Development Of Molecular Markers Research Articles

Fine mapping and analysis of a candidate gene controlling Phytophthora blight resistance in cucumber.

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development. We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene. Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs-4, as a closely linked marker for the cucumber blight resistance gene. This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight.

Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.)

BackgroundThis study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS).ResultsThe nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64–32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis.ConclusionsOverall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.

Development of nicotiana-specific molecular markers and their application in a loop-mediated isothermal amplification assay

An effective identification method for detecting illegal goods involving raw tobacco material is crucial for tobacco monopolies to conduct surveillance. We developed Nicotiana-specific molecular markers to determine whether seized goods contain raw tobacco material. The sequence data for genes related to the nicotine metabolism pathway and genomic data from the public Solanaceae database were used to establish Nicotiana-specific molecular markers. These markers were determined by experimentally verifying 17 types of nontobacco plant material and 91 types of tobacco material belonging to 11 sections of 3 subgenera. Two reliable Nicotiana-specific markers, Ntsp027 and Ntsp151, were selected from among the 209 newly developed markers. The results indicated that the primers corresponding to these two markers can amplify the target fragments in the 91 types of Nicotiana material without amplification of any PCR products in the 17 types of non-Nicotiana material. Furthermore, utilizing the marker Ntsp151, we verified the efficacy of the loop-mediated isothermal amplification (LAMP) assay in authenticating tobacco material. The identification of 21 tea-cigarette products via the combination of GC‒MS, a Nicotiana-specific molecular marker and LAMP methods underscores the utility of Nicotiana-specific DNA markers in determining whether illegal goods contain raw tobacco material. Our results indicate an impressive accuracy rate of 100%, which is consistent with the reliability assessment, underscoring the accuracy of these markers in effectively identifying tobacco material. Our findings can significantly augment the capacity for surveillance and anticounterfeiting efforts by aiding the fight against illicit trade and ensuring the integrity of all tobacco-related products in the market.

Molecular characterization of Indian races of Fusarium oxysporum f. sp. lentis (Fol) based on secreted in Xylem (SIX) effector genes and development of a SIX11 gene-based molecular marker for specific detection of Fol.

Fusarium wilt of lentil caused by Fusarium oxysporum f. sp. lentis (Fol) is a destructive pathogen limiting lentil production in India. In the present study, Secreted in Xylem (SIX) effectors genes were explored in Indian races of Fol and also a diagnostic tool for reliable detection of the disease was developed. Four SIX effectors genes, SIX11, SIX13, SIX6 and SIX2 were identified in 12 isolates of Fol belonging to seven races. SIX11 was present in all the races while SIX 13 was absent in race 6 and SIX6 was present only in race 4. The phylogenetic analysis revealed the conserved nature of the SIX genes within the forma specialis and showed sequence homology with F. oxysporum f. sp. pisi. The presence of three effectors, SIX11, SIX13 and SIX6 in race 4 correlates with high disease incidence in lentil germplasms. The in-silico characterization revealed the presence of signal peptide and localization of the effectors. Further SIX11 effector gene present in all the isolates was used to develop Fol-specific molecular marker for accurate detection. The marker developed could differentiate F. oxysporum f. sp. lycopersici, F. solani, F. oxysporum, Rhizoctonia solani and Sclerotium rolfsii and had a detection limit of 0.01ng μL- 1. The effector-based marker detection helps in the unambiguous detection of the pathogen under field conditions.

Durian (Durio zibethinus L.): Nutritional Composition, Pharmacological Implications, Value-Added Products, and Omics-Based Investigations

Durian (Durio zibethinus L.), a tropical fruit celebrated in Southeast Asia for its distinct flavor, is the focus of this comprehensive review. The fruit’s pulp is rich in high-value bioactive compounds, including gamma-glutamylcysteine, a precursor to the essential antioxidant glutathione. With durian cultivation gaining prominence in Southeast Asia due to its economic potential through cultivar enhancement, an in-depth examination of durian-related research becomes crucial. This review explores the health benefits of durian, analyzing the nutritional compositions and bioactive compounds present in the pulp, peel, and seed. It also underscores durian-based food products and the potential for valorizing durian waste. This review encapsulates the significant advancements made in omics-based research, aimed at deciphering the molecular complexities of durian fruit post-harvest ripening and the metabolic shifts impacting its sensory attributes. It is the first to summarize studies across genome, transcriptome, and metabolome levels. Future research should prioritize the development of molecular markers to accelerate the breeding of elite cultivars with preferred traits. It also proposes the exploration of durian waste valorization, including underexplored parts like flowers and leaves for their bioactive compounds, to promote a sustainable bioeconomy. Finally, it suggests the development of innovative durian products catering to the tastes of health-conscious consumers.

Assembly and characterization of the complete mitochondrial genome of Descurainia sophia: a medical plant producing glucosinolate

As a commonly used traditional Chinese medicine, Descurainia sophia has various reported pharmacological activities such as prevention of chronic diseases, cardiovascular protection, neuroprotection, anticancer, antioxidant, and has high nutritional values, but its mitochondrial genome (mitogenome) has not been reported. In this study, the D. sophia mitogenome was sequenced, assembled and annotated using next generation sequencing technologies on the Illumina HiSeq and PacBio Sequel platform. The results showed that the D. sophia mitogenome was a circular DNA molecule with the length of 265,457 bp and the GC content of 44.78%, encoding unique 56 genes, including 35 protein coding genes, 18 tRNA genes and 3 rRNA genes. We analyzed codon preference, repeated sequences, DNA sequence transformation, phylogenetic relationship, RNA editing and synteny in the D. sophia mitogenome. Based on the DNA sequences of mitogenomes, the phylogenetic and synteny analysis indicated that D. sophia was more closely related to Boechera stricta, and the mitogenome of D. sophia underwent frequent genome recombination. In this study, we obtained the complete mitogenome of D. sophia, which can provide valuable data support for future studies on genetic characteristics, phylogenetic relationships, species identification and development of new molecular markers in D. sophia.

The improvement of the CAPS-marker for St, J and V subgenome identification in Triticeae tribe plants using the 5S non-transcribed spacer polymorphism 

In the Triticeae tribe, several subgenomes (St, J, V and others) were described, and a subgenome-specific molecular marker development is an actual branch of studies. Non-transcribed spacers (NTS) of 5S rDNA are perspective to create species-specific or genome-specific molecular markers in closely related organisms. Early, the 5S rDNA NTS based CAPS marker (StJV-f/StJV-r primers with the SmiM1 enzyme digestion) was designed for identification of the St, J and V subgenomes. The V subgenome amplicons were differed from the St and J amplicons in length. The St amplicons were distinguishable from the J amplicons after the SmiM1 enzyme digestion (St fragments were digested, J fragments were not digested, which is a disadvantage, because a failure with the digestion of St amplicons can be mistaken for J amplicons). This article presents the results of the StJV marker improvement. Comparative analysis of restriction enzyme maps revealed that the Hpy166 II enzyme cuts the StJV amplicons of all studied subgenomes in such a way that different product patterns are obtained. Experimental testing confirmed this finding. Thus, the improved CAPS marker can serve as a promising tool for verifying samples in Triticeae plant collections, screening herbarium materials, as well as in the breeding process aimed at improving wheat by involving its wild relatives in traditional breeding programs efficiently.

Characterization of the complete mitochondrial genome of Paecilomyces variotii and comparative evolutionary mitochondriomics of 36 fungi.

Paecilomyces variotii has important economic value in stimulating crop growth, biodegradation, and other aspects. Up to now, there are no research reports on its mitochondrial genome. The mitochondrial genome of Paecilomyces variotii was determined with the next-generation sequencing method (Illumina, NovaSeq), and its characteristics were analyzed using various bioinformatics approaches. The length of complete mitochondrial genome sequence of P. variotii is 40,965bp and consists of 14 protein-coding genes, 2 ribosomal RNA genes, 1 ribosomal protein S3 gene, 26 transport RNA genes. The results of phylogenetics analysis using Bayesian inference and Maximum likelihood methods showed that P. variotii belongs to the Eurotiales order in the Thermoascaceae family, and 9 genera within the Eurotiomycetes class were effectively distinguished with high support rates (bootstrap value > 92% and posterior probabilities > 99%). The analysis of synonymous substitution rates and nonsynonymous substitution rates indicated that the Ka/Ks values of the 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class ranged from 0 to 0.4333. This study revealed the structural and sequence information characteristics of the mitochondrial genome of P. variotii, and the phylogenetic results strongly support its classification within the family Thermoascaceae, consistent with traditional morphological taxonomy studies. The 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class are subject to strong purifying (negative) selection. The results of this research provides an important molecular basis for the development of genomics, evolutionary genetics and molecular markers of P. variotii in the future.

Genetic diversity of the entomopathogenic fungus Metarhizium rileyi based on de novo microsatellite markers

Epizootics of the entomopathogenic fungus Metarhizium rileyi regulate lepidopteran populations in soybean, cotton, and peanut agroecosystems to the point that insecticide applications could be unnecessary. However, the contribution and how different strains operate during the epizootic are unknown. Several unanswered questions remain: 1. How many genotypes of M. rileyi are present during an epizootic? 2. Which genotype is the most common among them? 3. Are the genotypes involved in annual epizootics at the same location the same? Therefore, the development of molecular markers to accurately identify these genotypes is very important to answer these questions. SSR primers were designed by prospecting in silico to discriminate genotypes and infer the genetic diversity of M. rileyi isolates from the collection kept at Embrapa Soybean. We tested 13 SSR markers on 136 isolates to identify 43 clones and 12 different genetic clusters, with genetic diversity ranging from Hs = 0.15 (cluster I) to Hs = 0.41 (cluster IV) and an average diversity of 0.24. No clusters were categorically distinguished based on hosts or geographical origin using Bayesian clustering analysis. Nonetheless, some clusters comprised most of the isolates with a common geographic origin; for example, cluster VIII was mainly composed of isolates from Central-western Brazil, cluster II from Southern Brazil, and cluster XII from Quincy, Northern Florida, in the United States. Underrepresented regions (few isolates) from Pacific Island nations of Japan, the Philippines, and Indonesia (specifically from Java) were placed into clusters IX and X. Although the analyzed isolates displayed evidence of clonal structure, the genetic diversity indices suggest a potential for the species to adapt to different environmental conditions.

Status, Gaps and Perspectives of Powdery Mildew Resistance Research and Breeding in Cucurbits

Cucurbitaceae, the gourd family of flowering plants, is a very large and diverse family, the order Cucurbitales, contains 95 genera and 950–980 species of food and ornamental plants, and wild and weedy species mostly with high genetic diversity. This review is focused on the most important cucurbit crops (Cucumis sativus, Cucumis melo, Cucurbita spp., Citrullus lanatus, Momordica charantia, Lagenaria siceraria, and Luffa acutangula) and some their wild relatives as hosts of cucurbit powdery mildews (CPM). Powdery mildews (PM) (Ascomycota, Erysiphales) are one of the most frequently encountered and easily visible groups of plant pathogenic fungi with > 900 species. They are obligate biotrophs, they colonize above-ground plant tissues, mostly leaves, though they may also colonize stems, petioles, flowers and fruits, and they are usually debilitators, not killers. These parasitic fungi have been problematic on cucurbits for a long time world-wide, causing serious economic losses in yield and quality. All economically important cucurbit crops host CPM. Seven PM species with different taxonomic positions, host ranges, geographic distributions and ecological requirements are known on cucurbits. CPM species taxonomy and denomination rapidly changed during last few decades through detailed analyses and clarifications. At least three PM species frequently parasitize cucurbits: the endoparasite Leveillula taurica (Lt) with marginal economic importance; and two ectoparasitic species, Golovinomyces orontii (Go), and Podosphaera xanthii (Px), which are economically important world-wide. The two pathogens differ in ecological requirements and distribution, though they may occur together in mixed infections. They are highly variable at the population level for virulence, race identities, and fast adaptation of pathogens. Cucurbit-CPM species interactions are diverse and complicated, and differ between hosts and their respective pathogen genera and species. Here we present a critical overview of obstacles, gaps and recent progress in these matters for six cucurbit genera with respect to resistance resources, genetics of resistance, genetic mapping and development of molecular markers, physiology and mechanisms of resistance, developments in mlo-mediated resistance, patents, and CPM resistance breeding.

Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae.

Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq

Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of qLLS02 and qLLS03 are coincided with that of qLLS.LG02 and qLLS.LG03 respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region qLLS02 of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. This study holds significant implications for improving peanut breeding for LLS resistance through development of associated molecular markers.

Inflammatory Response Associated with West Nile Neuroinvasive Disease: A Systematic Review.

West Nile virus (WNV) infection is a seasonal arbovirosis with the potential to cause severe neurological disease. Outcomes of the infection from WNV depend on viral factors (e.g., lineage) and host-intrinsic factors (e.g., age, sex, immunocompromising conditions). Immunity is essential to control the infection but may also prove detrimental to the host. Indeed, the persistence of high levels of pro-inflammatory cytokines and chemokines is associated with the development of blood-brain barrier (BBB) damage. Due to the importance of the inflammatory processes in the development of West Nile neuroinvasive disease (WNND), we reviewed the available literature on the subject. According to the 2020 updated PRISMA guidelines, all peer-reviewed articles regarding the inflammatory response associated with WNND were included. One hundred and thirty-six articles were included in the data analysis and sorted into three groups (in vitro on-cell cultures, in vivo in animals, and in humans). The main cytokines found to be increased during WNND were IL-6 and TNF-α. We highlighted the generally small quantity and heterogeneity of information about the inflammatory patterns associated with WNND. Further studies are needed to understand the pathogenesis of WNND and to investigate the extent and the way the host inflammatory response either helps in controlling the infection or in worsening the outcomes. This might prove useful both for the development of target therapies and for the development of molecular markers allowing early identification of patients displaying an inflammatory response that puts them at a higher risk of developing neuroinvasive disease and who might thus benefit from early antiviral therapies.

Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut.

We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.

Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats.

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.

Chloroplast genome analyses of Caragana arborescens and Caragana opulens

BackgroundNumerous species within the genus Caragana have high ecological and medicinal value. However, species identification based on morphological characteristics is quite complicated in the genus. To address this issue, we analyzed complete plastid genome data for the genus.ResultsWe obtained chloroplast genomes of two species, Caragana arborescens and Caragana opulens, using Illumina sequencing technology, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species indicated that they could be assigned to the inverted repeat-lacking clade (IRLC). The genomes included 111 distinct genes (4 rRNA genes, 31 tRNA genes, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in the two genomes, the majority of which contained a single intron. Repeat analyses revealed 129 and 229 repeats in C. arborescens and C. opulens, respectively. C. arborescens and C. opulens genomes contained 277 and 265 simple sequence repeats, respectively. The two Caragana species exhibited similar codon usage patterns. rpl20-clpP, rps19-rpl2, and rpl23-ycf2 showed the highest nucleotide diversity (pi). In an analysis of sequence divergence, certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) were highly variable. A phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together with four other Caragana species. The genera Astragalus and Caragana were relatively closely related.ConclusionsThe present study provides valuable information about the chloroplast genomes of C. arborescens and C. opulens and lays a foundation for future phylogenetic research and molecular marker development.

A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance.

European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU) has released cultivars with a dominant allele at a single resistance locus identified by classical breeding, linkage mapping, and molecular markers. 'Jefferson' is resistant to the predominant EFB biotype in Oregon and has been selected by the OSU breeding program as a model for hazelnut genetic and genomic research. Here, we present a near complete, haplotype-resolved chromosome-level hazelnut genome assembly for C. avellana 'Jefferson'. This new assembly is a significant improvement over a previously published genome draft. Analysis of genomic regions linked to EFB resistance and self-incompatibility confirmed haplotype splitting and identified new gene candidates that are essential for downstream molecular marker development, thereby facilitating breeding efforts.

Comparative Analyses of Acacia Plastomes to Detect Mutational Hotspots and Barcode Sites for the Identification of Important Timber Species

The genus Acacia is a crucial source of industrial papermaking and timber, possessing significant economic value. Due to their nitrogen-fixing ability, rapid growth, and high tolerance to stress, Acacia species have become integral to short-term industrial timber forests, particularly in southern China and various other regions worldwide. Nevertheless, comparative genomic analyses of Acacia species remain limited, impeding the development of molecular markers for identifying and distinguishing between distinct Acacia species as well as distinguishing their wood counterparts from other tree species. To address this gap, we generated plastomic sequences from eight species commonly cultivated in Chinese plantation forests and compared them with existing data. Our findings revealed a generally conserved structure and gene content within the plastid genomes of Acacia. Notably, the dN/dS ratio of genes from distinct functional groups varied, particularly between ribosomal proteins and photosynthesis genes. Furthermore, phylogenetic analyses and sequence comparisons suggest that the introduction of Acacia to China may have been less diverse than previously thought or that interspecies introgression has occurred more frequently than previously documented. This study offers a valuable starting point for future research in this area and for improving timber quality through marker-assisted breeding.

Analyzing genetic diversity of chloroplast genomes in Liliales

AbstractLiliales is a monocotyledonous order and contains both photosynthetic and mycoheterotrophic species that distribute locally or worldwide. In this study, thegenetic diversity of chloroplast genomes in Liliales was explored regarding theirnucleotide diversity and repeated composition. The analysis of nucleotide diversity revealed various hotspots in large and small single-copy regions whereas the IR regions had low sequence divergence. Although each family has specific hotspots, the rps15-ycf1 region was commonly found as a highly variable area in the cpDNA of observed taxa. In the cpDNA of Liliales, mononucleotide simple sequence repeat (SSR) is the most common type. The majority of SSRs are located in non-coding regions. Similarly, more long repeats were found in non-coding areas than in coding sequences. Additionally, the complement repeat exceeds forward type in the cpDNA of Liliales. The highest number of long repeats was found in Corsia dispar whereas that of SSRswas detected in Smilax china. The results of nucleotide diversity and repeat analyses provided fundamental information for further studies on population genetics, molecular marker development and evolutionary history of Liliales.® 2022 Journal of Science and Technology - NTTU

Development and validation of genome-wide SSR molecular markers of Tapes dorsatus.

Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleleswas 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information contentwas 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.