Genetic Distance Analysis Research Articles

Coinfection of cotton plants with cotton leafroll dwarf virus‐atypical and a novel cotton begomovirus

AbstractCotton is a commercial crop of global importance whose versatile fibre is widely used in the textile industry. Cotton is vulnerable to infectious pathogens, including viruses, that are a major threat to cotton production. Cotton blue disease is caused by cotton leafroll dwarf virus (CLRDV), a polerovirus transmitted by aphids. This virus is controlled by sowing cotton varieties resistant to CLRDV, although, in recent years an atypical variant (CLRDV‐at), that breaks the resistance, has been identified. An outbreak of a disease occurred in cotton fields of the province of Chaco, in the north‐west of Argentina, in the 2014–2015 growing season. NuOpal cotton plants (a variety resistant to CLRDV and susceptible to CLRDV‐at) showed mosaic symptoms and had virus‐transmitting insect vectors, such as aphids and whiteflies (Bemisia tabaci). The symptoms were common for virus infections but different from those caused by CLRDV or CLRDV‐at. According to a reverse transcription‐PCR analysis with polerovirus primers and sequencing, the plants contained CLRDV‐at. To identify the complete virome of these plants, we performed a massive RNA‐based deep sequencing assay using Illumina technology. As a result, a new begomovirus that infects cotton in Argentina was identified. Structural and functional annotation indicated that its sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, which we propose to name cotton mosaic virus (CoMV). In addition, we report the first begomovirus and polerovirus coinfection in cotton.

Sequencing of the Complete Mitochondrial Genome of the Big Brown Mactra Clam, Mactra grandis (Venerida: Mactridae).

Mitochondrial genomes are playing an increasingly important role in molluscan taxonomy, germplasm, and evolution studies. The first complete mitochondrial genome of the commercial big brown mactra clam, Mactra grandis, was characterized using Illumina next-generation sequencing in this study. The 17,289 bp circular genome has a typical gene organization of 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, with an obvious (A + T)-bias of 64.54%. All PCGs exhibited a homogeneous bias in nucleotide composition with a (A + T)-bias, a positive GC skew, and a negative AT skew. Results of phylogenetic analysis showed that Mactra grandis was most closely related to Mactra cygnus. The functional gene arrangement of the two species was identical but different from other Mactra species. The congeneric relationships among Mactra species were demonstrated by genetic distance analysis. Additionally, the selective pressure analysis suggested that cox1 was highly efficient for discriminating closely related species in genus Mactra, while nad2 was the most appropriate marker for population genetic analysis.

Angiopterisnodosipetiolata (Marattiaceae), a new fern species from Yunnan, China.

Angiopterisnodosipetiolata Ting Wang tris, H.F.Chen & Y.H.Yan, a new fern of Marattiaceae, is described and illustrated. Morphologically, A.nodosipetiolata is similar to A.chingii with more than one naked pulvinus on the stipe and numerous jointed hairs on the undersides of the mature pinnae. However, the pinnae of A.nodosipetiolata are lanceolate and can reach up to 4-6 pairs, whereas they are elliptic and occur in 2-3 pairs in A.chingii. Phylogenetic and genetic distance analysis, based on the plastid genomes, also indicates that A.nodosipetiolata is not closely related to A.chingii. Currently, there are ca. 500 mature individuals in Gulinqing Nature Reserve and we suggest A.nodosipetiolata should be categorised as an Endangered (EN) species according to the criteria of IUCN.

Mitogenomic profiling of Marcia recens (Holten, 1802): a step towards taxonomic resolution of India's Ashtamudi short-neck clam

ABSTRACT The Ashtamudi short-neck clam forms a significant fishery resource holding India’s first Marine Stewardship Council Certification. The taxonomic classification of this particular clam has engendered debate regarding its proper nomenclature. The present study aims to provide its first comprehensive mitogenome profile from the type locality to address the existing taxonomic ambiguity. The mitogenome assembled using the genome skimming method had 17,991 base-pair length with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and control region. Phylogenetic analysis based on the concatenated data set of PCGs and rRNAs from 47 representative species of Veneridae grouped all species including short-neck clams from the subfamily Tapetinae into a single clade. This analysis also revealed the polyphyly of the genus Marcia. Nevertheless, the short-neck clam co-clustered with Marcia recens from Chinese waters. Subsequent mitochondrial gene order, genetic distance and morphological analyses substantiated the closer relationship of this clam to the genus Marcia, analogous to the phylogenetic output. The genomic data from the type locality provides additional molecular and phylogenetic evidence for the classification of short-neck clam in the genus Marcia. This will also help to address long-standing taxonomic uncertainties surrounding this species, offering valuable information critical for management and conservation of the resource.

Refining taxonomic identification of microalgae through molecular and genetic evolution: a case study of Prorocentrum lima and Prorocentrum arenarium.

Species delimitation based on lineage definition has become increasingly popular. However, these methods have been limited, especially for species that lack genomic data and are morphologically similar. The trickiest part for the species identification is that the interspecific and intraspecific boundaries are vague. Taking Prorocentrum (Dinophyta) as an example, analysis of cell morphology, growth, and toxin synthesis in both species of P. lima and P. arenarium does not provide a reliable basis for species delineation. However, through phylogenetic and genetic distance analyses of their ITS and LSU sequences, establishment of evolutionary tree based on orthologous gene sequences, and combining the results of automatic barcode gap discovery and Poisson tree processes models, it was sustained that P. arenarium does not belong to the P. lima complex and should be considered as an independent species. Interspecies genetic evolution analysis revealed that P. lima and P. arenarium may contribute to evolutionary direction that favors combating reverse environmental factors. In P. lima, viral invasion may be one of the reasons for its large genome size. In the study, P. lima complex has been selected as an example to enhance the taxonomic identification of microalgae through molecular and genetic evolution, offering valuable insights into refining taxonomic identification and promoting microbial biodiversity research in other species.IMPORTANCEMicroalgae, especially the species known as Prorocentrum, have received significant attention due to their ability to trigger harmful algal blooms and produce toxins. However, the boundaries between species and within species are ambiguous. Clear and comprehensive species delineation indicates that Prorocentrum arenarium should be considered as an independent species, separate from the Prorocentrum lima complex. Improving the classification and identification of microalgae through molecular and genetic evolution will provide reference points for other cryptic species. Prorocentrum occupy multiple ecological niches in marine environments, and studying their evolutionary direction contributes to understanding their ecological adaptations and community succession.

Haplotype diversity of 17 Y-STR in the Iranian population

The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.

High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins.

Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.

Molecular Identification and Phytochemical Analysis and Bioactivity Assessment of Catharanthus roseusLeaf Extract: Exploring Antioxidant Potential and Antimicrobial Activities.

Plants have long been at the main focus of the medical industry's attention due to their extensive list of biological and therapeutic properties and ethnobotanical applications. Catharanthus roseus, sometimes referred to as Nithyakalyani in Tamil, is an Apocynaceae family member used in traditional Indian medicine. It also examines the plant's potential antimicrobial and antioxidant activities as well as its preliminary phytochemical makeup. Leaf material from C. roseus was analyzed and found to include a variety of phytochemicals including alkaloids, terpenoids, flavonoids, tannins, phenols, saponins, glycosides, quinones, and steroids. Four of the seven secondary metabolic products discovered in C. roseus leaves showed bioactive principles: 3-methylmannoside, squalene, pentatriacontane, and 2,4,4-trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene. Catharanthus roseus is rich in the anticancer compounds vinblastine and vincristine. Whole DNA was isolated from fresh leaves, then amplified, sequenced, and aligned to find prospective DNA barcode candidates. One DNA marker revealed the restricted genetic relationship among C. roseus based on genetic distance and phylogenetic analysis. The antioxidant activity of the plant extract was evaluated using the DPPH, ABTS, phosphomolybdenum, FRAP, and superoxide radical scavenging activity assays, while the antibacterial potential was evaluated using the agar well diffusion assay. The ethanol extract of C. roseus was found to have the highest reducing power. In addition, a 4- to 21-mm-wide zone of inhibition was seen when the C. roseus extract was tested against bacterial and fungal stains. In conclusion, C. roseus has the most promise as an antibacterial and antioxidant agent.

DNA barcoding using chloroplast matK and rbcL regions for the identification of bamboo species in Sabah

Bamboo species play pivotal roles in maintaining ecological diversity and driving socio-economic development in Sabah, Malaysia. However, due to overlapping traits among distinct bamboo species, identifying them based solely on morphological characteristics poses challenges. DNA barcoding emerges as a highly effective method, demonstrating potential accuracy in identifying diverse plant species across various taxa and ecosystems. In this study, we used the chloroplast matK and rbcL regions as barcode markers to identify 15 bamboo plants in Sabah. Both matK and rbcL exhibited a notable 100% accuracy at the genus level, indicating their reliability in capturing broader taxonomic categories during BLAST searches and genetic distance analysis. However, at the species level, the success rate was limited to 60%, revealing challenges in differentiating closely related bamboo species using the existing DNA barcodes. Our findings underscore the need for an advanced DNA barcode reference library with extensive species coverage for accurate species identification. This study not only unveiled crucial insights into bamboo diversity and taxonomy in Sabah but also contributes to ongoing bamboo resource conservation and supports sustainable resource management in the region.

Genetic characterization of 2 Ceutorhynchus (Coleoptera: Curculionidae) weevilswith mitogenomes and insights into the phylogeny and evolution of related weevils.

The rape stem weevil (Ceutorhynchus asper Roel.) andits close relatives primarily breed on cruciferous plants and cause severe damage to rapeseed production. However, their genetic and molecular information is still scarce. Here, we generated mitogenomes for both C. asper and Ceutorhynchus albosuturalis. The lengths of the 2 mitochondrial genomes are 14,207bp (C. asper) and 15,373bp (C. albosuturalis), and both weevils exhibit identical numbers of protein-coding genes with the absence of trnI. A + T contents for both mitogenomes are high (80% and 79.9%, respectively). Haplotype and genetic distance analyses showed that the genetic differentiation of C. asper populations in northwestern China is low. Based on 5 datasets from mitogenomes, phylogenetic analyses with maximum-likelihood and Bayesian methods show that both species (C. asper and C. albosuturalis) fall in the CCCMS clade (Curculioninae, Conoderinae, Cossoninae, Molytinae, and Scolytinae) of Curculionidae and belong to clades H and I of the genus Ceutorhynchus, respectively. Larvae of the clade H weevils mainly are borers in petioles or stems of cruciferous plants, while larvae of the clade I weevils mainly inhabit the fruits of the same plants, suggesting that ecological niche specialization can play a critical role in the diversification of Ceutorhynchus species. This study generates baseline molecular and genetic information for future research of Ceutorhynchus-related taxa and provides insights into the phylogeny and evolution of Curculionidae.

The Mexican Balsam, Impatiens mexicana Rydb: A Redescription Based on Morphological and Phylogenetic Studies, with an Update of the Current Geographical Range of the Species

Impatiens mexicana is a native balsam restricted to the cloud forests of central and southwest Mexico, which is currently known to exist in four states (Zacatecas, Veracruz, Puebla, and Oaxaca), and is probably threatened by geographic restriction. Morphological and distributional information about this species is still scarce, with only a couple of investigations since its first description in 1910, which means the phylogenetic position of this species has yet to be placed. In order to contribute to knowledge of I. mexicana, morphological and molecular studies were carried out with material collected in the localities of Hidalgo, Veracruz, and Oaxaca, during expeditions from July to October 2021 and in 2022. The specimens selected were measured, photographed, and compared with morphological information from the six American balsams. At the same time, phylogenetic studies were carried out by using two regions of the cpDNA and one of the nrDNA. We report I. mexicana for the first time in Hidalgo state, and identify new registers in the Veracruz and Oaxaca localities, thus increasing the knowledge in its geographic distribution. We also redescribe the Mexican balsam by using new and complementary traits: we note that while the species is morphologically similar to I. capensis, it is distinguished by differences in flower color, the distribution of spot patterns on the upper petal, lower sepal, and lateral petals, and geographic information such as endemic geographic distribution in Mexico’s Tropical Montane Cloud Forest (TMCF). We also carried out phylogenetic analyses by using ITS and ITS + atpb-rbcL, which showed the Mexican balsam was independent from its Asian-American congeners. Interestingly, our genetic distance analyses reveal differences of 0.01–0.16% between I. mexicana and the other North American congeners that use ITS, atpb-rbcL and trnL-F, both independently and as concatenated genes: this low divergence most likely occurred because of the recent diversification of the group. However, both future redescriptions and phylogenetic studies in American species are imperative, as this will enable better discrimination.

GENETIC CHARACTERIZATION IN FOUR INDONESIAN CATTLE BREEDS INFERRED FROM ILLUMINA PARENTAGE SNP MARKERS

Genetic characterization in native livestock is essential to conserve the genetics standard of livestock for pure-breeding programs. This research aimed to characterize four Indonesian cattle breeds using 156 sites of Parentage SNP Markers, includingARS-USMARC-Parent (119 sites) and ARS-USMARC (37 sites). Total of 113 mixed-sex animals were used for the evaluation, including 16 Bali (Bos javanicus), 16 Madura (Bos indicus), 33 Ongole grade (Bos indicus), and 48 Sumba Ongole (Bos indicus) cattle breeds. Results showed Bali, Madura, and Ongole lineage (Ongole grade and Sumba Ongole) cattle can be discriminated against with the Parentage SNP Markers. The pairwise genetic distance analysis revealed that Bali cattle had a closer genetic relationship with Madura cattle (0.043 - 0.151) than Ongole lineage cattle (0.073 - 0.325). However, the phylogenetic tree explained that the Ongole lineage cattle are grouped into two different clades. At the same time, Bali, Madura and Ongole lineage cattle are grouped into their original cluster. The study suggests that the Parentage SNP Markers can be used to characterize Bali, Madura, and Ongole lineage cattle accurately.

The Nanling Mountains of southern China played a variable role as a barrier and refuge for birds depending upon landscape structure and timing of events

The Nanling Mountains, an important mountain range and watershed in south China, harbor a wealth of relictual plant species, and are considered a ‘museum' of subtropical biodiversity. With respect to birds, however, the roles of the Nanling Mountains in impeding the dispersal of the subtropical birds and, as a result, shaping their population and community structures have received little consideration. To examine these roles, we compiled and analyzed two datasets. 1) To test the mountains' influence on gene flow, we undertook a comparative phylogeographic study comparing mitochondrial COI and Cytb DNA sequences of five sylvioid resident bird species of the mountains (Huet's fulvetta Alcippe hueti, red‐billed leiothrix Leiothrix lutea, greater necklaced laughingthrush Pterorhinus pectoralis, Indochinese yuhina Staphida torqueola and mountain bulbul Ixos mcclellandii). 2) To examine differential community development over the history of modern birds, we examined distributional data of all species of the Nanling region using public species occurrence records. For part 1), we sampled 327 individuals from 36 sites and conducted correlation analysis of genetic and geographic distances, taking into account the landscape of the mountains. We found that the mountains do not seriously impede gene flow among populations but influenced species differently. For part 2), comparative analysis of 446 species in 81 families indicated that family membership influenced the community composition of birds in Nanling region. Variation in family distributions is attributable to both environmental and evolutionary factors. Overall, we found that the Nanling Mountains are not currently a substantial barrier to gene flow among the species we studied but act as a corridor and refuge for these birds. However, analyses on higher ranked community data suggest the mountains acted as a barrier in older times, corresponding to the known diversification events in southeast Asian avifauna.

Redes neurais artificiais para descritores morfológicos em germoplasma de alface biofortificada

ABSTRACT The classification based on morphological descriptors in lettuce is considered a complex activity and proves to be efficient for studying phenotypic characteristics. Therefore, the objective of this study was to analyze the biofortified lettuce germplasm bank at the Universidade Federal de Uberlândia using both conventional morphological descriptors and artificial neural networks. The experiment was conducted in the field. The experimental design employed was a randomized complete block design, consisting of 14 treatments (11 genotypes of mini lettuce, and the cultivars Purpurita, UDI 10.000, and Pira 72) with four replications. Nine morphological descriptors were evaluated. Following the data acquisition, dissimilarity matrix analyses, principal component analysis, dendrogram construction, and artificial neural network (ANN) analyses were performed. The genotypes exhibited phenotypic variability when compared to the parental strains UDI 10.000 and Pira 72. The purple color of the leaves and anthocyanin presence across the entire leaf surface were predominant among the genotypes. Descriptors such as leaf intensity and color, as well as anthocyanin intensity, coloration, and distribution, were the most influential in assessing genetic variability. The Self-Organizing Map (SOM) demonstrated greater sensitivity in discriminating between genotypes compared to the Unweighted Pair Group Method with Arithmetic Mean (UPGMA). While the UPGMA clustering method grouped genotypes into three clusters, the SOM method grouped into five clusters. The use of genetic distance analyses and SOM dendrogram proved to be effective in selecting individuals UFU 215#1, UFU 215#2, UFU 215#6, UFU 215#10, and UFU 215#13, which are clustered with the cultivar UFU Mini Biofort.

Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding.

Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.

Morphological and genetic identification of Halophila species and a new distribution record of Halophila nipponica at the Tanjung Adang Laut shoal, Johor, Malaysia.

The Halophila species exhibit complex characteristics due to their high degree of variation across different bioregions. This study delves into the intricate characteristics of Halophila species in the Tanjung Adang Laut shoal, Johor, Malaysia, and offers valuable insights through morphological and genetic evidence. Employing internal transcribed sequences (ITS), we investigated the phylogeny of Halophila species, revealing distinct clades for H. ovalis, H. major, H. spinulosa, and the newly recorded H. nipponica. Notably, H. nipponica from the Tanjung Adang Laut shoal formed a conspecific relationship with its counterparts from Japan and Korea (98.3-98.5% similarity; 5-11 bp differences). Morphologically, distinguishing features, including the ratio of the half-lamina width (1:4.76-6.13 mm) and cross-vein count (4-7 pairs), supported the identification of H. nipponica. Genetic distance analyses revealed differences between H. nipponica, H. ovalis, and H. major, indicating haplotype diversity. Geographical variations were evident, as H. nipponica presented unique haplotypes (H24) in its clade. The 47 haplotypes network identified significant mutation sites, providing a comprehensive understanding of genetic and morphological distinctions. In conclusion, this study highlights the intricate characteristics and phylogeny of Halophila species in the Tanjung Adang Laut shoal, Johor, and provides valuable insights into their genetic and morphological diversity.

Immunogenetic characteristics of sheep breeds of the Siberian-Far Eastern region

A comparative analysis of eight breeds of sheep (medium-wool, coarse-wooled, semifine-wool and fine-wool) bred in the Siberian-Far Eastern region was carried out. The research used the data on immunogenetic testing of sheep in breeding farms for a number of years. The testing was performed using 14 specific sera – reagents. The allelic profile of sheep, their similarities and differences related to phylogeny and previous selection were studied. All breeds studied had a distinctive allelic profile. Both frequent and infrequent antigens were identified in each breed. Based on antigen frequencies, an index of genetic similarity (r) was calculated, which was higher in the breeds of the same productivity direction, e.g. between Buubei and Edilbaevskaya breeds (r = 0.912), and lower between the breeds that were selected in isolation from each other. The lowest index of genetic similarity was found between the Buryat and West Siberian meat breeds (r = 0.707). Breeds of the same productivity direction from different regions also have distinctive features. The index of genetic similarity between coarse-wooled breeds (Buubei and Edilbaevskaya) is 0.912; between medium-wool breeds (Buryat and Aginskaya) it is at the level of 0.739; between semifine-wool breeds (Gorno Altai and West Siberian meat breeds) – 0.845; between fine-wool breeds (Kulunda and Zabaikalskaya) – 0.902. Using the cluster analysis of genetic distances, the relationships of breeds, their origin, and phylogeny were determined. West Siberian Meat and Kulunda breeds formed one cluster, Buubei and Buryat breeds were also included in one cluster. More distant breeds were Aginskaya (Zugalai type) and Edilbaevskaya.

Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig

Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090th to 1099th position, deletion of a 10 bp sequence at the 755th position, insertion of (CA) at the 137th position, and substitution of AT to GA at the 638th position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.

The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

AbstractThailand’s northeast (NE) region is an area of high-quality cultivated rice (Oryza sativa L.) production. However, an outbreak of weedy rice has recently spread throughout the region. Weedy rice is phenotypically and morphologically similar to cultivated rice, making identification difficult. The prospective management of weedy rice in the future will involve the study of its genetic diversity and population structure in this region. This study assesses the genetic diversity and population structure of 380 weedy rice samples in the northeast of Thailand through simple sequence repeat (SSR) markers. Thirty-one SSR markers generated 213 alleles with an average of 6.87 per locus and an overall genetic diversity of 0.723. Based on its geographic origin, weedy rice in the Southern NE are showed greater genetic diversity than that in the Central NE and Northern NE areas. The outcrossing rate in all regions was relatively high, with the highest being in the Southern NE at 9.769%. According to genetic distance analysis, the clustering of weedy rice samples in northeast Thailand was not associated with the geographic region. Neighbor-joining and principal coordinate analysis revealed that the 380 weedy rice samples fell into two major clusters. Cluster I contained three weedy rice samples and four wild. In Cluster II, 377 weedy rice samples were closely related to the four cultivated rice cultivars as well as brownbeard rice (Oryza rufipogon Griffiths) wild species. The results suggest that weedy rice in northeast Thailand may have originated as a cross between cultivated and wild rice, as seen in the closely related species, O. rufipogon. Overall, the findings of this study demonstrate the high genetic diversity of weedy rice in this region. Notably, some samples adapted, performing more like cultivated rice, which may be problematic for the future production of high-quality rice in this region. The prevention of weedy rice should, therefore, be given greater consideration in future studies.

Molecular genetics, seed morphology and fatty acids diversity in castor (Ricinus communis L., Euphorbiaceae) Iranian populations.

Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs.