High Polymorphism Research Articles

Evaluation of Genetic Diversity and Identification of Cultivars in Spray-Type Chrysanthemum Based on SSR Markers

Background/Objectives: Chrysanthemum (Chrysanthemum morifolium), a key ornamental and medicinal plant, presents challenges in cultivar identification due to high phenotypic similarity and environmental influences. This study assessed the genetic diversity and discrimination of 126 spray-type chrysanthemum cultivars. Methods: About twenty-three simple sequence repeat (SSR) markers were screened for the discrimination of 126 cultivars, among which six SSR markers showed polymorphic fragments. Results: Results showed high polymorphism across six markers, with an average of 3.8 alleles per locus and a mean polymorphism information content (PIC) of 0.52, indicating strong discriminatory efficiency. The average observed heterozygosity (Ho) was 0.72, reflecting significant genetic diversity within the cultivars. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) grouped the cultivars into seven clusters, correlating well with the PCA. Bayesian population structure analysis suggested two primary genetic subpopulations. Conclusions: These findings confirm SSR markers as an effective tool for the genetic characterization and precise discrimination of spray type chrysanthemum cultivars, offering significant applications in breeding, cultivar registration, and germplasm conservation. The SSR marker-based approach thus provides a reliable and efficient strategy to enhance the management and commercialization of diverse chrysanthemum germplasm collections.

Histological Study of Skin Structures From Selected Body Areas in the Varanus komodoensis.

The skin of the Komodo dragon (Varanus komodoensis) is covered by a form of armour formed mainly of scales, which often co-occur with osteoderms. Scales are keratinized, non-mineralized structures in the uppermost layer of the epidermis that are in contact with each other to form a system in which individual scales are isolated from each other by a softer skin fold zone. In the Varanus, the surface of the scales is flat and smooth (thoracic limb, abdomen, and tail areas), domed and smooth (head area) or domed with conical ornamentation (dorsal surface, pelvic limb-dorsal surface areas). In contrast, osteoderms are mineralized structures that are an integral part of the skin, located below the epidermal surface and positioned parallel (head, tail, thoracic limb-dorsal surface, thoracic limb-palmar surface, and tail) or obliquely (pelvic limb-dorsal surface, groin, abdomen) to the surface. Regardless of the body region, osteoderms are structures that are completely anchored in the dermis, and their surface is smooth and devoid of ornamentation. Tangential sections of the osteoderms demonstrate concentric resting lines. Histological sections of the varanid dermis show the presence of collagen bundles, parallel interlacing or crossing bundles of collagen fibers of varying thickness and degree of compactness, accompanied by muscle fibers. In the area of skin close to the osteoderm, loosely arranged bundles of collagen fibers are present, while in the zone distal to the osteoderm, a compact arrangement of these fibers is present. This study documents the morphological diversity and distribution of osteoderms and scales in selected areas of the body of V. komodoensis. Scales are characterized by a high polymorphism related to body region, while osteoderms show a high morphological similarity independent of the area of occurrence.

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism.

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Conservation Genetics and Breeding using Molecular Genetic Markers in Japanese Quail (Coturnix japonica).

The Japanese quail (Coturnix japonica) is a small migratory bird whose main habitats are located in East Asia, Russia, China, Japan, Korea, and India. The Japanese quail was first introduced into the Iraqi research sector in the early 1980s. This investigation aimed to identify the genetic divergence between the available genetic lines of the Japanese quail in Iraq as a first step to conducting further conservation and breeding, benefiting from studying the genetic diversity related to productivity, adaptation, and immune susceptibility. In this study, we harnessed the random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) protocol to investigate the genetic structure, diversity, and differentiation of seven distinct genetic lines of these birds with white, brown, wild grey, and yellow plumage guided by 20 molecular genetic markers. Our findings showed a relatively high polymorphism level of these 20 markers, which was adequate for describing genetic variation within and between the quail lines under study. Overall, the pairs of the White male and Brown male, Brown female and Grey male, and Grey female and Grey male lines were the most genetically distant. Conversely, the White male and Grey male lines were the most similar. The genetic differences established between these lines can enable us to suggest recommendations for further conservation genetics and breeding of this species. In particular, we propose that choosing animals (lines) with the greatest genetic distances, i.e., the least genetic similarities, can help preserve the highest genetic variability within the population. This proposed approach mirrors many contemporary conservation strategies, and information derived directly from this study can potentially be used to improve breeder selection regimes for additional conservation initiatives ex situ.

Development of Intragenic InDel Markers From RNA‐Seq Data for Map‐Based Cloning and Marker‐Assisted Selection in Maize (Zea mays L.)

ABSTRACTMaize is one of the most extensively grown and produced crops in the world. Functional molecular markers (FMM) are essential tools for enhancing the efficiency of both breeding and basic research. The transcriptome obtained from high‐throughput sequencing is a valuable resource for developing FMM. In this study, we precisely identified high‐density and highly polymorphic RNA‐derived InDel markers from 368 high‐quality, high read depth maize RNA‐seq datasets using stringent criteria. The nonredundant marker dataset comprised 13,904 InDel markers with a Polymorphism Information Content (PIC) ≥ 0.5 and a principal allelic difference (length difference between the most and second most frequent alleles) ≥ 3 bp, covering 7749 genes. Subsequently, the polymorphism of InDel markers was verified experimentally. Fifty InDel markers were randomly selected, and their average PIC values in 20 maize inbred lines selected from 368 RNA‐seq samples and 20 newly selected maize inbred lines were 0.53 and 0.54, with range intervals of 0.18 to 0.77 and 0.22 to 0.74, respectively. The high density and polymorphism of RNA‐derived InDel markers identified in this study make them effective tools for maize gene cloning, genetic diversity studies, genome‐wide association analysis, and marker‐assisted selection.

Chromosome-Level Genome Assembly and Genetic Maker System of the Endangered Largemouth Bronze Gudgeon (Coreius guichenoti) with Focus on Conservation Applications.

The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.

Environmental determinants of intraspecific variation in five functional traits of Pinus yunnanensis Franch.

Pinus yunnanensis Franch. is a native species in southwestern China, characterized by high polymorphism. However, the environmental drivers of intraspecific variation in its functional traits remain poorly understood. In this study, we examined the relationships between five functional traits (bark thickness, tree height, leaf dry matter content, leaf length, and specific leaf area) and habitat conditions across 20 populations, representing three varieties: var. yunnanensis (the original variety), var. pygmaea, and var. tenuifolia. Our experiments aimed to determine whether the functional traits varied among the three varieties under different environmental conditions. As specific leaf area and leaf dry matter content showed no significant correlations with any environmental factors, we focused our analysis on the remaining three traits. Using random forest models, we assessed the significance of each environmental factor and found the following: Temperature seasonality was a key determinant of tree height; soil particle size (clay and sand) had the strongest influence on bark thickness; and for leaf length, precipitation during the driest quarter was the most important factor. These findings offer insights into the variation in functional traits of P. yunnanensis and enhance our understanding of its adaptation to diverse environments.

MOLECULAR TYPING OF HLA-B*27 SUB-ALLELES REVEALS AN ASSOCIATION WITH ERAP1 AND DISEASE SUBSET OF ANKYLOSING SPONDYLITIS IN NORTH-INDIAN (KASHMIR) POPULATION

Background: Human Leukocyte Antigen(HLA)-B*27 is significantly linked to Ankylosing spondylitis(AS) and its presence aids in the diagnosis of the disease. Identification of HLA-B*27 allele plays an important role in the clinical monitoring,diagnosis and therapy of this spondyloarthropathy because of high HLA polymorphism and differential contribution of alleles and molecules encoded by them. HLA-B*27 is also present in general population 7-8%.We evaluated the presence and correlation of various HLA-B*27 alleles with clinical parameters and ERAP1 (SNPs rs27434, rs27529 and rs26510) of Ankylosing spondylitis in Kashmiri Population. Methods: This study involved total 200 cases (100 Ankylosing Spondylitis patients and 100 healthy controls). Genomic DNA was extracted by phenol-chloroform method. All subjects were genotyped for HLA-B*27 subtyping by Polymerase Chain Reaction(PCR)-Sequence Specific Primer(SSP) method. Result: HLA-B*27 were present in 90% of cases and in 20% of controls OR 36.0(15.91-81.48)P= &lt;0.0001. HLA-B*27:02 OR 9.12(2.63-31.6) p=&lt;0.0001, CAFRW OR 12.61(4.73-33.9)p= &lt;0.0001 and HLA-B*27+CAFRS OR 45.07(2.64-759.4)p=0.0001 were showing significant association with AS disease. Conclusion: The current study indicates that a majority of Kashmiri AS patients are associated with HLA-B*27 alleles. In addition we found that HLA-B*27 associated AS patients presented with more severe axial manifestation.

Structure of Genes Encoding Oxidosqualene Cyclases-Key Enzymes of Triterpenoid Biosynthesis from Sea Cucumber Eupentacta fraudatrix.

Oxidosqualene cyclases (OSCs) are enzymes responsible for converting linear triterpenes into tetracyclic ones, which are known as precursors of other important and bioactive metabolites. Two OSCs genes encoding parkeol synthase and lanostadienol synthase have been found in representatives of the genera Apostichopus and Stichopus (family Stichopodidae, order Synallactida). As a limited number of sea cucumber OSCs have been studied thus far, OSCs encoding gene(s) of the sea cucumber Eupentacta fraudatrix (family Sclerodactylidae, order Dendrochirotida) were investigated to fill this gap. Here, we employed RACEs, molecular cloning, and Oxford Nanopore Technologies to identify candidate OSC mRNAs and genes. The assembled cDNAs were 2409 bp (OSC1) and 3263 bp (OSC2), which shared the same CDS size of 2163 bp encoding a 721-amino-acid protein. The E. fraudatrix OSC1 and OSC2 had higher sequence identity similarity to each other (77.5%) than to other holothurian OSCs (64.7-71.0%). According to the sequence and molecular docking analyses, OSC1 with L436 is predicted to be parkeol synthase, while OSC2 with Q439 is predicted to be lanostadienol synthase. Based on the phylogenetic analysis, E. fraudatrix OSCs cDNAs clustered with other holothurian OSCs, forming the isolated branch. As a result of gene analysis, the high polymorphism and larger size of the OSC1 gene suggest that this gene may be an ancestor of the OSC2 gene. These results imply that the E. fraudatrix genome contains two OSC genes whose evolutionary pathways are different from those of the OSC genes in Stichopodidae.

Image Analysis Characterizes Phenotypic Variation in the Growth of Mushroom-Forming Fungus Schizophyllum commune.

Schizophyllum commune, a common wood-decay mushroom known for its extremely high genetic variation and as a rare cause of human respiratory diseases, could be a promising model fungus contributing to both biology and medicine. To better understand its phenotypic variation, we developed an image analysis system that quantifies morphological and physiological traits of mycelial colonies in Petri dishes. This study evaluated growth of six wild and one clinical isolates of Japanese S. commune, subjected to different temperatures and glucose concentrations, including a condition mimicking the human respiratory environment. Our analysis revealed that combinations of two growth indices, area and whiteness, and profiling by clustering algorithms highlighted strain-specific responses. For example, the clinical isolate was the whitest under the respiratory-like condition. We also found that the growth rate was strongly determined by glucose concentration, while the effects of temperature on growth varied among the strains, suggesting that while glucose preference is common in this species, responses to temperature differ between strains. This system showed sufficient sensitivity to detect variation in mycelial growth. Our study provides a key to unraveling morphological and physiological traits behind the high polymorphisms in S. commune, including the ability to colonize the human respiratory tract.

Exploitation of novel drought responsive EST-SSR markers in tetraploid cotton (Gossypium hirsutum L.)

Drought is a major environmental challenge that affects the quality and yield of cotton fibres. The aim of the present study was to develop drought-responsive EST-SSRs from cotton transcriptome data. A total of 1946 functionally annotated EST-SSR markers were developed, with tri-nucleotide SSR repeats being the most abundant (40.7 %), followed by di-nucleotides (18.1 %). Gene Ontology (GO) associated with EST-SSR showed the presence of genes related to drought stress, such as PIP, CDK, LEA, etc. A set of 46 EST-SSRs was validated under In-vitro conditions on fourteen cotton genotypes, and 15 EST-SSRs were found to be polymorphic. The polymorphic EST-SSRs markers amplified a total of 44 loci with 32.6 % polymorphism. Genetic analysis revealed that the markers NAU-G-16, NAU-G-39, NAU-G-117 and NAU-G-142 amplified four unique alleles at 121, 163, 224 and 238 bp, respectively, only in drought-tolerant cotton genotypes. The effectiveness of the markers was demonstrated by their high polymorphism information content (PIC), which ranged from 0.35 to 0.89. The large number of markers, 60 %, had a PIC value of >0.6 and were classified as highly informative. The genetic similarity coefficients between cotton genotypes ranged from 0.409 to 0.89, indicating moderate genetic diversity. The Shannon index ranged from 0.21 to 0.65, while the Nei coefficient ranged from 0.12 to 0.46. Clustering and PCo analysis showed the distribution of genotypes into four main clusters, with drought-tolerant genotypes grouped into a single cluster. These drought-responsive markers are promising for the further development of marker-assisted breeding with the aim of increasing the productivity of cotton under drought-prone conditions.

Microsatellite based molecular characterization of Nattukuttai- a unique short statured Bos indicus cattle population of southern India.

Molecular characterization was conducted to characterise 'Nattukuttai', a native cattle population of the north-eastern agro-climatic zone of Tamil Nadu (India), using thirty microsatellite markers. The analyses revealed a high level of genetic diversity, with a total of 294 alleles observed across all the loci, averaging 9.8 alleles per locus. The allele sizes ranged from 83bp to 302bp, with frequencies ranging from 0.010 to 0.875. The microsatellite markers demonstrated high polymorphism, as indicated by an average polymorphic information content (PIC) of 0.763. Deviation from Hardy-Weinberg equilibrium was observed in a significant number of loci, indicating possible genetic influences such as selection or population structure. Bottleneck analysis suggested that the Nattukuttai population did not undergo any recent significant population contraction. Comparative analyses with three other cattle populations (Kangayam, Malai Madu, and Malnad Gidda) revealed varying genetic distances. Nattukuttai showed a distinct genetic profile, diverging from a common source that also gave rise to the Kangayam and Malai Madu clusters. Multivariate statistical analyses and phylogenetic reconstruction supported the genetic differentiation of Nattukuttai from the other populations, while Malai Madu and Kangayam were found to be genetically closer to each other. Overall, these findings provide insights into the genetic structure and relationships of the Nattukuttai cattle population, highlighting its distinct genetic identity and potential conservation significance.

Genetic Polymorphism and Differentiation of Populations of Sterlet Acipenser ruthenus (Acipenseridae) in the Lower Irtysh and Middle Ob Basins

The article presents data on polymorphism of intermicrosatellite sequences in the sterlet Acipenser ruthenus of the lower reaches of the Irtysh River and the middle reaches of the Ob River. We assessed intra- and interpopulation variability and genetic differentiation of A. ruthenus and revealed a high ISSR polymorphism in the species from the central part of the Ob-Irtysh basin. The proportion of polymorphic amplicons was 0.966, genetic diversity was 0.355, and the average number of alleles per locus was 1.97. The highest polymorphism was typical for the sterlet from the Tobol River at the confluence with the Irtysh River. Genetic differentiation between the sterlet groups of the Irtysh and Ob rivers is well pronounced, the interpopulation component accounts for 42% of variability (Gst = 0.42), gene flow is limited (Nm = 0.67). The sterlet groups inhabiting the Lower Irtysh from the mouth of the Tobol River to the mouth of the Konda River do not differ genetically and form one population (Gst = 0.08–0.12, Nm = 3.76–5.55). The sterlet from the Irtysh River within the Vagay region is genetically different from the other Irtysh samples (Gst = 0.22, Nm = 1.68) and belongs to a different population group. The differentiation between samples of sterlet from the Ob basin is higher than between samples from the Irtysh basin. Groups of sterlet from the Ob River and the Yuganskaya Ob canal are genetically different (Gst = 0.30, Nm = 1.19) and form various subpopulations. Spawning migrations, as well as confinement to wintering pits, play a decisive role in the formation of the sterlet population structure in the studied part of the distribution area. The identified sterlet population groups should be considered as separate units of environmental and economic management.

InvertiaDB: A Database of Inverted Repeats Across Organismal Genomes.

Inverted repeats are repetitive elements that can form hairpin and cruciform structures. They are linked to genomic instability, however they also have various biological functions. Their distribution differs markedly across taxonomic groups in the tree of life, and they exhibit high polymorphism due to their inherent genomic instability. Advances in sequencing technologies and declined costs have enabled the generation of an ever-growing number of complete genomes for organisms across taxonomic groups in the tree of life. However, a comprehensive database encompassing inverted repeats across diverse organismal genomes has been lacking. We present InvertiaDB, the first comprehensive database of inverted repeats spanning multiple taxa, featuring repeats identified in the genomes of 118,070 organisms across all major taxonomic groups. The database currently hosts 30,067,666 inverted repeat sequences, serving as a centralized, user-friendly repository to perform searches, interactive visualization, and download existing inverted repeat data for independent analysis. invertiaDB is implemented as a web portal for browsing, analyzing and downloading inverted repeat data. invertiaDB is publicly available at https://invertiadb.netlify.app/homepage.html.

High resistance levels to pyrimethanil and fludioxonil among fourteen Penicillium spp. from pome fruits in the U.S. Pacific Northwest

In this study, 162 Penicillium isolates, i.e., 31 P. expansum isolates and 131 isolates from 13 other Penicillium spp. referred to as “non-expansum” were collected from apples and pears from multiple packinghouses in Washington State and Oregon. The sensitivity of the isolates to the postharvest fungicides pyrimethanil (PYR) and fludioxonil (FDL) was assessed in vitro. The mean EC50 value for PYR was 0.75 μg/mL in P. expansum compared to 1.63, 3.47, 6.95, 7.06 and 32.21 μg/mL in P. solitum, P. palitans, P. commune, P. roqueforti and P. carneum, respectively. For FDL, the mean EC50 value was 0.04 μg/mL in P. expansum compared to >0.80, 1.00, 10.40, 13.99, and 158.10 μg/mL in P. commune, P. palitans, P. roqueforti, P. solitum, and P. paneum, respectively. Overall, > 40 % of isolates from five “non-expansum” species showed dual resistance to PYR and FDL versus 9.6 % in P. expansum. The recommended rates of PYR and FDL failed to control isolates of six Penicillium spp. on detached apples after five months at 1.5 °C. Sequencing of the Mdl1, NikA, and Os1 genes from different isolates of eight species revealed a high polymorphism in the Mdl1 and NikA of several “non-expansum” species. Three and two concurrent mutations, in addition to a G409R and S959, were detected in the Mdl1 and NikA, respectively, that potentially confer resistance to PYR and FDL. The high level of resistance and the control failure observed on fruits highlight the potential risk posed by several “non-expansum” Penicillium species to pome fruit packers.

Study of the Genetic Mechanisms of Siberian Stone Pine (Pinus sibirica Du Tour) Adaptation to the Climatic and Pest Outbreak Stresses Using Dendrogenomic Approach.

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms-SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype-dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant's genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change.

Development of Simple Sequence Repeat of Monochamus alternatus (Coleoptera: Cerambycidae) Based on Restriction Site-Associated DNA Sequencing.

Monochamus alternatus, a pest posing a serious threat to coniferous species, such as Pinus massoniana, has had devastating effects on pine forests due to its association with Bursaphelenchus xylophilus. The creation of unique simple sequence repeat (SSR) primers for M. alternatus is crucial, as there has been little study of the species' phylogeography. The aim of this study was to identify and create polymorphic SSR primers by sequencing samples of M. alternatus obtained from three different sampling points using the restriction site-associated DNA sequencing (Red-seq) approach. Subsequently, supplementary samples were integrated, and genetic typing was performed utilizing the identified polymorphic primers. Through comprehensive analysis, a total of 95,612 SSR loci were identified. Among these, mononucleotide repeats (51.43%), dinucleotide repeats (28.79%), and trinucleotide repeats (16.74%) predominated among the SSR motif types. Ultimately, 18 pairs of SSR primers were screened out, demonstrating stable amplification and high polymorphism. Genetic typing revealed that the mean number of alleles (Na) for these primer pairs ranged from 3 to 8, observed heterozygosity (Ho) ranged from 0.133 to 0.733, polymorphic information content (PIC) ranged from 0.294 and 0.783, and Shannon's index (I) ranged from 0.590 to 1.802. This study effectively produced 16 pairs of SSR primers that can be applied to different populations of M. alternatus. As a result, important tools for furthering studies on the phylogeography of pine wood nematodes, creating genetic maps, gene mapping, and carrying out in-depth investigations into gene function have been made available.

Genome-wide dissection of genes shaping inflorescence morphology in 242 Chinese south–north sorghum accessions

The inflorescences morphology (IM) of sorghum (Sorghum bicolor L. Moench) affects its resistance to pests, diseases, and grain yields. However, the specific genetic factors underlying in IM are not yet fully elucidated. Here we conducted a comprehensive genome-wide association analysis (GWAS) to identify the stable and adaptive Quantitative Trait Loci (QTL) for five IM traits (panicle length, the number of cob nodes, the number of primary branches, the largest length of the primary branch, and panicle type) in a sorghum panel, which adapted to different environments from the south to north in China. Totally, 2,015,850 high quality single nucleotide polymorphisms (SNPs) were obtained. Population structure analysis showed that two distinct genetic sub-populations were divided according to their geographic origin. Seventy-one QTLs distributed in 41 genetic regions on 9 chromosomes were identified. These regions harbored 21 high-confident candidate genes that were homologous to rice domestication genes, including 7 related to IM. Two domestication-related genes (Sobic.003G052700 and Sobic.006G247700) were located into two major QTL regions (QTL3.4721839 and QTL6.58709500) which were identified in multi-environments. Allelic variations in the two genes displayed a geographical pattern, indicating that different IM traits were selected by south and north sorghum breeders, such as south sorghums had long and loose panicles in order to adapt the hot and humid climate, while north sorghums had short and compact panicle to increase planting density and grain yield per unit area due to dry climate. This work provides new breeding strategies and resources for developing locally adapted sorghum varieties.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

MHC Class II Supertypes Affect Survival and Lifetime Reproductive Success in a Migratory Songbird.

The major histocompatibility complex (MHC) plays a critical role in the immune response against pathogens. Its high polymorphism is thought to be mainly the consequence of host-pathogen co-evolution, but elucidating the mechanism(s) driving MHC evolution remains challenging for natural populations. We investigated the diversity of MHC class II genes in a wild population of pied flycatchers Ficedula hypoleuca and tested its associations with two key components of individual fitness: lifetime reproductive success and survival. Among 180 breeding adults in our study population, we found 182 unique MHC class II exon 2 alleles. The alleles showed a strong signal of positive selection and grouped into nine functional supertypes based on physicochemical properties at the inferred antigen-binding sites. Three supertypes were found in > 98% of the sampled individuals, indicating that they are nearly fixed in the population. We found no rare supertypes in the population, as all supertypes were present in > 70% of individuals. Three supertypes were related to different components of individual fitness: two were associated with lower offspring production over time, while the third was positively associated with survival. Overall, the substantial allelic and functional diversity and the relationship between specific supertypes and fitness are in accordance with the notion that balancing selection maintains MHC class II diversity in the study population, possibly with fluctuating selection as the underlying mechanism. The absence of rare supertypes in the population suggests that the balancing selection is not driven by rare-allele advantage.