Low Genetic Diversity Research Articles

Occurrence and Subtype Distribution of Blastocystis in Smallholder Dairy Cattle in Bangladesh

Blastocystis is a widespread protozoan known to induce digestive disorders in humans and animals, including cattle globally. The parasite exhibits a significant amount of genetic variability and is divided into 42 recognized subtypes (STs) in mammals and birds. Sixteen of these subtypes are identified in cattle and 14 are zoonotic. This study explored the distribution and genetic variations of Blastocystis and its zoonotic potential in dairy cattle. Two hundred fresh fecal samples were collected from smallholder dairy calves (aged <6 months) in two milk pocket areas of Bangladesh: Sirajganj (n=100) and Pabna (n=100). A molecular study based on PCR assay targeting the small subunit ribosomal RNA (SSU rRNA) gene was employed to screen and subtype the parasite in the fecal samples. Analyses revealed Blastocystis among 10% of the cattle, with 8% positive cases in samples from Sirajganj and 12% in samples from Pabna. Various factors including sex, age, breed groups, and fecal consistency were considered, although these were found to be statistically insignificant. Out of the 20 positive Blastocystis isolates, only three subtypes, namely ST10, ST21, and ST26, were identified where subtype ST10 was the most prevalent. Notably, no zoonotic subtypes were detected in the fecal samples, suggesting a lack of zoonotic significance. The findings provide insights into the molecular epidemiology of Blastocystis infection in cattle, indicating its low genetic diversity in the study areas. Further research is needed to determine the exact frequency and genetic composition of Blastocystis and its zoonotic potential in cattle in Bangladesh. J. of Sci. and Tech. Res. 6(1): 13-20, 2024

Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

BackgroundThe recent success of a population control gene drive targeting the doublesex gene in Anopheles gambiae paved the way for developing self-sustaining and self-limiting genetic control strategies targeting the sex determination pathway to reduce and/or distort the reproductive capacity of insect vectors. However, targeting these genes for genetic control requires a better understanding of their genetic variation in natural populations to ensure effective gene drive spread. Using whole genome sequencing (WGS) data from the Ag1000G project (Ag3.0, 3.4 and 3.8), and Illumina pooled amplicon sequencing, we investigated the genetic polymorphism of the intron-4–exon-5 boundary of the doublesex gene in the natural populations of An. gambiae sensu lato (s.l.).ResultsThe analyses showed a very low variant density at the gRNA target sequence of the Ag(QFS)1 gene drive (previously called dsxFCRISPRh) within the populations of West and East Africa. However, populations from the forest area in Central Africa exhibited four SNP at frequencies ranging from 0.011 to 0.26. The SNP (2R:48714641[C > T]) at high frequencies, i.e. 0.26 is identified within the An. coluzzii population from Angola. The analyses also identified 90 low frequency (1 − 5%) SNPs in the genomic region around the gRNA target sequence (intron-4–exon-5 boundary). Three of these SNPs (2R:48714472 A > T; 2R:48714486 C > A; 2R:48714516 C > T) were observed at frequencies higher than 5% in the UTR region of the doublesex gene. The results also showed a very low variant density and constant nucleotide diversity over a five-year survey in natural An. gambiae s.l. populations of Burkina Faso.ConclusionThese findings will guide the implementation of doublesex-targeted gene drives to support the current control tools in malaria elimination efforts. Our methods can be applied to efficiently monitor the evolution of any sequence of interest in a natural population via pooled amplicon sequencing, surpassing the need for WGS.

Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species.

The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged in the management of threatened species. The functional consequences of SVs are more complex than for single nucleotide polymorphisms (SNPs), as SVs typically impact a larger proportion of the genome due to their size and thus may be more likely to contribute to load. While the impacts of SV-specific genetic load may be less consequential for large populations, the interplay between weakened selection and stochastic processes means that smaller populations, such as those of the threatened Aotearoa hihi/New Zealand stitchbird (Notiomystis cincta), may harbour a high SV load. Hihi were once confined to a single remnant population, but have been reestablished into six sanctuaries and reserves, often via secondary bottlenecks, resulting in low genetic diversity, low adaptive potential, and inbreeding depression. In this study, we use whole genome resequencing of 30 individuals from the Tiritiri Matangi population to identify the nature and distribution of both SNPs and SVs within this small avian population. We find that SNP and SV individual mutation load is only moderately correlated, likely because SVs arise in regions of high recombination and that are less evolutionarily conserved. Finally, we leverage a long-term monitoring dataset of pedigree and fitness data to assess the impact of SNP and SV mutation loads on individual fitness, and find that SNP and SV realised load had similar negative correlations with lifetime fitness. However, of the masked load metrics, only SVs had a positive significant correlation with lifetime fitness, indicating that masking of deleterious alleles may be more important for SVs than for SNPs. The results of this study indicate that only examining SNPs neglects important aspects of intra-specific variation and that studying SVs has direct implications for linking genetic diversity and genomic health to inform management decisions.

High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies

Abstract Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species’ unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10-3) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of A. pentaphyllum but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments.

Genetic Structure and Diversity of Eurasian Otter (Lutra lutra) in Northern Eurasia and Caucasus: Are There Any Differences Between the Two Subspecies?

The Eurasian otter (Lutra lutra) is a widespread semiaquatic carnivorous mammal in Eurasia. The nominate subspecies (L. l. lutra) occupies vast areas between Western Europe and the Russian Far East, but its phylogeography and genetic diversity are still unclear across Northern Eurasia. Another subspecies, L. l. meridionalis, located in the Caucasus mountains, is morphologically almost identical to L. l. lutra but needs genetic revision. We compared the genetic diversity of Eurasian otters from Russia and Armenia using a mtDNA fragment (820 bp) and 20 autosomal microsatellite loci (N = 117). A total of 32 haplotypes were observed with 17 novel haplotypes. The MtDNA median-joining network was mostly star-shaped with a branch of haplotypes from Far Eastern Russian otters. Both mtDNA analysis and Bayesian clustering of microsatellite data indicated that Far Eastern otters are more genetically differentiated than European and Siberian otters (Φst = 0.565 and 0.467; Rst = 0.306 and 0.256), as well as Caucasian otters (L. l. meridionalis) from Russia and Armenia (Φst = 0.515, Rst = 0.253). Haplotype and nucleotide diversities of Far Eastern otters are also the highest between sample groups (H = 0.882, π = 0.003) and, of Caucasian otters, the lowest (H = 0.464, π = 0.001). Our results suggest Caucasian otters are more similar to the otters from European Russia than to the other groups (but with lower genetic diversity) and lack the genetic variability typical to different subspecies. On the contrary, otters from the Russian Far East are more genetically differentiated, have higher genetic diversity than otters from Europe, and likely belong to another genetic lineage.

Exploring the forensic effectiveness and population genetic differentiation in Guizhou Miao and Bouyei group by the self-constructed panel of X chromosomal multi-insertion/deletions

In this research, a self-developed panel comprising 22 X chromosomal multi-InDels and one X-STR was used to explore the genetic polymorphisms and forensic characteristics of these loci in Guizhou Miao and Guizhou Bouyei populations. Besides, genetic affiliations among Guizhou Miao, Guizhou Bouyei and Guizhou Han populations were investigated using principal component analysis, STRUCTURE and machine learning methods. The findings indicated that these loci in the male and female samples had comprehensive discrimination powers greater than 0.999999999. Meanwhile, the cumulative mean exclusion chance of these 23 loci for trio and duo cases were also greater than 0.9999 in Guizhou Miao and Guizhou Bouyei populations. Population genetic analyses of three Guizhou populations revealed that there were relatively low genetic divergences among these populations based on the self-constructed panel. In conclusion, this system could be utilized as the valuable tool for forensic personal identification and parentage testing in Guizhou Miao and Guizhou Bouyei populations.

Phylogeny and Genetic Population Structure of Dominant Copepods in Two Ponds with Contrasting Salinities in the Solar Saltern of Sfax (Tunisia) Based on Mitochondrial (COI and Cytb) and Nuclear (18S) DNA Sequences

Due to the complexity of taxonomic classification based on the classical morphological characters of copepods, phylogenies have been ambiguous. In this study, we investigate the phylogeny of copepods, including four species from three orders, in the saltern of Sfax using the small subunit of nuclear ribosomal RNA genes (18S). In the studied area, copepods seemed to be a polyphyletic group, and the genetic structure of these crustaceans is complex and problematic. We have also used two mitochondrial markers, the cytochrome c oxidase subunit I (mtCOI) gene and the cytochrome b (Cytb) sequence data, in order to investigate the genetic diversity and differentiation in a total of 96 individuals from two sets of Paracartia grani, sampled from two ponds with different salinities (42 PSU and 61 PSU). All of the results presented here suggest a low genetic diversity among P. grani species and a weak genetic structure between the sets. The nucleotide and haplotype diversity of P. grani were extremely low, indicating the homogeneity of the two sets, which could be combined into one set living in different ranges of salinity. This small genetic diversity is possibly due to the confined natural distribution range and strong selective pressure in a saltern environment. These data also suggest that gene flow is the main factor shaping the genetic structure of the studied sets.

The whole chromosome-level genome provides resources and insights into the endangered fish Percocypris pingi evolution and conservation

BackgroundPercocypris pingi (Tchang) was classified as Endangered on the Red List of China′s Vertebrates in 2015 and is widely distributed in the Upper Yangtze River. Although breeding and release into wild habitats have been performed for this commercially important fish in recent years, low genetic diversity has been found in wild populations. Genomic resources are strongly recommended before formulating and carrying out conservation strategies for P. pingi. Thus, there is an urgent need to conserve germplasm resources and improve the population diversity of P. pingi. To date, the whole genome of P. pingi has not been reported.ResultsIn our study, we constructed the first chromosome-level genome of P. pingi by high-throughput chromosome conformation capture (Hi-C) technology and PacBio long-read sequencing. The assembled genome was 1.7 Gb in size, with an N50 of 17,692 bp and a GC content from circular consensus sequencing of 37.67%. The Hi-C results again demonstrated that P. pingi was tetraploid (n = 98), with the genome consisting of 24-type and 25-type chromosomes. Chr.19 of the 24-type chromosomes in P. pingi resulted from the fusion of chr.19 and chr.22 in zebrafish. The divergence times between 24-type and 25-type chromosomes was around 6.1 million years ago. A total of 25,198 and 25,291 protein-coding genes were obtained from the 24-type and 25-type chromosomes, respectively. The ploidy of P. pingi is an allotetraploid. A total of 8,741 genes of P. pingi were clustered into 4,378 gene families that were shared with 14 other species, and the P. pingi genome had 68 unique gene families. Phylogenetic analyses indicated that P. pingi was most closely related to Schizothorax oconnori, and the genes were clustered on one branch. We identified 166 significantly expanded gene families and 173 significantly contracted gene families in P. pingi. The most enriched positive protein-coding genes, such as Bmp-4, Etfdh, homeobox protein HB9, and ATG3, were screened.ConclusionOur study provides a high-quality chromosome-anchored reference genome for P. pingi and provides sufficient information on the chromosomes, which will lead to valuable resources for genetic, genomic, and biological studies of P. pingi and for improving the genetic diversity, population size, and scientific conservation of endangered fish and other key cyprinid species in aquaculture.

Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia

Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.

Low genetic diversity and identification of two management units for tri-spine horseshoe crab Tachypleus tridentatus (Leach, 1819) in Palawan, Philippines

Low genetic diversity and identification of two management units for tri-spine horseshoe crab Tachypleus tridentatus (Leach, 1819) in Palawan, Philippines

Phylogeography of the Invasive Fruit Fly Species Bactrocera carambolae Drew & Hancock (Diptera: Tephritidae) in South America

The carambola fruit fly, Bactrocera carambolae Drew & Hancock, is native to Southeast Asia, infests about 150 plant species, and is considered a quarantine pest insect in several regions of the world. Bactrocera carambolae has invaded Suriname, French Guyana, and northern Brazil. In Brazil, it was first recorded in 1996 and has been restricted to the states of Amapá and Roraima due to official control efforts of the Ministry of Agriculture and Food Supply (Ministério da Agricultura e Pecuária—MAPA). This is the first study to estimate the genetic structure and diversity of South American populations of B. carambolae. A total of 116 individuals from 11 localities in Brazil and 7 localities in Suriname were analyzed. Additional sequences available at GenBank from Indonesia (Lampung) and Thailand (San Pa Tong and Muang District) were also used in the analysis. We sequenced a fragment of the mitochondrial gene cytochrome oxidase subunit I. A total of 35 haplotypes were found. Haplotypes from Indonesia were closest to the haplotypes from South America, separated only by a few mutational steps. This suggests that Indonesia is the likely source for the introduction of B. carambolae into South America. The Southeast Asian populations appeared as the most ancestral group in the phylogenetic trees. The high similarity and sharing of several haplotypes among populations within South America indicate a lack of genetic structure. The mismatch distribution and neutrality tests suggest that South American populations have undergone a rapid growth and expansion following a single founder event. The low genetic diversity and the population expansion evidenced by the neutrality tests lend support to the hypothesis of a recent introduction of a single lineage of the carambola fruit fly into South America.

Low Genetic Variation Among Trees in Cocoa Hand Pollination in the Offinso Municipality of Ghana Revealed by SSR Markers.

Cocobod introduced nationwide artificial hand pollination in Ghana in 2017 to supplement natural pollination of Theobroma cacao L. (cocoa) by insects (Forcipomyiamidges) to increase yield. Hybrid farms of 8-20years old are mostly selected. Pollen donor and receiver trees are selected based on morphological characteristics. This study analyzed the genetic diversity among donor and recipient trees of cocoa hand pollination in three farms in the Offinso Municipality of Ghana using SSR markers. Twelve forward and reverse primer pairs out of fifteen primers screened were used to evaluate genetic intraspecific and interspecific diversity among 25 accessions based on clear amplification and reproducible scorable bands. A total of 115 polymorphic bands were detected which ranged between 5.00 and 17.00 with a mean of 9.58 alleles per locus. Cluster analysis showed similarity coefficient range of 0.10 to 0.83. Analysis of molecular variance (AMOVA) showed13% genetic variation between populations and 87% within populations of T. cacao. PhiPT value of 0.130 recorded showed weak genetic differentiation between populations. Gene diversity varied from 0.64 to 0.88 with primers MTcCIR33 and MTcCIR07 respectively. Highest observed heterozygosity (Ho) of 0.60 and least Polymorphism Information Content (PIC) of 0.57 were recorded. Pollen donor and recipient trees selected from the same or nearby farms accounts for present genetic structure of low genetic diversity between populations. Though hand pollination designs focus much on high yields, improving genetic diversity to prevent inbreeding in cocoa is recommended.

Genetic diversity of Brucella abortus strains from cattle and water buffalo in the Italian province of Caserta

Brucella abortus is an important zoonotic pathogen that infects cattle and buffaloes. In Italy the application of eradication programs combined with vaccination has greatly contributed to reduce the incidence of brucellosis. However, despite the eradication programs brucellosis continue to persist with a high endemicity in some areas of Italy including the province of Caserta. In the present study the genomes of 44 B. abortus strains isolated from different outbreak cases that affected the province of Caserta were sequenced to characterize the genetic diversity of the Brucella strains circulating during the period from 2017 to 2022. The relatedness among these isolates was compared to 52 publicly available genomes of Italian B. abortus isolates. The results highlighted a low genetic diversity in the B. abortus population present in the Caserta area with the persistence of a low number of Brucella lineages and suggests a reduction in circulating lineages in recent years due to eradication programs.

Identification of molecular marks associated with early flowering in Campomanesia adamantium (Cambess.) O. Berg

Campomanesia adamantium is a fruit species of the Cerrado Biome that stands out for having high economic potential and significant genetic variability. Therefore, knowledge on its development and genetic variability is fundamental to define domestication and genetic improvement actions. In this context, identification of molecular marks that may be related to the early flowering of C. adamantium can provide bases for the assisted selection of early plants at nursery level. The objective of this study was to identify molecular marks associated with early flowering in C. adamantium accessions, using the ISSR molecular marker. A total of 17 ISSR primers were used in 46 accessions of C. adamantium (39 early and 07 late). It can be observed in the results for the 46 accessions that the primers produced a total of 104 bands, with a polymorphism of 96%. When analyzing the amplification pattern of early accessions individually, it was possible to observe the amplification of 103 bands, of which 93% were polymorphic. For late accessions, only 87 bands were amplified, of which only 66.67% were polymorphic, showing that these accessions have lower genetic variability than early accessions. Based on the amplification pattern of the primers between early and late accessions, primers 02, 03, 04 and 05 stood out, as they amplified DNA fragments above 70% in early accessions and that were not found in late accessions. It was concluded that there are four molecular marks with strong relationship with early flowering.

Monitoring Seroprevalence of Infectious Diseases in the Florida Panther (Puma concolor coryi).

Infectious diseases can have detrimental effects on wildlife populations, particularly those that persist at small sizes, have low genetic diversity, and are affected by fragmented habitat. One such example is the endangered Florida panther (Puma concolor coryi), which has been intensively managed since the early 1980s, with the current population ranging between 120 and 230 individuals. For more than three decades, panthers have been captured, demographics recorded, and blood samples collected to monitor for multiple infectious diseases; however, an updated comprehensive study of many of these pathogens has not occurred since 1991. Our goal was to identify temporal patterns and spatial clustering in seroprevalence; determine if the pathogens of interest tend to co-occur; and describe relationships between an individual's genetic assignment (admixed or canonical) and seropositivity. We analyzed serology data for eight pathogens representing different modes of transmission (direct, indirect, vector borne) and infection duration (acute, chronic) from 232 panthers collected between 1992 and 2017. Panthers held consistently high seropositivity for feline calicivirus (62.3%) and panleukopenia virus (79.7%) throughout the study, whereas feline herpesvirus and feline leukemia virus were at lower prevalence (3.1% and 2.4%, respectively), although neither had been noted prior to 1992. Panthers were frequently seropositive for canine distemper virus and feline immunodeficiency virus, and seroprevalence fluctuated through time. West Nile virus seropositivity increased over the study period following its introduction in North America in 1999. Panthers were consistently negative for feline coronavirus, which causes feline infectious peritonitis. Genetics and demographics (sex and age) had little influence on serostatus, and coexposure among pathogens did not tend to occur. Both feline immunodeficiency virus and feline leukemia virus appeared to have spatial clusters of seropositive individuals. Our findings enhance the understanding of pathogen exposure in panthers, informing and supporting ongoing surveillance efforts for timely detection and management of potential disease threats in vulnerable populations.

The Characterisation of Carbapenem-Resistant Acinetobacter baumannii and Klebsiella pneumoniae in a Teaching Hospital in Malaysia.

Background/Objectives: The emergence and dissemination of carbapenem-resistant organisms, particularly Acinetobacter baumannii and Klebsiella pneumoniae, pose a significant threat to healthcare systems worldwide. This retrospective study aims to characterise carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Klebsiella pneumoniae (CRKP) strains in a teaching hospital and to determine the risk factors associated with patients' in-hospital mortality. Methods: A total of 90 CRAB and 63 CRKP were included in this study. Carbapenemase genes and MLST types of CRAB and CRKP were determined using specific primers. Risk factors associated with in-hospital mortality were analysed with collected data. Results: All the CRAB strains consisted of OXA carbapenemase genes, with 98% of the strains co-harbouring blaOXA-23-like and blaOXA-51-like carbapenemase genes. Conversely, blaNDM is the predominant carbapenemase gene in CRKP, followed by blaOXA-48-like carbapenemase genes. ST2 and ST20 are the dominant MLST types in CRAB and CRKP, respectively. In CRAB, multivariate analysis identified age, ethnicity, the presence of a mechanical ventilator, and patients who experienced previous exposure to clindamycin in the last 90 days as associated with an increased risk of in-hospital mortality. In contrast, older age, male, ICU admission, and the presence of an indwelling urinary catheter were significantly associated with an increased risk of mortality for patients with CRKP. Conclusions: Both CRAB and CRKP lead to high rates of mortality. The MLST profile showed that the genomic patterns of CRKP were highly diverse, whereas CRAB strains had low genetic diversity. To tackle these challenging pathogens, robust surveillance and an in-depth understanding of molecular epidemiology and genomics studies are needed to tailor infection control strategies and individualise treatment approaches.

Impacts of habitat loss by reservoir inundation on occurrence, abundance, and genetic diversity of an imperiled, river-adapted, benthic-specialist fish, Etheostoma lemniscatum (Tuxedo Darter)

AbstractDams homogenize habitat and alter natural depth and flow regimes of lotic habitats, leading to extirpation of many stream-adapted fishes such as darters (Percidae). The Tuxedo Darter, Etheostoma lemniscatum, is a habitat-specialist of shallow, flowing pools with cobble substrate in the Big South Fork Cumberland River. One threat to this species is Wolf Creek Dam on the Cumberland River that creates Lake Cumberland, which during summer pool, inundates the lower 72 river kilometers (rkms) of the Big South Fork. A six-year period of lower reservoir elevations for dam repairs allowed a 9 rkm reach to return to riverine habitat and E. lemniscatum to colonize this reach. Once dam repairs were complete, the lower 72 rkms were again regularly inundated by Lake Cumberland. To determine the impact of post-dam repair inundation on E. lemniscatum, we compared occurrence, abundance, and genetic diversity metrics estimated from samples from 2015 and from several years post-inundation in 2019 and 2020 from 11 sites spanning the species’ range. Declines in occurrence and abundance were detected within the re-inundated reach. We observed low genetic diversity for the species for both sample periods, but no significant changes in genetic diversity between years. A trend towards lower allelic richness and an increase in the proportion of private alleles was observed in the 2019/2020 samples. Coupled with local extirpation and declines in abundance, these trends may be early warning signs of future declines in genetic diversity. We suggest future genetic monitoring to identify any time delayed responses to inundation not detected herein.

Efficient multi-allelic genome editing via CRISPR-Cas9 ribonucleoprotein-based delivery to Brassica napus mesophyll protoplasts.

Canola (Brassica napus L.) is a valuable oilseed crop worldwide. However, trait improvement by breeding has been limited by its low genetic diversity and polyploid genetics. Whilst offering many potential benefits, the application of transgenic technology is challenged by the stringent and expensive regulatory processes associated with the commercialisation of genetically modified organisms, coupled with a prevailing low public acceptance of such modifications. DNA-free genome editing using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 ribonucleoproteins (RNPs) offers a promising way to achieve trait improvements without the limitations of transgenic methods. Here, we present a method for DNA-free genome editing via the direct delivery of RNPs to canola mesophyll protoplasts. This method allows high-throughput in vivo testing of the efficacy of gRNA design as part of the transformation process to facilitate the selection of optimal designs prior to the generation of edited events. Of the 525 shoots regenerated via tissue culture from RNP-transfected protoplasts and screened for the presence of mutations in the targeted gene, 62% had one or more mutated target alleles, and 50% had biallelic mutations at both targeted loci. This high editing efficiency compares favourably with similar CRISPR-Cas9 approaches used in other crop plants.

Genetic and morphological features of some Turkish populations of Amblyseius swirskii (Athias-Henriot) (Acari: Phytoseiidae)

Amblyseius swirskii is one of the most important phytoseiid mites commercialized worldwide for controlling pest mites and small insect pests. The study aims to investigate morphological and genetic variation among seven populations collected from different locations and plant species (cotton, orange) in Türkiye. The DNA sequences (12S rRNA and Cytb mitochondrial DNA markers) were also compared with those of commercial populations. The average genetic distance among the Turkish populations was quite low (0.7% for 12S rRNA and 0.9% for Cytb mtDNA), ranging from 0 to 2.8% and 0 to 1.5%, respectively. The phylogenetic trees show two distinct groups, separated by genetic distances of 0.9% and 1.3% for the 12S rRNA and the Cytb mtDNA fragments, respectively. The genetic differences were not explained by location or host plant. However, specimens from some populations were exclusively or predominantly included in one of the two clades, and commercialized specimens of A. swirskii only included in one clade, along with specimens collected in orange orchards. Specimens from cotton fields and Solanum nigrum, were found in both clades, but in different proportions. Results show a globally low genetic diversity within A. swirskii for the two DNA fragments. The existence of two clades raises questions about the presence of a clade derived from commercial releases. However, this result may be related to other factors. Morphological analyses demonstrated substantial variability among the populations, except for the population sampled from orange in Adana Kozan. Despite this, the morphological and molecular results are relatively consistent.

Genetic diversity of Colletotrichum kahawae populations in Burundi

AbstractMicrosatellite markers were used to assess genetic diversity of Colletotrichum kahawae isolates from Burundi. Sampling was carried out through all coffee growing areas in Burundi. The indices of genetic diversity such as the number of different alleles (Na), the number of effective alleles (Ne) revealed low genetic diversity with an average of 1.900 and 1.196 respectively. Higher than expected heterozygosity and significant linkage disequilibrium are consistent with clonal reproduction. The results showed a weak genetic diversity between the populations from different region and the low value of Fst indicated that the C. kahawae populations of Burundi were weakly differentiated. Our results confirm the clonality of C. kahawae and its low dispersion ability. The weak differentiation between the populations and the occurrence of one clonal lineage in Burundi are consistent with previous study suggesting that the East African populations of C. kahawae are the most recently populations derived from the ancestral Angolan population.