Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.     

Recent advances in molecular marker techniques: Insight into QTL mapping,GWAS and genomic selection in plants

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.     

RFLP characterization of Indian Musa germplasm for clonal identification and classification

Summary Nineteen single-copy clones isolated from a PstI genomic library (cv. Maiden Plantain), and eight Vigna chloroplast DNA clones were used to probe total genomic DNA digests of 57 genotypes of Musa from India. The 19 genomic clones detected a total of 107 polymorphisms among the 57 genotypes. Principal coordinates and phenetic analyses of these data placed cultivars and species into distinct groups that were in general agreement with a previously published RAPD-based classification of these same plant materials. The 107 polymorphisms were sufficient to differentiate each clone from every other clone. Heterologous Vigna chloroplast DNA probes were used to characterize the cytoplasm of Musa cultivars and species. PCO analysis of these RFLPs were detected both within and between the generally recognized genome groups, indicating multiple hybridization pathways in the origin of hybrid clones. Data presented demonstrate that RFLPs are sufficiently abundant to classify Musa germplasm and that genetic relationships among Musa cultivars, based upon RFLP data, are in general agreement with relationships determined by analysis of morphology and RAPDs.     

A unique introgression from Moricandia arvensis confers male fertility upon two different cytoplasmic male-sterile lines of Brassica juncea

A Brassica juncea line carrying an introgression from Moricandia arvensis restored male fertility to two cytoplasmic male‐sterile (CMS) B. juncea lines carrying either M. arvensis or Diplotaxis catholica cytoplasm. Genetics of fertility restoration was studied in the F₁, F₂, F₃ and backcross generations of the cross between CMS and fertility‐restorer lines. No male‐sterile plants were found in F1‐F₃ generations of the cross between CMS [M. arvensis] B. juncea and the restorer. However, a 1: 1 segregation for male sterility and fertility was observed when the F1 was pollinated with non‐restorer pollen from a euplasmic line. These results clearly show that restoration is mono‐genic and gametophytic. In CMS lines carrying D. catholica cytoplasm, the restorer conferred male fertility to the F1 and showed 3: 1 and 1: 1 segregations for male fertility and sterility in F₂ and BC1 generations, respectively, indicating a monogenic, sporophytic mode of fertility restoration. The results were also supported by pollen stainability in the F1 which was about 65% in M. arvensis‐based CMS and >90% in D. catholica‐based CMS. The above results are discussed in the light of previous molecular studies which showed association between CMS and atpA in both systems.     

Molecular epidemiology of ovine herpesvirus type 2 infection in Kashmir, India

The aims of this investigation were to determine the prevalence of ovine herpesvirus type 2 (OvHV-2) (the causative agent of malignant catarrhal fever) infection in cattle, the carrier status of sheep and goats, and to define the pattern of acquisition of OvHV-2 in lambs under natural flock conditions in Kashmir, India. None of the buffy coat samples from 21 lambs contained OvHV-2 DNA sequences up to 28 days after birth, only one lamb had sequences of OvHV-2 DNA as early as 29 days after birth, and they were detected in the other 20 lambs when they were between 43 and 94 days of age. Sequences of OvHV-2 DNA were detected in buffy coat samples from 28 (85 per cent) of 33 adult sheep and in 16 (61 per cent) of 26 samples from adult goats by hemi-nested PCR. Seventeen (31 per cent) of 55 cattle with malignant catarrhal fever-like clinical signs had sequences of OvHV-2 DNA in their blood, and nine of the 17 died, all of them during the months of April to November, between November 2002 and March 2004. No clinical cases of sheep-associated malignant catarrhal fever was recorded during the months of December to March. The overall prevalence of OvHV-2 infection in the cattle in the region was estimated to be less than 1 per cent.     

In vitro and in vivo anthelmintic activity of Euphorbia helioscopia L

The anthelmintic potentials of the aqueous and methanol extracts of Euphorbia helioscopia were investigated. In folklore medicine, E. helioscopia (Euphorbiaceae) is used in the treatment of various gastrointestinal ailments and diseases. A worm motility inhibition (WMI) assay and egg hatch assay (EHA) were used for in vitro assessment, and a faecal egg count reduction (FECR) assay was used for an in vivo study. The in vitro study revealed anthelmintic effects of crude methanolic extracts of E. helioscopia on live Haemonchus contortus worms as evident from their paralysis and/or death at 8h after exposure, different concentrations (12.5mgml(-1), 25mgml(-1) and 50mgml(-1)) of aqueous and methanolic extracts were used against H. contortus which exhibited dose-dependent anthelmintic effects on H. contortus. Aqueous and methanolic extracts of aerial parts (stem, leaves and flowers) of E. helioscopia were found to have very low percent inhibitory egg hatching as compared to levamisole. It is concluded that the entire plant of E. helioscopia possesses significant anthelmintic activity and could be a potential alternative for treating cases of helminth infections in ruminants.     

Contagious caprine pleuropneumonia – a comprehensive review

Contagious caprine pleuropneumonia (CCPP) is a serious disease of goats, occasionally sheep and wild ruminants, caused by Mycoplasma capricolum subspecies capripneumoniae (Mccp). The disease is characterized by severe serofibrinous pleuropneumonia, very high morbidity (～100%), and mortality (80–100%). CCPP affects goats in more than 40 countries of the world thereby posing a serious threat to goat farming around the globe. The characteristic clinical signs of CCPP are severe respiratory distress associated with sero-mucoid nasal discharge, coughing, dyspnea, pyrexia, pleurodynia, and general malaise. In later stages, severe lobar fibrinous pleuropneumonia, profuse fluid accumulation in pleural cavity, severe congestion of lungs and adhesion formation is observed. Mycoplasmal antigen interactions with host immune system and its role in CCPP pathogenesis are not clearly understood. CCPP is not a zoonotic disease. Diagnosis has overcome cumbersome and lengthy conventional tests involving culture, isolation, and identification by advanced serological (LAT, cELISA) or gene-based amplification of DNA (PCR, RFLP, and hybridization) and sequencing. The latex agglutination test (LAT) is rapid, simple, and better test for field and real-time diagnosis applicable to whole blood or serum and is more sensitive than the CFT and easier than the cELISA. Moreover, the studies on antibiotic sensitivity and exploration of novel antibiotics (fluoroquinolones, macrolides) can help in better therapeutic management besides preventing menace of antibiotic resistance. Re-visiting conventional prophylactic measures focussing on developing novel strain-based or recombinant vaccines using specific antigens (capsular or cellular) should be the most important strategy for controlling the disease worldwide.