Genetic Diversity Information Research Articles

Baseline genetic distinctiveness supports structured populations of thornback ray in the Mediterranean Sea

Abstract The thornback ray (Raja clavata) is the most important chondrichthyan in terms of landings in the Mediterranean Sea. Intense harvesting may induce negative genetic effects reducing the resilience of overfished species. For this reason, genetic diversity information should be considered in fisheries management and conservation policies. Microsatellite markers were used to unravel the genetic features (variability, connectivity, sex‐biased dispersal) of R. clavata populations, both at the small (around the coast of Sardinia, western Mediterranean Sea) and larger spatial scales (at the pan‐Mediterranean level, and between the Atlantic Ocean and the Mediterranean Sea). Individual clustering, multivariate and variance analyses rejected the hypothesis of genetic homogeneity, with significant genetic differences between Mediterranean and Atlantic rays, as well as within the Mediterranean Sea between its western and eastern basins. The data indicated that both the Strait of Gibraltar and the Sicilian Channel seem to be effective in limiting the dispersal of thornback ray individuals, but a further structuring was identified, with the significant genetic differentiation of the populations located in the Algero‐Provençal and Tyrrhenian basins. Such a fine‐scale arrangement suggests the occurrence of additional barriers to species dispersal. A lack of significant genetic differentiation, stable over the years, was measured at a local scale among R. clavata Sardinian samples. Several possible mechanisms, both biological and abiotic (e.g. migratory behaviour, waterfronts and oceanographic discontinuities), are discussed. Overall, the genetic data presented, both at the local and regional level, could represent the baseline information for the temporal monitoring of populations and assessing the effects of present or future fisheries‐related management actions. The data obtained are information of paramount importance for minimizing the gaps in our current knowledge of the genetic diversity of thornback rays and maximizing the information needed for the correct protection of R. clavata populations.

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

Background: The genetic diversity information of local cattle and crossbred in South Sulawesi, Indonesia is essential for the establishment of conservation and breeding strategies. This research targeted to evaluate the phylogenetic relationship and genetic diversity of local and crossbred (CB) cattle. Methods: The present research organized at the Animal Laboratory, Professor Nidom Foundation, Surabaya, Indonesia from February to October 2021. The genome was isolated from 20 whole blood samples from seven purebreed belongs to Singosari National Artificial Insemination Center Malang, Indonesia, four crossbred in Gowa and nine crossbred in Sidrap, South Sulawesi, Indonesia. Partial sequences of mtDNA cytochrome oxidase subunit I (COI) gene were amplified employing the polymerase chain reaction technique. Result: This study revealed that a lot of single nucleotide polymorphism (SNP) found in local cattle (Bali and Peranakan Ongole) and CB cattle in Gowa and Sidrap indicated various genetic diversity can be used as a marker candidate and potential to be developed into future research knowing the correlation of the SNP with the growth rate of CB. Thus, this information will be helpful for further strategy in breeding development program.

Genetic Diversity and Population Structure of Selected Ethiopian Indigenous Cattle Breeds Using Microsatellite Markers.

In Ethiopia, livestock contributes 45% of agricultural GDP. Despite the economic role played by the sector, there have been little efforts to genetically improve the indigenous cattle. Morphological characterization of selected Ethiopian indigenous cattle has been made for (Bonga, Jimma, and Kerayu) cattle types. But, the selected indigenous cattle were not characterized at molecular level (genetic diversity information). Hence, this work was initiated to detect and determine the genetic diversity and population structure of selected Ethiopian indigenous cattle ecotypes using microsatellite markers. Different alleles were identified (131) and thirty-three of these alleles were unique to specific ecotypes. All loci used were informative with PIC values ranging from 0.5 (TGLA126) to 0.84 (ETH10) with a mean of 0.70 per locus. The Shannon information index ranged from (I = 1.02) ILST006 to (I = 1.63) ETH10 with an average of 1.28 revealing there is genetic diversity. Moreover, analysis of molecular variance (AMOVA) revealed 84% genetic variation within a population and 13% variation among populations. The value of F-statistics (Fst) (0.129 = 13%) indicated that there was moderate genetic differentiation among ecotypes. The (UPGMA) revealed, Bonga and Jimma clustered together while Kerayu cattle were relatively distinct, Principal coordinates analysis (PCOA) and structure analysis grouped the individual into different clusters confirming the presence of ecotype admixture due to geographical origins and uncontrolled mating. In general, this study has successfully characterized the genetic diversity and population structure of Bonga, Jimma, and Kerayu cattle ecotypes using high polymorphic/informative microsatellite markers. According to this study, Kerayu cattle have high AR and PA when compared to Bonga and Jimma cattle populations. So, the Kerayu population is more diverse than others and it is the hotspot for genetic diversity study. The generated information is very relevant for breeder and genetic conservation.

Assessment of the Genetic Structure and Diversity of Orobanche cumana populations from Turkey Using Simple Sequence Repeat Markers

Orobanche cumana Wallr. known as sunflower broomrape is a holoparasitic plant that causes huge yield losses in sunflower (Helianthus annuus L.) fields. Genetic characterization, genetic diversity, and race determination studies in O. cumana are very significant for preventing threats in sunflower fields. In this study, the broomrape populations sampled from Edirne, Kırklareli, Tekirdağ, and Adana provinces were used for genetic characterization. The sensitive Özdemirbey sunflower variety was used for growing O. cumana individuals. Eight simple sequence repeat (SSR) loci (Ocum52, Ocum70, Ocum81, Ocum87, Ocum108, Ocum141, Ocum160, and Ocum196) were used for the evaluation of genetic characterization and diversity of broomrape populations. All studied SSR loci were found to be polymorphic and yielded a total of 22 alleles in 143 samples analyzed. Na = 2.089 (mean number of alleles per locus), Ne = 1.390 (mean effective alleles), I = 0.392 (mean Shannon’s information index), Ho = 0.156 (mean observed heterozygosity), He = 0.239 (mean expected heterozygosity), and PIC = 0.228 (mean polymorphic information content) were calculated to assess genetic diversity of O. cumana populations.. As a result of molecular variance analysis, it was concluded that found that the genetic diversity of the populations was 38% among the population. The remaining 23% and 39% were due to among individuals and within individuals, respectively. The UPGMA method and STRUCTURE analysis divided the studied populations into 2 groups. Cluster I included LK2013, HT2016, T2018, and LE2013 populations, while group 2 included AE2003, AD2018, and MT2013 populations. The results we obtained have enabled us to reach important genetic diversity information about O. cumana, and the information obtained will provide important contributions for planned studies in the future.

Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection

Sesbania sesban (L.) Merr. is a multipurpose legume tree grown primarily for fodder and forage in the tropical and subtropical world. In this study, the Sesbania sesban collection maintained in the International Livestock Research Institute (ILRI) forage Genebank was studied using genome-wide markers generated on the DArTseq platform. Genotyping produced 84,673 and 60,626 SNP and SilicoDArT markers with a mean polymorphic information content of 0.153 and 0.123, respectively. From the generated markers, 7587 and 15,031 highly informative SNP and SilicoDArT markers, respectively, were filtered and used for genetic diversity analysis and subset development. Analysis of molecular variance (AMOVA) revealed higher variability 'within' (52.73% for SNP markers and 67.36% for SilicoDArT markers) than 'between' accessions. Hierarchical cluster analysis showed the presence of four main clusters in the collection. Mantel correlation analysis showed a lack of relationship between genetic variation of the germplasm and their geographical origin. A representative subset of 34 accessions containing germplasm from diverse origins and agro-ecologies was developed using SNP markers. The genetic diversity information generated in this study could be used for marker-assisted screening for stress tolerance, gap analysis and identification and acquisition of new distinct genotype(s) to broaden the genetic basis of the collection for future improvement programs to develop high-yielding, stress-tolerant varieties for enhancing food and environmental security in crop-livestock-based production systems.

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

GENETIC DIVERSITY OF ALPINIA MALACCENSIS (BURM.F.) ROSCOE (ZINGIBERACEAE) IN JAVA ISLAND, INDONESIA

Alpinia malaccensis (Burm.f.) Roscoe is a rare plant in Java, Indonesia, that produces essential oils. Its sustained decline causes great concern for future uses. Therefore, the study of its diversity in its natural habitat to predict future survival needs serious focus. The present study aims to determine the genetic diversity of A. malaccensis in Java based on ISSR markers. The sampling of a total of 11 populations yielded 33 accessions, which underwent amplifying using 12 ISSR primers. Using the molecular data analyzed their relationships, population structure, and genetic diversity. The UPGMA cluster, structure, and principal component analysis (PCA) demonstrated that the accessions divide in three groups, a result that correlates with their geography in Java. Group I consisted of var. malaccensis populations, while groups II and III comprised the var. nobilis populations, which proved truer among populations of var. nobilis. The genetic diversity category of A. malaccensis showed moderate based on Nei's genetic diversity (h = 0.2892) and Shannon's information index (I = 0.4438). The coefficient of genetic differentiation (GST) and molecular variance among the populations displayed higher within the individual population, which revealed a significant genetic variance among the 11 populations of A. malaccensis. The latest results confirm that ISSR markers can help distinguish the genotypes of A. malaccensis.

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.

Molecular characterization and prevalence of bovine hemoprotozoan and rickettsial organism from Bhubaneswar, Eastern India

The blood parasites adversely affect the bovine population and are one of the major hindrances to productivity and health of livestock, globally. This study aimed to study the prevalence of some bovine hemoparasites, their molecular characterization, and associated risk factors in and around Bhubaneswar, a place in Eastern India. Microscopy (Giemsa stained thin blood smear) and polymerase chain reaction (PCR)-based prevalence studies were undertaken for a total of 106bovine blood samples belonging to different breed, age, and sex presented to Veterinary Clinical Complex. DNA was extracted by conventional method and primer targeting msp5 gene (382 bp) for Anaplasma marginale, Tams1 gene (572 bp) for Theileria annulata and VSG RoTat 1.2 gene (110 bp) for Trypanosoma evansi, were used. Sequencing and phylogenetic analysis were also carried out for representative PCR products. The risk factors were correlated with prevalence by logistic regression analysis. Blood smear examination revealed a prevalence an overall of 48.11% (51/106) out of which the prevalence of T. annulata, A. marginale and T. evansi, and concurrent infection were reported to be 26.42%, 10.38%, 3.77%, and 7.55% respectively. All the samples found positive in microscopy were also found positive in PCR. PCR assay revealed an overall prevalence of 73.58% (T. annulata: 37.74%, A. marginale:17.92%, T. evansi: 5.66% and concurrent infection:12.26%). A higher prevalence was observed in the age group of 2–4 years (37.74%), females (61.32%) and cross-bred Jersey (50%). Representative PCR products were sequenced and assigned by GenBank (OL550058: A. marginale; OL604429: T. annulata and OL550059: T. evansi). There is a paucity of disease mapping of these parasites in most parts of the country. The study is probably the first report of molecular characterization of T. evansi and A. marginale from the region which gives some information of possible genetic diversity of the isolates circulating in the region. Future research should include large-scale epidemiological surveys as well as concurrent diagnosis of these hemoparasites for better treatment and control strategies.

Diagnosis of a Single-Nucleotide Variant in Whole-Exome Sequencing Data for Patients With Inherited Diseases: Machine Learning Study Using Artificial Intelligence Variant Prioritization

Background In recent years, thanks to the rapid development of next-generation sequencing (NGS) technology, an entire human genome can be sequenced in a short period. As a result, NGS technology is now being widely introduced into clinical diagnosis practice, especially for diagnosis of hereditary disorders. Although the exome data of single-nucleotide variant (SNV) can be generated using these approaches, processing the DNA sequence data of a patient requires multiple tools and complex bioinformatics pipelines. Objective This study aims to assist physicians to automatically interpret the genetic variation information generated by NGS in a short period. To determine the true causal variants of a patient with genetic disease, currently, physicians often need to view numerous features on every variant manually and search for literature in different databases to understand the effect of genetic variation. Methods We constructed a machine learning model for predicting disease-causing variants in exome data. We collected sequencing data from whole-exome sequencing (WES) and gene panel as training set, and then integrated variant annotations from multiple genetic databases for model training. The model built ranked SNVs and output the most possible disease-causing candidates. For model testing, we collected WES data from 108 patients with rare genetic disorders in National Taiwan University Hospital. We applied sequencing data and phenotypic information automatically extracted by a keyword extraction tool from patient’s electronic medical records into our machine learning model. Results We succeeded in locating 92.5% (124/134) of the causative variant in the top 10 ranking list among an average of 741 candidate variants per person after filtering. AI Variant Prioritizer was able to assign the target gene to the top rank for around 61.1% (66/108) of the patients, followed by Variant Prioritizer, which assigned it for 44.4% (48/108) of the patients. The cumulative rank result revealed that our AI Variant Prioritizer has the highest accuracy at ranks 1, 5, 10, and 20. It also shows that AI Variant Prioritizer presents better performance than other tools. After adopting the Human Phenotype Ontology (HPO) terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108). Conclusions We successfully applied sequencing data from WES and free-text phenotypic information of patient’s disease automatically extracted by the keyword extraction tool for model training and testing. By interpreting our model, we identified which features of variants are important. Besides, we achieved a satisfactory result on finding the target variant in our testing data set. After adopting the HPO terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108). The performance of the model is similar to that of manual analysis, and it has been used to help National Taiwan University Hospital with a genetic diagnosis.

Pewarisan Karakter Kuantitatif Persilangan Tanaman Melon

One of the efforts to solve the problem of limited quality melon seeds is to assemble melon varieties with distinctive fruit characters in terms of shape, taste, and color of the flesh. In general, farmers choose meon seeds that have a sweet taste, flesh color, large fruit size, and have a long shelf life . Analysis of quantitative character inheritance is very important in plant breeding programs. This analysis is used to obtain genetic information consisting of the number of genes controlling the character, gene action, genetic diversity, heritability and other genetic information. This study aims to study the inheritance pattern of several quantitative characters in melon crosses. The research design was a randomized block design with eight genotypes as treatment. The results showed that there was a maternal effect on the two crosses of melon plants G1 ((PK-669 x D-612) and G3 ((PK-361 x PK-165) on the characters of fruit diameter, fruit length, fruit weight, and leaf area. Heritability values in a broad sense on all parameters ranged from 0.95-1.00.

Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean.

The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat.

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

Mitochondrial COI Haplotype Diversity of Rhynchobatus australiae Collected from Ketapang Fish Port, Bangka Belitung Islands

Rhynchobatus australiae is a member of the Rhinidae family and can be found in the Indo Pacific. This species is categorized as Critically Endangered according to The International Union for Conservation of Nature and Natural Resources (IUCN) Red List and listed as Appendix II Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), due to population declines. Sustainable fisheries management is urgently needed. Information related to genetic diversity is one of the most important aspects of information for appropriate sustainable fisheries management. Therefore, this research aims to investigate the genetic diversity of Rhynchobatus australiae collected from Ketapang Fish Port Bangka Belitung Islands. Total 21 samples were collected at Ketapang Fish Port. DNA extraction was carried out using the 10% chelex method and amplification was done through PCR method on the mitochondrial DNA using Fish BCL and Fish BCH primer. Sequences in size of 653 base pairs were successfully obtained from all fish samples showing the existence of 2 clades from the construction of the phylogeny tree with close genetic distance. Results showed high haplotype diversity (Hd: 0.733 ± 0.082) and low nucleotide diversity (π: 0.00176± 0.00036) with 6 polymorphic sites (S) from 7 unique haplotypes (h). This research provides basic information of genetic diversity of Rhynchobatus australiae collected from Ketapang Fish Port and complements other information to better understand the status of the threatened Rhynchobatus australiae population.

Genetic diversity and marker trait association for phytophthora resistance in chilli.

Chilli is an important commercial crop with positive returns tendency. Phytophthora root rot causes drastic damage to chilli plant. Dearth of detecting marker trait associations is a major hinderance in practicing marker assisted selection in chilli breeding. Herein, 110 chilli accessions were assessed for 15 agronomic traits under control and disease infected conditions for two crop seasons (2018-2019). The SSR genotyping revealed high values of major allele frequency (MAF = 0.70), genetic diversity (GD = 0.39) and Polymorphic Information Content (PIC = 0.31). Principal coordinate analysis and population structure analysis showed distribution of diverse genotypes in all groups by dividing 110 genotypes in three populations and nine sub-populations. The UPGMA based Archaeopteryx tree was in concordance with population structure analysis. Linkage disequilibrium analysis evaluated that LD decays within 3-10bp. Marker trait association (MTA) revealed the associations of 35 SSRs with 14 morphological traits. The significant MTA for marker CAeMS073 with relative leaf damage (RLD, 0.183 R2) under control and treated conditions was consistently observed in both models. The markers, CAMS173 and CAMS194 were found to be strongly associated with RLD and Disease Index (DI), respectively. The absence of MTA was detected for height of first branch. The MTAs reported in this study can facilitate marker assisted breeding for developing chilli germplasm resistant against Phytophthora capsici.

Using SPAdes, AUGUSTUS, and BLAST in an Automated Pipeline for Clustering Homologous Exome Sequences.

Cross-species exome sequencing approaches provide unprecedented avenues for obtaining genetic diversity, evolutionary relationships, and functional information from a variety of organisms including non-model species. These approaches offer cost-effective opportunities to study multiple individuals or species in parallel, but also create bioinformatics challenges in the application of multiple but powerful bioinformatics tools for the identification of homologous gene families across individual or species boundaries. Popular tools of this kind include SPAdes for sequence assembly, AUGUSTUS for ab initio gene prediction, and BLAST for building homologous sequence families. These tools can also be sophisticated in terms of installation and usage. Here, we present detailed steps on how to run these tools for the recovery and clustering of exon sequences from cross-species raw exome-capture data into homologous sequence families. We also present a utility pipeline, CODSEQCP, that automates these steps to cluster exon sequences, facilitating population genomics and evolutionary studies. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Reads assembly using SPAdes Basic Protocol 2: Coding sequence extraction using AUGUSTUS Basic Protocol 3: Sequence clustering using BLAST Alternate Protocol: How to run CODSEQCP.

Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2.

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion–deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.

Susceptibility assessment and genetic population structure associated with Rhizoctonia solani AG3-PT - Potato stem canker disease

Rhizoctonia solani Kühn AG3-PT causes stem canker (SCD), and significantly impacts potato, Solanum tuberosum L. production globally. However, up to date, there are few resistant or tolerant potato cultivars to R. solani. Given the importance of the subject, we screened ninety-two potato genotypes to SCD, R. solani in the field and greenhouse conditions. Of which, fifty genotypes were subjected to genetic diversity analyzing using 20 Inter Simple Sequence Repeats (ISSR) primers. SCD severity on genotypes ranged from 5 to 73% in the field, and out of 20 used ISSR primer pairs, 14 primers generated 485 loci, of which 216 (45%) showed polymorphic bands. The highest percentage (67%) of polymorphisms was in uBC834 primer. Polymorphism information content value varied from 0.262 to 0.459 with an average of 0.338. Nei's measure of average population genetic diversity per locus ranged from 0.06 to 0.5. Effective number of alleles, Nei's genetic diversity and Shannon's Information Index were 1.530, 0.266, and 0.392, respectively. uBC834 and uBC811 primers identified the most polymorphic loci. According to simple-matching coefficient, the highest similarity (99%) was among “KSG64”, “KSG82”, ‏“KSG81”, ‏“KSG21”, “KSG31”, and “KSG109”, and lowest similarity (54%) in “8708/177” and “KSG300”. Thus, resistant sources can play a significant role in disease management in an integrated pest management planning program. Moreover, diverse potato resistant/susceptible genotypes reported in this study will be useful to generate mapping populations for potato and work in breeding programs for developing and releasing new resistant cultivars for SCD, R. solani infection.

Molecular detection and phylogenetic analysis of pigeon circovirus from racing pigeons in Northern China

BackgroundPigeon circovirus (PiCV) infections in pigeons (Columba livia) have been reported worldwide. Currently, pigeon racing is becoming increasingly popular and considered to be a national sport in China, and even, the greatest competitions of racing pigeons are taking place in China. However, there are still no epidemiologic data regarding PiCV infections among racing pigeons in China. The purpose of our study was to provide information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China.ResultsTo trace the prevalence, genetic variation and evolution of PiCV in sick and healthy racing pigeons, 622 samples were collected from 11 provinces or municipalities in China from 2016 to 2019. The results showed that the positive rate of PiCV was 19.3% (120/622) at the sample level and 59.0% (23/39) at the club level, thus suggesting that the virus was prevalent in Chinese racing pigeons. A sequence analysis revealed that the cap genes of the PiCV strains identified in our study displayed a high genetic diversity and shared nucleotide homologies of 71.9%–100% and amino acid homologies of 71.7%–100%. 28 and 36 unique amino acid substitutions were observed in the Cap and Rep proteins derived from our PiCV strains, respectively. A cladogram representation of PiCV strains phylogeny based on 90 cap gene sequences showed that the strains in this study could be further divided into seven clades (A, B, C, E, G, H, and I) and some of them were closely related to worldwide strains from different types of pigeons. A large number of recombination events (31 events) were also detected in the PiCV genomes from Chinese racing pigeons.ConclusionsThese findings indicate that PiCV strains circulating in China exhibit a high genetic diversity and also contribute to information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China.

Genetic diversity in natural population of Notopterus notopterus evaluated through mitochondrial DNA marker ATPase 6/8 regions and cytochrome b gene.

Population structure and genetic diversity of bronze featherback Notopterus notopterus, fish was not studied yet from Pakistan. So, genetic diversity and population structure of N. notopterus was analysed using two mitochondrial DNA genetic markers, ATPase 6/8 and Cytochrome b. 150 specimens were collected from five different rivers of Pakistan, resulting 56 haplotypes were detected for ATPase 6/8, Cytb and concatenated gene. Haplotype and nucleotide diversity for ATPase 6/8, Cytb and concatenated gene was observed below 1% among five natural populations of N. notopterus. ATPase 6/8 and Cytb genetic variance among populations was 6% and among and within individuals was 94%. Concatenated genetic variance among populations was 11%, among individual 5% and within individuals 84%. Fst value among all population was found 0.091 (p-value=0.02, p<0.05). The combined data set mean coefficient of genetic differentiation (FST) was 0.5572. The pair-wise FST was 0.000 (Chenab) to 0.88911 (Ravi). Maximum likelihood phylogeographic history of concatenated gene haplotypes showed four distinct diversified clusters. AMOVA, PCoA (Principal Coordinate Analysis) and maximum likelihood tree indicated that the natural populations of N. notopterus were comprised of four genetic stocks among five Pakistani rivers (Chenab, Indus, Jehlum, Ravi and Satluj). This study provides the higher level of genetic diversity with confirmatory proofs among genetic stocks of five natural populations of N. notopterus. The information of genetic diversity and genetic variation, from this research can be utilised to help conserve and manage the species in the wild.