Ecological Genetics and Genomics最新文献

Enset (Ensete ventricosum) is a multi-use perennial herbaceous crop used as a staple food for over 20 million people in Ethiopia. Despite its high use values, very few studies have been conducted to improve this crop, particularly using molecular marker systems. In this context, the study aimed at evaluating the magnitude of genetic diversity and population structure of enset germplasm collections from four major enset growing zones in southern Ethiopia using 12 simple sequence repeat (SSR) markers. A total of 147 individual leaf samples were collected from the entire enset populations and gave 289 alleles, ranging from 12 to 41 alleles per locus, with a mean of 24.5. The polymorphism information content for each locus varied from 0.86 to 0.95, with a mean of 0.91. The number of effective alleles ranged from 5.13 to 11.79 with a mean of 8.27. The expected and observed heterozygosity showed average values of 0.85 and 0.84, respectively. The greatest genetic distance (1.16) was between Gurage and wild populations, while the shortest (0.37) was between Gurage and Silte. Among the six populations, the wild had the highest percentage of polymorphic loci (100%). AMOVA attributed 89% of the genetic variation to intra-population and only 11% to among populations. The whole set of germplasm indicates low genetic differentiation and high gene flow (Nm). The UPGMA and principal coordinates largely correspond to each other and indicate three major groups. Overall, the information gained from this study would be useful for enset improvements and conservation strategies.

The investigations on interspecific hybrid basil were carried out in two distinct agro-climatic regions of India: Lucknow (Uttar Pradesh) and Rangareddy (Telangana). The experiment used an RCBD replicated thrice in each trial in each of the three seasons/environments: Jaid, Karief, and Rabi. The morphological and chemical changes of an interspecific basil hybrid/variety were studied across environments/seasons, and locations. All morphological traits and essential oil production are affected by the environment/seasons and location. The essential oil production and linalool concentration were found to be consistent. A high-quality linalool essential oil was discovered throughout the environment and locales. The biplot contrasted the test seasons/environments, as well as the researched locations and their interactions, visually. The ‘r' correlation between measured (M) and predicted (P) values was 0.998, and the predicted (P), means, and instability values (I) were all calculated using ATC coordinates. The ‘r' between GGE distance (GD) and entry means was also −0.952. This means that a higher absolute number indicates less stability, whereas a lower absolute value indicates a high level of stability. In summary, significant amounts of linalool-rich essential oil were obtained in the Northern Region (Lucknow) during the Jaid season (69.76 %) and the Southern Region (Hyderabad) during the Rabi season (69.88 %). This hybrid/variety's linalool content and essential oil yield averaged 190.78 kg/ha across seasons/environments and locations, with a linalool content of 67.91 %. Due to its high yield of top-notch linalool essential oil, the basil hybrid/variety that is particularly stable in terms of essential oil yield with high linalool content across seasons and places should be suggested for large-scale cultivation.

Background

Cytochrome oxidase subunit II is encoded by the MT-CO2 gene and belongs to a large internal membrane complex called cytochrome c oxidase. To date, no pathogenic single nucleotide variant has been confirmed in this gene according to the MITOMAP database. The goal of this study was to review the literature and attempt to interpret all defined variants of the MT-CO2 gene, either directly associated with symptoms or only by the occurrence of variant in specific diseases.

Methods

Available databases were searched for clinically relevant variants in the MT-CO2 gene. Variant interpretation was based on HelixMTdb frequency, identification of conserved sites in primates, particularly Pan paniscus and Pan troglodytes sequences from GenBank, MITOMAP data and the status of the Predict program.

Results

We found 23 single nucleotide variants in 30 papers where the authors suspected or directly linked variants with a specific phenotype. The most common method sequencing method was Sanger sequencing in 17 papers, and the next-generation sequencing in 6 papers.

Conclusions

Only two potentially pathogenic variants m.8163A > G and m.7887G > A were found, meeting almost all the restrictive criteria for confirmed mitochondrial pathogenic variants. Unfortunately, none of the variants described in all of the papers/databases analysed can be unquestionably classified as pathogenic. Considering that this is a critical respiratory chain subunit gene, further research is needed.

Sweetcorn is an important vegetable crop with high sugar content and economical value in US, Asia countries. Develop parental lines is core technology in hybrid sweetcorn breeding. This study applied the multivariate selection method to categorize and select elite tropical sweetcorn inbred lines for specialty corn breeding in Vietnam. Forty-two sweetcorn inbred lines was laid out in randomized complete block design with three replications in the field experiment from in Spring season 2021, Vietnam National University of Agriculture, Vietnam. Hierarchical clustering on principal component analysis was classified sweetcorn inbred lines into four major groups. Applied MGIDI index with 20 % selection intensity has identified two purple sweetcorn inbred lines, viz, N14, N41, a white sweetcorn inbred line N09, and five yellow sweetcorn inbred lines, viz, N05, N24, N25, N28, N39. General combining ability (GCA) analysis in Spring season 2022 showed that N39 have high positive GCA value on marketable yield and N28 have high positive GCA on total soluble solids.

Date palm (Phoenix dactylifera) is a significant crop grown in warm, tropical, and arid regions. The microorganisms associated with plants can have positive and negative effects on the growth and yield of crops. Thus, there is a need to study the role and contribution of the microbiome on date palms. The present review describes the current state of knowledge on the Date palm microbiome, including techniques and organisms studied, and their potential impacts/functions. We compiled an overview of the microbial species associated with date palms, plant compartments, their functions, and whether their effects were positive or negative. Many microbial species were identified as positively affecting date palms, including species that enhance growth, inhibit pathogens, and promote Indole acetic acid and aminocyclopropane-1-carboxylate hormones. Environmental DNA will enable studies on the whole microbiome associated with date palms, thus improving our understanding of plant microbiota and its applications for date palm production. The increasing knowledge about the microbiome of date palms offers the potential to be utilized to increase growth and yield. Furthermore, our review revealed that there currently needs to be studies on protists and archaea and their potential association with date palms, suggesting a need to target these organism groups in future studies.

Knowing the production system and breeding objectives is a prerequisite for designing in-situ conservation and genetic improvement programs. This study aimed to characterize goats' breeding practices and relative importance and identify goat keepers' breeding objectives. Data were collected through three approaches: formal personal interviews, measurement of morphological traits of live animals, and own flock ranking methods. Several SAS procedures were used to analyze the data. The result revealed that goats were the second most economically important livestock species next to cattle. Income generation and home meat consumption were the major reasons for keeping goats. The mating method was an uncontrolled natural mating method. Most (90–100%) goat keepers select male and female goats to be a parent for the next generation. Coat color, physical appearance, twinning ability, milk yield, and kid growth were identified as breeding objectives for breeding females through the personal interview method. Similarly, the most crucial traits for selecting a buck were growth, physical appearance, and coat color. Based on own animal ranking method, coat color, physical appearance, milk yield, twining ability, and mothering ability were the most important traits. The rank of animals was in line with the phenotype of morphological traits and market price. In conclusion, coat color, physical appearance, milk yield, and twining ability were identified to be the most important traits. Therefore, these breeding objectives can be used as input for designing a genetic improvement program for this goat population.

Coffea arabica is said to have low genetic variability, however more information is still needed about the extent of diversity present in the arabica coffee gene pool by evaluating existing genetic resources present in India. The study therefore was conducted to assess the phenotypic and genotypic variability in arabica coffee germplasm accessions. Significant variation was observed among coffee accessions for the traits studied indicating the presence of diversity. Out of 20 traits, per cent ‘A’ grade bean contributed maximum to the diversity (63.29 %). The 41 arabica coffee accessions were grouped into six clusters. The maximum intra-cluster and inter cluster distance (D² = 737.34) was revealed by cluster V (7 genotypes) and cluster II and VI (D² = 8544.21), respectively. Principle Component Analysis displayed 79.50% of variability. Observations on Coffee Leaf Rust disease incidence showed that mean disease severity infection was ranged from 1.34 to 32.67%. On the other hand, molecular analysis of 10 SRAP primers established high rate of polymorphism with an average PIC value of 0.74. The UPGMA clustering grouped arabica coffee genotypes into two major clusters. The similarity matrix coefficient was ranged from 0 to 94%. SRAP marker demonstrated high polymorphism rate can be utilized for future crop improvement program in coffee. Study established high phenotypic but low genetic diversity among the arabica coffee accessions based on morphological and molecular markers, respectively and identified high yielding, coffee leaf rust disease resistant accessions which showed possibility of developing improved varieties through breeding.

Biotic stresses are responsible for important crop losses each year. Downy mildews (DMS), elicited by obligate pathogens of the oomycete Peronosporaceae family, are recognized as an increasing threat for crop production worldwide. These diseases are responsible for major food losses and also damage valuable natural ecosystems. Fungicides have been widely employed for managing DMS, but they can be harmful to non-target organisms, human health and soil functioning. For this reason, biological control is attractive as an alternative and ecofriendly approach to deal with plant diseases. Potential biocontrol agents include endophytic fungi (EF). Endophytes produce metabolites that can protect host plants against fungi and other pests including DMS. Endophytes work as biocontrol agents by inducing the lignification of cell walls and producing fungicides and other antimicrobial compounds. Research on EF in the leaves of the host plants is crucial to the search for biocontrol methods for managing DMS. Several factors limit the development of DMS as biocontrol agents. This review summarizes the published research on the use of fungal endophytes as biological agents to control DMS with a particular emphasis on their identification, modes of action, and efficacy.

Hidden for many years and serendipitously discovered, giant viruses have emerged as a captivating subject of scientific interest, leading to significant discoveries and paradigm shifts in our understanding of viruses. The identification of Mimivirus in 2003 marked a turning point, leading to the exploration and characterization of various giant viruses, including Mimiviridae, Marseilleviridae, Pandoravirus, Pithovirus, Mollivirus, Faustovirus, and Cedratvirus. These viruses exhibit unique structural and genomic features, challenging our understanding of viral diversity and evolution. Metagenomic studies have revealed their presence in diverse environments, indicating their global distribution and suggesting the likelihood of further discoveries. The co-discovery of virophages, viruses associated with giant viruses, has added another layer of complexity to their interactions and ecological roles. The study of giant viruses has shed light on their impact on ecosystems and potential roles in eukaryotic evolution. However, many knowledge gaps persist, including understanding host-virus interactions, identifying original hosts, expanding isolation efforts, and investigating the implications of giant viruses for human health. Further research in these areas will contribute to our comprehensive understanding of these fascinating entities and their significance in virology and ecology.

Composting, a biologically driven process, can transform green waste into nutrient-rich soil amendments. Molecular biology is becoming increasingly popular among researchers for understanding microbial dynamics to understand the structure and function of biomolecules, such as DNA, RNA, proteins, and other macromolecules. Genomics is the favoured method of among researchers in environmental engineering, specifically during composting. It allows the researchers to analyse complex microbial communities at different stages of composting without the need for cultivation. Many researchers used 16S rRNA and 18S rRNA gene sequencing, ITS region sequencing, DGGE analysis, and whole genome shotgun (WGS) sequencing to analyse community dynamics of bacteria and fungi. The microbial communities vary concerning additives used with green waste composting and during the phases of composting. This mini-review summarises the techniques used for genomics study during the composting of green waste. It involves a type of substrate, the DNA extraction kit used, the region selected for the sequencing, and the primer selection. Microbial community dynamics during different phases of green waste composting are also discussed in this review.