content (PIC) ranged from 0.36 to 0.90 for RAPD and from 0.50 to 0.87 for ISSR. ISSR recognized a 90%, but RAPD recognized 82% similarity value. No absolute similarity value was between the mother plant and the regenerated shoots for the overall genotypes. At a 90% similarity value, 15 out of the 20 regenerated shoots from ‘Giza 88’ group with their mother plant using ISSR markers; however, 11 regenerated shoots grouped with their mother plant in one central cluster for ‘Giza 4’ using RAPD markers. The observed variations in the total number of polymorphic RAPD and ISSR bands and the number of bands specific to the mother and regenerated shoots, detected intra-clonal variation and genetic instability seem to be genotype-dependent.

Ch’ujuk: variedad clonal de ‘estevia’ como alternativa al cultivo masivo de Morita II para el Trópico de México

La demanda por edulcorantes naturales va en aumento en el mundo, debido principalmente a los efectos secundarios que producen los edulcorantes sintéticos, lo cual ha hecho que varios países prohíban el consumo de estos. Un ejemplo es Japón, el cual prohibió el uso de edulcorantes sintéticos desde los años 70 y sustituyó la mitad del consumo de azúcar de caña por cristales de Stevia rebaudiana (Bertoni) Bertoni. Debido a la relevancia actual de S. rebaudiana, el contar con materiales adaptados a las condiciones de México es una necesidad urgente para que el cultivo se incremente en el país. En el CIRSE-INIFAP desde 2010, se trabaja con el desarrollo tecnológico de este cultivo y a partir, de 2012 se inició el proyecto de impulso a la innovación con parcelas de Morita II. Posteriormente se adquirió por parte de INIFAP material genético proveniente de Paraguay, lo cual vino a fortalecer su fuente de variabilidad genética. Esta variabilidad ha permitido establecer parcelas y realizar una selección individual de aquellos materiales que muestran un mejor comportamiento agronómico, de tal forma que en la actualidad se cuenta con una nueva varieagronómicas ampliamente superiores a los materiales criollos y a la variedad Morita II, posee hojas grandes, abundantes, y tallo muy ramificado. Florece de forma uniforme, lo cual facilita la realización del corte en el momento más oportuno (al aparecer los primeros botones florales). El promedio de rendimiento es de 7 a 9 t ha-1 año con 60 000 plantas ha-1.

Molecular characterization of heat tolerance in eggplant (Solanum melongena) lines using SSR markers

High temperature is one of the most important environmental stresses causing heavy reduction in yield of eggplant (Solanum melongena L.) in India. Therefore, development of heat tolerant eggplant variety is an important breeding objective. The present investigation was conducted to assess genetic variation among 62 eggplant lines including heat tolerant and susceptible lines in order to identify novel heat tolerant lines in changing climate in India. We employed 15 simple sequence repeat (SSR) markers to study polymorphisms among eggplant lines obtained from eggplant breeding program. The observations were analyzed using Power Marker version 3.5. The range of amplified number of bands was from 2 to 3 in each of 15 markers. The allele frequency was ranged from 0.5 to 0.7931 with an average of 2.067 alleles per locus. Among the 15 polymorphic SSR markers, 67% markers had PIC value higher than 0.3 with heterozygosity of individual loci was ranged from 0.00 to 0.1667. The marker emf01C03 had higher number of allele (3) and the marker emd03C01 had maximum PIC value and gene diversity. The NJ dendrogram obtained by 15 SSR markers divides 62 lines into 7 clusters where the cluster VII comprised of most heat tolerant lines (DBL-21, Guhala Chatua Local). The amplification pattern of heat tolerant lines also differ which implies different genetic architecture of heat tolerant lines. The research work will be very useful to combine these diverse sources of genetic variability to develop heat tolerant variety (s) in eggplant.