High Polymorphism Research Articles

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.

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.

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.

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.

Experimental constraints on the role of temperature and pyrogenic mineral assemblage in wildfire-induced major and trace element mobilisation

Wildfires impact a large and increasing proportion of the Earth’s surface. With documented soil surface temperatures of up to ∼850 °C, wildfires may fundamentally alter the mineralogy and geochemistry of soils and regolith, more conventionally thought to be dominated by low temperature weathering processes. Here we use an experimental approach to test the effect of temperature on the formation of pyrogenic minerals, and on the distribution and mobility of major, trace and rare earth elements following post-fire chemical weathering. We focus on ferruginous nodules, common Fe-oxide cemented components of soils, which transform from non-magnetic to maghemite-bearing, magnetic nodules under wildfire conditions. These transformations provide a valuable record of fire impacts and facilitate the study of thermal processes and element mobility. Our results show heating produces a typical pyrogenic mineral assemblage of hematite, maghemite, metakaolin and transition alumina. At 900 °C the high temperature Fe2O3 polymorph luogufengite forms, which has never been reported in natural fire-affected substrates and therefore places an upper boundary on palaeowildfire temperatures at the soil-fire interface. Chemical leaching, employed to simulate the impacts of post-fire weathering, demonstrates that formation and subsequent breakdown of these pyrogenic minerals results in increased mobility of several elements including Li, Si, Sc, Cr, Co, Cu, Zn, Rb, Cs, La, Pb and U. Further, we propose that incongruent dissolution of pyrogenic metakaolin may be responsible for the formation of fusic material, an aluminous cement commonly found in soils. We conclude by discussing the significance of these results for the release of potentially toxic metals following a fire, identify trace elements that have the greatest potential to be used as palaeowildfire geochemical proxies (decreased alkali metal concentrations, decreased U/Th ratios, and decreased La compared to other rare earth elements), and the potential impact of wildfire on global geochemical cycles.

Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae

The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.

Molecular Diversity of the Casein Gene Cluster in Bovidae: Insights from SNP Microarray Analysis.

The casein gene cluster spans 250 to 350 kb across mammalian species and is flanked by non-coding DNA with largely unknown functions. These regions likely harbor elements regulating the expression of the 4 casein genes. In Bovidae, this cluster is well studied in domestic cattle and to a lesser extent in zebu and water buffalo. This study used a cattle-specific SNP microarray to analyze 12 Bovidae taxa and estimate casein gene cluster variability across 5 bovid subfamilies. Genotyping identified 126 SNPs covering the entire casein gene cluster and 2 Mb of upstream and downstream regions. Dairy cattle, watusi, and zebu showed the highest polymorphism: 63.7-68.2% in the 5'-upstream region, 35.6-40.0% in the casein cluster, and 40.4-89.4% in the 3'-downstream region. Among wild bovids, only a 'semi-aquatic' lechwe revealed high polymorphism similar to cattle. Other species exhibited lower variability, ranging from 9.1-27.3% in the 5'-upstream, 8.9-20.0% in the casein, and 4.2-10.6% in the 3'-downstream regions. For the first time, genome variability data were obtained for impala, waterbuck, and lechwe. It appears that higher variability in cattle's casein gene cluster may relate to its intense expression. This study confirms the effectiveness of cattle-derived microarrays for genotyping Bovidae.

Genotyping for Weak and Partial D Rh Status to Optimize Usage of Limited Blood Supplies

Abstract Introduction The Rh antigen group, expressed on erythrocytes and encoded by highly polymorphic RHD and RHCE genes on chromosome 1 (1p36-p34), is notable in transfusion medicine due to its high polymorphism, strong immunogenicity and ability to cause hemolytic transfusion reactions in patients and hemolytic disease of the fetus and newborn (HDFN). The D antigen specifically contains multiple epitopes with variations that include decreased expression (weak D) or loss of certain epitopes (partial D) which expose patients to risk of alloimmunization depending on the subtype of the Rh(D) antigen. Hence, serologic weak D testing followed by molecular testing is not performed except for donors testing negative for Rh(D) antigen and newborns typing negative for Rh(D) and born to Rh(D) negative mothers. Given the current shortages of blood supplies, understanding patients’ genotypes in the context of weak or partial D-typing and risk of alloimmunization can be essential in the management of increasingly limited supplies of red blood cell (RBC) units. Objective To further characterize patients that initially type negative for Rh(D) but positive for weak D with molecular testing to investigate risk of alloimmunization, retype the Rh(D) and avoid unnecessary use of Rh(D) negative RBC units during critical shortages of RBC units. Methods We collected the results of ABO/Rh(D) typing for patients with negative Rh(D) testing but positive weak D test over a period of four weeks in December 2023 and had D-variant molecular testing performed by a reference laboratory. Initial serologic ABO/Rh(D) was performed in tube followed by weak D testing by indirect Coombs test in tube. Results The total number of patients who initially tested negative for Rh(D) but positive (weak to +4) for weak-D was three patients. Two patients showed a probable genotype of RHD*01W.1 (RHD* weak type 1, 809T&amp;gt;G (V270G)) homozygous which indicated the presence of weak D+ type 1. Patients with weak D+ type 1 can receive Rh(D) positive red cell units, and they are not at risk of alloimmunization and developing anti-D. The third patient showed a probable genotype RHD*DVI type 2 homozygous (lack of Rh(D) exons 4 through 6) and indicated the presence of partial D antigen. Patients with partial D antigen should receive RH(D) negative red cell units as they are at risk of alloimmunization and developing anti-D. Conclusions Although the vast majority of Transfusion Medicine services do not perform the serologic weak D test with reflex to molecular testing, characterizing patients who test negative with initial serologic Rh(D) testing with serologic and molecular D-tests may aid in retyping the Rh(D) of patients during critical shortages, particularly for patients with ABO blood group O.

Developmental and validation of a novel small and high-efficient panel of microhaplotypes for forensic genetics by the next generation sequencing

BackgroundIn the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability.Results and discussionIn this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10− 43 and 1-1.6 × 10− 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods.ConclusionsIn summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution.

Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species

(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, finding extensive use in forestry and landscape design across China. (2) Methods: This study employed Illumina’s second-generation sequencing technology to sequence the chloroplast genomes of eight Phyllostachys species, followed by their assembly and annotation. (3) Results: The chloroplast genomes of the genus exhibit a characteristic tetrad structure with an average sequence length of 139,699 bp and an average GC content of 38.9%. A total of 130 genes have been annotated across eight bamboo species, comprising 75 protein-coding genes, 28 tRNA genes, and four rRNA genes. Global alignment and nucleotide polymorphism analyses indicate that the chloroplast genome of Phyllostachys is highly conserved overall. The boundaries of the four chloroplast regions are relatively conserved and exhibit minimal differences. Among these regions, three coding region genes—atpH, trnQ-UUG, and petB—and five non-coding regions—rpl32-trnL-UAG, rpl14-rpl16, rpl22-rps19, rps12-clpP, and trnR-UCU-trnM-CAU—exhibit high polymorphism and can be used as potential hotspot areas for subsequent research. A total of 266 simple sequence repeat (SSR) loci were identified by SSR analysis in the chloroplast genomes of eight bamboo species; the largest number of mononucleotide repeats was 154, predominantly consisting of A/T. Codon bias in the chloroplast genomes of the eight bamboo species indicates a preference for codons ending with A and U. Additionally, the UUA codon, which encodes leucine (Leu), is positioned between codons encoding phenylalanine (Phe), lysine (Lys), leucine (Leu), serine (Ser), and tyrosine (Tyr), indicating certain differences among these species. (4) Conclusions: This study aims to offer novel insights into the population genetics, phylogenetic relationships, and evolutionary patterns of Phyllostachys.

Identification of false smut – resistant donors in Rice (Oryza sativa L.) and analysis of their morpho-molecular diversity for resistance breeding

False smut disease of rice caused by the pathogen Ustilaginoidea virens is a growing threat to the rice farmers as it affects both quality and quantity. Development of resistant variety becomes difficult, since very few resistant donors were available for false smut resistant breeding programme. Therefore, to identify potential donors for resistance breeding a total of 60 genotypes were screened at hotspot location (Gudalur) during kharif 2023 which led to identification of 12 highly resistant genotypes and the notable ones are Koolavalai, Periya chandikar, Kapikar selection and Earapalli. Genetic variability studies indicated the presence of additive gene action for all the agronomic and disease related traits. Principal component analysis revealed the first 5 principal components collectively contributing 78.79 % of the total variance with disease-related traits contributing significantly to divergence. Ten clusters were delineated using Mahalanobis D2 statistics with clusters IX and V showing higher inter cluster distance (3453.64). Forty-one polymorphic markers were used to analyse the genotypes and The Unweighted Pair Group method with Arithmetic Mean (UPGMA) clustering by Jaccard distance formed 6 clusters. The Bayesian clustering classified the entire population into 2 subpopulations. False smut linked marker RM336 and RM218 were found to be the most informative marker with high Polymorphism Information Content (0.71, 0.69) and Heterozygosity Index (0.76, 0.73). The resistant genotypes such as IG71, Thulasi vasanai sambha, Arupatham vellai, Kaltikar and Chinna aduku nel can be used in the future breeding programmes to develop the resistant cultivar and to identify the candidate genes governing resistance.