Desirable Genes Research Articles

Establishment of a Dual-Vector System for Gene Delivery Utilizing Prototype Foamy Virus.

Foamy viruses (FVs) are generally recognized as non-pathogenic, often causing asymptomatic or mild symptoms in infections. Leveraging these unique characteristics, FV vectors hold significant promise for applications in gene therapy. This study introduces a novel platform technology using a pseudo-virus with single-round infectivity. In contrast to previous vector approaches, we developed a technique employing only two vectors, pcHFV lacking Env and pCMV-Env, to introduce the desired genes into target cells. Our investigation demonstrated the efficacy of the prototype foamy virus (PFV) dual-vector system in producing viruses and delivering transgenes into host cells. To optimize viral production, we incorporated the codon-optimized Env (optEnv) gene in pCMV-Env and the Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE) at the 3' end of the transgene in the transfer vector. Consequently, the use of optEnv led to a significant enhancement in transgene expression in host cells. Additionally, the WPRE exhibited an enhancing effect. Furthermore, the introduced EGFP transgene was present in host cells for a month. In an effort to expand transgene capacity, we further streamlined the viral vector, anticipating the delivery of approximately 4.3 kbp of genes through our PFV dual-vector system. This study underscores the potential of PFVs as an alternative to lentiviruses or other retroviruses in the realm of gene therapy.

A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants

BackgroundVirus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites.ResultsWe evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS. The seedlings were vacuum-infiltrated with Agrobacterium tumefaciens GV3101 cells carrying the tobacco rattle virus (TRV) vectors. The protoporphyrin IX magnesium chelatase subunit H (ChlH) gene, a key gene in chlorophyll biosynthesis, was used as the target for VIGS, and we observed yellow cotyledons 6 days after infiltration. As expected, the expression of CrChlH and the chlorophyll contents of the cotyledons were significantly decreased after VIGS. To validate the cotyledon based-VIGS method, we silenced the genes encoding several transcriptional regulators of the terpenoid indole alkaloid (TIA) biosynthesis in C. roseus, including two activators (CrGATA1 and CrMYC2) and two repressors (CrGBF1 and CrGBF2). Silencing CrGATA1 led to downregulation of the vindoline pathway genes (T3O, T3R, and DAT) and decreased vindoline contents in cotyledons. Silencing CrMYC2, followed by elicitation with methyl jasmonate (MeJA), resulted in the downregulation of ORCA2 and ORCA3. We also co-infiltrated C. roseus seedlings with TRV vectors that silence both CrGBF1 and CrGBF2 and overexpress CrMYC2, aiming to simultaneous silencing two repressors while overexpressing an activator. The simultaneous manipulation of repressors and activator resulted in significant upregulation of the TIA pathway genes. To demonstrate the broad application of the cotyledon-based VIGS method, we optimized the method for two other valuable medicinal plants, Glycyrrhiza inflata (licorice) and Artemisia annua (sweet wormwood). When TRV vectors carrying the fragments of the ChlH genes were infiltrated into the seedlings of these plants, we observed yellow cotyledons with decreased chlorophyll contents.ConclusionsThe widely applicable cotyledon-based VIGS method is faster, more efficient, and easily accessible to additional treatments than the traditional VIGS method. It can be combined with transient gene overexpression to achieve simultaneous up- and down-regulation of desired genes in non-model plants. This method provides a powerful tool for functional genomics of medicinal plants, facilitating the discovery and production of valuable therapeutic compounds.

Nanomaterials for intelligent CRISPR-Cas tools: improving environment sustainability.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a desirable gene modification tool covering a wide area in various sectors of medicine, agriculture, and microbial biotechnology. The role of this incredible genetic engineering technology has been extensively investigated; however, it remains formidable with cargo choices, nonspecific delivery, and insertional mutagenesis. Various nanomaterials including lipid, polymeric, and inorganic are being used to deliver the CRISPR-Cas system. Progress in nanomaterials could potentially address these challenges by accelerating precision targeting, cost-effectiveness, and one-step delivery. In this review, we highlighted the advances in nanotechnology and nanomaterials as smart delivery systems for CRISPR-Cas so as to ameliorate applications for environmental remediation including biomedical research and healthcare, strategies for mitigating antimicrobial resistance, and to be used as nanofertilizers for enhancing crop growth, and reducing the environmental impact of traditional fertilizers. The timely co-evolution of nanotechnology and CRISPR technologies has contributed to smart novel nanostructure hybrids for improving the onerous tasks of environmental remediation and biological sustainability.

Reliable reference gene selection for quantitative real-time PCR (qRT-PCR) in floral developmental phases of dioecious species Coccinia grandis

The flowering process is intricate and regulated by a combination of external and internal factors. Delving into gene expression research has the potential to enhance our comprehension of the molecular foundations underlying floral development. Because of its accuracy, specificity, reproducibility, and efficiency, qRT-PCR is now a biological research tool for studying expression pattern of desired genes. The gene expression investigations using qRT-PCR required a reference gene with relatively uniform expression levels in multiple biological samples, including different developmental stages, tissues, and experimental conditions. In this study, experimental sets offloral and floral organ development in the male and female plants of C. grandis, a dioecious Cucurbitaceae species, qRT-PCR profiling was performed using six reference genes as internal control with B-class floral identity gene, PISTILLATA (PI). To analyse the data, algorithms such as geNorm, NormFinder, RefFinder, and BestKeeper were used to pick out the best internal controls from a group of candidates. The optimal reference gene for qRT-PCR studies with floral samples has been recommended as β-actin combined with β-tubulin. This is the first report on the validation of candidate reference genes across flower developmental stages in the dioecious species C. grandis, which will provide basic data for research on the molecular mechanism underlying flower development in this species and lay the groundwork for similar studies in other related species.

Development of Gossypium hirsutum-Gossypium raimondii introgression lines and its usages in QTL mapping of agricultural traits

Gossypium raimondii (2n=2x=26, D5), an untapped wild species, is the putative progenitor of the D-subgenome of G. hirsutum (2n=4x=52, AD1), an extensively cultivated species. Here, we developed a G. hirsutum (recipient)-G. raimondii (donor) introgression population to exploit favorable QTLs/genes and mapped potential quantitative trait loci (QTLs) from wild cotton species. The introgression population consists of 256 lines with an introgression rate of 52.33% of the genome G. raimondii. The range of introgression segment length was 0.03-19.12 Mb, with an average of 1.22 Mb. The coverage of total introgression fragments was 386.98 Mb from G. raimondii. Further genome-wide association analysis (Q+K+MLM) and QTL mapping (RSTEP-LRT) identified 59 common QTLs, including 14 stable QTLs and 6 common QTL (co-QTL) clusters, and one hotspot of MIC. The common QTLs for seed index showed all positive additive effects, while the common QTLs for boll weight were all negative additive effects, indicating that the linkage between seed index and boll weight could be broken. QTLs for lint percentage showed positive effect and could be beneficial for improving cotton yield. Most QTLs for fiber quality had negative additive effects, implying these QTLs were domesticated/improved in G. hirsutum. A few fiber quality QTLs showed positive additive effects, which could be used to improve cotton fiber quality. These introgression lines developed would be useful for molecular marker-assisted breeding and facilitate us to map QTLs precisely for mining desirable genes from the wild species G. raimondii to improve cultivated cotton in future via a design-breeding approach.

أثر التضريب في بعض الصفات الإنتاجية للدجاج البياض

5The hybridization process is considered One of the crucial techniques in programs aimed at enhancing and refining animal breeds, as it works on increasing production and transferring and collection of a large number of desirable genes present in the resulting hybrids, thereby improving them. The generation of chickens resulting from the hybridization of breeds Generally excels in various economic aspects like growth rate, feed efficiency, age of initial egg laying, egg output, and meat production, and meat production. To improve the local chickens, which have a rich reservoir of genes and traits that have given them the ability to adapt to local environmental conditions and resistance to diseases, the production performance is still low. Therefore, this study aims to emphasize the significance of crossbreeding local chickens with high-yield breeds while preserving their unique traits. This approach holds great promise for enhancing the productivity of layer chickens.

Frequency of heterotic hybrids in relation to general combining ability of parents in sweet corn.

The success of developing prominent hybrids directly depends on the selection of parents with good combining ability which can transfer desirable genes with additive effects to their progeny. The data of 42 hybrids generated using 7×7 full diallel design; their seven parents along with three check hybrids were subjected to combining ability analysis from the experiment that was carried out during rainy season 2019. The analysis of variance showed significant general combining ability, and specific combining ability mean sum of squares for all the thirteen characters studied. It is obvious from the results that three lines (SC Sel 2, SC Sel 1 and SC Sel 3) showed high overall general combining ability status, suggesting these lines as good general combiners across traits. Eighteen hybrids had high overall specific combining ability status, while nearly 52% (22 hybrids), 57% (24 hybrids) and 47% (20 hybrids) of crosses showed high overall mid-parent, better-parent and standard heterosis. The unique superiority of crosses involving high overall general combiner parent in the crosses highlighted the importance of using such parents to realize high heterotic crosses. A non-linear relationship between high overall specific combining ability status and heterotic status of hybrids was noticed. The probability of obtaining a cross with high standard heterosis was more with employing parents with high general combining ability status.

An objective way to preserve the genes of domestic small in number cattle breeds

The results on the preservation of the genetic characteristics of the breed of Sychevka of cattle under conditions admixture of Holstein blood using marker genes of blood groups are presented. The studies were conducted from 1977 to 2021 in pedigree farms of the Smolensk region. The possibility of preserving by the method of immunogenetic monitoring of valuable hereditary traits of cows outstanding in milk productivity, from the families of the breed of Sychevka cattle, which allows preserving their genes in generations, thereby maintaining hereditary variability and increasing the dairy productivity of animals, has been established. Under immunogenetic control, the desirable genes of the Dobrynya 5141 cow, born in 1963 of the breed of Sychevka, marked with the A/B/ EAB-allele, have been preserved for 6 generations and are distributed in the genotypes of female offspring of the herd pedigree farm Rybkovskoe. The genetic predisposition of cows to high milk productivity is also preserved. It is proposed to use a method tested on animals of the breed of Sychevka in breeding to preserve the gene pool of other small or endangered breeds cattle.

Prebreeding and genetic enhancement of cultivated sunflower (Helianthus annuusL.) using diploid wild Helianthus species in India

Pre-breeding activities using promising diploid wild Helianthus like Helianthus annuus (wild), H. argophyllus, H. praecox, H. debilis and H. petiolaris and popular cultivar (ARM-243B) have been initiated at ICAR Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad to increase the frequency of desirable genes, wider adaptability and a broad genetic base. Wider variability was observed for yield and yield contributing traits besides disease reactions within and between species. Evaluation of a few populations for biotic stresses and yield related traits resulted in the identification of desirable introgression lines. The highest seed yield (42.5 g/plant) was reported in combinations with H. annuus (wild), H. petiolaris (40.2 g/plant) and H. debilis (39.8 g/plant). Interspecificderivatives derived from H. praecox were found resistant to powdery mildew. Interspecific derivatives of H. argophyllus, namely PB-1001, PB-1003, PB-1005, PB-1007, PB-1008, PB-1014, and PB-1019 were resistant to leafhoppers, while PB-1003, PB-1005, and PB-1007 exhibited resistant reactions to downy mildew under sick plot conditions. H. debilis derivatives viz., PB-120, PB-127, PB-128, PB-129 and PB-130 recorded >40% oil content. The pre-breeding lines derived from these interspecific cross combinations serve as an invaluable reservoir of genes for carrying out basic studies on the key traits as well as the exploitation of agronomically desirable traits in the AICRP sunflower breeding programmes.

Amplification of Genes Associated with Saxitoxin Biosynthesis in Bacteria Associated with Pyrodinium bahamense var. compressum Using Primers Designed from Other Saxitoxin-Producing Organisms

Pyrodinium bahamense var. compressum, the primary producer of saxitoxin (STX) in tropical water, poses a palpable threat to public health and safety. Seafood and aquaculture products contaminated with lethal concentrations of the principal neurotoxin, saxitoxin, have been implicated in mortality and morbidity. Previous research revealed that the relationship between bacteria and algae may contribute directly or indirectly to the synthesis of saxitoxin. This study investigates the potential relationship between the dinoflagellate and its associated bacteria; hence the initial step is to determine whether the genes responsible for the STX production in P. bahamense can be found in the associated bacteria. A total of six bacterial species associated with P. bahamense were successfully identified in a previous study. The presence of the sxt genes in the associated bacterial genome was determined using primers that have previously been utilized in other saxitoxin-producing species, such as in dinoflagellates (Alexandrium fundyense) and cyanobacteria (Anabaena and Aphanizomenon gracile). This study showed that the utilized primers were unsuitable as the primers produced non-specific amplification in the bacterial genome. We suggest that specific primers targeting the sxt homolog genes in bacterial species should be designed to obtain the desired genes from the associated bacteria in a future study.

A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops.

Breeding new and sustainable crop cultivars of high yields and desirable traits has been a major challenge for ensuring food security for the growing global human population. For polyploid crops such as wheat, introducing genetic variation from wild relatives of its subgenomes is a key strategy to improve the quality of their breeding pools. Over the past decades, considerable progress has been made in speed breeding, genome sequencing, high-throughput phenotyping and genomics-assisted breeding, which now allows us to realize whole-genome introgression from wild relatives to modern crops. Here, we present a standardized protocol to rapidly introgress the entire genome of Aegilops tauschii, the progenitor of the D subgenome of bread wheat, into elite wheat backgrounds. This protocol integrates multiple modern high-throughput technologies and includes three major phases: development of synthetic octaploid wheat, generation of hexaploid A. tauschii-wheat introgression lines (A-WIs) and homozygosis of the generated A-WIs. Our approach readily generates stable introgression lines in 2 y, thus greatly accelerating the generation of A-WIs and the introduction of desirable genes from A. tauschii to wheat cultivars. These A-WIs are valuable for wheat-breeding programs and functional gene discovery. The current protocol can be easily modified and used for introgressing the genomes of wild relatives to other polyploid crops.

Maize genetic breeding for tolerance to abiotic stress with focus on sustainable use of environmental resources

This bibliographic review explored maize genetic breeding to increase tolerance to abiotic stress. The main stresses faced by the crop, such as water stress and nitrogen deficiency, and their negative impacts on grain yield were discussed. Strategies to minimize these effects were examined, focusing on the selection of tolerant genotypes and the strategic positioning of these genotypes in different growing environments. The germplasm bank and genetic diversity were highlighted as crucial resources to identify desirable traits and genes associated with resistance to abiotic stress. The selection of secondary characters, considering their heritability and correlation with characters of interest, allows maximizing the efficiency in the selection of promising genotypes in genetic breeding programs. Test environments simulating stresses, such as water stress and low nitrogen, are essential to evaluate the performance of genotypes and identify the most tolerant ones. The genetic breeding of maize for tolerance to abiotic stress promotes promising solutions to face environmental challenges and ensure the sustainability of agricultural production.

Genetic enhancement of okra [Abelmoschus esculentus (L.) Moench] germplasm through wide hybridization.

The introgression of genetic material from one species to another through wide hybridization and repeated back-crossing, plays an important role in genetic modification and enriching the cultivated gene-pool with novel genetic variations. Okra (Abelmoschus esculentus [(L.) Moench)] is a popular vegetable crop with high dietary fibre and protein, rich in essential amino acids, lysine and tryptophan. The wild Abelmoschus genepool has many desirable traits like ornamental value, short internodal length, more number of productive branches, extended bearing, perennation tendency, reduced fruit length (more consumer preferred trait), high mucilage content (medicinal value), abiotic stress tolerances such as drought, high temperature and biotic stress resistances such as okra Yellow Vein Mosaic Virus (YVMV) and Enation Leaf Curl Virus (ELCV) diseases. The repeated use of elite breeding lines led to narrowing of the genetic base of the okra crop, one of the major factors attributed to breakdown of resistance/ tolerance to biotic stresses. YVMV and ELCV are the two major diseases, causing significant yield loss in okra. Hence, wide hybridization was attempted to transfer tolerance genes from wild species to the cultivated genepool to widen the genetic base. The screening of germplasm of wild Abelmoschus species at hotspots led to the identification of tolerant species (Abelmoschus pungens var. mizoramensis, A. enbeepeegeearensis, A. caillei, A. tetraphyllus and A. angulosus var. grandiflorus), which were further used in a wide-hybridization programme to generate interspecific hybrids with the cultivated okra. Presence of pre- and post-zygotic barriers to interspecific geneflow, differences in ploidy levels and genotype specific variations in chromosome numbers led to varying degrees of sterility in F1 plants of interspecific crosses. This was overcome by doubling the chromosome number of interspecific hybrids by applying Colchicine at the seedling stage. The 113 cross derivatives generated comprising amphidiploids in the F1 generation (30), F3 (14), one each in F2 and F4 generations, back cross generation in BC1F2 (03), BC1F3 (25), and BC2F3 (02), crosses between amphidiploids (27), multi-cross combinations (07) and inter-specific cross (between A. sagittifolius × A. moschatus subsp. moschatus) selfed derivatives at F8 generation (03) were characterized in the present study. Besides they were advanced through selfing and backcrossing. The amphidiploids were found to possess many desirable genes with a considerable magnitude of linkage drag. Majority of the wide cross derivatives had an intermediate fruit morphology and dominance of wild characters viz., hispid fruits, stem, leaves, tough fruit fibre, vigorous perennial growth habit and prolonged flowering and fruiting. The fruit morphology of three BC progenies exhibited a high morphological resemblance to the cultivated okra, confirming successful transfer of useful genes to the cultivated okra genepool. The detailed morphological characteristics of the various combinations of Abelmoschus amphidiploids and the genetic enhancement of the genepool achieved in this process is reported here.

Response of bacterial biovars to inheritance pattern of bacterial wilt disease in tomato

ABSTRACT Knowledge of the genetic control of disease tolerance is necessary for effective transfer of desirable genes in resultant progenies leading to development of disease tolerant cultivars and hybrids. Bacterial wilt (BW) disease-resistant varieties of tomato (Solanum lycopersicum L.) express differential reactions to bacterial biovars distributed in specific regions. Genetic control of host tolerance to BW disease was studied using the generations P1, P2, F1, F2, BC1, BC2 of three tolerant × susceptible crosses (“Utkal Kumari × CLN- 2460E;” “Utkal Kumari × CLN-2764A;” “Utkal Deepti × CLN-2460E”) involving two tolerant (“Utkal Kumari,” “Utkal Deepti”), and two susceptible (“CLN-2460E” and “CLN-2764A”) genotypes exposed to the virulent bacterial biovars III and VI. The inheritance pattern indicated tolerance to BW disease was conditioned by a single dominant gene in three crosses when exposed to both biovars. Genetic control of bacterial wilt resistance did not depend on the interaction between genotype and bacterial biovars tested. Predominance of non-additive gene action and duplicate epistasis for conditioning of first appearance and incidence of BW disease in crosses indicated hindrance in progress through conventional selection. Selection for improvement of BW disease-related traits should be delayed to later segregating generations. The modified bulk method of selection appeared to be best for improving BW disease-related traits of tomato. Tomato hybrids tolerant to BW disease could be developed with the involvement of one parent tolerant to this disease.

Claudin18.2 bispecific T cell engager armed oncolytic virus enhances antitumor effects against pancreatic cancer

Bispecific Tcell engagers (BiTEs) represent a promising immunotherapy, but their efficacy against immunologically cold tumors such as pancreatic ductal adenocarcinoma remains unclear. Oncolytic viruses (OVs) can transform the immunosuppressive tumor microenvironment into the active state and also serve as transgene vectors to selectively express the desired genes in tumor cells. This study aimed to investigate whether the therapeutic benefits of tumor-targeting Claudin18.2 BiTE can be augmented by combining cancer selectively and immune-potentiating effects of OVs. Claudin18.2/CD3 BiTE was inserted into herpes simplex virus type 1 (HSV-1) to construct an OV-BiTE. Its expression and function were assessed using reporter cells and peripheral blood mononuclear cell (PBMC) co-culture assays. Intratumoral application of OV-BiTE restrained tumor growth and prolonged mouse survival compared with the unarmed OV in xenograft models and syngeneic mice bearing CLDN18.2-expressing KPC or Pan02 pancreatic cancer cells. Flow cytometry of tumor-infiltrating immune cells suggested both OV-BiTE and the unarmed OV remodeled the tumor microenvironment by increasing CD4+ Tcell infiltration and decreasing regulatory Tcells. OV-BiTE further reprogrammed macrophages to a more pro-inflammatory antitumor state, and OV-BiTE-induced macrophages exhibited greater cytotoxicity on the co-cultured tumor cell. This dual cytotoxic and immunomodulatory approach warrants further development for pancreatic cancer before clinical investigation.

Submergence Tolerance in Rice (Oryza sativa L.) Genotypes at the Seedling Stage: A Combined Approach of Morphological and Molecular Characterization

Background: Rice (Oryza sativa L.) is the major cereal crop often suffers from submergence in the rainfed growing situation of India and South East Asia. Developing rice cultivars with tolerance to submergence is the best strategy to circumvent the situation. In Eastern India a vast reservoir of rice genotypes exists grown in diverse agro-climatic situation under rainfed condition. Screening rice genotypes under submergence stressed condition by observing morphological traits combined with molecular marker approach helps to identify the genotypes having innate capacity to survive under flooding condition more precisely than either of the approach alone. The present study was framed to identify the landraces and genotypes having the presence of desired genes which will helpful for future breeding program. Methods: Fifty rice (Oryza sativa L.) genotypes were evaluated for submergence tolerance using both morphological and molecular characterization in the field and laboratory respectively. Six stress indices, namely elongation%, survival%, mortality%, relative growth index, dry mass% and recovery rate, were examined in the field seven days and fourteen days after submergence. The genotypes were screened with SSR markers to identify the presence of the desired gene. Result: Based on morphological and molecular screening, out of all rice genotypes, Brahmabalak, Jaladhi 1-2, Jaldubi, Kerala Sundary, China IRRI, Sonachur, Pravat, Pankaj, Ranjit SUB1 and Bahadur SUB1 showed higher levels of tolerance to submergence than the tolerant control Swarna SUB1. They have one or more loci different from the SUB1 locus, which can be bred to create improved submergence-tolerant rice varieties with high yield in the rainfed lowland agroecosystem.

Conventional and molecular breeding strategies for improvement of drought tolerance cultivars in rice: Recent approaches and outlooks

Rice is a vital staple food, especially in Asia, but it is highly susceptible to drought, leading to significant yield losses. To ensure food sustainability, drought-tolerant rice varieties are essential. Conventional breeding methods improve drought tolerance by focusing on biometric traits like root depth, avoidance, escape, and tolerance. This involves screening and crossing drought-tolerant varieties with high-yielding ones, followed by selection and evaluation. Techniques such as pedigree selection, recurrent selection, and backcrossing introduce desirable genes to enhance drought tolerance. Induced mutation through radiation exposure is also used. The molecular basis of drought tolerance involves identifying and manipulating genes responsible for rice's response to water stress. Techniques like QTL analysis, transcriptomics, genomics, and proteomics identify genes and QTLs associated with drought tolerance. Important genes involved in drought response include DREB, LEA, and ROS scavenging genes. Identifying QTLs enables the development of molecular markers for efficient screening of drought-tolerant rice genotypes. In conclusion, conventional breeding and molecular approaches are employed to develop drought-tolerant rice varieties. Conventional breeding improves biometric traits, while molecular techniques identify and manipulate specific genes associated with drought tolerance. This combination holds promise for high-yielding and drought-tolerant rice cultivars, contributing to global food security. However, further research is needed to understand the complex genetic mechanisms underlying drought tolerance in rice and enhance breeding precision and efficiency.

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research.ResultsTo solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4.ConclusionsWe present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.

ASMEvoNAS: Adaptive segmented multi-objective evolutionary network architecture search

Network architecture search (NAS) has attracted much attention as an automatic design technique of network architecture. In particular, multi-objective evolutionary algorithms (MOEAs) have been a popular kind of optimizer in NAS due to their global optimization capability. However, as a population-based iterative search method, MOEAs are subject to the unbearable computational cost of individual evaluation on multiple objectives at each generation, which affects their generalization ability and transferability of MOEA-based NAS. Therefore, an adaptive segmented multi-objective evolutionary network architecture search (ASMEvoNAS) method is proposed in this paper. Firstly, an adaptive segmented evaluation strategy is designed to adaptively select different but more suitable objectives to efficiently assess the candidate architectures at different evolutionary stages, instead of evaluating them by all the considered objectives simultaneously. Thus, the computational cost and complexity of the search process can be controlled and reduced to some extent. Secondly, a preference-based pre-selection strategy is designed to filter out the initialized architectures with high parameter quantities to reduce the total parameter scale of the whole population and memory consumption. Last, a novel desirable gene reservation-based crossover and a directed connection-based mutation are proposed to produce offspring. Experimental results show that ASMEvoNAS shows promising performance on CIFAR-10, CIFAR-100, and ImageNet with error rates of 2.21%, 15.57%, and 24.43% top-1, respectively. The proposed method reduces the search cost to 0.36 GPU-Days on CIFAR-10 while maintaining competitive classification performance compared to state-of-the-art networks. In addition, ASMEvoNAS presents superior performance when dealing with the considered transfer tasks, as well as the benchmark dataset of NAS.

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from the Democratic Republic of Congo using a set of 8389 high-quality DArTseq-based single nucleotide polymorphism (SNP) markers. The average polymorphic information content (PIC) of the markers was 0.25. About 42.4% of the SNPs had a PIC value between 0.25 and 0.5, which were moderately informative. The ADMIXTURE program was used for structure analysis, which revealed five sub-populations (K = 5), with admixtures. In principal component analysis (PCA), the first three principal components accounted for 36.3% of the total variation. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. The significant genetic diversity among the evaluated rice genotypes can be further explored to obtain potentially desirable genes for rice improvement.