Ecological Genetics and Genomics最新文献

Hessian fly (HF), Mayetiola destructor (Say), is an important wheat insect pest that annually results in significant production losses. In Morocco, this insect reduces wheat yields by 32–36 % during drought years. The purpose of the current study is to identify the genomic region, marker-trait associations (MTAs), and putative genes associated with the trait of hessian fly resistance in 210 bread wheat (Triticum aestivum L.) genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The screening was carried out in the growth chamber using the Hessian fly Mayetiola destructor (Say) populations collected from the Chaouia Ouardigha region in Morocco. The 210 genotypes tested showed various degrees of resistance to the Hessian fly, with eighty-six accessions showing high levels of resistance. The HF severity ranged from 0 to 100 %, whereas the coefficient of variance (CV) was recorded at 84.15 %. Genome-wide association studies (GWAS) using a mixed linear model (MLM) identified 20 significant MTAs at P < 0.001 associated with Hessian fly resistance. The highest number of MTA (10) was recorded in the A sub-genome, followed by 9 MTAs in the B genome. The highest significant marker is AX-95143016 which is located on chromosome 3B with a -Log10(p) of 10.23. After mapping the 20 significant markers associated with Hessian fly resistance, there were 12 potential candidate genes found. This study identified highly resistant genotypes and significant markers that could be used in future wheat breeding programs.

Water deficit stress is one of the most important environmental factors that reduce grain yield in bread wheat. Despite the recent progress in breeding this plant, there is still a need to improve bread wheat cultivars that tolerate water stress in the country. In the current research, 100 genotypes of spring bread wheat during the years 2020–2021 and 2021–2022 in two conditions of non-stress and water deficit stress in the form of a simple 10x10 lattice square design at the beginning of flowering in Gachsaran Research Center located in the south of Iran. Eight quantitative indices of tolerance to water deficit were calculated. Principal component analysis (PCA), hierarchical cluster analysis (HCA), analysis of variance, and Pearson correlation were carried out in this study. According to the data, significant genotypic variation was seen among genotypes for both individual yield and drought indices. Geometric Mean Productivity (GMP) recorded the lowest coefficient of variation (CV) value with 10.6 %, while Tolerance Index (TOL) recorded the highest CV value with 45.4 %. The heritability of several of the indices is moderate to high; the Stress Susceptibility Index (SSI) has the greatest heritability at 0.96. Four distinct clusters were formed from the 100 genotypes. PC1 and PC2 make up 98.4 % of the total variance. Specifically, PC1 covers 68.9 %, while PC2 accounts for the remaining 29.5 %. These chosen genotypes will act as parent plants in breeding initiatives to create novel varieties resistant to drought.

Genome-wide Association Studies (GWAS) and Transcriptome-wide Association Studies (TWAS) are pivotal tools in genetics research. GWAS, with its comprehensive genome coverage, reveals insights into complex trait variations among different populations. It finds applications beyond gene identification, including historical population studies and linkage disequilibrium pattern assessments. However, GWAS faces challenges like multiple testing corrections and difficulties in pinpointing causal variants. Conversely, TWAS offers higher gene resolution and the potential for deeper insights into genetic mechanisms. Yet, TWAS prediction accuracy is contingent on gene heritability, and its complexity lies in navigating gene regulatory networks and epigenetic factors. Understanding the strengths and limitations of both GWAS and TWAS is crucial for harnessing their full potential in genetic research endeavours.

In this study, genetic polymorphisms using DNA barcoding has been performed on selected ten species of Selaginella collected form Tamil Nadu and the Hills of Kerala. The main aim of this study was to estimate a phylogenetic and evolutionary relationship between selected species of Selaginella using DNA barcoding. The genomic DNA of selected species of Selaginella was isolated and were examined for DNA polymorphisms. The method described by Sanger has been used to sequence the PCR rbcL products. The phylogenetic analysis was carried out using four methods viz., minimum evolution, neighbor joining, UPGMA and maximum parsimony. For the studied species, the PCR amplification result was good, the molecular weight range from 500 to 600 base pairs and the amplicons were sequenced. The obtained sequences were aligned, annotated and submitted in GenBank. The phylogenetic analysis of studied Selaginella species using minimum evolution, NJ and UPGMA methods showed similar trees whether maximum parsimony tree displayed varied tree. The sequence alignment results illustrated that the sequence of S. involvens, S. intermedia, S. inaequalifolia, S. wightii and S. tenera were distinct from the other studied Selaginella species viz., S. brachystachya, S. repanda, S. radicata, S. bryopteris and S. delicatula. The cladistics tree also explains the relationship between S. delicatula with and without cones. This concludes that rbcL data is most valuable for inferring phylogenetic relationship between closely related species. DNA barcoding using rbcL gene was applied to distinguish the inter-specific variation among the selected Selaginella species.

Mangrove ecosystem contains diverse group of microorganisms that have not been studied extensively. The present study used metagenomic approach for understanding the diversity of bacteria in a mangrove ecosystem from South India. Water, top soil and sediment samples were analyzed and the dominant Phyla were Firmicutes(75–81 %) followed by Proteobacteria(12–15 %). Oenococcusoeni(33–35 %) was the most abundant bacterial species, followed by Bacillus(18–22 %) in all the samples. But the remaining species showed variedabundanceamong the samples. Lysinibacillus halotolerance (9–17 %), Loktanella cinnabarina (11–13 %), Cohnella hongkongensis (2–7%), Parcubacteria(1–2.5 %) and Oreniasivashensis (0.7–2%). Top soil sample had the most abundance of bacteria, but sediment sample had the most species diversity. Water samplefrom Mangrove contained bacteria of more diverse evolutionary lineage, which showed significant diversity among other samples.

The genetic composition and diversity of chicken breeds/populations have been shaped through selective breeding and management practices. Understanding the genetic diversity of chicken breeds can inform breeding strategies and conservation priorities as well as improve desirable traits in offspring. Assessing genetic diversity between indigenous and exotic breeds provides insights into the benefits of selective breeding and/or crossbreeding. Various studies have investigated genetic diversity indicators in indigenous chicken breeds. Markers are central to study diversity, among them DNA-based markers have proven to be more effective than protein-based markers due to their polymorphism, codominance, and ease of genotyping. Among the 19 diverse chicken breeds currently registered in India, the indigenous Aseel and Kadaknath breeds have more peculiar distinctive characteristics. Synthetic chicken breeds developed by various research organizations exhibit variations in physical features and closely resemble native breeds in terms of eggshell color and meat quality. Overall, chicken is a significant species, because of its economic importance, short reproductive cycle and high fertility. This review shall deal with various aspects of genetic diversity explored in chicken breeds in Indian context.

Lemongrass (Cymbopogon spp.), is a well-known aromatic grass distinguished by its unique lemon scent. The importance of lemongrass in gastronomic, pharmacological, and cosmetic uses is examined in this research paper. The chemical makeup of lemongrass is discussed, emphasizing the presence of citral and other bioactive chemicals that give the herb its flavor, aroma, and medicinal qualities. The study highlights the possible advantages of growing lemongrass in semi-arid areas like Lalitpur (U.P.) and Datia (M.P.) in the Indian state of Bundelkhand, since it may flourish there with little water and improve soil fertility. Five lemongrass varieties—Nima, Praman, CIMAP-Suwarna, Krishna, and CIM-Shikhar—are compared in the study according to their morphological traits, oil yield, herb yield, and citral content. Results demonstrate that the total citral content and essential oil output of the two kinds, LG1 and LG4, are constant between the two genotypes, LG3 and LG5, respectively, across the locations. Regarding the stable types, the location-specific recommendations for essential oil yield were LG1 and LG3, while LG2 and LG4 were suggested for the total citral content. With a few exceptions in the first and second locations, where some traits showed low to medium heritability, most traits in the different sites had broad-sense heritability that was generally high. In all three locations, there were substantial percentages of genetic advance over mean (GAM) for specific features. The retention of genotype stability depends on these characteristics. These cultivars possess advantageous characteristics for growing in the Bundelkhand area, potentially providing farmers with financial gains and improving land in semi-arid regions. The findings highlight the importance of lemongrass as a useful plant with a wide range of applications and aid in the selection of cultivars that are appropriate for a certain area.

Salmonella ranks among the prominent etiological agents responsible for foodborne illnesses on a global scale. Within the scope of this investigation, a bacteriophage capable of eliminating Salmonella enteritidis was isolated using the double-layer agar overlay technique. The phage's morphological characteristics were elucidated through the application of Transmission Electron Microscopy. The genomic DNA of the phage underwent complete sequencing utilizing the MiSeq platform, with library preparation executed through the NexteraXT library prep kit method accompanied by the NexteraXT index kit. Paired-end sequencing was performed over 2 × 251 cycles read length, employing a Miseq V3 kit within the Illumina MiSeq system. Notably, the phage manifested conspicuous plaques upon S. enteritidis when subjected to the double agar overlay technique. NINP13076 displayed a 22-min latency period with a calculated average burst size of 53 PFU/cell. Phages exhibited resilience to the diverse pH conditions, manifesting no discernible impact on their viability over a storage duration of up to one week. storage at temperatures of 4 °C, 26 °C, and 37 °C demonstrated minimal effects on the phage population, with no statistically significant alterations observed. Genome assembly yielded a draft genome encompassing 161,329 base pairs with a GC content of 44.4 % and achieved coverage at a depth of 104x. Phylogenetic tree analysis unveiled a highly proximate relationship with the Salmonella Phage SSE-121 genome, demonstrating a distance score of 0.1 and signifying its classification as a novel member within the SSE121 virus group.

Alpha amylase inhibitor (α-AI) extracted from wheat grains (Triticum sp.) as possible new agent in pest control, and some other organic inhibitors are evaluated against α-amylase of the fourth larval instar of the peach fruit fly (PFF) larvae; Bactrocera zonata (Saund.). 4.2 mg protein ml⁻¹ of the inhibitor extracted by 70 % ammonium sulphate inhibited, in vitro, 97.9 % of amylolytic activity of the larvae. Percent inhibition efficiency (Ei%) of the crude inhibitor was directly proportional with its concentration in the range from 4.2 to 0.21 mg protein ml-1. The calculated IC50 was 1 mg protein ml-1. Increasing of the surrounding temperature from 10 to 35 °C not enhanced inhibitor efficiency, and the inhibitor could inhibit the enzyme efficiently at a relatively low temperature (10 °C). On the other hand, wheat extract showed quick binding affinity to α-amylase of PFF larvae. Incubation of the inhibitor with the enzyme for 10 min was sufficient for wheat α- AI to exert its maximum inhibition. Screening of other possible organic compounds act as α-AI such as citric, gallic and acetic acids showed that gallic acid was the most potent inhibitor, and it was able to inhibit α-amylase of the larvae, at a relatively, low concentration (10⁻⁴M). It could be concluded that there are natural potent inhibitors of PFF α-amylase which act as a key enzyme for carbohydrates digestion. This might be useful as an alternative method for controlling B. zonata population. Additional experiments are necessary to make these alternative compounds applicable in the field.