Induction of genetic variability of maize genotypes through radiation revealed mutants resistant to maize streak disease

The absence of genetic variability among crop genotypes is an impediment to breeding progress, hence mutagenesis could serve as a useful tool to create genetic variation to obtain desirable traits of interest. In this study, four maize genotypes, Obatampa, Dapango, Pann 54 and Honampa which were susceptible to maize streak disease (MSD) were acutely irradiated at 254.3 Gy, using a cobalt 60 (60Co) at a rate of 300 Gy/hr. The irradiated seeds were planted with their parental controls at streak disease highly endemic environment. Field trials for the selected maize genotypes were conducted from the M1 to M4 generations to screen for MSD resistance and improved grain yield. Sixteen putative mutants and four individual parental controls were selected across the four maize genotypes at the end of the M4 generation based on disease severity score and yield indices. Detailed morphological screening and field evaluation of putative mutants showing improved plant architecture, increased grain yield and resistance to maize streak disease were tagged and selected. Obatanpa-induced-genotype was the best mutant identified with a grain yield of 6.8 t ha-1. Data on days to 50% flowering indicated that all 16 putative mutants were maturing plants.

NLRP3/GSDMD mediated pyroptosis induces lung inflammation susceptibility in diesel exhaust exposed mouse strains

BACKGROUND

Genetic diversity among species influences the disease severity outcomes linked to air pollution. However, the pathway responsible for this variability remain elusive and needs further investigation.

OBJECTIVE

To investigate the genetic factors and pathways linked with differential susceptibility in mouse strains associated with diesel exhaust exposure.

METHODS

C57BL/6 and Balb/c mice were exposed to diesel exhaust (DE) for 5 days/week for 30 min/day for 8 weeks. Body weight of mice was recorded every week and airway hyperresponsiveness towards DE exposure was recorded after 24 hours of last exposure. Mice were euthanised to collect BALF, blood, lung tissues for immunobiochemical assays, structural integrity and genetic studies.

RESULTS

C57BL/6 mice showed significantly decreased body weight in comparison to Balb/c mice (p < 0.05). Both mouse strains showed lung resistance and damage to elastance upon DE exposure compared to respective controls (p < 0.05) with more pronounced effects in C57BL/6 mice. Lung histology showed increase in bronchiolar infiltration and damage to the wall in C57BL/6 mice (p < 0.05). DE exposure upregulated pro-inflammatory and Th2 cytokine levels in C57BL/6 in comparison to Balb/c mice. C57BL/6 mice showed increase in Caspase-1 and ASC expression confirming activation of downstream pathway. This showed significant activation of inflammasome pathway in C57BL/6 mice with ∼2-fold increase in NLRP3 and elevated IL-1b expression. Gasdermin-D (GSDMD) levels were increased in C57BL/6 mice demonstrating induction of pyroptosis that corroborated with IL-1b secretion (p < 0.05). Genetic variability among both species was confirmed with sanger's sequencing suggesting presence of SNPs in 3'UTRs of IL-1b gene influencing expression between mouse strains.

CONCLUSIONS

C57BL/6 mice exhibited increased susceptibility to diesel exhaust in contrast to Balb/c mice via activation of NLRP3-related pyroptosis. Differential susceptibility between strains may be attributed via SNPs in the 3'UTRs of the IL-1β gene.

Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.

Natural variability and heritability of root-nodulation traits in chickpea (Cicer arietinum L.) minicore

The existence of large variations for nodulation traits in chickpea minicore was revealed and genetic materials for beneficial biological nitrogen fixation (BNF) traits like early nodulation, high nodulation, and delayed nodule senescence were identified. Early-nodulating genotypes viz. ICC12968, ICC7867, ICC13816, ICC867, ICC15264, ICC15510, and ICC283 produced > 10 nodule number per plant (NNPP) at 15 as well as 30 days after sowing (DAS). Maximum of 36 NNPP at stage 3 i.e., 253% higher than check cultivar were observed in Iran originated ICC6874. Chickpea minicore showed large variations for nodule mass that ranged up to 850 mg/plant at 60 DAS and 2290 mg/plant at 90 DAS. Strong positive correlation was found between nodule fresh weight and specific weight at stage 3 (0.69) and stage 4 (0.76). Besides these, few slight positive significant correlations were also observed viz., nodule number per plant at stage 3 and 4 (0.45), nodule fresh weight at stage 3 and 4 (0.39). Principal component analysis (PCA) indicated that dimensions 1 (21%), 2 (17.6%), and 3 (13%) accounted for a substantial portion of the phenotypic variance, each contributing more than 10%. Accessions viz. ICC1431, ICC13599, ICC13764, and ICC13863 with pink active root nodules and high nodule biomass at later crop growth stages are considered as genetic resources to extend the BNF support in chickpea. High broad-sense heritability values of 76.43 and 90.23 were observed for early nodulation and delayed nodule senescence, respectively. Hence, the identified genotypes for early nodulation and delayed nodule senescence can be used for improving symbiotic efficiency in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03908-1.

Genetic variability of Dirofilaria repens isolates from humans and dogs in Italy

Dirofilaria repens is a paradigmatic example of an emerging vector-borne pathogen (VBP) in both human and veterinary fields. The spatial expansion and the increasing zoonotic impact of this VBP can be related to several drivers including the genetic structure of parasite populations. Italy is one of the European countries traditionally endemic with the highest incidence of canine and human cases of subcutaneous dirofilariosis. The present study aimed to assess the genetic identity and variability of D. repens isolates of human and canine origin from areas of Central Italy, compared with those isolated from different areas of Europe by sequence analysis of mtDNA genes (i.e., 12 S rDNA and cox1). A total of twenty isolates of D. repens were obtained from biopsies of subcutaneous and ocular cases of dirofilariosis occurring in 10 dogs and 10 humans. The sequence analysis of 12 S rDNA showed that all the sequences obtained clustered as a monophyletic group with a strong nodal support, indicating that all sequence types represented D. repens. The cox1 and the 12 S sequence analysis did not show host-related polymorphisms between human and dog-derived specimens. The sequence analysis of cox1 was performed including 8 additional sequences previously obtained from human and canine isolates in the same areas. Out of the 28 sequences analyzed, 20 were grouped in a haplogroup comprising 15 haplotypes (i.e., DR1, DR2, DR4, DR5, DR7, DR8, DR10-DR18), 2 sequences matched to DR9, reported for the first time in Italy, and 6 showed peculiar polymorphisms that were not previously described. The results obtained have implications for a better understanding of the epidemiology and phylogeography of this emerging vector-borne zoonotic parasite.

Multi-locus sequencing typing reveals geographically related intraspecies variability of Sporothrix brasiliensis

Sporotrichosis is a subcutaneous mycosis caused by pathogenic Sporothrix species. Among them, Sporothrix brasiliensis is the main species associated with endemic regions in South America, especially Brazil. It is highly virulent and can be spread through zoonotic transmission. Molecular epidemiological surveys are needed to determine the extent of genetic variation, to investigate outbreaks, and to identify genotypes associated with antifungal resistance and susceptibility. This study investigated the sequence variation of different constitutive genes and established a novel multilocus sequence typing (MLST) scheme for S. brasiliensis. Specific primers were designed for 16 genes using Primer-BLAST software based on the genome sequences of three S. brasiliensis strains (ATCC MYA-4823, A001 and A005). Ninety-one human, animal, and environmental S. brasiliensis isolates from different Brazilian geographic regions (South, Southeast, Midwest and Northeast) andtwo isolates from Paraguay were sequenced. The loci that presented the highest nucleotide diversity (π) were selected for the MLST scheme. Among the 16 studied genetic loci, four presented increased π value and were able to distinguish all S. brasiliensis isolates into seven distinct haplotypes. The PCR conditions were standardized for four loci. Some of the obtained haplotypes were associated with the geographic origin of the strains. This study presents an important advance in the understanding of this important agent of sporotrichosis in Brazil. It significantly increased the discriminatory power for genotyping of S. brasiliensis isolates, and enabled new contributions to the epidemiological studies of this human and animal pathogen in Brazil and in other countries.

Exploring genetic variability under extended photoperiod in lentil (Lens Culinaris Medik): vegetative and phenological differentiation according to genetic material's origins

Lentil is an important pulse that contributes to global food security and the sustainability of farming systems. Hence, it is important to increase the production of this crop, especially in the context of climate changes through plant breeding aiming at the development of high-yielding and climate-smart cultivars. However, conventional plant breeding approaches are time and resources consuming. Thus, speed breeding techniques enabling rapid generation turnover could help to accelerate the development of new varieties. The application of extended photoperiod prolonging the duration of the plant's exposure to light and shortening the duration of the dark phase is among the simplest speed breeding techniques. In this study, genetic variability response under extended photoperiod (22 h of light/2 h of dark at 25 °C) of a lentil collection of 80 landraces from diverse latitudinal origins low (0°-20°), medium (21°-40°) and high (41°-60°), was investigated. Significant genetic variations were observed between accessions, for time to flowering [40 → 120 days], time of pods set [45 → 130 days], time to maturity [64 → 150 days], harvest index [0 → 0.24], green canopy cover [0.39 → 5.62], seedling vigor [2 → 5], vegetative stage length [40 → 120 days], reproduction stage length [3 → 13 days], and seed filing stage length [6 → 25 days]. Overall, the accessions from Low latitudinal origin demonstrated a favorable response to the extended photoperiod application with almost all accessions flowered, while 18% and 57% of accessions originating from medium and high latitudinal areas, respectively, did not successfully reach the flowering stage. These results enhanced our understanding lentil responses to photoperiodism under controlled conditions and are expected to play important roles in speed breeding based on the application of the described protocol for lentil breeding programs in terms of choosing appropriate initial treatments such as vernalization depending on the origin of accession.

Cadmium partitioning between hulls and kernels in three sunflower varieties: consequences for food/feed chain safety

Contamination of sunflower seeds with soil Cd is an important issue for food and feed because this species strongly accumulates this metal. The present work reports that seeds from three sunflower varieties (ES Biba, Extrasol, Vellox) cultivated in the field in a calcareous agricultural soil having a moderately high Cd content (1 mg Cd/kg) had Cd contents of 0.84, 0.88 and 0.76 mg Cd/kg, respectively, all exceeding the regulation limit of 0.5 mg Cd/kg seeds for human food. On average, for the three varieties, washing seeds did not affect their total Cd contents but slightly increased the Cd in the kernels at the expense of that in hulls. Despite the Cd content of the whole seeds not differing between the varieties, the Cd fraction in the edible kernel differed significantly between varieties from 78 to 87% of the total seed Cd. The results of this study suggest that (i) the size of the kernel, relative to that of the hull, may affect the dilution of Cd in kernel tissues and (ii) there might be genetic variability for the capacity of transfer of Cd from the hull to the kernel. This opens the perspective to increase food safety by selecting sunflower genotypes that retain more Cd into the hull and transfer less of it to the edible kernel.

Morpho-nutritional status of micronutrient efficient wheat (Triticum aestivum L.) genotypes under changing environments

In India, where cereal-based meals make up the majority of the daily diet, bread wheat (Triticum aestivum L.) is a key grain crop. Micronutrient deficiencies are a result of the lack of a diverse food culture in the nation. Genotypes of bread wheat that have been biofortified might be introduced to address this. It is anticipated that more information on the genotype x year interaction of these nutrients in grain will help us better understand the size of this interaction and perhaps even identify more stable genotypes for this attribute. Year revealed divergent responses to grain iron and zinc. Compared to zinc, iron showed lowest variation across year. Maximum temperature was the major determinant for the four traits. Iron is also significant correlation with zinc. Among the total fifty-two genotype, HP-06, HP-22, HP-24, HP-25, HP-33, HP-44, and HP-45 were found superior for zinc and iron content. These genotypes with high levels of zinc and iron can be used in a hybridization programme to further crop improvement. Wide-scale cultivation of the chosen genotype with high zinc and iron content in the agro-climatic conditions of Jammu will work with the region's current cropping systems.

Gamma-rays induced mutations increase soybean oil and protein contents

Mutation breeding is one of the effective techniques used for improving desired traits such as yield quality and quantity in economic crops. The present study aims to develop oil and protein contents in addition to high yield attributes in soybean using gamma rays as a mutagen. Seeds of the soybean genotypes Giza 21, Giza 22, Giza 82, Giza 83 and 117 were treated with gamma rays doses 50, 100, 200 and 300 Gy. Plants were then scored based on morphological parameters correlated with yield quantity including plant height, seed weight and valuable protein and oil contents. Mutant lines exhibiting the highest yield attributes were selected and used as parents for M2 generation. The M2 progeny was further assessed based on their ability to maintain their yield attributes. Twenty mutant lines were selected and used as M3 lines. The yield parameters inferred a positive effect of gamma irradiation on the collected M3 mutant lines compared to their parental genotypes. 100 Gy of gamma rays gave the highest effect on the number of pods, branches and seeds per plant in addition to protein content, while 200 Gy was more effective in increasing plant height, number of pods per plant, and oil content. Six mutant lines scored the highest yield parameters. Further assessment inferred an inverse relationship between oil and protein content in most of the tested cultivars with high agronomic features. However, four mutant lines recorded high content of oil and protein besides their high seed yield as well, which elect them as potential candidates for large-scale evaluation. The correlation among examined parameters was further confirmed via principal component analysis (PCA), which inferred a positive correlation between the number of pods, branches, seeds, and seed weight. Conversely, oil and protein content were inversely correlated in most of yielded mutant lines. Together, those findings introduce novel soybean lines with favorable agronomic traits for the market. In addition, our research sheds light on the value of using gamma rays treatment in enhancing genetic variability in soybean and improving oil, protein contents and seed yield.

Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics

Drought is a major abiotic stress that severely limits sustainable wheat (Triticum aestivum L.) productivity via morphological and physio-biochemical alterations of cellular processes. The complex nature and polygenic control of drought tolerance traits make breeding tolerant genotypes quite challenging. However, naturally occurring variabilities among wheat germplasm resources could potentially help combating drought. The present study was conducted to assess the drought tolerance of 18 Bangladeshi hexaploid wheat genotypes, focusing on the identification of potent sources of diversity by combining microsatellite markers, also known as single sequence repeat markers, and morpho-physiological characteristics that might help accelerating wheat crop improvement programs. Initially, the genotypes were evaluated using 25 microsatellite markers followed by an on-field evaluation of 7 morphological traits (plant height, spike number, spike length, grains per spike, 1000-grain weight, grain yield, biological yield) and 6 physiological traits (SPAD value, membrane stability index, leaf relative water content, proline content, canopy temperature depression, and leaf K+ ion content). The field-trial was conducted in a factorial fashion of 18 wheat genotypes and two water regimes (control and drought) following a split-plot randomized complete block design. Regardless of genotype, drought was significantly damaging for all the tested traits; however, substantial variability in drought stress tolerance was evident among the genotypes. Spike length, 1000-grain weight, SPAD value, leaf relative water content, canopy temperature depression, proline content, and potassium (K+) ion content were the most representative of drought-induced growth and yield impairments and also correlated well with the contrasting ability of genotypic tolerance. Microsatellite markers amplified 244 alleles exhibiting 79% genetic diversity. Out of 25 markers, 23 was highly polymorphic showing 77% average polymorphism. Morpho-physiological trait-based hierarchical clustering and microsatellite marker-based neighbor-jointing clustering both revealed three genotypic clusters with 71% co-linearity between them. In both cases, the genotypes Kanchan, BAW-1147, BINA Gom 1, BARI Gom 22, BARI Gom 26, and BARI Gom 33 were found to be comparatively more tolerant than the other tested genotypes, showing potential for cultivation in water-deficit environments. The findings of this study would contribute to the present understanding of drought tolerance in wheat and would provide a basis for future genotype selection for drought-tolerant wheat breeding programs.

Molecular characterization of human adenovirus causing infantile acute gastroenteritis in Venezuela before and after rotavirus vaccine implementation

Human adenoviruses (HAdV) of species F are commonly involved in pediatric acute gastroenteritis (AGE). The real impact on Venezuelan health is unknown. To investigate the prevalence and molecular diversity of HAdV in Venezuela, 630 fecal samples collected from children with AGE in 3 cities, from 2001 to 2013, were tested by PCR. Species F and types F40/41 were identified by REA. HAdV was detected in 123 cases (19.5%), most from outpatient females under 24 months old. A progressive and substantial increase in the detection rate was observed over time, significantly higher in rotavirus vaccinated than unvaccinated children (28.4% vs. 9.5%, P = 0.00019). Phylogenetic analysis of 28 randomly selected genomes showed high similarity among HAdV-F40/41 and those worldwide. HAdV-F of type 41 prevailed (79.8%) and clustered into 2 intratypic major clades. The significant involvement of HAdV-F41 in AGE suggests the importance of actively monitoring viral agents other than rotavirus, especially after vaccine introduction.

Variability in the PRDM9 gene in Sindhi cattle

BACKGROUND

Sindhi is a dual-purpose breed adapted to tropical environments. However, this breed has the smallest total population among indicine breeds in Brazil and the smallest effective number. In addition, the inbreeding coefficient is higher than 6.25% in ~ 60% of the population. Therefore, alternatives to increase genetic diversity are important. Within this context, the PRDM9 gene is particularly interesting since it is involved in meiotic recombination events, consequently enhancing genetic variability in the population by increasing the number of circulating haplotypes. Each allele of the gene induces recombination at a different hotspot. The larger the number of circulating alleles, the higher the recombination rate and the greater the genetic variability.

METHODS

The aim of this study was to characterize alleles of the PRDM9 gene in Sindhi cattle. The region of the zinc finger domains of the gene was amplified by PCR, genotyped, and sequenced for allele identification in 50 Sindhi animals.

RESULTS

Three alleles (A-cattle1, B-cattle14, and C-cattle19) and six genotypes (AA, BB, CC, AB, AC, and BC) were identified.

CONCLUSION

The allele variation of the PRDM9 gene in the Sindhi breed enables to guide the mating of animals with different genotypes/alleles and to promote genetic variability by recombination if there is intralocus variability.

Genetic variation in the OPN gene affects milk composition in Chinese Holstein cows

The aim of this study was to investigate the association between genotypes and haplotypes of OPN, and milk composition in dairy cows. A total of 317 Chinese Holstein cows were genotyped via DNA sequencing in this study. Three single nucleotide polymorphisms (SNPs), g.2916G > A, g.58675C > T and g.58899C > A, and eight haplotypes were identified. Of the eight possible haplotypes, four haplotypes i.e., Hap2 (ACC; 55.30%), Hap6 (GCC, 15.6%), Hap1 (ACA, 13.6%) and Hap4 (ATC, 5.70%), were considered to be major with a cumulative estimated frequency of >90%. Single markers (g.2916G > A and g.58899C > A) and Haplotype Hap6/4 were found to be associated with an increase in butter-fat percentage (p < 0.05). Taken together, our results provided evidence that polymorphisms in OPN are associated with milk composition, and could potentially be used for marker-assisted selection in Chinese Holstein cows.

Genetic diversity and its impact on disease severity in respiratory syncytial virus subtype-A and -B bronchiolitis before and after pandemic restrictions in Rome

OBJECTIVES

To scrutinize whether the high circulation of respiratory syncytial virus (RSV) observed in 2021-2022 and 2022-2023 was due to viral diversity, we characterized RSV-A and -B strains causing bronchiolitis in Rome, before and after the COVID-19 pandemic.

METHODS

RSV-positive samples, prospectively collected from infants hospitalized for bronchiolitis from 2017-2018 to 2022-2023, were sequenced in the G gene; phylogenetic results and amino acid substitutions were analyzed. Subtype-specific data were compared among seasons.

RESULTS

Predominance of RSV-A and -B alternated in the pre-pandemic seasons; RSV-A dominated in 2021-2022 whereas RSV-B was predominant in 2022-2023. RSV-A sequences were ON1 genotype but quite distant from the ancestor; two divergent clades included sequences from pre- and post-pandemic seasons. Nearly all RSV-B were BA10 genotype; a divergent clade included only strains from 2021-2022 to 2022-2023. RSV-A cases had lower need of O2 therapy and of intensive care during 2021-2022 with respect to all other seasons. RSV-B infected infants were more frequently admitted to intensive care units and needed O2 in 2022-2023.

CONCLUSIONS

The intense RSV peak in 2021-2022, driven by RSV-A phylogenetically related to pre-pandemic strains is attributable to the immune debt created by pandemic restrictions. The RSV-B genetic divergence observed in post-pandemic strains may have increased the RSV-B specific immune debt, being a possible contributor to bronchiolitis severity in 2022-2023.

Genetic variation and population structure of Fasciola hepatica: an in silico analysis

Fasciola hepatica is a trematode leading to heavy economic setbacks to the livestock sector globally. The population's genetic information and intimate kinship level are frequently assessed using analysis of mitochondrial DNA. In this analysis, we retrieved cox1 (n = 247) and nad1 (n = 357) sequences of F. hepatica from the NCBI GenBank database and aligned the sequences with the respective reference sequences using MEGA software. The median joining network was drawn using PopArt software while neutrality and diversity indices were estimated with the help of DnaSp software. Neighbor-joining phylogenetic tree was constructed using the MEGA software package. A total of 46 and 98 distinctive haplotypes were observed for cox1 and nad1 genes, respectively. Diversity indices indicated high haplotype and nucleotide diversities in both genes. Positive Tajima's D and Fu's Fs values were found for the entire population of both the genes under study. The cox1 and nad1 gene segments in this study showed high Tajima's D values, suggesting a low likelihood of future population growth. The Tajima's D value of the nad1 gene sequence is lower (2.14910) than that of the cox1 gene sequence (3.40314), which suggests that the former is growing at a slower rate. However, the region-wise analysis revealed that both the cox1 and nad1 genes showed deviation from neutrality suggesting a recent population expansion as a result of an excess of low-frequency polymorphism. Furthermore, the overall host-wise analysis showed positive and significant Tajima's D values for the cox1 and nad1 gene sequences. To the best of our knowledge, this is the first attempt to provide insights into genetic variations and population structure of F. hepatica at a global scale using cox1 and nad1 genes. Our findings suggest the existence of specific variants of F. hepatica in different parts of the world and provide information on the molecular ecology of F. hepatica. The results of this study also mark a critical development in upcoming epidemiological investigations on F. hepatica and will also contribute to understanding the global molecular epidemiology and population structure of F. hepatica.

Genetic variability of rice stripe virus after its pandemic in Jiangsu

BACKGROUND

Rice stripe virus (RSV) caused a serious disease pandemic in rice in East China between 2001 and 2010. The continuous integrated managements reduced virus epidemic year by year until it was non-epidemic. As an RNA virus, its genetic variability after undergoing a long-term non-epidemic period was meaningful to study. While in 2019, the sudden occurrence of RSV in Jiangsu provided an opportunity for the study.

METHODS AND RESULTS

The complete genome of JY2019, an RSV isolate from Jiangyan, was determined. A genotype profile of 22 isolates from China, Japan and Korea indicated that the isolates from Yunnan formed the subtype II, and other isolates clustered the subtype I. RNA 1-3 of JY2019 isolate well-clustered in the subtype I clade, and RNA 4 was also in subtype I, but it had a slight separation from other intra-group isolates. After phylogenetic analyses, it was considered NSvc4 gene contributed to the tendency, because it exhibited an obvious trend towards the subtype II (Yunnan) group. High sequence identity (100%) of NSvc4 between JY2019 and barnyardgrass isolate from different regions demonstrated genetic variation of NSvc4 was consistent in RSV natural populations in Jiangsu in the non-epidemic period. In the phylogenetic tree of all 74 NSvc4 genes, JY2019 belonged to a minor subtype Ib, suggesting the subtype Ib isolates might have existed in natural populations before the non-epidemic period, but not a dominant population.

CONCLUSIONS

Our results suggested that NSvc4 gene was susceptible to selection pressure, and the subtype Ib might be more adaptable for the interaction between RSV and hosts in the non-epidemic ecological conditions.

Comparative proteomic analysis of Trypanosoma cruzi TcI lineage epimastigotes unveils metabolic and phenotypic differences between fast- and slow-dividing strains

Trypanosoma cruzi, the causative agent of Chagas disease, is a genetically and phenotypically diverse species, divided into 5 main phylogenetic lineages (TcI to TcVI). TcI is the most widespread lineage in the Americas. Proteomics is a suitable tool to study the global protein expression dynamics in pathogens. Previous proteomic studies have revealed a link between (i) the genetic variability; (ii) the protein expression; and (iii) the biological characteristics of T. cruzi. Here, two-dimensional electrophoresis (2DE) and mass spectrometry were used to characterize the overall protein expression profiles of epimastigotes from four distinct TcI strains displaying different growth kinetics. Ascending hierarchical clustering analysis based on the global 2DE protein expression profiles grouped the strains under study into two clusters that were congruent with their fast or slow growth kinetics. A subset of proteins differentially expressed by the strains in each group were identified by mass spectrometry. Biological differences between the two groups, including use of glucose as an energy source, flagellum length, and metabolic activity, were predicted by proteomic analysis and confirmed by metabolic tests and microscopic measurements performed on the epimastigotes of each strain. Our results show that protein expression profiles are correlated with parasite phenotypes, which may in turn influence the parasite's virulence and transmission capacity.

Microsatellite marker-based genetic diversity assessment among exotic and native maize inbred lines of Bangladesh

Hybrid development is basically dependent on the variability among available genetic resources. Polymorphism among the maize inbreds is essentially needed for maize hybridization. This study aimed at the assessment of diversity among 22 maize inbreds by 18 microsatellite markers. The study identified 187 alleles at 18 SSR loci. The amplified allele frequency per microsatellite locus was 10.4 and the highest allele per locus was 17 in SSR primer pair phi026. SSR primer set p-umc1292, phi074 and phi090 showed the lowest 6 alleles per genotype per locus. The locus phi026 showed the highest degree of gene diversity (0.92), and the locus p-umc1292 had the lowest of gene diversity (0.77) with a mean value of 0.862 among the microsatellites. At each site, the most prevalent allele varied between 0.14 (bnlg371) and 0.36. (p-umc1292). At any given locus, an average of 0.22 out of the 22 selected maize inbred lines had a common major allele. The average value of the polymorphic information content (PIC) was 0.85, within the range of 0.74 at the lowest to 0.92 at the highest. The higher PIC values of phi026 and nc013 established them to be the best markers for maize inbred lines. The UPGMA clustering generated seven distinct groups having 12.5% of similarity coefficient. The results revealed that inbred lines E10, E27, E19, E34, E35, E4, E43, E28, E11, E21, E17, E38, E25, E34, E14, E16, E39 and E3 were more diversified. These lines are promising to be used as parent materials for hybrid maize development in the future.

Identification and validation of the first EST-SSR markers based on transcriptome of Anopheles darlingi, the primary transmitter of malaria in Brazil

BACKGROUND

Anopheles darlingi is a monotypic species in terms of its morphological, genetic, and behavioral aspects and is the primary transmitter of human malaria (99%) in Brazil, especially in the Brazilian Amazon. In this pioneering study, 15 expressed sequence tag (EST)-simple sequence repeat (SSR) markers were obtained and characterized in samples from the municipality of São Gabriel da Cachoeira, Amazonas state, Brazil, with polymorphisms that can be used for further genetic research.

METHODS AND RESULTS

The specimens (from egg to larval stage) collected were bred in the insectary at INPA (National Institute for Amazonian Research). The SSR repeats within the contigs of the A. darlingi EST banks were confirmed on the Vector Base site. DNA was extracted and amplified using polymerase chain reaction and then genotyped. Fifteen polymorphic SSR loci were identified and characterized. The number of alleles totaled 76 and ranged from 2 to 9. The observed heterozygosity varied between 0.026 and 0.769, the expected heterozygosity between 0.025 and 0.776, and the mean polymorphism information content was 0.468. Eight loci showed Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (P: (5%) ≤ 0.0033). No linkage disequilibrium was found among the loci.

CONCLUSIONS

The polymorphic SSRs of the loci have been shown to be efficient for investigation of the variability and genetic population structure of A. darlingi.

Cervical carcinogenesis risk association of HPV33 E6 and E7 genetic variations in Taizhou, Southeast China

BACKGROUND

Human papillomavirus (HPV) 33 belongs to the Alphapapillomavirus 9 (α-9 HPV) species group, which also contains types 16, 31, 35, 52, 58 and 67. The purpose of this study was to investigate the genetic variations of HPV33 and to explore its carcinogenicity among women in Taizhou, Southeast China.

METHODS

Exfoliated cervical cells were collected for HPV genotyping. Only single HPV33 infection cases were selected, and their E6 and E7 genes were sequenced using the ABI 3730xl sequencer and then analysed using MEGA X.

RESULTS

From 2014 to 2020, a total of 185 single HPV33-positive specimens were successfully amplified. We obtained 15 distinct HPV33 E6/E7 variants, which were published in GenBank under accession numbers OQ672665-OQ672679. Phylogenetic analysis revealed that all HPV33 E6/E7 variants belonged to lineage A, of which 75.7% belonged to lineage A1. Compared with CIN1, the proportion of sublineage A1 in CIN2/3 was higher, but there was no significant difference (76.5% vs. 80.6%, P > 0.05). Altogether, 20 single nucleotide substitutions were identified, of which 6 were novel substitutions, including T196G (C30G), A447T, G458T (R117L), G531A, A704A, and C740T. In addition, no significant trends were observed between the nucleotide substitutions of HPV33 E6/E7 variants and the risk of cervical lesions.

CONCLUSION

This study provides the most comprehensive data on genetic variations, phylogenetics and carcinogenicity of HPV33 E6/E7 variants in Southeast China to date. The data confirmed that cervical lesions among women in Taizhou are attributable to HPV33, which may be due to the high infection rate of sublineage A1 in the population.

Involvement of cutavirus in a subset of patients with cutaneous T-cell lymphoma with an unfavorable outcome

BACKGROUND

European studies suggest an association between cutavirus (CuV) and cutaneous T-cell lymphoma (CTCL); however, the worldwide prevalence of CuV in patients with CTCL and its prognostic impact remain unknown.

METHODS

We investigated the prevalence and viral loads of CuV DNA using biopsy specimens from the lesional skins of 141 Japanese patients with cutaneous malignancies, including 55 patients with various types of CTCL.

RESULTS

CuV DNA was detected significantly more frequently in biopsies from patients with mycosis fungoides (MF) (38% [13/34]; the most common subtype of CTCL) than in those from patients with other cutaneous malignancies (6% [6/107]; P<0.001). The viral-load range in patients with CuV DNA-positive MF was 23-3922 copies/10³ cells and 8-65 copies/μg of DNA. A phylogenetic analysis using the partial sequences of the CuV viral capsid protein 1 (VP1)/VP2 genes revealed that the CuV sequences identified here were clustered in a Japanese-specific clade distinct from that comprising CuV sequences from European patients with MF. Kaplan-Meier curves and a log-rank test showed that CuV positivity was associated with a shorter disease-specific survival in patients with MF (P = 0.031), whereas no significant difference in overall survival was observed (P = 0.275). No significant correlation was observed between CuV DNA load and survival in patients with CuV-positive MF.

CONCLUSIONS

Our results suggest that CuV is associated with MF in a subset of Japanese patients. Large-scale prospective studies are warranted to clarify the role of CuV status, especially regarding the viral genotype, on adverse outcomes in patients with CuV-positive MF.

Phenology, growth, yield, and yield-related traits of Ethiopian garlic genotypes. A review

Garlic is one of the most important medicinal plants and consists of high sulfur concentration compounds like diallyl disulfide, allicin, diallyl trisulfide, and S-allylcysteine. It contributes for anti-inflammatory, anticancer, anthelmintics, antifungal, liver protection, antioxidants, antistress, and wound healing properties. Therefore, garlic plays a significant role in human life. To popularize this multi-purpose crop in Ethiopia, there are ample opportunities and potential, like a wide agro-ecology and a labor force. However, today's garlic production in Ethiopia is low because of different factors like climate, soil, microbiome and cultural practices. While, mainly due to genotype variation, garlic yield is constrained. Thus, gathering and reviewing the impact of genotypes on phenology, growth, yield, and yield traits is important to summarize and organize. Hence, the main objective of this paper is to show the phenology, growth, yield, and yield-related traits of garlic as influenced by genotype. Finally, this review scoped to reveal phenology, growth, yield and yield traits as influenced by Ethiopian garlic genotypes. Generally, different genotypes influence the phenology, growth, yield, and yield traits of garlic. Therefore, garlic producers should use a high-yielding variety (genotype) in the area.

Insights into the molecular genetic basis of individual differences in metacognition

There is a striking lack of studies on the molecular genetic basis of metacognition, i.e., the higher-order ability to monitor mental processes. Here, an initial step toward resolving this issue was undertaken by investigating functional polymorphisms from three genes of the dopaminergic or serotonergic systems (DRD4, COMT, and 5-HTTLPR) in relation to behaviorally assessed metacognition in six paradigms across three cognitive domains. We report evidence for a task-dependent higher average confidence level (metacognitive bias) in carriers of at least one S or L_G-allele in the 5-HTTLPR genotype and integrate these findings within a differential susceptibility framework.

Replication properties and immunomodulatory effects of human cytomegalovirus infection impact the clinical presentation in congenital patients: A case series

BACKGROUND

Human cytomegalovirus (HCMV) is the leading cause of congenital infections resulting in severe morbidity and mortality among newborns worldwide. Although both the host's and the virus' genetic backgrounds contribute to the outcome of infections, significant gaps remain in our understanding of the exact mechanisms that determine disease severity.

OBJECTIVES

In this study, we sought to identify a correlation between the virological features of different HCMV strains with the clinical and pathological features of congenitally infected newborns, therefore proposing new possible prognostic factors.

STUDY DESIGN

This short communication presents five newborns with congenital cytomegalovirus infection, whose clinical phenotype during fetal, neonatal, and follow-up periods is correlated with in-vitro growth properties, immunomodulatory abilities and genome variability of HCMV strains isolated from organic samples (urine) of the patients.

RESULTS

The five patients described in this short communication displayed a heterogeneous clinical phenotype and different virus replication properties, immunomodulatory abilities, and genetic polymorphisms. Interestingly, we observed that an attenuate viral replication in-vitro influences the immunomodulatory abilities of HCMV, leading to more severe congenital infections and long-term sequelae. Conversely, infection with viruses characterized by aggressive replicative behavior in-vitro resulted in asymptomatic patients' phenotypes.

CONCLUSIONS

Overall, this case series suggests the hypothesis that genetic variability and differences in the replicative behavior of HCMV strains result in clinical phenotypes of different severity, most likely due to different immunomodulatory properties of the virus.

Genomic variability and population structure of six Colombian cattle breeds

Analyses of the genetic diversity of indigenous cattle are essential for implementing conservation programs, promoting their sustainable use and maintaining productive advantages offered by these breeds in local conditions. The aim of this study was to investigate the genetic diversity and population structure of six Colombian cattle breeds: Blanco Orejinegro (BON), Costeño con Cuernos (CCC), Romosinuano (ROM), Sanmartinero (SAM), Casanareño (CAS), and Hartón del Valle (HDV). Two additional breed groups were included for comparison: Zebu (CEB) and a crossbreed of Colombian cattle breeds × Zebu. Genetic diversity within breeds was analyzed using expected heterozygosity (He), inbreeding coefficient (f), and runs of homozygosity (ROH). Population structure was assessed using model-based clustering (ADMIXTURE) and principal components analysis (PCA). Zebu cattle showed the lowest genetic diversity (He = 0.240). Breeds with the highest genetic diversity level were HDV and BON (He = 0.350 and 0.340, respectively). Inbreeding was lower for Colombian cattle breeds ranging between 0.005 and 0.045. Overall, the largest average genetic distance was found among the group of Colombian cattle breeds and Zebu, while the smallest was found between ROM and CCC. Model-based clustering revealed some level of admixture among HDV and CAS cattle which is consistent with their recent history. The results of the present study provide a useful insight on the genetic structure of Colombian cattle breeds.

Superior leaf physiological performance contributes to sustaining the final yield of cotton (Gossypium hirsutum L.) genotypes under terminal heat stress

This study aimed to optimize methods for identifying heat-tolerant and heat-susceptible cotton plants by examining the relationship between leaf physiology and cotton yield. Cotton accessions were exposed to elevated temperatures through staggered sowing and controlled growth conditions in a glasshouse. Based on their yield performance, leaf physiology, cell biochemistry, and pollen germination, the accessions were categorized as heat-tolerant, moderately tolerant, or susceptible. High temperatures had a significant impact on various leaf physiological and biochemical factors, such as cell injury, photosynthetic rate, stomatal conductance, transpiration rate, leaf temperature, chlorophyll fluorescence, and enzyme activities. The germination of flower pollen and seed cotton yield was also affected. The study demonstrated that there was a genetic variability for heat tolerance among the tested cotton accessions, as indicated by the interaction between accession and environment. Leaf gas exchange, cell biochemistry, pollen germination, and cotton yield were strongly associated with heat-sensitive accessions, but this association was negligible in tolerant accessions. Principal component analysis was used to classify the accessions based on their performance under heat stress conditions. The findings suggest that leaf physiological traits, cell biochemistry, pollen germination, and cotton yield can be effective indicators for selecting heat-tolerant cotton lines. Future research could explore additional genetic traits for improved selection and development of heat-tolerant accessions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01322-8.

Cutavirus on the skin in an Asian cohort: identification of a novel geographically related genotype

BACKGROUND

Cutavirus (CuV) is the newest human parvovirus and is currently receiving increasing attention because of its possible association with cutaneous T-cell lymphoma. Despite the pathogenetic potential of CuV, it has been detected in normal skin; however, little is known about the prevalence, infection levels, and genetic variations of this virus in the skin of the general population.

METHODS

We investigated the CuV DNA prevalence and viral loads concerning age, sampling location, and gender using 678 skin swabs collected from the normal-appearing skins of 339 Japanese participants aged 2-99 years. Phylogenetic analyses were also conducted based on the near-full-length CuV sequences identified in this study.

RESULTS

Both the CuV DNA prevalence and viral loads were significantly higher in the skin of elderly persons aged ≥60 years compared with those of persons aged < 60 years. CuV DNA tended to persist in the skin of elderly individuals. No significant difference in viral loads was observed between the skin of the upper arm and the skin of the forehead in CuV DNA-positive specimens. Significantly higher viral loads were evident in men vs. women, although no gender-associated differences in viral prevalence were noted. Phylogenetic analyses demonstrated the existence of Japanese-specific viruses that were genetically distinct from viruses prevalent in other areas, especially Europe.

CONCLUSIONS

This large study suggests that high levels of CuV DNA are prevalent on the skin of elderly adults. Our findings also indicated the prevalence of geographically related CuV genotypes. A follow-up study of this cohort should provide helpful information on whether CuV may become pathogenic.

Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing

Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.

Gene polymorphisms associated with heterogeneity and senescence characteristics of sarcopenia in chronic obstructive pulmonary disease

BACKGROUND

Sarcopenia, or loss of skeletal muscle mass and decreased contractile strength, contributes to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD). The severity of sarcopenia in COPD is variable, and there are limited data to explain phenotype heterogeneity. Others have shown that COPD patients with sarcopenia have several hallmarks of cellular senescence, a potential mechanism of primary (age-related) sarcopenia. We tested if genetic contributors explain the variability in sarcopenic phenotype and accelerated senescence in COPD.

METHODS

To identify gene variants [single nucleotide polymorphisms (SNPs)] associated with sarcopenia in COPD, we performed a genome-wide association study (GWAS) of fat free mass index (FFMI) in 32 426 non-Hispanic White (NHW) UK Biobank participants with COPD. Several SNPs within the fat mass and obesity-associated (FTO) gene were associated with sarcopenia that were validated in an independent COPDGene cohort (n = 3656). Leucocyte telomere length quantified in the UK Biobank cohort was used as a marker of senescence. Experimental validation was done by genetic depletion of FTO in murine skeletal myotubes exposed to prolonged intermittent hypoxia or chronic hypoxia because hypoxia contributes to sarcopenia in COPD. Molecular biomarkers for senescence were also quantified with FTO depletion in murine myotubes.

RESULTS

Multiple SNPs located in the FTO gene were associated with sarcopenia in addition to novel SNPs both within and in proximity to the gene AC090771.2, which transcribes long non-coding RNA (lncRNA). To replicate our findings, we performed a GWAS of FFMI in NHW subjects from COPDGene. The SNP most significantly associated with FFMI was on chromosome (chr) 16, rs1558902A > T in the FTO gene (β = 0.151, SE = 0.021, P = 1.40 × 10-12 for UK Biobank |β= 0.220, SE = 0.041, P = 9.99 × 10-8 for COPDGene) and chr 18 SNP rs11664369C > T nearest to the AC090771.2 gene (β = 0.129, SE = 0.024, P = 4.64 × 10-8 for UK Biobank |β = 0.203, SE = 0.045, P = 6.38 × 10-6 for COPDGene). Lower handgrip strength, a measure of muscle strength, but not FFMI was associated with reduced telomere length in the UK Biobank. Experimentally, in vitro knockdown of FTO lowered myotube diameter and induced a senescence-associated molecular phenotype, which was worsened by prolonged intermittent hypoxia and chronic hypoxia.

CONCLUSIONS

Genetic polymorphisms of FTO and AC090771.2 were associated with sarcopenia in COPD in independent cohorts. Knockdown of FTO in murine myotubes caused a molecular phenotype consistent with senescence that was exacerbated by hypoxia, a common condition in COPD. Genetic variation may interact with hypoxia and contribute to variable severity of sarcopenia and skeletal muscle molecular senescence phenotype in COPD.

Full-sib progenies show greater genetic diversity than half-sib progenies in sour passion fruit: an approach by ssr markers

BACKGROUND

Genetic variability is the most important parameter in plant breeding based on selection. There is a need for morpho-agronomic and molecular characterization of Passiflora species, to exploit their genetic resources more efficiently. No study has yet been carried out to compare half-sib and full-sib families in relation to the magnitude of the genetic variability obtained in them, and then to elucidate the advantages or disadvantages of each one.

METHODS AND RESULTS

In the present study, SSR markers were used to evaluate the genetic structure and diversity of half-sib and full-sib progenies of sour passion fruit. Two full-sib progenies (PSA and PSB), and a half-sib progeny (PHS), together with their parents, were genotyped with a set of eight pairs of SSR markers. Discriminant Analysis of Principal Components (DAPC) and Structure software were used to study the genetic structure of the progenies. The results indicate that the half-sib progeny has lower genetic variability, although it has higher allele richness. By the AMOVA most of the genetic variability was found within the progenies. Three groups were clearly observed in the DAPC analysis, while two hypothetical groups (k = 2) were observed in the Bayesian approach. The PSB progeny showed a high genetic mixture between the PSA and PHS progenies.

CONCLUSION

Lower genetic variability is found in half-sib progenies. The results obtained here allow us to suppose that the selection within full-sib progenies will possibly provide better estimates of genetic variance in sour passion fruit breeding programs, since they provide greater genetic diversity.

RNA-seq analysis of the active chick embryo chorioallantoic membrane reveals genes that encode proteins assigned to ion transport and innate immunity

The chicken chorioallantoic membrane (CAM) is an extraembryonic membrane that is vital for the embryo. It undergoes profound cell differentiation between 11 and 15 days of embryonic incubation (EID), which corresponds to the acquisition of its physiological functions. To gain insight into the functional genes that accompany these biological changes, RNA sequencing of the CAM at EID11 and EID15 was performed. Results showed that CAM maturation coincides with the overexpression of 4225 genes, including many genes encoding proteins involved in mineral metabolism, innate immunity, homeostasis, angiogenesis, reproduction, and regulation of hypoxia. Of these genes, some exhibit variability in expression depending on the chicken breed (broiler versus layer breeds). Besides the interest of these results for the poultry sector, the identification of new functional gene candidates opens additional research avenues in the field of developmental biology.

Distribution and mitochondrial CO1-based genetic diversity of Aedes aegypti L (Culicidae: Diptera) in Saudi Arabia

Mosquitoes (Diptera: Culicidae) act as vectors for various pathogens and parasites that affect millions of people worldwide. Aedes aegypti (Linnaeus, 1762) is one of the devastating pests of humans, acting as a key vector of dengue viruses. Therefore, correct identification of this serious pest to determine its distribution is paramount in its management. Morphological identification is usually based on the maturity and quality of the specimens. This can still yield ambiguous results in distinguishing Ae. aegypti species due to limited taxonomic expertise and the presence of cryptic species. In this research, mitochondrial CO1 gene-based identification was adopted to analyze 7 samples, each containing 7 specimens of Ae. aegypti from various localities of Saudi Arabia: Jeddah (A1), Makkah (A2), Al Madinah Al Munawwarah (A4), Jazan (A5), Qunfudah (A6), Yanbu (A8), and Najran (A10). DNA barcoding and maximum likelihood (ML) tree analysis revealed that all 49 species belong to Ae. aegypti and showed high similarity with specimens of this species worldwide.

Genetic effects of demographic bottleneck and recovery in Kinkazan Island and mainland populations of Japanese macaques (Macaca fuscata)

Populations of Japanese macaques were significantly reduced in most areas from the 1900s to the 1960s and then recovered mainly in the northeastern part of Honshu. A drastic reduction in population size reduces genetic variability through a bottleneck effect. Demographic expansion after the reduction that accumulates new mutations can reduce the bottleneck effects or drive the recovery of genetic variability. We examined the genetic status of a small island population (Kinkazan Island) and a larger mainland population (southern Tohoku) of Japanese macaques that experienced recent demographic bottlenecks and recovery using eight microsatellite loci. The two populations were significantly genetically different from each other. The Kinkazan population exhibited lower genetic variability, remarkable evidence of bottleneck (i.e., significant heterozygosity excess and lower frequency of rare alleles), and a considerably smaller effective population size based on genetic data than based on the current census size. These results indicate that the genetic status has not completely recovered from the demographic bottleneck despite a full recovery in census size on Kinkazan Island. New mutations might rarely have accumulated because of the small carrying capacity of the island. Therefore, the genetic variability of the population would have been restrained by the severe bottleneck size, small carrying capacity, and long-term isolation. On the other hand, the bottleneck effect seems to be limited in the southern Tohoku population considering higher genetic variability, non-significant heterozygosity excess in many mutation conditions, and the highest frequency of rare alleles.

Whole-genome sequencing of Crimean-Congo Hemorrhagic Fever Virus circulating in Pakistan during 2022

Pakistan is an endemic country for Crimean-Congo Hemorrhagic Fever (CCHF) and its Balochistan province is considered a hotspot region for circulation of the virus whereas sporadic cases have been reported from other parts of the country. Our study aims to investigate the genomic diversity of the CCHF virus circulating in Punjab and Khyber Pakhtunkhwa provinces of Pakistan. Between April-September 2022, 46 samples from suspected CCHF patients were tested, with six (13%) showing positive RT-PCR results. Among the positive cases, all were male, aged 14-48 years among which four were butchers. Three CCHF patients succumbed to the disease. The complete S-M-L-gene fragments of four positive samples were sequenced. The S and L segments belonged to the Asia-1 clade and clustered with regional strains from Iran, India, and Afghanistan. One M segment sequence grouped into Africa-2 along with those reported from India during 2016-2019. We report the detection of a reassorted virus (NIH-PAK-CCHF-03|2022) having Asia-1-Africa-2-Asia-1 (S-M-L) segment pattern for the first time from Pakistan. Mutational analysis showed M segments harboring eight mutations (T55A, S80P, T110I, T185A, T189A, A212T, and N239I/T) in the mucin-like domain, five mutations (D250N, T333S, I375V, M401I, A433T), four mutations (N545D, Y657F, K688R, and I824V) in GP38-domain, and three mutations (T1418N, A1431V, and G1449S) in Gc-domain. These findings highlight the significance of whole-genome sequencing of indigenous strains for a better understanding of the CCHFV evolution in Pakistan. This article is protected by copyright. All rights reserved.

Genetic variability of the prion protein gene in Indonesian goat breeds

Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goats. Resistance or susceptibility of small ruminants to classical scrapie is influenced by polymorphisms in the prion protein gene (PRNP). PRNP variability in Indonesian indigenous goat breeds has not been investigated so far and therefore was the goal of this study. Sanger sequencing of the PRNP gene coding region in 72 goats of the seven Indonesian breeds Kacang, Gembrong, Samosir, Kejobong, Benggala, Jawarandu, and Peranakan Etawah revealed three amino acid substitutions, namely W102G, H143R, and S240P. Some silent mutations were also found at codons 42 (a/g), 138 (c/t), and 179 (g/t). The PRNP alleles K222 and D/S146 known to have significant protective effects on resistance to classical scrapie in goats were not detected. The allele R143, which may have a moderate protective effect, had a frequency of 12% among the analyzed Indonesian goat breeds. While R143 was missing in Kacang and Benggala, its frequency was highest in the breed Gembrong (32%). No scrapie cases have been reported in Indonesia until now. However, in the case that selection for protective PRNP variants would become a breeding goal, the analyzed breeds will not be very useful resources. Other goat breeds which are present in the country should be investigated regarding resistance to scrapie, too.

Adaptive mechanisms in quinoa for coping in stressful environments: an update

Quinoa (Chenopodium quinoa) is a grain-like, genetically diverse, highly complex, nutritious, and stress-tolerant food that has been used in Andean Indigenous cultures for thousands of years. Over the past several decades, numerous nutraceutical and food companies are using quinoa because of its perceived health benefits. Seeds of quinoa have a superb balance of proteins, lipids, carbohydrates, saponins, vitamins, phenolics, minerals, phytoecdysteroids, glycine betaine, and betalains. Quinoa due to its high nutritional protein contents, minerals, secondary metabolites and lack of gluten, is used as the main food source worldwide. In upcoming years, the frequency of extreme events and climatic variations is projected to increase which will have an impact on reliable and safe production of food. Quinoa due to its high nutritional quality and adaptability has been suggested as a good candidate to offer increased food security in a world with increased climatic variations. Quinoa possesses an exceptional ability to grow and adapt in varied and contrasting environments, including drought, saline soil, cold, heat UV-B radiation, and heavy metals. Adaptations in salinity and drought are the most commonly studied stresses in quinoa and their genetic diversity associated with two stresses has been extensively elucidated. Because of the traditional wide-ranging cultivation area of quinoa, different quinoa cultivars are available that are specifically adapted for specific stress and with broad genetic variability. This review will give a brief overview of the various physiological, morphological and metabolic adaptations in response to several abiotic stresses.

Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms

Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of F_ST were higher in Wallachian sheep (F_ST = 0.14) than in Sumava sheep (F_ST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the N_e estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (F_HOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.

be associated with the climatic region of its human carriers?

Blastocystis sp. is a widespread microorganism that colonizes the intestinal tract of several animals, including human beings, while its pathogenic role in humans is still under debate. The objective of the present study was to describe the frequency of Blastocystis sp. subtypes (STs) and their genetic variation within and among samples recovered from scholars inhabiting two rural villages with tropical climates and compare this information with previously documented data from arid and temperate zones in Mexico. Blastocystis sp. positive samples and ST identification were achieved by coprological analysis screening and Polymerase Chain Reaction-sequencing, respectively. Classical population genetics indexes (nucleotide diversity (π), haplotype polymorphism (θ), gene flow (Nm), genetic differentiation (ST), and Tajima's D) were calculated by comparing the sequences here obtained (n = 42) and those from previous studies from the arid (n = 80) and temperate (n = 61) climates from Mexico. Although Blastocystis sp. was the parasite most frequently found between 33% and 26% in both communities, only STs 1-3 were found. Haplotype network inference of Blastocystis sp. STs showed different haplotype profiles among STs vs. climate zones, although no specific haplotypes were identified for any particular climatic zone. Population genetics indexes showed different values within STs and climate zones (π and θ values ranged from 0.004 to 0.147; Nm > 4 and ST from 0.006 to 0.12). Our results show that Blastocystis sp. subtypes exhibit a different genetic variability profile according to the climate zone, suggesting a balancing process between the genetic variability within the Blastocystis sp. subtype and the number of haplotypes identified in each climate.

Genetic variability in the E6 and E7 oncogenes of HPV52 and its prevalence in the Taizhou area, China

Background

Human papillomavirus (HPV) 52 is one of the prevalent oncogenic HPV genotypes in East Asia. Chinese women have the highest susceptibility to the HPV52 type, but research data on HPV52 genetic variability and its carcinogenicity in China is lacking.

Methods

The present study aimed to investigate the genetic variability of HPV52 currently circulating among Chinese women by PCR sequencing the entire E6 and E7 oncogenes. HPV52 sequence alignment, genetic heterogeneity analyses and maximum-likelihood phylogenetic tree construction were performed by BioEdit software and MEGA X software.

Results

Between 2016 and 2018, the overall HPV infection rate was 21.3%, of which HPV52 was the most prevalent high-risk type (17.2%) in the Taizhou area, China. A total of 339 single HPV52-positive samples were included in this study. We obtained 27 distinct variation patterns of HPV52 with the accession GenBank numbers ON529577-ON529603. Phylogenetic analysis showed that 96.6% of HPV52 variants belonged to lineage B, which seemed to be uniquely defined by G350T, A379G (K93R) in the E6 gene and C751T, A801G in the E7 gene. Due to the dominance of lineage B in our study population, the results could not be used to assess the association of the HPV52 (sub)lineage with the risk of cervical lesions. In addition, no significant trends were observed between the nucleotide substitutions of HPV52 variants and the risk of cervical carcinogenesis.

Conclusion

Our data showed that HPV52 variants were strongly biased towards lineage B. These results confirmed that cervical lesions in the Taizhou area are highly attributable to HPV52, which may be due to the high infection rate of lineage B in the population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01929-5.

Genetic origin of donkeys in Brazil

INTRODUCTION

The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses.

MATERIAL AND METHODS

This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga).

RESULTS AND DISCUSSION

We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure, and distances of the groups, reported here for the first time. CONCLUSION : This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.

Chemical mutagenesis: role in breeding and biofortification of lentil (Lens culinaris Medik) mutant lines

BACKGROUND

Induced mutagenesis is a quick and effective breeding strategy to enhance genetic variability, an important prerequisite for the genetic improvement of existing lentil cultivars. Lentil is an important cool season food legume with low productivity due to the low yielding potential of existing lentil cultivars. The present study aimed at increasing the yielding potential, resulted in the isolation of six high-yielding mutant lines with dense micronutrients.

METHODS AND RESULTS

Two lentil varieties were treated with different doses of ethyl methanesulphonate, hydrazine hydrate, and sodium azide, followed by phenotypic selection for consecutive three generations. In the M₂ generation, six high-yielding mutant lines with stable phenotypes were isolated. The results revealed a substantial increase in mean values for quantitative and physiological traits coupled with a manifold increase in the genotypic coefficient of variation (GCV), heritability (h²), and genetic advance (GA). Correlation analysis revealed that plant yield was significantly and positively influenced (P < 0.001) by fertile branches per plant, pods per plant, and seed weight. Principal component analysis revealed two principal components contributed 63.5 and 62.5% of the total variation in the varieties Pant L-639 and Pant L-406, respectively.

CONCLUSION

The isolated high-yielding mutant lines with dense micronutrients that serve as rich genetic resources could be subjected to further breeding trials. After attaining yield stability, these might be registered and released as new improved lentil varieties.

Identification and characterization of a new geminivirus from soybean plants and determination of V2 as a pathogenicity factor and silencing suppressor

BACKGROUND

Soybean is one of the four major crops in China. The occurrence of viruses in soybean causes significant economic losses.

RESULTS

In this study, the soybean leaves from stay-green plants showing crinkle were collected for metatranscriptomic sequencing. A novel geminivirus, tentatively named soybean geminivirus A (SGVA), was identified in soybean stay-green plants. Sequence analysis of the full-length SGVA genome revealed a genome of 2762 nucleotides that contain six open reading frames. Phylogenetic analyses revealed that SGVA was located adjacent to the clade of begomoviruses in both the full genome-based and C1-based phylogenetic tree, while in the CP-based phylogenetic tree, SGVA was located adjacent to the clade of becurtoviruses. SGVA was proposed as a new recombinant geminivirus. Agroinfectious clone of SGVA was constructed. Typical systemic symptoms of curly leaves were observed at 11 dpi in Nicotiana benthamiana plants and severe dwarfism was observed after 3 weeks post inoculation. Expression of the SGVA encoded V2 and C1 proteins through a potato virus X (PVX) vector caused severe symptoms in N. benthamiana. The V2 protein inhibited local RNA silencing in co-infiltration assays in GFP transgenic 16C N. benthamiana plants. Further study revealed mild symptoms in N. benthamiana plants inoculated with SGVA-ZZ _V2-STOP and SGVA-ZZ _V2-3738AA mutants. Both the relative viral DNA and CP protein accumulation levels significantly decreased when compared with SGVA-inoculated plants.

CONCLUSIONS

This work identified a new geminivirus in soybean stay-green plants and determined V2 as a pathogenicity factor and silencing suppressor.

Phenotypic evaluation of agronomic and root related traits for drought tolerance in recombinant inbred line population derived from a chickpea cultivar (C. arietinum L.) and its wild relative (C. reticulatum)

Drought is a major abiotic stress that drastically reduces chickpea yields. The present study was aimed to identify drought-responsive traits in chickpea by screening a recombinant inbred line population derived from an inter-specific cross between drought cultivar of GPF2 (C. arietinum L.) and drought sensitive accession of ILWC292 (C. reticulatum), at two locations in India. Twenty-one traits, including twelve morphological and physiological traits and nine root-related traits were measured under rainfed (drought-stress) and irrigated conditions (no-stress). High genotypic variation was observed among RILs for yield and root traits indicated that selection in these germplasms would be useful in achieving genetic progress. Both correlation and principal component analysis revealed that plant height, number of pods per plant, biomass, 100-seed weight, harvest index, membrane permeability index, and relative leaf water content were significantly correlated with yield under both irrigated and drought stress environments. Root length had significant positive correlations with all root-related traits except root length density in drought-stressed plants. Path analysis and multiple and stepwise regression analyses showed that number of pods per plant, biomass, and harvest index were major contributors to yield under drought stress conditions. Thus, a holistic approach across these analyses identified number of pods per plant, biomass, harvest index, and root length as key traits for improving chickpea yield through indirect selection for developing drought-tolerant cultivars. Overall, on the basis of yield components morphological and root traits, a total of 15 promising RILs were identified for their use in chickpea breeding programs for developing drought tolerant cultivars.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01218-z.

Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches

This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.

DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers' field and genebank collections

A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers' field and genebank collections Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers' needs.

The Mediterranean limpet Patella caerulea (Gastropoda, Mollusca) to assess marine ecotoxicological risk: a case study of Tunisian coasts contaminated by metals

Participants in the coastal socio-economy of the Mediterranean Sea, such as industries, aquaculture, urban populations, conglomerates, and tourists, create intense anthropogenic pressures on marine ecosystems (such as the release of trace metals). This raises concerns about their impact on the surrounding environment and on marine organisms, including those collected for human consumption. This study introduces the possibility of using Patella caerulea (Linnaeus 1758), indigenous to the Mediterranean Sea, as a biosentinel of marine pollution. This study proposes coupling environmental (bioaccumulation) and toxicological (redox homeostasis) measures of bioavailability with genetic variability (COI mtDNA) assessments. Concentrations of six trace metals (cadmium, copper, iron, lead, nickel, and zinc) were measured in surface seawater and in P. caerulea individuals collected from four coastal stations on the Tunisian coast where different levels of metal contamination have occurred. The quantified biomarkers involved the determination of antioxidant defense enzymes, catalase (CAT), glutathione peroxidase (GPX), superoxide dismutase (SOD), and the measurement of lipid peroxidation indicated by malondialdehyde (MDA) levels. Our study identified critical levels of metal contamination among locations in the Gulf of Gabes. Concomitantly, the induction of antioxidant biomarkers (especially SOD and GPX) was observed, highlighting the potential of P. caerulea to acclimate to stressful pollution conditions. Molecular analysis of COI (mtDNA) revealed low discrimination between the four P. caerulea populations, highlighting the role of marine currents in the Mediterranean Sea in the dispersal and passive transportation of limpet larvae, allowing an exchange of individuals among physically separated, P. caerulea populations.

Roles of two distinct alphasatellites modulating geminivirus pathogenesis

BACKGROUND

Alphasatellites are small coding DNA satellites frequently associated with a begomovirus/betasatellite complex, where they are known to modulate virulence and symptom development. Two distinct alphasatellites, namely, Cotton leaf curl Multan alphasatellite (CLCuMuA), and Gossypium darwinii symptomless alphasatellite (GDarSLA) associated with Cotton leaf curl Multan virus-India (CLCuMuV-IN) and Ludwigia leaf distortion betasatellite (LuLDB) were found to be associated with yellow mosaic disease of hollyhock (Alcea rosea) plants. In this study, we show that alphasatellites CLCuMuA and GDarSLA attenuate and delay symptom development in Nicotiana benthamiana. The presence of either alphasatellites reduce the accumulation of the helper virus CLCuMuV-IN. However, the levels of the associated betasatellite, LuLDB, remains unchanged. These results suggest that the alphasatellites could contribute to the host defence and understanding their role in disease development is important for developing resistance strategies.

METHODS

Tandem repeat constructs of two distinct alphasatellites, namely, CLCuMuA and GDarSLA associated with CLCuMuV-IN and LuLDB were generated. N. benthamiana plants were co-agroinoculated with CLCuMuV and its associated alphasatellites and betasatellite molecules and samples were collected at 7, 14 and 21 days post inoculation (dpi). The viral DNA molecules were quantified in N. benthamiana plants by qPCR. The sequences were analysed using the MEGA-X tool, and a phylogenetic tree was generated. Genetic diversity among the CLCuMuA and GDarSLA was analysed using the DnaSP tool.

RESULTS

We observed a reduction in symptom severity and accumulation of helper virus in the presence of two alphasatellites isolated from naturally infected hollyhock plants. However, no reduction in the accumulation of betasatellite was observed. The phylogenetic and genetic variability study revealed the evolutionary dynamics of these distinct alphasatellites , which could explain the role of hollyhock-associated alphasatellites in plants.

CONCLUSIONS

This study provides evidence that alphasatellites have a role in symptom modulation and suppress helper virus replication without any discernible effect on the replication of the associated betasatellite.

Human papillomavirus 68 prevalence and genetic variability based on E6/E7 genes in Sichuan

HPV68 is a common HR-HPV, its persistent infection is closely related with the occurrence of cervical cancer. In this study, 2939 (27.60%, 2939/10650) positive samples were detected, and 174 (5.92%, 174/2939) were HPV68. 150 HPV68 E6-E7 were successful sequenced, 4 non-synonymous mutations were detected in E6, and E7 were 12. N133S non-synonymous mutations of HPV 68 E6 and C67G, T68 A/M of HPV68 E7 are E6, E7 positive selection sites, they all located in the key domains and major motifs of E6/E7 protein, the above amino-acid substitutions changed the protein structure, disturbed the interaction with other protein or cellular factors and make a difference in epitopes affinity, may affect the pathogenicity and adaptability of HPV68 to the environment. The enrichment of HPV68 data is of great significance for understanding the inherent geographical and biological differences of HPV68 in China.

Genetic variability affects the skeletal response to immobilization in founder strains of the diversity outbred mouse population

Mechanical unloading decreases bone volume and strength. In humans and mice, bone mineral density is highly heritable, and in mice the response to changes in loading varies with genetic background. Thus, genetic variability may affect the response of bone to unloading. As a first step to identify genes involved in bones' response to unloading, we evaluated the effects of unloading in eight inbred mouse strains: C57BL/6J, PWK/PhJ, WSB/EiJ, A/J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, and CAST/EiJ. C57BL/6J and NOD/ShiLtJ mice had the greatest unloading-induced loss of diaphyseal cortical bone volume and strength. NZO/HlLtJ mice had the greatest metaphyseal trabecular bone loss, and C57BL/6J, WSB/EiJ, NOD/ShiLtJ, and CAST/EiJ mice had the greatest epiphyseal trabecular bone loss. Bone loss in the epiphyses displayed the highest heritability. With immobilization, mineral:matrix was reduced, and carbonate:phosphate and crystallinity were increased. A/J mice displayed the greatest unloading-induced loss of mineral:matrix. Changes in gene expression in response to unloading were greatest in NOD/ShiLtJ and CAST/EiJ mice. The most upregulated genes in response to unloading were associated with increased collagen synthesis and extracellular matrix formation. Our results demonstrate a strong differential response to unloading as a function of strain. Diversity outbred (DO) mice are a high-resolution mapping population derived from these eight inbred founder strains. These results suggest DO mice will be highly suited for examining the genetic basis of the skeletal response to unloading.

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Mouse strain affects bone's response to immobilization.

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Magnitude of bone loss from immobilization is heritable.

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Bone transcriptomic response to immobilization is influenced by genetic variation.