Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China

Introduction

Penicillium species exhibit a broad distribution in nature and play a crucial role in human and ecological environments.

Methods

Two Penicillium species isolated from the ancient Great Wall loess in the Mentougou District of Beijing, China, were identified and described as new species, namely, Penicillium acidogenicum and P. floccosum, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS, BenA, CaM, and RPB2 genes.

Results

Phylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to P. chrzaszczii and P. osmophilum, respectively.

Discussion

Penicillium acidogenicum is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C. Penicillium floccosum is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of Penicillium.

Molecular Markers Help with Breeding for Agronomic Traits of Spring Wheat in Kazakhstan and Siberia

The Kazakhstan-Siberia Network for Spring Wheat Improvement (KASIB) was established in 2000, forming a collaboration between breeding and research programs through biannual yield trials. A core set of 142 genotypes from 15 breeding programs was selected, genotyped for 81 DNA functional markers and phenotyped for 10 agronomic traits at three sites in Kazakhstan (Karabalyk, Shortandy and Shagalaly) and one site in Russia (Omsk) in 2020-2022. The study aim was to identify markers demonstrating significant effects on agronomic traits. The average grain yield of individual trials varied from 118 to 569 g/m2. Grain yield was positively associated with the number of days to heading, plant height, number of grains per spike and 1000-kernel weight. Eight DNA markers demonstrated significant effects. The spring-type allele of the Vrn-A1 gene accelerated heading by two days (5.6%) and was present in 80% of the germplasm. The winter allele of the Vrn-A1 gene significantly increased grain yield by 2.7%. The late allele of the earliness marker per se, TaMOT1-D1, delayed development by 1.9% and increased yield by 4.5%. Translocation of 1B.1R was present in 21.8% of the material, which resulted in a 6.2% yield advantage compared to 1B.1B germplasm and a reduction in stem rust severity from 27.6 to 6.6%. The favorable allele of TaGS-D1 increased both kernel weight and yield by 2-3%. Four markers identified in ICARDA germplasm, ISBW2-GY (Kukri_c3243_1065, 3B), ISBW3-BM (TA004946-0577, 1B), ISBW10-SM2 (BS00076246_51, 5A), ISBW11-GY (wsnp_Ex_c12812_20324622, 4A), showed an improved yield in this study of 3-4%. The study recommends simultaneous validation and use of selected markers in KASIB's network.

Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review

The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.

The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

Hybrids of an Impressive Age

We benefited from the availability of a species-specific DNA marker to describe the morphometry of T. cordata × platyphyllos hybrids of an impressive age (ca. 150 years) grown in the Pazaislis baroque monastery yard in Central Lithuania. In an earlier study on a country-wide set of 543 T. cordata individuals from natural forest populations in Lithuania, we detected a nuclear microsatellite locus Tc8 well-differentiating between T. cordata and T. platyphyllos. The Tc8 locus contained a 140 bp allele in T. cordata (541 sampled individuals) and alleles above 160 bp in the two trees with a T. platyphyllos-like morphology (sampled in a national park). To verify the Tc8 locus as species specific, we sampled a further four T. platyphyllos-like individuals, which all contained the Tc8 locus alleles above 160 bp. We subsequently genotyped the six old-growth individuals from the Pazaislis monastery with mixed T. cordata × platyphyllos morphology. Results revealed that all six old-growth Tilia individuals from the Pazaislis monastery were heterozygous for the Tc8 locus with alleles of 140 bp (indicative of T. cordata) and 162 bp (indicative of T. platyphyllos). This finding confirms the morphological observations that these individuals are hybrids between T. cordata and T. platyphyllos. Additionally, the genotyping of a set of 14 nuclear microsatellite loci revealed that all six trees from the Pazaislis monastery are clones, possessing identical microsatellite genotypes. After the molecular identification, we morphotyped leaves, bracts, twigs, and nuts of the 6 old-growth T. cordata × platyphyllos hybrids from the Pazaislis monastery, 16 T. cordata old-growth trees, 4 T. × europaea var. europaea 'Pallida' trees growing near the Pazaislis monastery, and 4 mature T. platyphyllos trees from a nearby Girionys park. The morphotyping showed that T. cordata × platyphyllos hybrids may be the easiest to distinguish from T. cordata by raised and horizontally tertiary veins of leaves.

and Tinospora cordifolia (Willd.) Miers

The adulteration of plants and their materials used in herbal formulations poses a severe health concern. Hence, there is a need to establish a reliable, cost-effective, and robust molecular biomarker to distinguish among species and identify herbal plants and raw drugs from adulterants. The present study used suppressive subtractive hybridization and next-generation sequencing technology to identify novel DNA markers for Boerhavia diffusa L. and Tinospora cordifolia (Willd.) Miers. We identified two primer sets for B. diffusa and one for T. cordifolia. The DNA markers were validated in different accessions of B. diffusa and T. cordifolia and their common adulterants to determine the sensitivity and specificity of developed DNA markers. The designed DNA markers showed 100% sensitivity and specificity in detecting B. diffusa and T. cordifolia from their adulterants. The strategy described here can be extrapolated for developing DNA markers to authenticate other plant species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03732-7.

Function identification and characterization of Oryza sativa ZRT and IRT-like proteins computationally for nutrition and biofortification in rice

Zinc plays a very critical role and function in all organisms. Its deficiency can cause a serious issue. In Oryza sativa, the ZRT/IRT transporter-like proteins play a role in the zinc metal uptake and transport. Few OsZIPs genes have been validated and characterized for their biological functions and most of OsZIPs are not well physiologically, biochemically and phenotypically characterized. In the current study, they analyzed for their function through subcellular localization, phylogenetic analysis, homology modeling, expression analysis, protein-protein interaction (PPI) network prediction, and prediction of their binding sites. Hierarchical clustering of OsZIP genes based on different anatomical parts and developmental stages also orthologs prediction was identified. The presence of SNPs, SSRs, ESTs, FSTs, MPSS, and SAGE tags were analyzed for useful development of markers. SNPs were identified in all OsZIPs genes and each gene was further classified based on their number and position in the 3'UTR and 5'UTR regions of the gene-specific sequences. Binding clusters and their location on the protein sequences were predicted. We found Changing in residues number and position which were due to partial overlapping and sequence alignment, but they share the same mechanism of binding and transporting Zinc. A wide range of CRISPR Cas9 gRNAs was designed based on single nucleotide polymorphism (SNP) for each OsZIP transporter gene for well-function identification and characterization with genome-wide association studies. Hence this study would provide useful information, understanding, and predicting molecular insights for the future studies that will help for improvement of nutritional quality of rice varieties.Communicated by Ramaswamy H. Sarma.

DNA and RNA Molecules as a Foundation of Therapy Strategies for Treatment of Cardiovascular Diseases

There has always been a tendency of medicine to take an individualised approach to treating patients, but the most significant advances were achieved through the methods of molecular biology, where the nucleic acids are in the limelight. Decades of research of molecular biology resulted in setting medicine on a completely new platform. The most significant current research is related to the possibilities that DNA and RNA analyses can offer in terms of more precise diagnostics and more subtle stratification of patients in order to identify patients for specific therapy treatments. Additionally, principles of structure and functioning of nucleic acids have become a motive for creating entirely new therapy strategies and an innovative generation of drugs. All this also applies to cardiovascular diseases (CVDs) which are the leading cause of mortality in developed countries. This review considers the most up-to-date achievements related to the use of translatory potential of DNA and RNA in treatment of cardiovascular diseases, and considers the challenges and prospects in this field. The foundations which allow the use of translatory potential are also presented. The first part of this review focuses on the potential of the DNA variants which impact conventional therapies and on the DNA variants which are starting points for designing new pharmacotherapeutics. The second part of this review considers the translatory potential of non-coding RNA molecules which can be used to formulate new generations of therapeutics for CVDs.

Signatures of Admixture and Genetic Uniqueness in the Autochthonous Greek Black Pig Breed Deduced from Gene Polymorphisms Affecting Domestication-Derived Traits

The Greek Black Pig (or Greek Pig) is the only recognized autochthonous pig breed raised in Greece, usually in extensive or semi-extensive production systems. According to its name, the characteristic breed coat color is solid black. In this study, with the aim to start a systematic genetic characterization of the Greek Black Pig breed, we investigated polymorphisms in major genes well known to affect exterior and production traits (MC1R, KIT, NR6A1, VRTN and IGF2) and compared these data with population genetic information available in other Mediterranean and Western Balkan pig breeds and wild boars. None of the investigated gene markers were fixed for one allele, suggesting that, in the past, this breed experienced introgression from wild boars and admixture from cosmopolitan pig breeds, enriching the breed genetic pool that should be further investigated to design appropriate conservation genetic strategies. We identified a new MC1R allele, containing two missense mutations already reported in two other independent alleles, but here present in the same haplotype. This allele might be useful to disclose biological information that can lead to better understanding the cascade transmission of signals to produce melanin pigments. This study demonstrated that autochthonous genetic resources can be an interesting reservoir of unexpected genetic variants.

Differentiation of Lingxiaohua and Yangjinhua by chloroplast genome sequencing and DNA barcoding markers

Lingxiaohua (Campsis Flos, Campsis grandiflora (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, Datura metel Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of rbcL, matK, psbA-trnH, and ITS2 regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the rps14 and rpoC1 regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua.

Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil

Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.

Natural resistance of tomato plants to Tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.

New Sources of Resistance and Identification of DNA Marker Loci for Sheath Blight Disease Caused by Rhizoctonia solani Kuhn, in Rice

Sheath blight disease caused by the necrotrophic, soilborne pathogen Rhizoctonia solani Kuhn, is the global threat to rice production. Lack of reliable stable resistance sources in rice germplasm pool for sheath blight has made resistance breeding a very difficult task. In the current study, 101 rice landraces were screened against R. solani under artificial epiphytotics and identified six moderately resistant landraces, Jigguvaratiga, Honasu, Jeer Sali, Jeeraga-2, BiliKagga, and Medini Sannabatta with relative lesion height (RLH) range of 21-30%. Landrace Jigguvaratiga with consistent and better level of resistance (21% RLH) than resistant check Tetep (RLH 28%) was used to develop mapping population. DNA markers associated with ShB resistance were identified in F2 mapping population developed from Jigguvaratiga × BPT5204 (susceptible variety) using bulk segregant analysis. Among 56 parental polymorphic markers, RM5556, RM6208, and RM7 were polymorphic between the bulks. Single marker analysis indicated the significant association of ShB with RM5556 and RM6208 with phenotypic variance (R2) of 28.29 and 20.06%, respectively. Co-segregation analysis confirmed the strong association of RM5556 and RM6208 located on chromosome 8 for ShB trait. This is the first report on association of RM6208 marker for ShB resistance. In silico analysis revealed that RM6208 loci resides the stearoyl ACP desaturases protein, which is involved in defense mechanism against plant pathogens. RM5556 loci resides a protein, with unknown function. The putative candidate genes or quantitative trait locus harbouring at the marker interval of RM5556 and RM6208 can be further used to develop ShB resistant varieties using molecular breeding approaches.

Coffea canephora: Heterotic Crosses Indicated by Molecular Approach

The genus Coffea comprises more than 100 species, of which the most commercially important are Coffea arabica and Coffea canephora. The latter is a self-incompatible plant with high natural genetic variability. The detection of polymorphism at the DNA level by molecular markers allowed significant progress with the selection of superior plants. The objective of this study was the molecular characterization of C. canephora using microsatellite markers. To this end, a population of forty-four C. canephora genotypes and one C. arabica genotype, was evaluated with 21 primers. These primers identified 61 alleles in the population and between 2 and 5 alleles per locus. The information index indicated a high level of polymorphism of the analyzed markers. According to the observed and expected heterozygosity, the genetic diversity in the population is high. The overall inbreeding coefficient of the population detected high heterozygosity and zero inbreeding within this population. Genetic diversity among the accessions was also evaluated by the unweighted pair-group method based on arithmetic averages (UPGMA). Six groups were formed based on Mojena's cutting rule and three using the Bayesian approach. These results confirmed the existence of genetic diversity, genetic variability and a potential for selection in future breeding efforts involving the 45 genotypes studied.

Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review

Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.

Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species

Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of "full site" insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 "full sites," respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.

Generic Multiplex Digital PCR for Accurate Quantification of T Cells in Copy Number Stable and Unstable DNA Samples

An accurate T cell quantification is prognostically and therapeutically relevant in various clinical applications, including oncology care and research. In this chapter, we describe how T cell quantifications can be obtained from bulk DNA samples with a multiplex digital PCR experiment. The experimental setup includes the concurrent quantification of three different DNA targets within one reaction: a unique T cell DNA marker, a regional corrector, and a reference DNA marker. The T cell marker is biallelically absent in T cells due to VDJ rearrangements, while the reference is diploid in all cells. The so-called regional corrector allows to correct for possible copy number alterations at the T cell marker locus in cancer cells. By mathematically integrating the measurements of all three markers, T cells can be accurately quantified in both copy number stable and unstable DNA samples.

State-of-the-Art Update of Pancreatic Cysts

Andrew Canakis.

Fundamentals for forage crop breeding and seed production in Russia

Plant breeding and seed production of new generation fodder crops is the groundwork for creating a fodder base for livestock production in sufficient quantities. The Federal Williams Research Center of Forage Production and Agroecology founded in 2018 based on of the All-Russia Williams Fodder Research Institute and other scientific institutions is the largest and most comprehensive center in the field of food production. It develops new techniques and methods for creating initial seed material based on a wide use of genetics, biotechnology, microbiology, immunology, ecology, biogeocenology, and cell selection. During the existence of the Fodder Research Institute and its experimental stations, up to 300 varieties of feed crops were created, which occupied leading positions in the production of fodder in meadows, pastures, and hayfields. Eighty-five modern varieties of fodder crops of the latest generation are widely used and zoned in all regions of Russia. However, the destroyed system of elite and commercial seed production does not allow these varieties to take their rightful place in fodder production, and the market still possesses a large share of non-varietal and mass scale reproduction seeds. In addition, imported seeds brought to the Russian market are often disguised as lawn varieties to reduce the cost and simplify their entry to the market. In this way, 107 varieties of winter ryegrass (Lolium perenne L.), 47 varieties of cane fescue (Festuca arundinacea Schreb.), 21 varieties of creeping clover (Trifolium repens L.), etc. appeared in Russia. In such circumstances, the attention of the Williams Center is focused on the development of techniques and methods for creating fundamentally new varieties based on its own research in genetics, biotechnology, immunology, and ecological selection. Much attention is paid to expanding the network of research stations throughout Russia in order to revive the system of elite seed growing, especially in the regions with the most favorable climate for growing seeds of particular crops. A seed production center was organized as a branch of the Williams Center at the end of 2020. In the future, it is planned to create a united coordinated interdepartmental complex for the breeding of fodder crops in accordance with the regional needs of animal husbandry

Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.

High Genetic Diversity of 16 Indian lettuce (Lactuca indica L.) Accessions from Vietnam

<b>Background and Objective:</b> Plant genetic resources provide the raw material for crop improvement and plant breeding program largely depends on it. Therefore, the evaluation of plant genetic resources plays a critical role in crop improvement and also in conserving valuable genetic resources for the future. In this study, the genetic diversity of 16 <i>Lactuca indica</i> L. accessions collected in Vietnam was investigated by using ISSR and RAPD markers. <b>Materials and Methods:</b> Genetic diversity of 16 <i>Lactuca sativa</i> L. genotypes collected in Vietnam were evaluated using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) molecular markers. <b>Results:</b> In this study, 42 RAPD and ISSR primers were initially used, of which 12 and 9 primers, respectively were finally selected as they produced scorable patterns. RAPD markers produced a total of 113 loci, out of which 52 loci (45.96%) were polymorphic. The average percentage of the polymorphic band for RAPD primer is 45.96% and the genetic similarity based on simple matching coefficient ranged from 69.0-94.7%. ISSR analysis detected a total of 60 loci, out of which 22 loci (36.32%) were polymorphic and the genetic similarity ranged from 56.7-95.0%. In general, ISSR markers amplified fewer loci and showed lower variation in the percentage of polymorphism compares to the RAPD assay. <b>Conclusion:</b> These results indicate that the 16 collected Indian lettuce genotypes are genetically diverse. Because of these genetic diversities, the collected genotypes could be used for preserving or crossing programs to improve this precious medicinal plant in Vietnam.

Genetic diversity and phylogenetic relationship among the western and the Asian honey bees based on two mitochondrial gene segments (COI and ND5)

The Asian honey bee species i.e., Apis cerana (the eastern honey bee), A. dorsata (the giant honey bee), and the western or European honey bee (A. mellifera) collected from Pakistan were studied using partial sequences from two mitochondrial genes (i) the Cytochrome c oxidase I (COI) and (ii) the mitochondrially encoded NADH dehydrogenase 5 (ND5) and then compared with other honey bees sequences (already submitted from different countries around the globe) obtained after the national center for biotechnology information (NCBI). DNA sequences were analyzed employing molecular evolutionary genetics analysis and Kimura 2-parameter model, neighbor-joining method was applied to investigate phylogenetic relationships, and DNA sequence polymorphism was applied to measure the genetic diversity within the genus Apis. The phylogenetic analyses yielded consistent results. Based on COI gene fragment in two Asian and European honey bee species from Pakistan and from other countries showed considerable genetic diversity levels and deviation among the species. While in contrast the phylogenetic analyses based on ND5 gene fragment in Asian and European honey bee species from Pakistan and other countries showed comparatively higher genetic diversity indices and variations than the COI gene. So, in the genus Apis, the mitochondrial ND5 region has shown the possibility to answer the interactions among species. A further detailed work (by linking the analysis of other genomic and mitochondrial genes) is required for good quality solution to establish the concise genetic diversity and interaction among the Apis species. The objective of this study was to explore the extent of genetic differences and phylogenetic links among the three kinds of honey bee species from Pakistan and comparing them with other bee species around the globe.

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.

Screening of Olive Biodiversity Defines Genotypes Potentially Resistant to Xylella fastidiosa

The recent outbreak of the Olive Quick Decline Syndrome (OQDS), caused by Xylella fastidiosa subsp. pauca (Xf), is dramatically altering ecosystem services in the peninsula of Salento (Apulia Region, southeastern Italy). Here we report the accomplishment of several exploratory missions in the Salento area, resulting in the identification of thirty paucisymptomatic or asymptomatic plants in olive orchards severely affected by the OQDS. The genetic profiles of such putatively resistant plants (PRPs), assessed by a selection of ten simple sequence repeat (SSR) markers, were compared with those of 141 Mediterranean cultivars. Most (23) PRPs formed a genetic cluster (K1) with 22 Italian cultivars, including 'Leccino' and 'FS17', previously reported as resistant to Xf. The remaining PRPs displayed relatedness with genetically differentiated germplasm, including a cluster of Tunisian cultivars. Markedly lower colonization levels were observed in PRPs of the cluster K1 with respect to control plants. Field evaluation of four cultivars related to PRPs allowed the definition of partial resistance in the genotypes 'Frantoio' and 'Nocellara Messinese'. Some of the PRPs identified in this study might be exploited in cultivation, or as parental clones of breeding programs. In addition, our results indicate the possibility to characterize resistance to Xf in cultivars genetically related to PRPs.

Molecular characterization of India Ginseng Withania somnifera (L) using ISSR markers

BACKGROUND

Ashwagandha (Withania somnifera (L.) Dunal), popularly known as Indian ginseng or winter cherry is a multipurpose plant of immense therapeutic value in the ayurvedic and indigenous medicine system and distributed in wide geographic locations and exhibiting extensive phenotypic and chemical variability.

METHODS AND RESULTS

The present study was carried out to assess the molecular genetic diversity among 4 CIMAP varieties and five local cultivars of ashwagandha and cluster dendrograms were created by using 20 ISSR primers. A total of 224 bands of varied length were produced, out of which 193 (86.1%) products were polymorphic and 31 (13.8%) products were monomorphic. Where each ISSR arbitrary primer had 5-16 valuable bands with an average of 11.2 bands per primer, of which 86.16% bands were polymorphic. The PIC values ranged from 0.16 to 0.36 with an average PIC value of 0.29 and RP values ranged from 2.22 to 7.99. The UPGMA cluster analysis of 20 ISSR primers grouped the nine accessions into 2 major clusters. The first and second major cluster consists of seven and two accessions respectively.

CONCLUSION

Therefore, this study provides evidence that ISSR based molecular diversity assessment can be used as an efficient tool for detecting similarity and phylogenetic relationships among genotypes of Withania somnifera collected from different geographical locations. This information can be used to improve root and other characteristics of ashwagandha genotypes and there is also scope for the development of high-yielding varieties by selecting diverse parents for crossing (based on the molecular diversity) from the present accessions.

Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo

The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.

QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan

Background

The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth.

Methods

In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method.

Results

In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

Background

Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes.

Results

We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies.

Conclusions

This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.

Genetically 'pure' Fasciola gigantica discovered in Algeria: DNA multimarker characterization, trans-Saharan introduction from a Sahel origin and spreading risk into north-western Maghreb countries

Fascioliasis is a freshwater snail-borne zoonotic helminth disease caused by two species of trematodes: Fasciola hepatica of almost worldwide distribution and the more pathogenic F. gigantica restricted to parts of Asia and most of Africa. Of high pathological impact in ruminants, it underlies large livestock husbandry losses. Fascioliasis is moreover of high public health importance and accordingly included within the main neglected tropical diseases by WHO. Additionally, this is an emerging disease due to influences of climate and global changes. In Africa, F. gigantica is distributed throughout almost the whole continent except in the north-western Maghreb countries of Morocco, Algeria and Tunisia where only F. hepatica is present. The present study concerns the DNA multimarker characterization of the first finding of F. gigantica in sheep in Algeria by the complete sequences of rDNA ITS-1 and ITS-2 and mtDNA cox1 and nad1 genes. Sequence comparisons and network analyses show sequence identities and similarities suggesting a south-north trans-Saharan geographical origin, with introduction from Ghana, through the Sahel countries of Burkina Faso and Mali into Algeria. This way perfectly fits with nomadic pastoralism according to interconnecting intranational and transborder herd transhumance routes traditionally followed in this western part of Africa from very long ago. The risk for further spread throughout the three north-western Maghreb countries is multidisciplinarily analysed, mainly considering the present extensive motorization of the intranational transhumance system in Algeria, the lymnaeid snail vector species present throughout the north-western Maghreb, the increasing demand for animal products in the growing cities of northern Algeria and the continued human infection reports. Control measures should assure making anti-fasciolid drugs available and affordable for herders from the beginning and along their transhumant routes and include diffusion and rules within the regional regulatory framework about the need for herd treatments.

Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species

Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.

Development and Validation of a Real-Time PCR Based Assay to Detect Adulteration with Corn in Commercial Turmeric Powder Products

Turmeric, or Curcuma longa, is commonly consumed in the South East Asian countries as a medical product and as food due to its therapeutic properties. However, with increasing demand for turmeric powder, adulterated turmeric powders mixed with other cheap starch powders, such as from corn or cassava, are being distributed by food suppliers for economic benefit. Here, we developed molecular markers using quantitative real-time PCR to identify adulteration in commercial turmeric powder products. Chloroplast genes, such as matK, atpF, and ycf2, were used to design species-specific primers for C. longa and Zea mays. Of the six primer pairs designed and tested, the correlation coefficients (R²) were higher than 0.99 and slopes were -3.136 to -3.498. The efficiency of the primers was between 93.14 and 108.4%. The specificity of the primers was confirmed with ten other species, which could be intentionally added to C. longa powders or used as ingredients in complex turmeric foods. In total, 20 blind samples and 10 commercial C. longa food products were tested with the designed primer sets to demonstrate the effectiveness of this approach to detect the addition of Z. mays products in turmeric powders. Taken together, the real-time PCR assay developed here has the potential to contribute to food safety and the protection of consumer's rights.

Resilience Effects of SGK1 and TAP1 DNA Markers during PRRSV Outbreaks in Reproductive Sows

The porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious stressor that causes serious health problems and productivity drops. Based on previous genome-wide analyses, we selected SGK1 and TAP1 as candidate genes for resilience, and genotyped three mutations, including a 3'UTR variant SGK1_rs338508371 and two synonymous variants TAP1_rs1109026889 and TAP1_rs80928141 in 305 Landrace × Large White sows. All polymorphisms affected the reproductive performance in the outbreak, but not during the endemic phase, thereby indicating a potential use of these markers for resilience. Moreover, some genotypes were associated with a stable performance across PRRSV phases. Thus, in the outbreak, the SGK1_rs338508371 AA sows had less piglets born alive (p < 0.0001) and more stillborns (p < 0.05) while other sows were able to keep their productivity. During the outbreak, TAP1_rs80928141 GG sows had less piglets born alive (p < 0.05) and both TAP1 polymorphisms influenced the number of mummies in an additive manner (p < 0.05). Remarkably, TAP1_rs80928141 AA sows had around one mummy more than GG sows (p < 0.01). Resilience to PRRSV could be improved by including the SGK1 and TAP1 markers in crossbreeding and/or selection schemes, as they contribute to maintaining a stable number of piglets born alive and lost, particularly mummies, despite the outbreak.

Genetic diversity and interrelationship among Indian and exotic melons based on fruit morphology, quality components and microsatellite markers

Seventy melon (Cucumis melo L.) accessions comprising of landraces, inbred lines, cultivars, wild relatives and exotic populations were characterized using fifteen fruit traits and 30 SSR markers. Overall, aim of this study was to investigate the genetic relatedness across origins, horticultural groups and accession categories. Significant differences were observed for days to first fruit maturity, fruit weight, fruits per vine, yield per plant, flesh thickness, fruit shape index, total soluble solids, β-carotene, ascorbic acid and titrable acidity. Twenty-four polymorphic SSRs detected 67 distinct alleles with moderate polymorphic information content (0.43) and genetic diversity (0.44). Observed heterozygosity (0.53) was higher than expected heterozygosity (0.48) which can be attributed to out-cross nature of melons. Neighbor joining tree based on SSRs diverged 70 accessions into six clusters independent of geographic sites of collections. Momordica and inodorus accessions formed distinct clusters, with some exceptions. Intermixing of landraces, modern cultivars and exotic accessions belonging to different taxa and geographic regions indicated genetic resemblance with each other. Hybridization among exotic and indigenous genetic resources can be utilized for genetic enhancement and introgression of new traits in modern melon cultivars.

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.

Insights into genetic diversity and population structure of Indian carrot (Daucus carota L.) accessions

Carrot (Daucus carota L.) is acknowledged as a highly valuable vegetable crop. Despite having high demand, limited breeding efforts have been made to develop the varieties and hybrids suitable to wider climatic conditions due to improper characterization of the available germplasm. An accession panel (AP) consisting of 144 accessions of five different root colors representing Asiatic and Western gene pools collected from different parts of India was utilized in the present study. This diverse AP was used to assess the population structure and genetic diversity from 80 polymorphic DNA markers distributed throughout the genome. Population structure, neighbor-joining (NJ) tree, and principal coordinate analysis (PCoA)-based diversity assessment divided the AP into three subpopulations/clusters. Greater than ninety percent polymorphism and the higher average polymorphic information content (͂> 0.50) coupled with higher gene diversity (He) indicating the broad genetic base of the population. Moderate to high F_st and gene flow (Nm) between the subpopulations revealed a moderate genetic differentiation among Indian carrot accessions owing to the highly outcrossing nature of carrot. Analysis of molecular variance (AMOVA) exhibited higher variation among individuals within the subpopulations (69.00%) or total populations (19.00%) than among the subpopulations (13%) as expected in the single Daucus species used here. The information obtained in the study would benefit the carrot breeders to explore the genetic diversity of the Indian carrots in the carrot breeding program for widening the genetic base and multi-color target trait improvement.

[Molecular markers in the genetic diversity studies of representatives of the genus Rubus L. and prospects of their application in breeding]

Род Rubus L. (семейство Rosaceae Juss.), по оценкам разных систематиков, состоит из 12–16 подродов, объединяющих ~750 видов. Самые крупные по числу видов подроды – Idaeobatus (Focke) Focke, к которому относятся малины, и типовой подрод Rubus (=Eubatus Focke), включающий виды ежевик. Представители рода Rubus обладают высокой пищевой и хозяйственной ценностью, а также лекарственными свойствами. Селекционные исследования направлены на расширение генетического разнообразия и создание новых сортов малин и ежевик, устойчивых к биотическим и абиотическим стрессорам и отличающихся высоким качеством плодов. Современные селекционно-генетические программы все шире включают достижения молекулярной генетики и геномики. В данной статье представлен обзор фундаментальных и прикладных исследований генетического разнообразия культивируемых и дикорастущих видов рода Rubus, выполненных на основе методов молекулярного маркирования. Рассмотрены основные типы молекулярных маркеров (RFLP, RAPD, SSR, ISSR, AFLP, SCAR, SSCP, ретротранспозонные маркеры и т. д.) и области их применения в изучении представителей рода Rubus. Приведены результаты работ по использованию методов ДНК-маркирования для решения самых разных задач, включая: исследование межвидового и внутривидового генетического разнообразия, филогенетических связей видов и надвидовых таксонов, выяснение спорных вопросов систематики, генотипирование и уточнение родословных сортов малин и ежевик, изучение сомаклональной изменчивости и др. Наиболее важным результатом в практическом плане является создание насыщенных молекулярно-генетических карт для разных видов малин и ежевик, на которых локализованы многочисленные гены и QTL, детерминирующие различные хозяйственно ценные признаки. В то же время необходимо отметить, что число маркеров, перспективных для проведения эффективного молекулярного скрининга, пока еще недостаточно.

Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis

Conventional genetic improvement of disease resistance in aquatic animal species involves challenge tests or using qPCR to quantify viral load that is costly, time-consuming and causing biosecurity concerns. Recent developments in high throughput next generation genome sequencing platforms such as genotyping by sequencing (GBS) have opened new possibilities for improving disease traits based on DNA information. The principal aim of this study was thus to examine potential application of genomic selection to improve resistance to hepatopancreatic parvovirus (HPV) in banana shrimp Fenneropenaeus merguiensis. Specifically, we used a total of 9472 single nucleotide polymorphisms (SNPs) developed de novo from GBS platforms to assess accuracy of genomic prediction for HPV resistance and growth, carcass and quality-related traits in this white shrimp species. Our multi-locus mixed model analysis showed moderate heritabilities for HPV resistance (h² = 0.46) and other traits studied (0.10 to 0.55). Genetic correlations of HPV titre with growth and carcass traits, estimated using SNPs markers, were negative (i.e., favourable), suggesting that selection for improved growth and carcass traits may have increased HPV resistance (i.e., reduced HPV titre). More importantly, our gBLUP model demonstrated that the accuracy of gBLUP prediction was moderate for HPV disease resistance (0.46). The genomic prediction accuracy was somewhat greater for growth and carcass related traits especially for body weight (0.76) and meat or tail weight (0.77). On the other hand, the prediction accuracy was from 0.25 to 0.41 for quality traits (raw and cooked colour and flesh streaks). Collectively, it is concluded that there are prospects to apply genomic selection in the genetic improvement for increased disease resistance, carcass and quality-related traits in this population of banana shrimp F. merguiensis.

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR

Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R² > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.

Alterations to DNA structure as a cause of expression modifications of selected genes of known intrauterine-growth-restriction-association shared by chosen species - a review

The review aimed at searching for DNA structure markers of epigenetic modifications leading to intrauterine growth restriction (IUGR) in three livestock species, mouse and human. IUGR affects mammals by harming their wellbeing and the profitability of breeding enterprises. Of the livestock species, we chose cow, pig and sheep owing to there being many reports on the epigenetics of IUGR. IUGR investigations in human and mouse are particularly numerous, as we are interested in our own wellbeing and the mouse is a model species. We decided to focus on five genes (Igf2r, Igf2, H19, Peg3 and Mest) of known IUGR association, reported in all of those species. Despite the abundance of papers on IUGR, naturally occurring mutations responsible for epigenetic modifications have been described only in human and cow. The effect of induced DNA structural modifications upon epigenetics has been described in mouse and pig. One paper regarding mouse was chosen from among those describing DNA modifications performed to obtain parthenogenetic progeny. Papers regarding pig parthenogenetic progeny described the epigenetics of genes involved in foetal development, with no interference with the genome structure. No reports on DNA modifications altering IUGR epigenetics in sheep were found. Only environmental effects were studied and we could not conclude from the experiment designs whether the gene setup could affect the expression of involved genes, as different populations were not included or not specified within particular experiments. Apparently, DNA markers of IUGR epigenetics exist. It has been reported that the small number of them, occurring naturally, may result from neglecting existing evidence of such selection or health status forecasting markers.

Genetic Markers Associated with Field PRRSV-Induced Abortion Rates

In gilts and sows, the more severe clinical manifestation of porcine reproductive and respiratory syndrome virus (PRRSV) occurs in late gestation and can result in up to a 40% abortion incidence. Despite the known genetic component in resilience to PRRSV, there is scarce information regarding the abortive outcome of this disease. We tested the relationship between eight molecular markers (six from published studies and two identified in the present study in the HDAC6 gene) and the probability of abortion during a PRRSV outbreak, using data from two commercial Landrace x Large White sow farms with an incidence of abortion of 35% and 17%. From the markers tested, USP18_-1533G>A did not segregate in these populations, and CD163_c.3534C>T and HDAC6_g.2360C>T did not affect the abortion rate. In contrast, the minor allele of two markers in SSC4 (WUR1000125 in GBP1 and rs340943904 in GBP5), which lower viremia in growing pigs, and the major alleles of CD163_rs1107556229 and HDAC6_rs325981825 were associated with a lower probability of abortion during PRRSV outbreaks. The more striking result was for the MX1 gene, where the odds ratio of aborting versus not aborting was nine times lower in the sows homozygous for a 275-bp insertion than in the other genotypes. Interactions between markers were not relevant. All together, we bring here the first evidence that mutations in the host genome can predispose or protect from complete reproductive failure in sows infected with PRRSV.

Description of larva and pupa of Laenahaigouica (Tenebrionidae, Laenini) from China based on morphology and four DNA makers

The larvae, pupae, and adults of Laenahaigouica Schawaller, 2001 were collected during recent fieldwork in the Sichuan Province (China). Since the pupal morphology of Laena has never been investigated this created an opportunity to provide the first description. Moreover, prior to this study larval characters of only one species, Laenastarcki Reitter, 1887, were known. Therefore, description of the larva of L.haigouica enabled the first verification of the intrageneric stability of larval characters revealed for other Laena species. Association of the studied immature stages with the adults was confirmed by analysing COI sequences. Additionally, three other loci (16S, Cytb, 28S) were sequenced for L.haigouica during this study.

Development and evaluation of taxon-specific primers for the selected Caudovirales taxa

The phage taxonomy is primarily based on the morphology derived from Transmission Electron Microscopic (TEM) studies. TEM based characterization is authentic and accepted by scientific community. However, TEM based identification is expensive and time consuming. After the phage isolation, before analysis TEM, a DNA based rapid method could be introduced. The DNA based method could dramatically reduce the number of samples analyzed by TEM and thereby increase the speed and reduce the cost of identification. In the present work, four environmental phage isolates were identified based on TEM studies and genome size. The identification of these four phages was validated using DNA based method. The taxon-specific DNA markers were identified through multiple sequence alignments. The primers were designed at conserved genes (DNA polymerase or integrase) of 4 different phage taxa viz. family Ackermannviridae, genus Jerseyvirus, genus T4virus, and genus P22virus. These primers were evaluated using both in vitro and in silico approach for the amplification of the target taxons. Majority of the primer sets were found to amplify member species of the targeted taxa in vitro. In In silico analysis, six primer sets intended for identification of family Ackermannviridae showed positive amplification of ≥86.7% classified species. Further, the primers targeting the genus Jerseyvirus and T4virus showed the amplification of 53.8% and ≥84.6% species, respectively. The present work is a case study performed to explore the possibility of use of taxon-specific primers for identification and taxonomic studies of newly isolated phages to supplement the TEM.

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

BACKGROUND

Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited.

RESULTS

To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii.

CONCLUSIONS

The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata.

DNA markers for tuberculosis diagnosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.

Easy strategy used to detect the genetic variability in chickpea (Cicer arietinum L.)

A priority in the management and use of elite plant materials for breeding has been based on molecular markers or DNA sequencing of entire genomes, in order to perform genetic differentiation which is still quite costly. Chickpea (Cicer arietinum) is one of the species with genomic monotony and very low polymorphism, and its detection even with DNA markers has not been easy. In germplasm banks, the genetic distinction is a priority in order to use properly selected lines. In this study, 57 chickpea accessions from a germplasm bank were analyzed by using nrRAMP (non-radioactive Random Amplified Microsatellite Polymorphism) markers, and their genetic variability was determined. Our results showed DNA polymorphisms, which are enough to differentiate between the accessions and between C. arietinum and Cicer reticulatum (out-group); this last wild species is closely related to chickpea. We concluded that the nrRAMP technique was an effective and a highly useful method to assess the genetic diversity and variability among closely related plants, such as chickpea; in addition, this technique can be easily implemented in laboratories.

Molecular biomarkers for prognosis of gastrointestinal stromal tumor

Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. However, the development of molecular markers, especially circulating biomarkers, remains largely undone for the prognosis of GIST. We discussed the clinical-pathological characteristics of GIST and identified potential biomarkers for guidance of therapy and prognosis of GIST. Around 90% of GISTs contain mutations in KIT or PDGFRA and the remaining 10% of GISTs are wild-type. Recent studies have indicated that various DNAs and miRNAs could serve as potential biomarkers for prognosis of GIST, including KIT, PDGFRA, other DNAs (such as BRAF, SDH, SETD2 and ROR2), and microRNAs (miRNAs). The pressing need and challenges in the development of circulating prognostic biomarkers for GIST are also discussed. Although challenges remain, DNAs and miRNAs are promising circulating biomarkers for surveillance and prognosis of GIST. Advances in clarification of aberrant molecular alterations may open new avenues for exploration of reliable and robust biomarkers to improve the management of GIST.

Phylogenetic Analysis and Molecular Typing of Trichothecene-Producing Fusarium Fungi from Russian Collections

We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1α) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. A study of 60 strains of different origins using DNA markers confirmed, and in the case for several strains, clarified their taxonomic characteristics. As a result, a strain of F. commune (F-900) was identified in Russia for the first time. Furthermore, the strain F-846 proved to be phylogenetically distinct from any of the known Fusarium species. F. equiseti strains from Northwest Russia were found to belong to the North European group (I), whereas a strain from the North Caucasus - to the South European one (II). Partial TRI14 sequences from 9 out of 12 species were determined for the first time. Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. Specific chemotypes of trichothecene B producers were characterized using two primer sets. The chemotyping results were verified by HPLC.

Multiplex PCR identification and culture-independent quantification of Bacillus licheniformis by qPCR using specific DNA markers

Probiotics benefits in fish farming have been usually inferred appraising the effects observed on the host and not through the direct assessment of probiotic dynamics in the host gut microbiota. To overcome this gap, quantitative PCR (qPCR) can be a powerful approach to study the bacterial dynamics in fish gut microbiota. The presented work proposes four B. licheniformis-specific DNA markers and details a qPCR method to track putative probiotics B. licheniformis on fish gut. The four B. licheniformis-specific DNA markers - BL5B (hypothetical protein BL00303), BL8A (serA2), BL13C (rfaB) and BL18A (ligD) - were selected and validated by PCR and multiplex-PCR with 20 B. licheniformis isolates and a broad range of non-target bacteria. To assess the dynamics of B. licheniformis in the digesta of farmed fish, a qPCR was validated using markers BL8A and BL18A and calibration curves obtained for both markers with digesta samples spiked with B. licheniformis cells showed a high correlation (R² > 0.99) over 6 log units (CFU/reaction), and a limit of detection (LOD) as low as 247 CFUs/reaction. Furthermore, the consistent qPCR repeatability and reproducibility underline the specificity and reliability of the qPCR proposed. Ultimately, the possibility to monitor the dynamics of B. licheniformis probiotics in the gut microbiota of farmed fish might be instrumental to optimize best practices in aquaculture.