Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers.

Evaluation and characterization of genetic resources maintained at both in situ and ex situ GenBanks have important implications for future utilization in association mapping studies, genetic selection, breeding and conservation activities. The main objective of this study was to evaluate the genetic diversity, population structure and relationship of 384 Ethiopian barley genotypes collected from different barley growing regions of Ethiopia using 49 simple sequence repeat (SSR) markers. Analysis of these 49 SSR markers amplified a total of 478 alleles with an average of 9.755 alleles per locus were obtained of which 97.07% of the loci were observed to be polymorphic. Nei's genetic diversity index (h) was 0.654 and the Shannon diversity index (I) was 0.647, indicating that the genetic diversity in barley genotypes studied was moderately high. At the population level, mean per cent of polymorphic loci (PPL) showed 98.37%, h = 0.388 and I = 0.568. Highest level of genetic diversity was observed in the Arsi population (with PPL = 100%, h = 0.439, I = 0.624); the lowest value observed was in population from Jimma (with PPL = 75.51%, h = 0.291, I = 0.430). Analysis of molecular variance (AMOVA) result showed significant genetic differentiation within and between populations (P<0.001), with 84.21% and 15.79% of the variation occurring within and among populations, respectively. Further, genetic variation analysis showed a coefficient of gene differentiation of 0.053 and a gene flow value of 4.467 among populations. The 384 barley genotypes were divided into seven genetic clusters according to STRUCTURE, neighbour-joining tree and principal coordinate analysis, correlating significantly with geographic distribution. These results signified presence of significant variations within and among populations (P<0.001), with the highest of the variation occurring within populations. The results will also assist with the design of conservation strategies, such as genetic protection via both in situ and ex situ conservation.

Genome-wide identification, characterization and expression analysis of non-RD receptor like kinase gene family under Colletotrichum truncatum stress conditions in hot pepper.

Receptor like kinases (RLKs) are preserved upstream signaling molecules which regulate several biological processes from plant development to various stress adaptation programs. Non arginine aspartate (non-RD) a prominent class of RLKs plays a significant role in disease resistance and apoptosis in plants. In present investigation, a comprehensive in silico analysis for non-RD Kinase gene family as well as identification of gene structures, sequence similarity, chromosomal localization, gene duplication analysis, promoter analysis, transcript expression profiles and phylogenic studies were done. In this study, twenty-six genes were observed on nine out of twelve chromosomes. All these genes were clustered into five subfamilies under large monophyletic group termed as Interleukin-1 Receptor-Associated Kinase (IRAK) family. Some of the important physiochemical properties of twenty-six proteins are determined and ranged in the following order: (a) Amino acids size ranged from (620 to 1781) (b) Molecular weight ranged as of (70.11 to 197.11 KDa) and (c) Theoretical PI ranged from (5.69 to 8.63) respectively. Structural diversity in genomic structure among non-RD kinase gene family was identified and presence of pathogen induced cis regulatory elements including STRE, MYC, MYB, and W box were found. Expression profiles revealed the potential ability of three genes CaRLK1 from LRRXII and CaRLK15,16 from stress antifung subfamily were pointedly upregulated beyond the severe stress time period (9 DAI) in anthracnose resistant genotype PBC-80 in response to Colletotrichum truncatum infection. Subsequently, in silico studies from the available genome sequencing data helped us to identify candidate genes tangled in inducing disease resistance.

Data on germination, growth and morphological changes of oil palm (Elaeis guineensis Jacq.) zygotic embryos during in vitro culturing.

Oil palm (Elaeis guineensis Jacq.) from being almost unknown crop a mere three decades ago is now the most consumed and the most traded edible oil in the world. It is a highest yielding crop producing on an average 4 to 6 tons of oil per ha per year. Due to its innumerable uses in the food, oleochemicals and biofuel industries, cultivation of oil palm has expanded enormously in recent years. Since oil palm is a perennial monocotyledonous species with a single growing apex, the plant cannot be multiplied vegetatively and the conventional propagation through seed is limited by dormancy. Thus in vitro germination has become the key method for multiplication of elite oil palm genotypes. Although there are several reports on in vitro germination of oil palm, still there is a lack of an efficient & repeatable method. Hence an attempt is made to standardize the suitable culture media for direct germination from mature oil palm zygotic embryos. The data presented here represents the effect of genotypes, pretreatments and culture media on Mean Germination Time, Speed of Germination Index, Shoot Formation Index and Root Formation Index during in vitro culturing of oil palm zygotic embryos.

Integrated approaches to study the drought tolerance mechanism in hot pepper (Capsicum annuum L.).

Drought is one of the predominant abiotic stresses which have phenomenal impact on crop productivity. Alterations in aquaporin gene expressions are part of complex molecular responses by plant in response to drought. To better understand the role of aquaporins in economically important crop chilli (Capsicum annuum), drought induced gene expression of twelve aquaporins was determined in drought tolerant-KCa-4884 and drought susceptible-G-4 genotypes. Conjointly, the effect of drought on leaf water status and photosynthetic parameters were evaluated. Gene expression of all examined 12 aquaporins was up-regulated in KCa-4884 and in contrast, all the aquaporin genes were down-regulated in G-4 under drought stress. Significant variations among two chilli genotypes have been recorded in photosynthetic rate (P n ), stomatal conductance (G s ), and relative water content (RWC), sub-stomatal CO2 concentration (C i ). KCa-4884 revealed significantly high rates of P n and RWC and decreased G s under water deficit conditions providing evidence for superior drought adaptive strategies. Differences in physiological parameters illustrate prevention of water loss during drought. Up-regulation of aquaporins in drought tolerant genotype implicates their possible role in water relations and photosynthetic performance even under extended drought conditions.

Apoplast proteomic analysis reveals drought stress-responsive protein datasets in chilli (Capsicum annuum L.).

Drought is one of the major environmental constrains that limit plant performance worldwide. Plant apoplast which acts as connecting link between environment and plant protoplast carries multiple functions in plant metabolism and signalling. To investigate the drought induced changes in apoplast, proteome analysis in conjunction with antioxidant enzyme activity changes were studied in chilli (Capsicum annuum L). Drought induced apoplast proteome revealed augmented phenyl alanine ammonia lyase, peroxidase activities and reduced catalase activity. LC-MS analysis of apoplast proteome revealed differential expression of proteins under water stress conditions. Up-regulation of 43 protein species which encompass stress related proteins such as defensins, peroxidises, polygalaturonase inhibitor proteins, superoxide dismutase proteins were observed. Unlike control, twenty unique protein species were identified to be present in proteome of drought treated plants. Qualitative and quantitative changes in apoplast proteome emphasize the dynamics of plant apoplast and its role in drought stress. This work would provide insights into drought induced proteomic changes in apoplast and also would prove to be useful for protein phenotyping.

Seed Antioxidants Interplay with Drought Stress Tolerance Indices in Chilli (Capsicum annuum L) Seedlings.

Altering climatic conditions and water stress drastically affects the chilli crop yield. In this scenario we adapted a strategic approach for screening of elite chilli genotypes, by exploring role of seed antioxidants in stress tolerance during vegetative phase. A total of 20 chilli genotypes' seed antioxidant potential and its effect on water stress tolerance were studied at three water regimes, namely, control (100% Field Capacity), moderate (80% Field Capacity), and severe (60% Field Capacity) stress conditions. Drought tolerance traits relative water content, chlorophyll content, and activities of superoxide dismutase and catalase enzymes were measured. A strong correlation was observed between seed antioxidants and water stress tolerant traits in seedlings. Genotypes KCa-5, KCa-6, and KCa-10 showed low quantity of H2O2 and Malondialdehyde in seeds and maintained high membrane integrity and chlorophyll content in seedlings. High content of proline in KCa-5, KCa-7, and KCa-10 seeds retained high relative water content at seedling stage under severe water stress. Present work reveals genotypic differences of hot pepper to different water regimes. Based on Principal Component Analysis (PCA) of seed antioxidant variables and drought tolerance indices twenty genotypes segregated into three clusters, namely, drought tolerant and susceptible and moderately tolerant.

In silico structural homology modeling of nif A protein of rhizobial strains in selective legume plants.

Symbiosis is a complex genetic regulatory biological evolution which is highly specific pertaining to plant species and microbial strains. Biological nitrogen fixation in legumes is a functional combination of nodulation by nod genes and regulation by nif, fix genes. Three rhizobial strains (Rhizobium leguminosarum, Bradyrhizobium japonicum, and Mesorhizobium ciceri) that we considered for in silico analysis of nif A are proved to be the best isolates with respect to N2 fixing for ground nut, chick pea and soya bean (in vitro) out of 47 forest soil samples. An attempt has been made to understand the structural characteristics and variations of nif genes that may reveal the factors influencing the nitrogen fixation. The primary, secondary and tertiary structure of nif A protein was analyzed by using multiple bioinformatics tools such as chou-Fasman, GOR, ExPasy ProtParam tools, Prosa -web. Literature shows that the homology modeling of nif A protein have not been explored yet which insisted the immediate development for better understanding of nif A structure and its influence on biological nitrogen fixation. In the present predicted 3D structure, the nif A protein was analyzed by three different software tools (Phyre2, Swiss model, Modeller) and validated accordingly which can be considered as an acceptable model. However further in silico studies are suggested to determine the specific factors responsible for nitrogen fixing in the present three rhizobial strains.

Marker-assisted breeding for introgression of opaque-2 allele into elite maize inbred line BML-7.

Improvement of quality protein maize (QPM) along with high content of lysine and tryptophan had foremost importance in maize breeding program. The efficient and easiest way of developing QPM hybrids was by backcross breeding in marker aided selection. Hence, the present investigation aimed at conversion of elite maize inbred line BML-7 into QPM line. CML-186 was identified to be a donor variety as it revealed high-quality polymorphism with BML-7 for opaque-2 gene specific marker umc1066. Non-QPM inbred line BML-7 was crossed with QPM donor CML-186 and produced F1 followed by the development of BC1F1 and BC2F1 population. Foreground selection was carried out with umc1066 in F1, and selected plants were used for BC1F1 and BC2F1 populations. Two hundred plants were screened in both BC1F1 and BC2F1 population with umc1066 for foreground selection amino acid modifiers. Foreground selected plants for both opaque-2 and amino acid modifiers were screened for background selection for BML-7 genome. Recurrent parent genome (RPG) was calculated for BC2F1 population plants. Two plants have shown with RPG 90-93% in two generation with back cross population. Two BC2F2 populations resulted from marker recognized BC2F1 individuals subjected toward foreground selection followed by tryptophan estimation. The tryptophan and lysine concentration was improved in all the plants. BC2F2 lines developed from hard endosperm kernels were selfed for BC2F2 lines and finest line was selected to illustrate the QPM version of BML-7, with 0.97% of tryptophan and 4.04% of lysine concentration in protein. Therefore, the QPM version of BML-7 line can be used for the development of single cross hybrid QPM maize version.

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes.

Soil is major reservoir for microbes and harbors a vast microbial diversity. Soil microbiota plays a pivotal role in biogeochemical cycles, bioremediation, and in health and disease states of humans, animals, and plants. It is imperative to understand the microbial signatures which are specific in such an ecosystem to unravel their potential role and impact on environment. During the recent years, exploration of soil microbial communities has been geared up with the advent of advanced sequencing technologies. Introduction of custom-made protocols and optimized procedures have enhanced the accuracy levels along with cost-effectiveness of DNA extraction. Standardization of DNA extraction method from soil microbiota has its own limitations due to different nature of soils and the complexity of ecosystems. Though a few standardized protocols are in usage, huge variations and complexities among the microbial communities frequently suggest the optimization, based on various known and unknown factors. Therefore, a set of four standardized DNA isolation protocols was comparatively analyzed with respect to our custom-made protocol owing to the scientific fact that the same protocol does not hold good for all soil samples. Furthermore, the developed protocol has been successfully applied for the identification of efficient plant-specific Rhizobial stains for five legume plants from the soils of various locations under same geographical region. Out of 40 Badrachalam forest soils, five samples, KPFS36, CHFS17, TPFS33, GVFS06, and GPFS40, one for each of Arachis hypogaea, Vigna radiata, Vigna mungo, Glycine max, and Cicer arietinum plants, were selected, respectively, for the soil DNA extraction. A considerable improvement in the DNA yield was identified using the modified protocol with a yield of 21.08 µg/g providing abundant DNA fragments for further investigation on Rhizobial species.

Population genetic structure of cotton pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) using mitochondrial cytochrome oxidase I (COI) gene sequences from India.

Pink bollworm (PBW), Pectinophora gossypiella is one of the most destructive pest's globally inflicting huge economic losses in cotton even during later stages of crop growth. In the present investigation, the population genetic structure, distribution, and genetic diversity of P. gossypiella in cotton growing zones of India using partial mitochondrial DNA cytochrome oxidase-I (COI) gene was addressed. The overall haplotype (Hd), number of nucleotide differences (K), and nucleotide diversity (π) were 0.3028, 0.327, and 0.00047, respectively which suggest that entire population exhibited low level of genetic diversity. Zone-wise clustering of population revealed that central zone recorded low level of Hd (0.2730) as compared to north (0.3619) and south (0.3028) zones. The most common haplotype (H1) reported in all 19 locations could be proposed as ancestral/original haplotype. This haplotype with one mutational step formed star-like phylogeny connected with 11 other haplotypes. The phylogenetic relationship studies revealed that most haplotypes of populations are closely related to each other. Haplotype 5 was exclusively present in Dharwad (South zone) shared with populations of Hanumangarh and Bathinda (North zone). The result indicated that there is no isolation by distance effect among the Indian populations of PBW. The present study reports a low genetic diversity among PBW populations of India and H1, as ancestral haplotype from which other haplotypes have evolved suggests that the migration and dispersal over long distance and invasiveness are major factors.