Genetic diversity of Ralstonia solanacearum infecting solanaceous vegetables from India reveals the existence of unknown or newer sequevars of Phylotype I strains

Bacterial wilt is one of the important constraints in the cultivation of solanaceous vegetables in India. The disease is caused by Ralstonia solanacearum, a soil bacterium. We have collected 232 isolates of R. solanacearum infecting solanaceous vegetables (eggplant, tomato and chilli) and other crops from different parts of India. Pathogenicity of the isolates was tested on eggplant, tomato and chilli and the pathogen was confirmed by PCR. Multiplex PCR and biochemical tests indicated that all the isolates were phylotype I and biovar 3. Ninety-five representative isolates selected based on geographical region, host range and pathogenicity were subjected to further phylogenetic and diversity analysis. Sequence analysis of egl, pga and hrpB genes of 95 isolates and genetic diversity of 50 representative isolates was reported and discussed. Indian isolates within the Phylotype I did not group based on the host or geographical location, except clustering of isolates from the Andaman Islands. Indian isolates clustered into two sub groups based on egl and pga trees indicating the presence of two major population groups. Sub group 1 is the dominant group in the data set and consists of unknown/newer sequevars, and sub group 2 consist of mainly the isolates which are designated with sequevar numbers based on egl sequences. In the hrpB based tree, the sub group 2 is the dominant group in the data set and it is the same for the sub group 1 of the egl tree. Indian phylotpe I R. solanacearum strains are phenotypically diverse including the previously described sequevars 14, 17, 44, 47 and 48. Our studies indicated the existence of R. solanacearum isolates with unknown/newer sequevars; the diversity existing among the phylotype I isolates might be due to a continuous evolutionary process. To our knowledge this is the first detailed report on the diversity of phylotype I R. solanacearum strains infecting solanaceous vegetables and the existence of unknown/newer sequevars in India.     

Development and validation of class I SSR markers targeting (GATA) n repeat motifs in rice

SSR markers targeting (GATA) _n motifs are known to be highly polymorphic and useful in many organisms. (GATA) _n motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective to identify class I rice microsatellites in the rice genome with (GATA)_n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions. Many of the (GATA) _n motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCR-based markers targeting all the class I (GATA) _n microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on marker analysis. These informative markers targeting (GATA) _n motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Passoupathy Rajendrakumar, Akshaya Kumar Biswal and Kannabiran Sakthivel contributed equally.     

Improving hybrid rice parental lines for blast resistance by introgression of broad-spectrum resistance genes Pi54 and Pi9 by marker-assisted selection

Hybrid rice technology offers a great promise to produce 15% to 20% more yield than pure line varieties. The success of hybrid rice hinges on developing superior parental lines. To improve the blast resistance of hybrid rice parental line RP5933-1-19-2R, crosses were made with donors of two major blast resistance genes namely, Pi54 (Tetep) and Pi9 (IR71033–121-15) and the resulting F₁s were confirmed for their hybridity by using Pi54MAS and NMSMPi9-1 genic markers. The confirmed F₁s were intercrossed to obtain ICF₁s and selected positive plants by markers were backcrossed to the recurrent parent, as well as selfed for advancing further to BC₁F₃ and ICF₄ generations. The segregating plants were phenotyped for blast resistance at Uniform Blast Nursery. The identified complete restorers namely, RP 6619-1, RP 6616-26, RP 6619-3 and RP 6619-11 with Pi9 and Pi54 genes would serve as donors for broad spectrum blast resistance. This could ultimately lead to the development of new rice hybrids with improved resistance to blast disease, which is crucial for sustainable rice production and food security.     

Accelerating gene discovery in climate-resilient and nutrient-rich major and minor millets through genome-wide association studies: Progress and prospects

Millets are known for their resilience and nutritional benefits and hence believed to have a promising role in ensuring food and nutritional security under changing climatic conditions. Research on millets has intensified in recent years, especially in dissecting the genetic components of yield, stress tolerance and nutritional quality traits. Recent advances in next-generation sequencing, bioinformatics and associated statistical procedures for genome-wide association studies (GWAS) have provided wide opportunities to resolve the genetic complexity of polygenic traits by measuring historical and evolutionary recombination events in the natural population(s). During the past decade, GWAS has been successfully employed to identify key genes controlling growth, development, stress tolerance, nutrient use efficiency and nutritional quality traits in sorghum, pearl millet, foxtail millet and finger millet. However, progress in other minor millets is still in its infancy. Genetic dissection of these complex traits in millets may pave the way for genetic alteration of climate resilience, photosynthesis and nutrient accumulation in rice and wheat. In this review, progress in GWAS analysis in detecting QTLs underlying complex traits in sorghum and other millets is highlighted.     

Molecular prevalence of Cryptosporidium spp. in dairy calves in Southern states of India

Dung samples were collected from dairy calves of south Indian states viz., Andhra Pradesh, Karnataka, Kerala, Tamil Nadu and union territory, Puducherry and are subjected to nested polymerase chain reaction (PCR) targeting 18S rRNA gene for detection of Cryptosporidium infection. Of the 459 dung samples screened 182 were found positive with a prevalence of 39.65%. Highest prevalence of Cryptosporidium was observed in Puducherry (86.67%) and lowest in Kerala (17.65%). Genotyping by PCR-restriction fragment length polymorphism (RFLP) and sequence analysis revealed the presence of all the four major Cryptosporidium species of cattle viz., Cryptosporidium andersoni, Cryptosporidium ryanae, Cryptosporidium parvum and Cryptosporidium bovis. C. andersoni was widely distributed in calves of Tamil Nadu, Karnataka and Puducherry whereas in Andhra Pradesh C. ryanae was the major species. Of the 64 samples subjected to PCR-RFLP, 39 (60.94%) could be classified as C. andersoni, 18 (28.13%) as C. ryanae, 4 (6.25%) as C. parvum and 3 (4.69%) were confirmed as C. bovis. The results were also confirmed by sequencing of 19 Cryptosporidium DNA samples.     

Nonrandom processes maintain diversity in tropical forests

An ecological community's species diversity tends to erode through time as a result of stochastic extinction, competitive exclusion, and unstable host-enemy dynamics. This erosion of diversity can be prevented over the short term if recruits are highly diverse as a result of preferential recruitment of rare species or, alternatively, if rare species survive preferentially, which increases diversity as the ages of the individuals increase. Here, we present census data from seven New and Old World tropical forest dynamics plots that all show the latter pattern. Within local areas, the trees that survived were as a group more diverse than those that were recruited or those that died. The larger (and therefore on average older) survivors were more diverse within local areas than the smaller survivors. When species were rare in a local area, they had a higher survival rate than when they were common, resulting in enrichment for rare species and increasing diversity with age and size class in these complex ecosystems.     

Litter decomposition and nutrient release in relation to atmospheric deposition of S and N in a dry tropical region

Temporal and spatial variations in litterfall, leaf litter decomposition and nutrient release were quantified along an air pollution gradient around an industrial area in a dry tropical region of India. Significant differences were found in litterfall between the sites. Litter decomposition rates also significantly varied among the study sites. Litter decomposition was faster at sites away from the industrial region with coal-fired power plants. The concentrations of N and P increased, whereas that of Ca and SO₄-S decreased in decomposing litter over time. The nutrient release pattern was also modified by atmospheric deposition. Concentrations of SO₂ and NO₂ were negatively correlated with relative mass loss. Turnover time of nutrients, except SO₄-S in decomposing litter was maximal at the site receiving highest atmospheric depositions. The study documents that industrial emissions significantly modified nutrient cycling in adjacent terrestrial ecosystems.     

Evaluating landraces of bread wheat <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. for tolerance to aluminium under low pH conditions

Bread wheat (Triticum aestivum L.) landraces held within ex situ collections offer a valuable and largely unexplored genetic resource for wheat improvement programs. To maximise full utilisation of such collections the evaluation of landrace accessions for traits of interest is required. In this study, 250 accessions from 21 countries were screened sequentially for tolerance to aluminium (Al) using haematoxylin staining of root tips and by root regrowth measurement. The staining test indicated tolerance in 35 accessions, with an intermediate response to Al exhibited in a further 21 accessions. Of the 35 accessions classified as tolerant, 33 also exhibited increased root length following exposure to Al. The tolerant genotypes originated from Bulgaria, Croatia, India, Italy, Nepal, Spain, Tunisia, and Turkey. AFLP analysis of the 35 tolerant accessions indicated that these represent diverse genetic backgrounds. These accessions form a valuable set of germplasm for the study of Al tolerance and may be of benefit to breeding programs for expanding the diversity of the gene pool from which tolerant cultivars are developed.