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Aim: Indian mustard [Brassica juncea (Linn.)] is the third vital oilseed crop in the world which contributes 28.6% in the production of oilseeds. Genetic diversity assessment plays a fundamental role in the preservation and improvement of the targeted plant species. Study Design: In the present investigation, 196 Indian mustard genotypes including checks were grown in the field and evaluated based on different morpho-physiological traits. Place and Duration of the Study: All the genotypes were grown in randomized block design with two replications in Rabi 2016-17 and 2017-18 at the experimental field of Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, M.P., India. Methodology: The study was conducted to record different morphological and physiological traits that play a major role in differentiating the targeted genotypes. Results: Based on the present study, the highest genotypic and phenotypic coefficients of disparity were documented for seed yield per plant tracked by harvest index and numbers of silique per plant. Maximum heritability and genetic advance were documented for seed yield per plot tracked by harvest index, biological yield per plot, days to 50% flowering, length of the main raceme, numbers of silique per plant, seed yield per plant, numbers of seeds per silique, 1000-seed weight and numbers of silique per the main raceme. Conclusions: In principal component analysis, 15 principal components were evidenced while cluster analysis gave 16 clusters. The highest inter-cluster distance was evidenced between cluster 9 and cluster 16 which suggests that the hybridization scheme considering parents from these clusters is supposed to be given a higher occurrence of better-wanted combination(s) for expansion of beneficial genetic stocks.

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

The characterization of garlic germplasm improves its utility, despite the fact that garlic hasn't been used much in the past. Garlic has an untapped genetic pool of immense economic and medicinal value in India. Hence, using heuristic core collection approach, a core set of 46 accessions were selected from 625 Indian garlic accessions based on 13 quantitative and five qualitative traits. The statistical measures (CV per cent, CR per cent, VR per cent) were used to sort the core set using Shannon-Wiener diversity index and the Nei diversity index. In addition, the variation within the core set was tested for 18 agro-morphological and six biochemical characteristics (allicin, phenol content, pyruvic acid, protein, allyl methyl thiosulfinate (AMTHS), and methyl allyl thiosulfinate (MATHS)). Further study of the core set's molecular diversity was performed using sequence related amplified polymorphism (SRAP) markers, which revealed a wide range of diversity among the core set's accessions, with an average polymorphism efficiency (PE) of 80.59 percent, polymorphism information content (PIC) of 0.29, effective multiplex ratio (EMR) of 3.51, and marker index (MI) of 0.99. The findings of this study will be useful in identifying high-yielding, elite garlic germplasm lines with the trait of interest. Since this core set is indicative of total germplasm, these selected breeding lines will be used for genetic improvement of garlic in the future.

Moringa oleifera Lam. (common name: drum stick, horseradish tree) belongs to the monogeneric family, Moringaceae. Immature pods, fresh leaves and flowers of M. oleifera are used for culinary purposes. The leaves and young pods are a rich source of minerals and vitamins. In the present study, 23 genotypes of drumstick, which were selected based on superiority of yield/tree from 120 genotypes surveyed in South India were subjected to analysis morphology, yield and quality attributes and found they are substantially varying thus necessitate further analysis. Diversity analysis based on the coefficient of variation (CV), genotypic coefficient of variation (GCV), environmental coefficient of variation (ECV), phenotypic coefficient of variation (PCV) and heritability were determined. Quantitative fruit traits such as fruit length (30.56–127.57 cm), fruit weight (72.22–163.27 g), fruit breadth (3–8 cm), number of fruits/tree (NF/T) (320–1000), and number of seeds/fruit (NS/F) (11–29) varied among the genotypes. Correlation studies revealed that the fruit yield had a significant, positive correlation with the number of fruits per tree, length of fruit and single fruit weight. The estimate of PCV was slightly higher than the GCV for all characters studied, indicating that the apparent variation is not only genetic but also influenced by the growing environment in the expression of the traits. Heritability was greater than 90% for all characters studied. The overall analysis outcome of the study emphasizes that selection of high yielding genotypes should give due weightage to the number of fruits per tree and single fruit weight.

Thirteen elite lines of Brassica napus L. were tested. Nine phenotypic traits viz., days to 50% flowering, days to maturity, plant height, branches, pods, pod length, pod width, pod weight and seed yield were studied. ANOVA revealed significant results for all the traits while summary statistics exhibited high level of genetic variability in days to 50% flowering, days to maturity, plant height and number of pods. On the other hand, number of branches, pod length, pod width, pod weight and seed yield need more attention for improvement. Coefficient of correlation revealed significant combinations among various traits which could be utilized directly. Cluster analysis based on linkage distances described grouping pattern into three clusters for dissimilarities. Elite line 24866 of Pakistani origin placed in separate cluster prominently that is due to best performance for maximum traits, hence recommended for farmers’ field large scale cultivation.

Whole genome sequence in mango offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, simple sequence repeats (SSRs) were predicted from genome sequence of mango. Based on the SSR length (? 50 bp), highly-variable mango SSRs (MSSRs) were sorted. A sub-set of 129 MSSRs was validated on a set of 24 diverse mango genotypes yielding marker validation and polymorphism of 88.96 and 85.27 per cent, respectively. One hundred and ten polymorphic markers were identified for the present set of mango genotypes. Polymorphic information content (PIC) ranged from 0.10 to 0.78 and the highest value was observed with MSSR133. The mean PIC value was 0.40 but 33 MSSR markers showed PIC values ? 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in mango. MSSRs data was further used for diversity analysis of mango genotypes belonging to different agro-ecological conditions including chance seedlings, landraces, exotic and indigenous germplasm and hybrids. Cluster analysis using UPGMA of 24 mango genotypes revealed that these MSSRs were informative in diversity analysis and distinguished mango genotypes based on their origin, parentage and embryo types. A novel set of 110 hyper-variable SSR markers have been added to the mango repository depicting usefulness in discriminating closely related mango germplasm and their use in mango improvement programme.

The present investigation reveals the association between yield and its contributing traits in a set of advanced generation of green gram genotypes. Seed yield per plant showed significant and positive correlation with plant height followed by pod length, pods per cluster and pods per plant whereas, 100 seed weight and harvest index showed positive but non-significant correlation. Path analysis indicated that the pod length has the highest positive direct effect on seed yield per plant, followed by harvest index, primary branches per plant, 100 seed weight, pods per cluster, protein content and pods per plant. Cluster analysis revealed divergence in 25 accessions by making four clusters. Cluster II and cluster IV showed highest inter cluster distance signifying that hybridisation between genotypes from these two clusters will exploit heterosis at a greater level. Selection criteria based on pod length, pods per cluster, protein content, 100 seed weight and seed yield per plant can be devised for further improvement of these genotypes.

In breeding programs, direct selection based on yield is very difficult due its polygenic nature. Therefore breeders need to consider association of numerous yield related attributes with yield and among themselves. In this study, 43 rice genotypes including some released varieties and advanced lines were evaluated based on morpho-genetic parameters. A field experiment was conducted at the field laboratory of Genetics and Plant Breeding Department, Bangladesh Agricultural University using a randomized complete block design with three replications. Analysis of variance revealed that all genotypes exhibited significant variations (P ≤ 0.001) for all considered traits except leaf length indicating a wider extent of variability for selection. Greater phenotypic coefficient of variation (PCV) compared to corresponding genotypic coefficient of variation (GCV) for all the traits representing environmental influence on the studied traits. High GCV and PCV values were observed for the most important yield related traits like seedling height, leaf length, flag leaf area, flag leaf angle, number of effective tiller hill-1, 1000-grain weight and yield plant-1. These results suggested that selecting genotypes with these traits could be way for attaining enhancement in rice yield. Majority of the traits displayed high heritability (>60%) with high genetic advance (>20%) pointing towards non-additive gene action suggesting selection should be practiced carefully. Correlation study explored significant positive and negative association among yield and related attributes. Principal component analysis revealed the most important traits contributing to the variations among the genotypes. According to cluster analysis, 43 genotypes were grouped into 4 clusters among which genotypes within cluster I and cluster III might be selected for future rice breeding programs regarding yield potentiality and other related traits. [J Bangladesh Agril Univ 2020; 18(4.000): 923-933]

The study was undertaken to identify genotypic diversity at molecular level of potato for varietal improvement program at the Advanced Plant Breeding Laboratory, Department of Genetics and Plant Breeding, Bongobondhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh. Eight cultivars of potato viz. Lalpakri, Sindurkouta, Indurkani, Ausha, Patnai, Sadaguti, Shilbilati, Challisha were collected from Bangladesh Agricultural Research Institute (BARI), for studying genotyping divergence. Genomic DNA was extracted from young leaves of the cultivars and PCR reaction was performed. The PCR amplified DNA profile was visualized on agarose gel, staining with ethidium bromide. Three RAPD primers named OPA 01, OPA 03 and OPD 18 were used to evaluate the genetic diversity of potato varieties. All the primers were polymorphic and the primers produced the highest number of alleles. The genetic diversity value in Lalpakri with all cultivars except Sadaguti was found to have the highest genetic distance (1.0). The amount of genetic diversity within potato germplasm is quite distinct as revealed by the genetic similarity coefficients. The results indicate that, high level of genetic distance exists among the cultivars. The Primers OPA 01, OPA 03 and OPD 18 showed the highest level of genetic diversity and PIC value while the Lalpakri and Sadaguti cultivars had the highest genetic distance among other cultivars which could be used for further potato breeding program.

Red rot disease is a severe disease of sugarcane that affects the crop productivity in sugarcane growing countries. In this study, resistance gene analogues (RGAs) similar to kinase resistance prot...

Assessment of genetic diversity by using metabolic and molecular markers is important for the characterization of local unexplored germplasms of garden cress (Lepidium sativum L.) and their further utilization in crop breeding programme. However, such studies are limited to garden cress, an important medicinal crop of India. In the present study, biochemical, morphological and molecular characters were used to unravel the diversity and relationship among fifteen elite genotypes of garden cress, and the volatile constituents of seed oil were also analysed by GC-MS. Here, we report the genetic differentiation of garden cress genotypes collections in India using 10 RAPD and 9 ISSR markers. Analysis of variance revealed significant mean square values for all the morphological and biochemical traits. Random amplified polymorphic DNA (RAPD) (10) and inter-simple sequence repeats (ISSR) (9) markers produced a total of 114 bands, out of which 89 showed polymorphism. The average polymorphism was 90.8% (RAPD) and 66.03% (ISSR). The mean values of RAPD and ISSR markers for polymorphism information content (PIC) were 0.37 and 0.27, effective multiple ratio (EMR) were 4.92 and 3.10, marker index (MI) were 1.84 and 1.17 and the resolving power (Rp) were 1.39 and 1.56, respectively. In the clustering based on the combined biochemical, morphological and molecular data, the 15 genotypes were divided into two main clusters ranged from 0.50 to 0.86. Based on the observed variations, it is concluded that the magnitude of morphological, biochemical and molecular variations in the garden cress genotypes studied is significant. The volatile constituents of seed oil were also analysed by GC-MS for qualitative analysis which showed 72 similar components in oil of 15 local genotypes of garden cress. The results obtained in the present study could be useful for breeding and improvement of garden cress in the future.

Rice (Oryza sativa) is a major cereal crop that contributes significantly to global food security. Here, the aim of this study was to create scientific information on nature and magnitude of genetic variability and inter-relationship among yield and related agro-morphological attributes and also to explore the pattern of diversity among some local rice germplasms. Fourty seven local rice genotypes were evaluated following randomized complete block design with three replications. Analysis of variance manifested significant differences (P ≤ 0.001) among the genotypes based on all studied traits except leaf width reflecting broad spectrum of variability which offer an ample chances for selection. The phenotypic coefficient of variation (PCV) was higher than the corresponding genotypic coefficient of variation (GCV) for all the traits except filled grain panicle-1 indicating that there was an influence of environment on majority of the studied traits. Similarly, moderate broad-sense heritability with high genetic advance as percent of mean of majority of the traits also indicated the accumulation of additive gene effects and suggested direct selection for those characters for economic feasibility. Correlation analysis revealed significant positive and negative correlation among the traits. Principal component analysis showed that the first two principal components of the considered traits accounted for about 37.9% of the total variation and pointed out a wide variation among the genotypes. The dendrogram of cluster analysis grouped 47 rice genotypes into four clusters. Cluster II incorporated the highest number of genotypes followed by Cluster I. In terms of high yield potentiality cluster III had highest cluster mean for rice yield, followed by cluster IV. Data from this study offer a valuable gene pool from the traditional local rice germplasms which can be employed in future rice breeding program for either varietal improvement or developing new variety. [J Bangladesh Agril Univ 2020; 18(2.000): 289-299]

Pine wilt disease (PWD) is a worldwide forest disease caused by pine wood nematode (PWN). In this article, we investigated the composition, organization, correlation, and function of the endophytic microbial community in Pinus massoniana field with and without PWN. Samples were taken from branches, upper, middle, and lower trunks, as well as soil, from both healthy and infected trees. The results showed that the fungal diversity of healthy pines is around 1.1 times that of infected pines, while the bacterial diversity is about 0.75 times that of infected pines at the OTUs level. An increase of the abundance of pathogenic fungus such as Saitozyma, Graphilbum, Diplodia, Candida, Pseudoxanthomonas, Dyella and Pantoea was witnessed in infected pines according to the result of LEfSe. Furthermore, Ophiostoma and saprophytic fungus such as Entomocorticium, ganoderma, tomentella, entomocorticium were exclusively prominent in infected pines, which were substantially and highly connected with other species (p

Background Biocontrol is an effective strategy in the integrated management of plant diseases, now more as a necessity than choice, in the present era of environmental and health awareness. Microbial diversity is a wonder by nature that inspires to explore and accordingly, the diversity analysis of the isolated microbes revealed their morphological and molecular differences. The DNA provides a common platform to store the microbial information in the form of databases in public domain that can be used by anyone from anywhere. Results Exploration for native microbes in the present study resulted in isolation of different isolates of Trichoderma and Bacillus. The microbes were identified using morphological traits and molecular markers and the key conserved 18S and 16S gene sequences submitted with the appropriate repositories. Nucleotide analysis indicated a close phylogenetic relationship between BIK 2 and BIK 3 (Bacillus isolates) and within all the 5 Trichoderma isolates. The percent disease reduction of Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (Xoo) was more in plants treated with consortia of the Trichoderma (61.13%) and Bacillus (53.59%) isolates, respectively. Screening of plant growth promotion activities, percentage increase in root (41.00%) and shoot length (44.77%) were found to be maximum in Trichoderma consortia treated plants. Conclusions Three Bacillus and one Trichoderma strains, viz., B. velezensis, B. subtilis and B. paralicheniformis and Trichoderma asperellum, were identified and found to be effective against R. solani and Xoo pathogens of rice. In vitro and in vivo studies indicated that TAIK1 and BIK3 were found to be the most potential isolates among others isolated. Ability to improve plant growth was more pronounced by consortia of microbes.

The success of a breeding programme can be determined by the level of genetic diversity that exists among breeding materials. This study was carried out to (i) determine the level of genetic divers...

Diversity in plant genetic resources (PGR) provides opportunity for plant breeders to develop new and improved cultivars with desirable characteristics viz., high yield, pest and disease resistance, photosensitivity and high oil quality. Genetic diversity is a ubiquitous feature of all species in nature. Therefore, different genotypes of sesame were used for diversity analysis. Different clustering techniques were widely used for the analysis of diversity. In this paper, Bayesian hierarchical clustering algorithm is applied which can be interpreted as a novel fast bottom-up approximate inference method. Finally, this method clusters the genotypes into various groups with their corresponding genotypes in respective clusters.

The present study was aimed at genetic characterization and diversity analysis of Pandharpuri buffalo population using the Food and Agriculture Organization (FAO) recommended bovine microsatellite markers. Genomic DNA was isolated from blood samples of 50 unrelated animals and a total of 23 microsatellite loci were amplified using polymerase chain reaction. Among 23 recommended microsatellite markers, 14 markers (BM2113, BM1818, CSSM66, HEL13, INRA037, ILSTS05, HAUT27, INRA023, INRA035, HEL5, ETH3, NRA063, MM12 and ETH10) were found to be highly polymorphic in Pandharpuri population. The amplified products were run on polyacrylamide gel electrophoresis (PAGE) apparatus along with a ladder; subsequently, the allele typing was done based on silver staining of the gel. The effective and observed number of alleles, heterozygosity (expected and unbiased) estimates and polymorphic information content (PIC) levels were estimated for each locus. A total of 87 alleles were secured for 14 polymorphic loci studied giving an overall average of 6.21 alleles per locus. The number of alleles ranged from 2 (INRA063) to 9 (BM1818 and HEL13). The mean effective number of alleles across all polymorphic loci was found to be 4.28. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.77 and 0.76, ranging from 0.50 (INRA063) to 0.88 (BM1818) and 0.50 (INRA063) to 0.88 (BM1818), respectively. The average PIC estimate across all polymorphic loci was 0.73 ranging from 0.373 (INRA063) to 0.864 (BM1818). In the present study, the characterization and diversity estimates are reported for Pandharpuri population. It was found to maintain optimum diversity based on 14 polymorphic microsatellite markers.

SUMMARY Despite extensive studies on cultivated rice, the population structure and genetic diversity of the indica photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines in China remains unclear. Using 48 simple sequence repeat (SSR) markers, we genotyped a panel of 208 indica P/TGMS lines and confirmed three subgroups, named indica-I, indica-II and indica-III, in indica P/TGMS lines. Further diversity analysis indicated indica-II had the highest genetic diversity. The genetic differentiation between indica-II and indica-III was demonstrated as the largest among the three subgroups. Moreover, indica/japonica component identification was detected that five P/TGMS lines possess indica components less than 0.900. These results improve our knowledge on the genetic background for P/TGMS lines in China and will be beneficial for hybrid rice breeding programs.

Amomum tsao-ko (Zingiberaceae) is a commonly used spice and medicinal plant. Morphological variations exist in the fruits of A. tsao-ko. In this study, we compared the phenotypic traits of fruits collected from nine regions in Yunnan Province, China. Based on the mean square values of fruit weight, number of ridges, seed weight, pericarp thickness, and seed diameter, the fruits of A. tsao-ko in Yunnan were grouped into three categories, corresponding to different regions in Yunnan. A principal component analysis revealed that the number of ridges, number of seeds per fruit, and vertical fruit diameter are the most variable parameters. Considering the genetic improvement potential at the regional level, A. tsao-ko in the regions of Gongshan, Tengchong, Jinping, Lushui, and Pingbian is the most efficient for breeding new cultivars, as the plants growing in these regions have a heavier fruit weight, larger fruit diameter, larger transverse diameter, greater number of ridges, greater seed number per fruit, heavier seed weight, moderate pericarp thickness, and larger seed diameter. Based on the selected area, the nested square analysis showed that the fruit vertical diameter, fruit diameter, and the number of seeds per fruit in the region are greater than the regional mean square, and the differences reached an extremely significant level as well. Thus, these three traits can be selected as genetic materials in this region for breeding.

Genetic variability has been greatly valued in yard-long bean, due to their narrow genetic base. To diversify the genetic base, yard long bean genotypes were evaluated to quantify the variation, to assess the extent of association between the yield complaint traits, diversity and for their utilization in crop improvement programmes. High phenotypic and genotypic coefficient of variations, heritability coupled with genetic advance over mean were observed most of the traits except internodal length, days to first and 50 per cent flowering, days to first and last picking, seeds per pod. Correlation and path analysis of variables namely pod length, pod width and pods per plant contributes high positive significant association with pod yield per plant, and maximum direct and indirect effect recorded for pods per plant, green pod length and green pod width. The genotypes were grouped into 12 clusters, the maximum divergence recorded between genotypes of Cluster XI and Cluster XII for traits pod yield per plant, vine length and yield per plot and pod length contributed high towards total divergence, the genetically diverse genotype of these clusters aids in the creation of larger recombinants, and would be an aid in the genetic improvement of yard-long bean genotypes.

Background Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. Results Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P Conclusion A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.

A primary goal of modern cheese manufacturing is consistent product quality. One aspect of product quality that remains poorly understood is the variability of microbial subpopulations due to temporal or facility changes within cheese production environments. Therefore, our aim was to quantify this variability by measuring day-day and facility-facility changes in the cheese facility microbiome. In-process product (i.e., milk and cheese) and food-contact surfaces were sampled over the course of three production days at three cheese manufacturing facilities. Microbial communities were characterized using 16S rRNA metabarcoding and by plating on selective growth media. Each facility produced near-identical Cheddar cheese recipes on near-identical processing equipment during the time of sampling. Each facility also used a common pool ofLactococcusstarter cultures which were rotated daily as groups of 4–5 strains and selected independently at each facility. Diversity analysis revealed significant facility-facility and day-day differences at each sample location. Facility differences were greatest on the food contact surfaces (i.e., draining-matting conveyor belts), explaining between 25 and 41% of the variance. Conversely, daily differences within each facility explained a greater proportion of the variance in the milk (20% vs. 12%) and cheese (29% vs. 20%). Further investigation into the sources of these differences revealed the involvement of several industrially relevant bacteria, including lactobacilli, which play a central role in flavor and texture development during Cheddar cheese ripening. Additionally,Streptococcuswas found to contribute notably to differences observed in milk samples, whereasAcinetobacter,Streptococcus,Lactococcus,Exiguobacterium, and Enterobacteriaceae contributed notably to differences on the food contact surfaces. Facility differences in the cheese were overwhelmingly attributed to the rotation ofLactococcusstarter cultures, thus highlighting circumstances where daily microbial shifts could be misinterpreted and emphasizing the importance of repeated sampling over time. The outcomes of this work highlight the complexity of the cheese facility microbiome and demonstrate daily and facility-facility microbial variations which might impact cheese product quality.

The soft rot caused by Pectobacterium and Dickeya spp. is among the most important potato disease, responsible for outbreaks worldwide. In 2018, potato tubers (cultivar Lady Claire) with and without visible soft rot symptom, together with their geocaulospheres were sampled from the field in Bačka region (Serbia). The 16S rRNA Next Generation Sequencing (NGS) of tubers with and without soft rot symptom and their corresponding soils was performed to detect differences in microbial diversity and, using this data to predict causal agent(s) of disease and which samples are potentially best for isolating biocontrol strains. The ubiquitous soil bacteria from the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were dominant in all samples. The sequences identified as Pectobacterium aroidearum, P. carotovorum, and P. polaris were present in all tested samples and it can be hypothesized that they caused soft rot. The K3 sample showed the presence of genera with potential antimicrobial activity (Pseudomonas, Arthrobacter, Chryseobacterium, Bacillus, and Exiguobacterium). This result shows that diversity analysis could be used for checking for the presence of potential antagonistic bacteria at infected sites. Also, following the presence or absence of particular taxa could point out a capacity of soil to endure a growth season without an outbreak of soft or to maintain it without significant losses. This is a new approach to interpreting the results of the diversity of bacterial communities of tubers and can be useful for screening the health status of the soil.

Orchid family is the largest plant family which consists of a diverse group of flowering plants, with blooms that are often colorful and fragrant. Orchids are commercially traded as ornamental plants, medicinal products, and food. Climates allows to grow most of the climatic environment like humid, subtropical or moderate climates allows to grow most of the orchids species. The worldwide commercial production of these ornamental plants is based on clonal propagation, which leads to proliferation of pathogens and disease outbreaks. The viruses infecting orchid plants have a big influence on the produce and the quality of bulbs, force flowers and are relentless intimidation to the propagation. To control the viral pathogens, specific diagnostic procedure is required which can be fulfilled by advanced molecular techniques. Viruses from orchid’s crop can be diagnosed by techniques such as electron microscopy (EM), immunosorbent electron microscopy (ISEM), enzyme-linked immunosorbent assay (ELISA), nucleic acid hybridization, PCR, RT-PCR, next-generation sequencing (NGS) techniques, etc. The expansion of NGS in detection of known and emergent viruses from infected material is proving to be a major breakthrough for the detection of asymptomatic and multiple viruses. Globally, studies on orchid reported that currently more than 60 viruses are known to infect orchid plants. This chapter describes latest research work on genome analysis and diversity study of viruses infecting orchid plants belonging to different virus groups.

The caloric needs of the global population are solely dependent on only 30 crops including rice, wheat, and maize. It is important to diversify and ensure the global food supply by enhancing the wide adaptation of nutritionally important vegetable crops. Focusing on the underutilized and locally available vegetable crops would meet the need of eradicating malnutrition and food security for the local population and small-hold farmers. With the advent of long-read sequencing technologies, several orphan crops and crops with complex genetic nature are being explored and genome resources are made available for crop improvement. Moringa oliefera is a well-known medicinal and nutritive plant which is getting adequate attention in recent years. Functional analytical tools including genome, transcriptome, metabolome, and proteome were made available for moringa; besides diversity analysis, evolutionary and syntenic studies were also reported. With an objective of exploring the available resources of an important nutritive crop and evaluating the need to enhance the functional studies further, this chapter reviews the application of long-read sequencing and their application in moringa genomics for its wider utilization in pharma industries.

Background: Greengram is the fourth dominant pulse crop grown in India and is highly susceptible to bruchids and yellow mosaic virus. Ricebean belonging to the tertiary genepool of greengram shows resistance to this pest and disease. Ricebean being a minor pulse crop has limited SSR markers. Hence, the present study was conducted to test the cross-species amplification of SSR markers derived from related species which could be helpful in studying the molecular diversity available in each crop and for molecular confirmation of the inter- and intra-specific hybrid developed from the crosses.Methods: Molecular diversity analysis was carried out using 30 genotypes belonging to two species of Vigna (V. radiata and V. umbellata) based on 20 SSR primers derived from adzukibean, commonbean and greengram. Result: Cross species amplification was observed for all the SSR primers pairs used. The number of alleles detected varied from one (VJ 31122A) to four (CEDAAG 001 and MB 91) with an average of 2.55 alleles per primer. Allele size varied from 100 to 292 bp. The PIC value ranged from zero to 0.611 with an average value of 0.377. Dendrograms constructed based on UPGMA and Neighbour-Joining tree method, grouped the genotypes into five clusters and five groups, respectively. The V. umbellata genotypes were grouped in separate cluster from the V. radiata genotypes in both the methods. The obtained DNA polymorphism at intra- and inter-specific level will facilitate the application of molecular breeding approaches for greengram improvement.

Estimation of the level of durum wheat germplasm genetic diversity is important for its classification and efficient use in breeding programmes. The aim of this study was to assess genetic diversity of durum wheat genotypes developed at the Institute of Field and Vegetable Crops in Novi Sad, Serbia, with 26 morphological characteristics based on the International Union for Protection of New Varieties of Plants guidelines. The Shannon diversity index was used as an indicator of morphological diversity and it ranged from 0.283 for glaucosity of lower side of the flag leaf blade and density of hairiness of uppermost node of the culm, to 0.950 for the ear colour, with the mean value of 0.616, indicating a medium to high level of morphological diversity. On average, the diversity was higher for traits relating to generative organs than for those associated with vegetative plant organs. The 21 morphological characteristics were sufficient to distinguish unique profiles of all durum wheat genotypes. The estimation of varietal diversity and identification of morphological characteristics with the highest discriminative power were done by multiple correspondence analysis. The traits that contributed the most to the distinction of genotypes were the ear colouration, length of beak of the lower glume, lower glume shape, ear length of awns at tip relative to ear length and colour of awns. Morphological characterization using the traits with the highest discriminative power could be a useful complementary method for durum wheat germplasm classification and diversity analysis. Ocena genetičke raznolikosti germplazme tvrde pšenice je važna za njenu klasifikaciju i efikasno korišćenje u oplemenjivačkim programma. Cilj ovog rada bio je da se proceni genetička raznolikost genotipova tvrde pšenice stvorenih u Institutu za ratarstvo i povrtarstvo u Novom Sadu, sa 26 morfoloških osobina prema uputstvu Međunarodne unije za zaštitu novih biljnih sorti (UPOV). Šenonov indeks diverziteta je korišćen kao indikator morfološke raznolikosti i kretao se od 0,283 za prevlaku na rukavcu zastavičara i dlakavosti vršne internodije, do 0,950 za boju klasa. Prosečna vrednost Šenonovog indeksa od 0,616 ukazuje na srednje visok nivo morfološke raznolikosti. U proseku, raznovrsnost je bila veća za osobine koje se odnose na generativne biljne organe nego za vegetativne. Utvrđeno je da je 21 morfološka osobina bila dovoljna za razlikovanje jedinstvenih profila svih genotipova tvrde pšenice. Procena sortne raznolikosti i identifikacija morfoloških osobina sa najvećim diskriminativnim vrednostima je urađena pomoću višestruke korespodentne analize. Osobine koje su najviše doprinele razlikovanju genotipova su bile: boja klasa, dužina zadnje strane glume, oblik donje glume, odnos dužine osja i klasa, kao i boja osja. Morfološka karakterizacija pomoću osobina sa najvećim diskriminativnim vrednostima može biti korisna dopunska metoda za klasifikaciju i analizu diverziteta germplazme tvrde pšenice.

The process of blocking 5-lipoxygenase (5-LOX) catalyzed leukotriene biosynthesis has been recognized for the past few decades as a promising therapeutic strategy for acute inflammatory, allergic, and respiratory diseases. Due to the toxicity effect of FDA approved 5-LOX inhibitor zileuton, novel 5-LOX inhibitors have been sought by the scientific community. As a result, a significant and relevant amount of information on the structure-activity of 5-LOX inhibitors has been released and stored in public databases. In this study, we aimed at the comprehensive cheminformatic characterization of the diversity and complexity of the chemical space of 5-LOX inhibitors and its activating protein FLAP inhibitors by comparing it with the Approved drug space and virtual LOX library. The visual representation of the property space indicates some compounds in the 5-LOX inhibitors space broaden the traditional medicinal space. The structural diversity of the databases is computed using complementary approaches, including Physicochemical Property (PCP) descriptors, molecular fingerprints, and molecular scaffold. With the apparent exception of approved drugs, the 5-LOX dataset shows more diversity compared to FLAP and LOX virtual library set. This study was able to identify the underlying patterns in the chemical and pharmacological properties space that were decisive for the drug discovery and development of 5-LOX inhibitors.

Background Monochamus alternatus Hope is one of the insect vectors of pinewood nematode (Bursaphelenchus xylophilus), which causes the destructive pine wilt disease. The microorganisms within the ecosystem, comprising plants, their environment, and insect vectors, form complex networks. This study presents a systematic analysis of the bacterial microbiota in the M. alternatus midgut and its habitat niche. Methods Total DNA was extracted from 20 types of samples (with three replicates each) from M. alternatus and various tissues of healthy and infected P. massoniana (pines). 16S rDNA amplicon sequencing was conducted to determine the composition and diversity of the bacterial microbiota in each sample. Moreover, the relative abundances of bacteria in the midgut of M. alternatus larvae were verified by counting the colony-forming units. Results Pinewood nematode infection increased the microbial diversity in pines. Bradyrhizobium, Burkholderia, Dyella, Mycobacterium, and Mucilaginibacter were the dominant bacterial genera in the soil and infected pines. These results indicate that the bacterial community in infected pines may be associated with the soil microbiota. Interestingly, the abundance of the genus Gryllotalpicola was highest in the bark of infected pines. The genus Cellulomonas was not found in the midgut of M. alternatus, but it peaked in the phloem of infected pines, followed by the phloem of heathy pines. Moreover, the genus Serratia was not only present in the habitat niche, but it was also enriched in the M. alternatus midgut. The colony-forming unit assays showed that the relative abundance of Serratia sp. peaked in the midgut of instar II larvae (81%). Conclusions Overall, the results indicate that the bacterial microbiota in the soil and in infected pines are correlated. The Gryllotalpicola sp. and Cellulomonas sp. are potential microbial markers of pine wilt disease. Additionally, Serratia sp. could be an ideal agent for expressing insecticidal protein in the insect midgut by genetic engineering, which represents a new use of microbes to control M. alternatus.

Seed traits of bread wheat, including the seed size that is considered to be associated with early vigor of the crop and end-use quality, are valuable to farmers and breeders. In this study, a collection of 789 bread wheat landraces, held in-trust at the genebank of the International Center for Agricultural Research in the Dry Areas (ICARDA) were scanned for seed morphometric traits using GrainScan. Diversity analysis using the 12k DartSeq SNP markers revealed that these accessions can be grouped into five distinct clusters. To evaluate the performance for early selection from genebank accessions, we examined the accuracy of genomic selection models with genomic relationship that these landraces accounted for. Based on cross-validations, prediction accuracies for seed traits ranged from 0.64 for seed perimeter to 0.74 for seed width. The variability of prediction accuracies across random validations averaged at 0.14, with a range from 0.12 to 0.18, suggesting stable predictability and reproducible results even with a collection of much greater genetic diversity from genebank accessions. Adding the climatic relationship matrix between accessions based on passport information improved the predictive ability by 8%. Our results on seed traits demonstrated the capacity for estimating important agronomic phenotypes for genebank accessions directly based on genomic information, further advocating the advance in genomic technologies for identifying parental germplasm as potential donors of beneficial alleles for introgression.

Genetically diverse germplasm is an important source for identification of parental lines having desired traits like high oil content, high seed yield and disease resistance in sesame. In the present study, 90 genotypes have been selected for genetic diversity analysis using Mahalanobis D2 statistics. Data on five quantitative traits namely, plant height (cm), days to 50 per cent flowering, number of capsules plant-1, single plant yield(g) and oil content (%) have been analysed for clustering using Tocher’s method. A total of nine clusters were obtained. Of these clusters, cluster IX and V showed highest inter cluster distance indicating that they are the most diverse cluster whereas clusters VIII and II were the least diverse as indicated by the inter cluster distance. Cluster means were highest in cluster IX for number of capsules per plant and single plant yield while it was highest in cluster III for oil content and days to 50 per cent flowering. Based on cluster mean values for desirable traits, genetically diverse genotypes can be used in hybridization programme for oil and yield improvement in sesame.

Genetic diversity was assessed in 48 popular varieties of tetraploid cotton from each cultivated zone of India using 68 SSR markers distributed across linkage groups. The markers produced a total of 144 alleles with an average of 2.19 per locus. The polymorphism information content (PIC) ranged from 0.04 to 0.57 with a mean of 0.23 indicating lesser diversity in the studied material. Jaccard’s similarity index based neighbourhood joining cluster analysis grouped the genotypes into three major clusters, each of which was further classified into sub-groups. Inconsistencies were observed between the clusters and known pedigree of the cultivars. A narrow genetic base was also revealed among the cotton cultivars. The SSR markers revealed a genetic similarity of 73% among the varieties studied. The DNA fingerprint developed using a selected set of 14 markers showed a probability of identical match of 2.47×10-3 with high goodness of fit (r2=0.86). The identified markers have great potential in DNA fingerprinting in cotton which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.

BackgroundNarrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) inBrassica juncea(AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak,RSPR-01andUrvashi) and Exotic (Donskaja IV,Zem 1andEC287711) genepools.ResultsSequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set ofB. junceagenotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.ConclusionsDespite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity inBrassica juncea.

A long shelf life for fresh meat products is very important both to processors, retailers and consumers. In this work, the effect of repeat acid spraying on the shelf life of vacuum skin-packaged (VSP) chilled beef, as well as the quality and microbial community dynamics was evaluated. Carcasses were sprayed with 300 ppm peroxyacetic acid (PA) or 3% lactic acid (LA) three times during the chilling process, or one more time of LA spray before packaging (LLA). Quality, sensory attributes and microbial load of VSP beef during 32 days of storage at 4 °C were evaluated. The results showed that quality and sensory scores decreased over time for all treatments, but LLA treated samples were still above the rejection threshold at the end of the storage period. Moreover, the total volatile basic nitrogen value and the total viable counts were 15.0 mg/100 g and 7.2 log CFU/g for the control group, while acid treated groups remained below these two values until the end of the storage period. In particular LLA treated beef steaks exhibited the best preservation potential even at the end of storage. This is attributed to the reduction of Proteobacteria in LLA beef steaks shown by the bacterial diversity analysis via high-throughput sequencing, as well as the lower counts of B. thermosphacta and Enterobacteriaceae during storage. This indicates that LLA treatment has the potential to achieve a shelf life extension of VSP steaks without impacting on quality.

Fermented yaks’ milk is a characteristic fermented dairy product with a rich microflora (especially lactic acid bacteria [LAB]), that has been produced by Tibetan people in China throughout history. Systematic analysis of the LAB composition of fermented yaks’ milk from central Tibet is essential. In the present study, 38 samples of fermented yaks’ milk were collected from three regions in central Tibet. From these, a total of 211 isolates of LAB were generated using traditional pure culture methods. To accurately analyze their biodiversity, 16S rRNA gene sequence analysis and denaturing gradient gel electrophoresis (DGGE) were used. The isolates were identified as belonging to six genera and 22 species/subspecies. Among them, Lactobacillus species predominated (117 isolates) accounting for 55.45% of all isolates. Overall, L. delbrueckii subsp. bulgaricus (60 isolates; 28.43% of the total) was the most commonly isolated species of LAB from fermented yaks’ milk from central Tibet. Seven Lactobacill...

Tomato is one of the most economically important vegetable crops in the world. Objective of this study was to determine the genetic diversity of tomato based on its horticultural traits. Seventy-one tomato genotypes were planted and grown in two replications with randomized complete block design for two years. Diversity analysis produced six distinct clusters based on average-linkage method. Five principal components (PC) explained more than 92% of the phenotypic variation. Clusters produced in this analysis can be of importance for breeding programs developing specific fruit types based on consumer’s demand.

Jackfruit (Artocarpus heterophyllus Lam.) being an important dryland horticultural tree, grows well with minimum care and maintenance. The study aimed at identifying the genetic diversity present in twenty jackfruit genotypes for different pulp colours. The genotypes were identified for commercial cultivation, based on fruit and flake quality characters viz., fruit weight, fruit rind weight per kg fruit, number of flakes per kg fruit, weight of flakes per kg fruit, individual fresh flake weight and TSS as per the Jackfruit descriptors given by IPGRI, Rome. The best genotypes identified from the study were Swarna, Lalbagh Madhura, Byrachandra, NSP, Ashoka Yellow and NEL and these can be used for commercial purpose. Molecular diversity analysis was also carried out using 22 SSR primers, out of which six primers (SSR 9, SSR 10, SSR 30, SSR 34, SSR 45 and SSR 48) showed polymorphism among twenty genotypes. The genetic similarity co-efficient ranged from 0 to 0.96, indicating a vast variation in genetic diversity for pulp colour. A dendrogram was constructed by UPGMA analysis revealed three major clusters. The genotypes with cream and yellow colour pulp grouped in cluster I and II, followed by yellow, orange and red in cluster III. These markers effectively segregated the genotypes based on different pulp colours and hence, can be used for both diversity analysis and in breeding applications.

Soybean (Glycine max L.) is an economically important crop providing a great source for vegetable oil and protein. Yield losses of soybean under current climate change keep increasing, despite the progressive increase in yield through breeding and management practices since the 1960s. Conventional breeding facilitated the development of high-quality soybeans with enhanced tolerance to severe environmental fluctuations such as drought, flooding, heat, and salinity. However, conventional approaches are laborious, time consuming, and looks inefficient to fulfill the increasing demands of the growing world population. The advances in marker-assisted and genomics-assisted breeding, sequencing technologies, and bioinformatics tools have enabled the soybean improvement at a faster pace. The rapidly accumulating genomic resources have enabled the development of molecular markers associated with many important quantitative trait loci, provided a clear picture of genomic variations in soybean germplasm, and identified key genes for genetic engineering. This knowledge is being utilized to facilitate the development of climate-smart soybeans. In this chapter, we discuss and summarize the advances in soybean improvement through conventional and genomics-assisted breeding, genetic engineering approaches, and available bioinformatics tools for soybean. This chapter also highlights soybean genetic resources, diversity analysis, association mapping, as well as recent strategies such as gene editing and nanotechnology application in soybean breeding programs. This information could facilitate the incorporation of climatic-smart traits in breeding for more stable soybean production with the changing climate.

This work characterized mechanisms controlling cadmium (Cd) tolerance and accumulation in lettuce at both the physiological and genetic levels. These traits were evaluated in 18 Lactuca accessions representing a large genetic diversity. Cd tolerance and accumulation in roots and shoots as well as Cd translocation from roots to the shoot varied independently, and with a significant range of variation. Analyses of F1 progenies of crosses between cultivars with contrasted phenotypes showed that high tolerance to Cd, low Cd accumulation and low Cd root-shoot translocation were recessive traits. Results of analyses of F2 progenies of different crosses suggest that root Cd concentration and root-shoot Cd translocation were under a complex genetic determinism involving at least two loci. This work thus revealed that limiting both Cd accumulation and Cd root-shoot translocation in lettuce is possible and depends on recessive loci. Differences in the ability to accumulate Cd in roots in the long term could not be linked to differences in short-term 109Cd uptake into, or efflux from, roots. In contrast, the cultivar with the highest root-shoot Cd translocation was the same in the long term and in the short term, which suggests that this trait relies on processes that are implemented quickly (i.e. in less than three days) after the start of Cd exposure.

Soybean is one of the strategic food crops in Indonesia, but its production is far below the demand due to inadequate area for soybean cultivation. Shifting soybean cultivation to marginal land such as saline soil has been suggested as a realistic solution to increase soybean production. Development of soybean variety tolerant to salinity is the key step to support the cultivation of soybean in saline soil. The objective of this research was to evaluate the genetic diversity in mutant soybean lines generated using gamma rays based on agronomic traits and RAPD markers. A total of 200 irradiated seeds of cultivar Detam-3 were planted in saline soil with electrical conductivity of 1.2–4.3 dS/m. Agronomic traits were evaluated on plants until harvesting time. Genetic analysis using two RAPD markers (OPAA-02 and OPAA-14) was done on 11 plants of each radiation treatment. The results showed that 54 plants survived in saline soil. High level of variation based on agronomic traits was observed in these plants. RAPD analysis revealed 60% and 83.3% polymorphism among 11 plants for OPAA-02 and OPAA-14 markers, respectively.

Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers&rsquo, Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop&rsquo, s improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths.

Because increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, it is believed that interactions between bacteria and alien plants play an important role in plant invasions. However, the diversity of bacterial communities associated with invasive plants is poorly understood. Therefore, we investigated the diversity of rhizo- and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L (Asteraceae) based on bacterial 16S rRNA gene data obtained from 57 samples of four S. vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Rhizosphere harbored much more bacterial OTUs and showed higher alpha diversity than the leaf and root endosphere. Bacterial community composition differed substantially between compartments and locations in relative abundance profiles, especially at phyla and family level. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Acidobacteria) comprised more than 90% of abundance in all the bacterial communities. And similar endophytic communities with a shared core set of bacteria were observed from different S. vulgaris populations. According to the function prediction based on the identification and abundance information of the OTU, bacteria characterized as plant pathogens, as well as those involved in ureolysis and nitrate reduction, were rich in endophytic communities. This study reveals the microbiomes and their putative function in the invasive S. vulgaris plants and is also the first step for future studies on the role of interactions between bacteria and alien plants in plant invasions.

In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined.

Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1 to 10 % Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back fifty years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry. The analyses were performed using traditional cultivation methods, and further augmented by next-generation DNA sequencing methods. Bacterial counts for starter cultures cultivated on two different media, MRS and MPCA, revealed large differences in the relative abundance of leuconostocs. Most of the leuconostocs in two of the starter cultures were unable to grow on MRS, emphasizing the limitations of culture-based methods and the importance of careful media selection or use of culture independent methods. Pan-genomic analysis of 59 Leuconostoc genomes enabled differentiation into twelve robust lineages. The genomic analyses show that the diary-associated leuconostocs are highly adapted to their environment, characterized by the acquisition of genotype traits such as the ability to metabolize citrate. In particular, Leuconostoc mesenteroides subsp. cremoris display telltale signs of a degenerative evolution, likely resulting from a long period of growth in milk in association with lactococci. Great differences in the metabolic potential between Leuconostoc species and subspecies were revealed. Using targeted amplicon sequencing, the composition of the Leuconostoc population in the five commercial starter cultures was shown to be significantly different. Three of the cultures were dominated by Ln. mesenteroides subspecies cremoris. Leuconostoc pseudomesenteroides dominated in two of the cultures while Leuconostoc lactis, reported to be a major constituent in fermented dairy products, was only present in low amounts in one of the cultures. This is the first in-depth study of Leuconostoc genomics and diversity in dairy starter cultures. The results and the techniques presented may be of great value for the dairy industry.

Strawberries contain high levels of vitamin C, cellulose and pectin, and produce anthocyanins which have important therapeutic values, including antitumor, antiulcer, antioxidant and antiinflammatory activities. There is a pressing need to develop reliable methods for identifying strawberry germplasm and for assessing genetic diversity/relatedness in berry genotypes for practical breeding purposes and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic material independent of environmental influences. This review presents the progress in-depth of various aspects of molecular diversity analyses in strawberries. Significant progress has been made in diversity analysis in strawberry cultivars and advanced lines developed in Canada. Inter simple sequence repeat (ISSR) markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in the current breeding programs. The paper also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques including expressed sequence tag-polymerase chain reaction (EST-PCR) analysis to develop improved strawberries environmental friendly cultivars suited to the changing needs of growers and consumers.

Thirty-five grape varieties were evaluated for their molecular diversities based on inter-primer binding site (iPBS) markers. Fifteen selected iPBS primers generated a total of 99 polymorphic DNA bands with 86.3% polymorphism. The effectiveness of iPBS marker is comparable to or even more efficient than other retrotransposon-based markers in grape. The differentiation between cultivated and wild grape varieties were clearly showed by both UPGMA cluster analysis and PCoA analysis revealing that Chinese cultivated and wild grape germplasm are highly divergent and possess abundant genetic diversities. This study also confirmed that the iPBS marker is a simple, informative, reproducible and suitable method for grape genetic diversity evaluation.

Meat protein hydrolyzate can be used as an ingredient in making instant cream soup. The application of mutton protein hydrolyzate as an ingredient in making cream soup has never been done. The purpose of this study was to develop instant cream soup products from goat meat hydrolyzate as a functional food product prototype, and to know the characterization of instant cream soup in terms of its physical and chemical properties. This research is an experiment with a completely randomized design, with replications 3 times. The treatment is the addition of goat meat protein hydrolyzate which consists of 6 levels, namely, 0%, 0.2%, 0.4%, 0.6%, 0.8% 1.0% and commercial cream soup as a comparison. Data on physical properties and chemical composition were analyzed statistically by diversity analysis. The results showed that the addition of goat meat protein hydrolyzate at different concentrations was able to increase bulk density and pH value and reduce the water binding capacity of instant cream soup produced. The addition of goat meat protein hydrolyzate at different concentrations increases the water content and protein content, decreases the carbohydrate content of instant cream soup, but does not affect the ash content and fat content. It can be concluded that the addition of goat meat hydrolyzate to 1% produces instant cream soup with the same pH value and water binding capacity as commercial cream soup products and produces higher protein content than commercial products.

Stone fruits and pome fruits are cultivated commercially worldwide. In India, they are grown in temperate regions, which mainly includes Jammu and Kashmir, Uttarakhand, Himachal Pradesh and some North-Eastern states. In this study, an attempt has been made to identify the Prunus necrotic ringspot virus (PNRSV) infecting stone and pome fruits in India and to characterise them on the molecular level. Surveys were conducted in the temperate fruit-growing areas and incidence of PNRSV was detected by serological and molecular means in almond, apple, cherry, nectarine, peach, plum and wild cherry. Further diversity analysis of PNRSV was performed using bioinformatics tools such as clustalW, DNA Data Bank of Japan, MultAlin and Recombination Detection Programme. PNRSV was detected in plum, peach, cherry, almond, nectarine, wild cherry and apple. In the diversity analysis study on the basis of coat protein gene, it was found that the isolates showed identity levels from 82 to 100%. In a plum isolate, a stretch of...

This study was undertaken to compare patterns of agronomic characters and yellow pigment content diversity between Iranian durum landraces and modern varieties. In four field experiments, a collection of 127 accessions of landraces and 23 modern cultivars tetraploid wheat representing Iranian and global genetic diversity were tested under optimum and rain-fed conditions. Across the environments, the yellow pigment concentrations ranged from 1.85 mg kg−1 to 8.95 mg kg−1 in the field-grown samples. Multivariate analysis detected five groups, four including landraces and one comprising modern cultivars. As a group, modern cultivars were the most productive and showed high mean values for harvest index, grains per spike and yellow pigment, but they had the lowest plant height. Landraces had the highest mean number of spikes per m2 and 1000-kernel weight, but were characterized by low plant height and yellow pigment content. Clustering analysis also showed that, based on yield and yellow pigment content, the a...