DNA Molecular Markers Research Articles

Diversity of Improved Diploids and Commercial Triploids from Musa spp. via Molecular Markers.

Banana breeding consists of obtaining diploid, triploid, and tetraploid intra- and interspecific hybrids by conventional breeding methods with the objective of aggregating characteristics of agronomic and commercial interest. Given the narrow genetic base of bananas, Embrapa's Banana Genetic Breeding Program (BGBP) aims at crosses between improved diploids (ID) (ID × ID) and between improved diploids (ID) and commercial triploids (ID × CTP) and tetraploids (ID × CTT), in order to increase the genetic base and variability in bananas regarding agronomic traits of interest and resistance to main biotic and abiotic factors. These improved diploids are resistant to main fungal diseases such as yellow (YSD) and black Sigatoka (BSD) disease and Fusarium wilt (race 1 and subtropical race 4), the latter being one of the most devastating diseases in bananas. The genetic diversity between 22 improved diploids and seven commercial banana triploids was analyzed using DNA molecular markers. Five IRAP (Inter-Retrotransposon Amplified Polymorphism, 7 ISSR (Inter-Simple Sequence Repeats) and 12 SSR (Simple Sequence Repeat) markers were used. The genetic dissimilarity matrix was based on the Jaccard dissimilarity index; clusters were separated using the UPGMA (Unweighted Pair Group Method With Arithmetic Mean) method and cophenetic correlation of 0.8755. This study of the genetic diversity between improved diploids and commercial triploids, based on the genetic dissimilarity matrix, revealed that the most dissimilar diploids were DM23 and DM15 (74%) and DM16 and DM15 (74%). The smallest genetic distances between the improved diploids and commercial triploids were between TCGN25 and DM17 (50%) and TCN26 and DM17 (50%). The genetic distance matrix also revealed important genotypes to be used in crosses in order to maintain good characteristics in commercial triploids when crossed with improved diploids. The results of our study provide better breeding strategies for one of the largest banana-breeding programs worldwide focused on the development of banana varieties resistant to main biotic and abiotic factors.

Genome Survey of Male Rana dybowskii to Further Understand the Sex Determination Mechanism.

Rana dybowskii is one of the important aquaculture species in Northeast China. The fallopian tubes of female R. dybowskii are used to prepare oviductus ranae (an important traditional Chinese medicine). Therefore, R. dybowskii females have higher economical value than males. An increasing female R. dybowskii population can increase the benefits from R. dybowskii culture. However, the genome of amphibians is complex, making it difficult to investigate their sex determination mechanism. In this study, we analyzed the genome of male R. dybowskii using next-generation sequencing technology. A total of 200,046,452,400 bp of clean data were obtained, and the K-mer analysis indicated that the depth was 50×. The genome size of R. dybowskii was approximately 3585.05 M, with a heterozygosity rate, repeat sequence ratio, and genome GC content of 1.15%, 68.96%, and approximately 43.0%, respectively. In total, 270,785 contigs and 498 scaffolds were generated. The size of the contigs and scaffolds was 3,748,543,415 and 3,765,862,278 bp, respectively, with the N50 length of 31,988 and 336,385,783. The longest contig and scaffold were of the size 137,967,485 and 1,808,367,828 bp, respectively. The number of contigs and scaffolds > 10K nt was 99,620 and 451, respectively. Through annotation, 40,913 genes were obtained, including 156,609 CDS (i.e., 3.83 CDS per gene). Sequence alignment was performed with the assembled scaffolding genome in this study. Two and one fragment had high homology with two male-specific DNA molecular markers of R. dybowskii discovered previously (namely, MSM-222 and MSM-261, respectively). In addition, the Dmrt1 gene of R. dybowskii was obtained with a length of 18,893 bp by comparison and splicing. The forward primers amplifying MSM-222 and MSM-261 were located at 322-343 and 14,501-14,526 bp of Dmrt1, respectively. However, sequence alignment revealed that MSM-222 and MSM-261 were not located on Dmrt1, and only some homologous parts were observed. This indicated that in addition to Dmrt1, other important genes may play a crucial role in the sex determination mechanism of R. dybowskii. Our study provided a foundation for the subsequent high-quality genome construction and provided important genomic resources for future studies on R. dybowskii.

Molecular markers and their importance for pig production and breeding: an overview

The DNA polymorphisms are changes in the sequence of nucleotide bases that result in genetic differences among two or more individuals. These polymorphisms have been used as molecular markers and contribute to studies in swine related to genetic diversity, pedigree analysis, selection, and discovery of genomic regions controlling economically important traits. Among the molecular markers, Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been most studied in pigs mainly due to their greater abundance in the genome, ease of detection and possibility of automation. The knowledge and application of information from molecular marker shave contribute to a more efficient and competitive pig production. Furthermore, in pig breeding programs, the molecular markers are especially important to allow higher efficiency in selection for traits with low heritability, difficult or expensive to measure, sex-limited, and that express later in the animal’s life, resulting in a higher prediction accuracy for these traits. Considering the relevance of DNA molecular markers for the development of pig production and the advances in research in this area, we aimed to present an overview of the main research results related to the discovery, contribution and implementation of molecular markers in pig breeding and production. This review contextualizes and summarizes important results and recent findings in order to update the reader and stimulate future research based on the identification and relevance of molecular markers applied to pig production.

SALINITY, VERTICILLIUM WILT TOLERANCE AND GENETIC DIVERSITY ANALYSIS OF UPLAND COTTON GENOTYPES

Cotton is one of the most economically important crops. Screening and selection salt-tolerant cotton genotypes using DNA molecular markers not only introduces tolerant cultivars valuable for hybridization and breeding programs, but also identifies DNA regions implicated in the salinity tolerance mechanism. Screening and selection of cotton genotypes resistant to salinity stress and Verticillium wilt disease using DNA molecular markers not only introduces tolerant cultivars valuable for hybridization and breeding programs, but also identifies DNA regions implicated in the tolerance mechanism. The lowest Disease Severity Index was recorded in AP-317 (0.37) and Tashkent-2 (0.32) varieties. A total of 63 bands were generated based on 12 ISSR primers, 50 of which were polymorphic. The highest PIC value was recorded for UBC841 (0.466). AP-317 of Azerbaijan origin and Kirqizistan-174 of Kyrgyzstan origin were the most distant (0.358) genotypes and at the same time showed high resistance to Verticillium wilt. The obtained results showed that ISSR markers were an effective tool for determining genetic variation and identification of cotton cultivars.

Allelic differences in the key genes of betalain biosynthesis in table beet accessions with contrasting root color from the VIR collection

Background. Table beet (Beta vulgaris L.) contains a great amount of naturally red-colored betanins. A number of enterprises are forced to import foreign dyes because the reserves of domestic plant raw materials are insufficient. With this in view, the development of cultivars with high betalain pigment content is now required.Materials and methods. Allelic differences were screened in the key genes of the betalain biosynthesis pathway among table beet accessions with various root color from the VIR collection using the Sanger DNA sequencing method.Results and discussion. For the first time we identified a nonsense mutation in the CYP76AD1 gene in cv. ‘Serdolik’ with yellow flesh; it led to the truncation of the functional P450 domain. We suggested that the detected polymorphism correlated with phenotypic switching because the well-known role of CYP76AD1 was essential for the red betalain accumulation. Moreover, a number of missense mutations in cv. ‘Avalanche’ in the first exon of the BvDODA1 gene were found. These mutations were probably associated with the expression of the uncolored phenotype. An in silico analysis revealed highly homologous copies of CYP76AD5, located tandemly on chromosome 9. Attention should be paid to these copies, together with the CYP76AD6 gene, as they seem the most preferable targets for a knockout to increase the red pigment content.Conclusion. It is possible to identify the best table beet accessions for further genome editing among a previously selected high-betanin group. In addition, this study revealed the allelic differences in the key genes of the betalain biosynthesis pathway. These results will be useful for the development of DNA molecular markers to facilitate the selection of table beet forms with required properties.

Analysis of Fennel Breeding Populations Based on Distinctness, Uniformity, and Stability (DUS) Testing via Morphological Descriptors and DNA Molecular Markers

AbstractA bred plant variety is a valuable tool for enhancing crop production and total yield. Recently, our breeding team developed three high seed yielding synthetic cultivars of bitter fennel. To characterize these newly breeding populations and differentiate them from each other and their parental populations, we conducted a Distinctness, Uniformity, and Stability (DUS) assessment using morphological traits evaluated over two consecutive years, as well as 20 Start Codon Targeted (SCoT) markers. The evaluation of morphological traits revealed that, five of qualitative traits exhibited monomorphism, while two other qualitative traits displayed polymorphism. Additionally, the investigation of eight quantitative traits showcased significant diversity. The Combined Over Years Distinctiveness analysis at a 1% significance level, based on eight quantitative characteristics, indicated distinctiveness for two breeding populations, namely Early and Medium Maturity Synthetic cultivars, compared to other populations. The Combined Over Years Uniformity analysis identified that all of the breeding populations and their parental populations were uniform in terms of the measured traits. The differences between Phenotypic Coefficients of Variation and Genotypic Coefficients of Variation were not particularly noticeable in the experimental material used currently. The majority of the measured traits showed high heritability, highlighting their stability over time. PCA utilized for quantitative morphological features, the first two principal components collectively accounted for more than 86.8% of the phenotypic variation. Subsequently, a dendrogram was constructed, which clustered breeding and parental populations into three distinct groups. The 15 SCoT markers produced a total of 164 extended fragments, with 139 (85%) of them showed polymorphic.The genetic similarity between the populations exhibited a range of 0.08–0.81, and cluster analysis utilizing Jaccard similarity coefficients and the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) technique revealed clear distinctions among the three breeding populations and their parental populations. Altogether, the findings indicate that morphological DUS descriptors effectively distinguish some the populations, while others with overlapping expressions cannot be discriminated. Notably, SCoT markers demonstrate a fine ability to detect distinctions among fennel populations, suggesting the possibility of utilizing them as a complement to morphological traits in the DUS test. As a conclusion, these three newly breeding populations of fennel are distinct from each other and from their parental populations, and they can advance for registration and seed purity testing.

Randomly Amplified Polymorphic DNA (RAPD) Molecular Markers as a Valuable Tool to Confirm the Genetic Diversity in Soybean Germplasms (Glycine max)

Randomly Amplified Polymorphic DNA (RAPD) Molecular Markers as a Valuable Tool to Confirm the Genetic Diversity in Soybean Germplasms (Glycine max)

An efficient in vitro organogenesis protocol for the endangered relic tree species Bretschneidera sinensis and genetic fidelity assessment using DNA markers.

Bretschneidera sinensis is a monotypic species of rare and tertiary relic trees mainly distributed in China. B. sinensis is a potentially valuable horticultural plant, which has significant ornamental and research value, and is a crucial tool for the study of phylogeography. The artificial cultivation of B. sinensis is of great scientific value and practical significance. In this study, we developed a direct organogenesis process of B. sinensis using mature zygotic embryos as initial materials. The highest sterile germination induction (54.5%) from the mature zygotic embryo was obtained in a Murashige and Skoog (MS) medium with 2.0 mg·L-1 6-benzylaminopurine (6-BA) and 0.2 mg·L-1 α-naphthaleneacetic acid (NAA). The highest percentage of shoot regeneration (90.37%) was attained using 1.0 mg·L-1 6-BA and 0.01 mg·L-1 NAA in the MS medium. The Woody Plant Medium (WPM) had the greatest adventitious shoot elongation rate of 93.33%. The most optimized rooting rate was 88.89% in a half-strength MS medium containing 2.0 mg·L-1 indole-3-butyric acid (IBA) and 1.0 mg·L-1 NAA. The genetic fidelity of in vitro regenerated plantlets was assessed using inter-simple sequence repeats and random amplified polymorphic DNA molecular markers, confirming the genetic uniformity and stability of regenerated B. sinensis plantlets. Our research presents an effective in vitro propagation system for B. sinensis, laying the groundwork for its germplasm conservation and large-scale production while maintaining high genetic integrity.

Next-Generation Multitarget Stool DNA Test for Colorectal Cancer Screening

BackgroundA next-generation multitarget stool DNA test, including assessments of DNA molecular markers and hemoglobin level, was developed to improve the performance of colorectal cancer screening, primarily with regard to specificity.MethodsIn a prospective study, we evaluated a next-generation multitarget stool DNA test in asymptomatic adults 40 years of age or older who were undergoing screening colonoscopy. The primary outcomes were sensitivity of the test for colorectal cancer and specificity for advanced neoplasia (colorectal cancer or advanced precancerous lesions). Advanced precancerous lesions included one or more adenomas or sessile serrated lesions measuring at least 1 cm in the longest dimension, lesions with villous histologic features, and high-grade dysplasia. Secondary objectives included the quantification of sensitivity for advanced precancerous lesions and specificity for nonneoplastic findings or negative colonoscopy and comparison of sensitivities for colorectal cancer and advanced precancerous lesions between the multitarget stool DNA test and a commercially available fecal immunochemical test (FIT).ResultsOf 20,176 participants, 98 had colorectal cancer, 2144 had advanced precancerous lesions, 6973 had nonadvanced adenomas, and 10,961 had nonneoplastic findings or negative colonoscopy. With the next-generation test, sensitivity for colorectal cancer was 93.9% (95% confidence interval [CI], 87.1 to 97.7), and specificity for advanced neoplasia was 90.6% (95% CI, 90.1 to 91.0). Sensitivity for advanced precancerous lesions was 43.4% (95% CI, 41.3 to 45.6), and specificity for nonneoplastic findings or negative colonoscopy was 92.7% (95% CI, 92.2 to 93.1). With the FIT, sensitivity was 67.3% (95% CI, 57.1 to 76.5) for colorectal cancer and 23.3% (95% CI, 21.5 to 25.2) for advanced precancerous lesions; specificity was 94.8% (95% CI, 94.4 to 95.1) for advanced neoplasia and 95.7% (95% CI, 95.3 to 96.1) for nonneoplastic findings or negative colonoscopy. As compared with FIT, the next-generation test had superior sensitivity for colorectal cancer (P<0.001) and for advanced precancerous lesions (P<0.001) but had lower specificity for advanced neoplasia (P<0.001). No adverse events occurred.ConclusionsThe next-generation multitarget stool DNA test showed higher sensitivity for colorectal cancer and advanced precancerous lesions than FIT but also showed lower specificity. (Funded by Exact Sciences; BLUE-C ClinicalTrials.gov number, NCT04144738.)

Identification, comparative and phylogenetic analysis of eight Vitis species based on the chloroplast genome revealed their contribution to heat tolerance in grapevines

The chloroplast genome plays an important role in exploring the origin and evolution of grapes. In this study, the chloroplast genomes of eight grape germplasms were analyzed. The results show that the sequence arrangement was highly conserved and has a typical annular quadripartite structure. At the same time, GC content, gene sequence, repeat type and codon bias pattern are highly conserved. Whereas, 19 mutation hotspot regions were identified by the comparative analysis, including 9 protein-coding genes (atpF, rpoC2, rps18, psbC, atpB, rbcL, rps20, ycf1 and ycf15) and 10 non-coding regions (trnK – rps16, rps16 – trnQ, trnE – trnT, psbZ - trnG, ndhC – trnV, accD – psaI, ycf2 – trnL, ndhF – rpl32, ccsA - ndhD, trnL - ycf2). Most of these highly variable genes were involved in the physiological process of photosynthesis. Further examination of photosynthetic fluorescence showed an obvious difference among those species under high-temperature conditions. In addition, maximum likelihood (ML) evolutionary trees depend on the chloroplast genome and CDS sequences suggest that heat tolerance may be related to the phylogeny of grapevine. In the future, the highly variable sequences and SSR loci were also identified by the chloroplast genome comparison, and those results may be used for the DNA molecular marker in taxonomic studies and contribute to the heat stress resistance breeding of grapevine.

Screening of among seventeen sunflowers (Helianthus annuus L.) genotypes for oil content and the first flowering day using random amplified polymorphic DNA markers

Background Sunflower refers to the tribe Helianthus, subtribe Helianthinae, and family Asteraceae, which collectively contains 20 genera and 400 species. An important oilseed crop that yields edible oil is Helianthus annuus L. Objective The primary goal of the current study was to assess the genetic diversity of 17 genotypes of sunflower (Helianthus annuus L) To measure the oil content during the initial flowering period and to reach the highest percentage of oil can be obtained from the first flowering day. Materials and methods Five RAPD (random amplified polymorphic DNA) primers were used to detect the genetic diversity of the 17 sunflower hybrid genotypes obtained from Spain. Phylogenetic relationships of 17 sunflower genotypes were determined using three replications and 6 m lines on August 15, 2019, at the National Research Centre farm in Nubaria as part of a donation from the German corporation (strobe), Spain. To analyze the genetic diversity and phylogenetic linkages in sunflower germplasm, DNA fingerprinting and the Random Amplified Polymorphic DNA (RAPD) molecular marker approach were also used. Results and conclusion The oil content of 17 sunflower genotypes (Helianthus annuus L.) was assessed, with values ranging from 46 to 50%, with the highest values falling into five genotypes. However, the two genotypes were found to have the lowest oil percentage (46%). The early age and oil percentage differed among the varieties. In the Tornado and Elves genotypes, the longest and shortest days were 59 and 47, respectively. The means and standard errors for all statistical data are reported. Statistical significance was evaluated using the LSD. P values were considered statistically significant at P less than or equal to 0.05. According to the findings, RAPD primers generated 49 bands with a size range of 0.1–3 kb and an 87.75% polymorphism percentage. For RAPD, 43 polymorphic bands with distinct bands were observed. Morphological features and RAPD analysis separated the UPGMA Dendrogram into three groups. Jaccard’s coefficient was used to analyze the genetic similarity matrix, and a morphological study revealed that Tornado and Elvas, both from Spain, shared the most genetic similarity (0.970). RAPD analysis and morphological features are useful in identifying genetic variants. Conclusion, according to our findings, Helianthus annuus L. has a significant variation ratio. Indicating substantial diversity across the 17 sunflower genotypes, the genetic similarity index calculated using pooled data from RAPD markers showed an extensive range from 0.645 to 0.986. This study may be a reference for future research on Helianthus annuus L. and may support breeding initiatives and species concepts.

Determination of TYLCV-Resistant Cherry and Cocktail Tomato Cultivars by Molecular Markers

ABSTRACT In this study, resistant cultivars to Tomato yellow leaf curly virus (TYLCV) of different cherry and cocktail tomato cultivars were determined using molecular DNA markers. For this purpose, resistance to Tomato Yellow Leaf Curly Virus (TYLCV) of a total of 409 different cherry and cocktail tomato cultivars was determined by polymerase chain reaction (PCR) using the primer Ty3P6-25. As a result of the assays, 291 cherry and cocktail tomato cultivars were found to be susceptible (rr), 66 cultivars were heterozygous resistant (Rr), and 45 cultivars were homozygous resistant (RR) to TYLCV. In addition, no molecular markers were detected in 7 cherry and cocktail tomato cultivars. It was found that the molecular DNA marker used is useful in determining resistance responses to TYLCV in cherry tomato and cocktail tomato and can provide reproducible and reliable results in a short time.

Genetic footprints of Quaternary climatic fluctuations on the endangered Tuco-tuco-das-dunas (Ctenomys flamarioni)

Abstract The biogeographic history of a species results from responses to past and current processes, and understanding those responses at both temporal scales is essential. We explored phylogeographic and current genetic variation structure in Ctenomys flamarioni—a subterranean rodent that inhabits a small region of the coastal plain of Brazil—and contrasted the roles of “present-day niche suitability” versus “historical climate stability” to understand current and past intraspecific genetic diversity. We used both mitochondrial DNA sequences (concatenated Cytb and D-loop, n = 78) and nuclear DNA (9 microsatellites loci, n = 154) molecular markers for individuals across the entire distribution of the species. We used phylogeographic trees, Bayesian clustering, and haplotype networks to explore genetic variation and diversity. We correlated genetic diversity with measures of current niche suitability and potential areas of Late Quaternary paleostability. Phylogeographic patterns confirmed low levels of genetic diversity structured at different hierarchical levels. We also found a weak but significant pattern of isolation by distance, indicating that geographical distance partially modulates genetic differences among populations. We also observed a positive correlation between genetic diversity and climate paleostability for microsatellites at local and regional scales. However, we found no significant association between genetic diversity and niche suitability for microsatellites at local or regional scales. We observed several signatures of bottleneck and population expansion at different geographic scales. Our results suggest that Quaternary climatic fluctuations—acting together with habitat suitability and other contemporary factors—played a fundamental role in elucidating the evolutionary history of the species—including patterns of historical dispersal, and current patterns of habitat occupation and genetic structure. In addition, based on our molecular and environmental data sets from the across the range of the species and considering the restricted endemism of C. flamarioni, we emphasize the urgency of conservation actions to protect this endangered species.

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

Barcoding a glass eel migration: a snapshot of taxa migrating upstream in the Palu River, Central Sulawesi, Indonesia

Eels of the genus Anguilla are high value food fish with a catadromous life cycle. As tropical anguillid glass eels migrate to freshwater in multi-species schools, effective management of these and other diadromous resources requires reliable data. Previous research using two morphological methods concluded that between three and five anguillid eels recruit to the Palu River in Central Sulawesi, Indonesia with interannual and seasonal variations in species composition, size structure, and co-migrating taxa. Some glass eels and other taxa could not be identified based on external morphology. To clarify the taxonomic uncertainty regarding species recruiting to the Palu River this study applied DNA barcoding using the Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) molecular marker. Taxa identified from the first sampling of glass eels and other taxa recruiting in these mixed schools included three anguillid eels, five other fishes, two crustacea and one mollusc, presenting a snapshot of taxa migrating upstream in the Palu River. Current GenBank accessions did not enable species level identification of two fish larvae (families Eleotridae and Tetraroginae). The sequences will add to Indonesian accessions in the GenBank repository and inform resource management, including the use of environmental DNA (eDNA) methods for monitoring Indonesian anguillid eels.

Assessment of the chemical and genetic variability among accessions of Cicerbita alpina (L.) Wallr., an alpine plant with anthelmintic properties

Cicerbita alpina(L.) Wallr, is a perennial alpine plant and a member of theAsteraceaefamily, typically found at altitudes above 1000 meters in the Italian Alps. Although previously utilized primarily as a local delicacy, recent studies have revealed strong antiparasitic activity throughin vitroexperiments. In Europe, numerous chemical drugs employed to combat nematodes — helminths that infest the digestive tract of livestock — are banned due to their environmental harm or show only reduced efficiency because of the development of resistance. Consequently, there is a growing demand for new alternative anthelmintic treatments in agricultural practices. Specialized metabolites found in the extracts ofC. alpinacould offer a sustainable and biological alternative to chemical drugs, specifically for nematode control. For this purpose, a unique germplasm collection originating from eight distinct natural populations in the Italian Alps was analyzed for its chemical diversity using state-of-the-art targeted LC-MS/MS spectrometry, including quantification based on multiple reaction monitoring. The predominant metabolites identified from the species were the caffeic acid derivatives chicoric acid, chlorogenic acid, and 3. 5-dicaffeoylquinic acid, the sesquiterpene lactone derivative 8-O-acetyl-15-ß-D-glucopyranosyl lactucin and the flavone glycosides, apigenin-7-O-glucoside and luteolin-7-O-glucoside, alongside their precursors apigenin and luteolin, respectively. Additionally, the genetic diversity of eighty individual plants within the germplasm collection was evaluated using ten DNA molecular markers (Simple Sequence Repeats), successfully transferred from two closely related species (Cichorium intybusandTanacetum parthenium). This investigation unveiled a significant range of genetic diversity within the examined populations, resulting in the establishment of three distinct genetic groups. The findings were further correlated with the original ecological environment and local climate conditions spanning a biennial period, indicating substantial variations among the different accessions and the intricate interplay between genetic background and environmental factors. These results could serve as a basis for future domestication of the species through plant breeding programs ensuring product quality, but also facilitating the cultivation ofC. alpinain more diverse geographic regions.

Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding

BackgroundAs an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated.ResultsIn this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results (http://www.sorghum.top:8079/;http://43.154.129.150:8079/;http://47.106.184.91:8079/). Users can query the information of related sites and primer pairs.ConclusionsAnyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.

Simple, fast and inexpensive hot sodium hydroxide and tris DNA extraction method for genotyping tomato and melon seeds.

Seed commerce is a highly profitable global market. Most commercialized seeds are hybrid seeds originating from a controlled cross between two selected parental lines. The market value of hybrid seeds depends on their hybrid genetic purity. DNA molecular markers are a reliable and widespread tool to genotype plant materials; however, DNA extraction from seeds is challenging, often laborious and expensive. With the ultimate goal of creatinga tomato and melon hybrid seeds purity test, various challenges arise. To overcome these problems and with the purpose ofcrude DNA extraction, a simple, fast, inexpensive and easily scalable adaptation of the hot sodium hydroxide and tris method coupled to a competitive allele-specific PCRgenotyping method is proposed.

Variation in habitat use and its consequences for mercury exposure in two Eastern Ontario bat species, Myotis lucifugus and Eptesicus fuscus.

The St. Lawrence River in Eastern Ontario, Canada, has been a designated an area of concern due to past industrial contamination of sediment in some areas and transport of mercury from tributaries. Previous research using bats as sentinel species identified elevated concentrations of total mercury (THg) in fur of local bats and species-specific variation between little brown bats (Myotis lucifugus) and big brown bats (Eptesicus fuscus). Here, we investigated the mercury exposure pathways for these two species by testing the hypothesis that diet variation, particularly the reliance on aquatic over terrestrial insects, is a determinant of local bat mercury concentrations. We analyzed THg concentration and stable isotope ratios of δ15N and δ13C in fur of little and big brown bats, and in aquatic and terrestrial insects. Big brown bats, especially males, accumulated significantly higher THg concentrations in their fur compared to little brown bats. However, this difference was not related to diet because big brown bats consumed terrestrial insects, which were lower in mercury than aquatic insects, the primary prey for little brown bats. We also evaluated whether fur THg concentrations translate into molecular changes in tissues linked to (methyl)mercury toxicity by quantifying tissue changes in global DNA methylation and mitochondrial DNA abundance. No significant changes in DNA molecular markers were observed in relation to fur THg concentration, suggesting mercury exposure to local bats did not impact molecular level changes at the DNA level. Higher mercury in bats was not associated with local aquatic contamination or genotoxicity in this study area.

Ajay Kumar Parida (1963-2022), an eminent plant biotechnologist with a passion for mangrove biology.

We remember Dr Ajay Parida, a leading plant biotechnologist, whose premature passing has deprived the Indian plant science community of a committed scientist and an able administrator. Born on 12 December 1963 in Bhagabanpur, Cuttack District (now Jajpur district), Odisha, he passed away in Guwahati on 19 July 2022. A collegial scientist, his down-to-earth and approachable nature, as well as his resourcefulness were instrumental in advancing the cause of Indian science and harnessing frontier biotechnological tools as vehicles of social consciousness. His expertise in quantitative DNA variation and molecular marker analysis, paved the way for subsequent research on mangrove molecular diversity at the M. S. Swaminathan Research Foundation (MSSRF), Chennai. His contributions to mangrove biology, genetics and genomics as well as extremophile plant species in the Indian context over two decades are a benchmark in his field. He also provided commendable leadership in his capacity as Director, Institute of Life Sciences (ILS), Bhubaneshwar during the COVID-19 pandemic.