Pathotyping and antimicrobial susceptibility testing of Escherichia coli isolates from neonatal calves

Neonatal calf mortality is a major concern to livestock sector worldwide. Neonatal calf diarrhoea (NCD), an acute severe condition causes morbidity and mortality in calves. Amongst various pathogens involved in NCD, E. coli is considered as one of the major causes. The study was targeted to characterize E. coli isolates from neonatal calves for diarrhoeagenic Escherichia coli (DEC) types (pathotyping), antimicrobial resistance (AMR) profiling and to correlate with epidemiological parameters. From neonates, a total of 113 faecal samples were collected, out of that 308, lactose fermenting colonies were confirmed as E. coli. Pathotypable isolates (12.3%) were represented by STEC (6.1%), EPEC (2.9%), ETEC (1.9%), EAEC (0.9%) and EHEC (0.3%). Occurrence of STEC was more in non-diarrhoeic calves, whereas ETEC was observed more in diarrhoeic calves. EPEC occurrence was observed in both diarrhoeic and non-diarrhoeic calves. Fishers extract test showed no significant association for occurrence of DEC types to type of dairies, health status, species, breed, age and sex of neonatal calves. Two hundred and eighty isolates were tested for antimicrobial susceptibility. The isolates showed maximum resistance towards ampicillin (55.4%) followed by tetracycline (54.3%), while minimum resistance was observed towards meropenem (2.5%). Multidrug resistant E. coli isolates were found to be 139 (49.6%), and Extended-spectrum beta-lactamase (ESBL) producers were 120 (42.9%). DEC pathotypes like STEC, ETEC, EHEC and EAEC that are also multidrug resistant present in neonatal calves have zoonotic potential and hence are of public health significance.

     

Capturing genetic variability and selection of traits for heat tolerance in a chickpea recombinant inbred line (RIL) population under field conditions

Chickpea is the most important pulse crop globally after dry beans. Climate change and increased cropping intensity are forcing chickpea cultivation to relatively higher temperature environments. To assess the genetic variability and identify heat responsive traits, a set of 296 F_8–9 recombinant inbred lines (RILs) of the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant) was evaluated under field conditions at ICRISAT, Patancheru, India. The experiment was conducted in an alpha lattice design with three replications during the summer seasons of 2013 and 2014 (heat stress environments, average temperature 35 °C and above), and post-rainy season of 2013 (non-stress environment, max. temperature below 30 °C). A two-fold variation for number of filled pods (FPod), total number of seeds (TS), harvest index (HI), percent pod setting (%PodSet) and grain yield (GY) was observed in the RILs under stress environments compared to non-stress environment. A yield penalty ranging from 22.26% (summer 2013) to 33.30% (summer 2014) was recorded in stress environments. Seed mass measured as 100-seed weight (HSW) was the least affected (6 and 7% reduction) trait, while %PodSet was the most affected (45.86 and 44.31% reduction) trait by high temperatures. Mixed model analysis of variance revealed a high genotypic coefficient of variation (GCV) (23.29–30.22%), phenotypic coefficient of variation (PCV) (25.69–32.44%) along with high heritability (80.89–86.89%) for FPod, TS, %PodSet and GY across the heat stress environments. Correlation studies (r = 0.61–0.97) and principal component analysis (PCA) revealed a strong positive association among the traits GY, FPod, VS and %PodSet under stress environments. Path analysis results showed that TS was the major direct and FPod was the major indirect contributors to GY under heat stress environments. Therefore, the traits that are good indicators of high grain yield under heat stress can be used in indirect selection for developing heat tolerant chickpea cultivars. Moreover, the presence of large genetic variation for heat tolerance in the population may provide an opportunity to use the RILs in future-heat tolerance breeding programme in chickpea.     

Classification of two different rough soil surfaces by using microwave X-band data through support vector machine (SVM)

Support vector machine (SVM) model is employed and tested for the soil surface roughness classification. SVM is calibrated (trained) and tested with the experimentally obtained data. The experimentally data is obtained by using X-band (9.5 GHz) scatterometer for two soil surface roughness 3.78 cm and 1.83 cm at constant soil surface moisture equal to 22.80%. The measurement of the scattering coefficient was carried out over a range of incidence angle from 20° to 70° at the step of 5° for both the HH and vv polarization. The performance of the SVM model is evaluated from the outcome classification result on trained data set and test data set. Radial Gaussian kernel function results 100% correct Classification and identification of soil surface roughness both in training and validation phase. SVM is a proficient technique for soil surface roughness classification by such experimentation and have numerous of advantages over artificial neural network (ANN) based approaches and other theoretical approaches as its less complexity and less time consumption ability.     

The alternative breeding approaches for improving yield gains and stress response in pigeonpea (Cajanus cajan)

Pigeonpea is an important food legume crop of semi‐arid tropical regions. Plateauing of pigeonpea yield has been worrying breeders for the past 6–7 decades. Serious breeding efforts made during this period resulted in various high‐yielding and disease resistant cultivars. However, the gains in pigeonpea productivity have been modest. The authors, while reviewing this situation, conclude that long generation turnover, complexity of biological traits, low selection response and overreliance upon pedigree breeding present the key bottlenecks for this situation. In this paper, some alternative breeding approaches and technologies are suggested for the genetic enhancement of yield stability and stress response of pigeonpea.     

Diversity among melon (Cucumis melo L.) landraces from the Indo-Gangetic plains of India and their genetic relationship with USA melon cultivars

We report here the first broad genetic characterization of farmer-developed landraces of melon (Cucumis melo L.) from the Indo-Gangetic plains of India, an area overlooked in previous melon genetic diversity analyses of Indian melon germplasm. Eighty-eight landraces from three melon Groups in two subspecies (C. melo subsp. agrestis Momordica Group, and C. melo subsp. melo Cantalupensis Group and Reticulatus Group) were collected from the four agro-ecological regions (six sub-regions) of two northern states of the Indo-Gangetic plains of India, Uttar Pradesh and Uttarakhand. Significant differences were found among the landraces and eight USA Reticulatus Group reference cultivars for 18 plant and fruit traits: no. of primary branches per plant, days to marketable maturity, sex expression, fruit shape, flesh colour, netting, no. of fruit per plant, fruit weight, shelf life, total soluble solids (°Bx), ascorbic acid (mg/100 g), titratable acidity (%), fruit length and diameter, seed cavity length and diameter, flesh thickness, and resistance to Cucumber mosaic virus. The three melon groups differed significantly for 10 of the plant and fruit traits. Cantalupensis Group and Reticulatus Group accessions were andromonoecious, and the Momordica Group was monoecious. Neighbour-joining (NJ) tree and factorial correspondence analysis (FCA) of simple sequence repeat loci also revealed a high level of genetic variability in this germplasm. The 96 melon genotypes clustered into five groups in the NJ tree analysis: the 16 Indian Reticulatus Group accessions and eight USA reference cultivars formed a distinct group; and the 60 Cantalupensis Group accessions clustered in four other groups with the 12 Momordica Group accessions in a distinct subgroup of one of the Cantalupensis groups. The FCA plot largely confirmed the NJ tree with three distinct groups, one for each melon group. The close affinity of the Indian and USA Reticulatus melons was not unexpected, but it is not clear whether it was inherent in the group and maintained as Reticulatus melons moved from India through Central Asia and Europe to North America, or the result of recent intercrossing of Indian landraces with the USA-derived cultivars and selection for a broad range of Reticulatus type melons.     

Identification of quantitative trait loci associated with iron deficiency chlorosis resistance in groundnut (Arachis hypogaea)

Iron deficiency chlorosis is an important abiotic stress affecting groundnut production worldwide in calcareous and alkaline soils with a pH of 7.5–8.5. To identify genomic regions controlling iron deficiency chlorosis resistance in groundnut, the recombinant inbred line population from the cross TAG 24 × ICGV 86031 was evaluated for associated traits like visual chlorosis rating and SPAD chlorophyll meter reading across three crop growth stages for two consecutive years. Thirty-two QTLs were identified for visual chlorosis rating (3.9%–31.8% phenotypic variance explained [PVE]) and SPAD chlorophyll meter reading [3.8%–11% PVE] across three stages over 2 years. This is the first report of identification of QTLs for iron deficiency chlorosis resistance-associated traits in groundnut. Three major QTLs (>10% PVE) were identified at severe stage, while majority of other QTLs were having small effects. Interestingly, two major QTLs for visual chlorosis rating at 60 days (2013) and 90 days (2014) were located at same position on LG AhXIII. The identified QTLs/markers after validation across diverse genetic material could be used in genomics-assisted breeding.     

Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin

A persistent puzzle in the field of biological electron transfer is the conserved iron-sulfur cluster motif in both high potential iron-sulfur protein (HiPIP) and ferredoxin (Fd) active sites. Despite this structural similarity, HiPIPs react oxidatively at physiological potentials, whereas Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy uncovers the substantial influence of hydration on this variation in reactivity. Fe-S covalency is much lower in natively hydrated Fd active sites than in HiPIPs but increases upon water removal; similarly, HiPIP covalency decreases when unfolding exposes an otherwise hydrophobically shielded active site to water. Studies on model compounds and accompanying density functional theory calculations support a correlation of Fe-S covalency with ease of oxidation and therefore suggest that hydration accounts for most of the difference between Fd and HiPIP reduction potentials.     

Response of rice genotypes to rice root-knot nematode (Meloidogyne graminicola) infection under varying temperature regimes

The rice root-knot nematode (RRKN), Meloidogyne graminicola, is one of the major pests of the rice–wheat cropping system. Resistance against M. graminicola in rice could be most valuable in alleviating this problem. The host response of 75 Oryza genotypes was examined at three day/night temperature regimes, 29/26°C, 34/31°C and 38/35°C, in Pluronic gel as well as in soil. Out of the 75 selected rice genotypes, only Zhenshan 97 B exhibited high resistance to this set of temperature regimes, with the least number of galls/root system. At 34/31°C, more second-stage juveniles (J2s) were hatched and J2 population densities in roots of the susceptible rice genotypes increased significantly compared with those of plants grown at the 29/26°C. In resistant genotypes, only a few J2s penetrated roots and developed into mature females. The histopathological studies revealed that in susceptible rice genotypes at high-temperature regimes, the multinucleate giant cells were well developed. The results presented in this study revealed that an increase in temperature had a significant effect on the resistance of rice genotypes and resistance appeared more pronounced in genotype Zhenshan 97 B. This resistant genotype can be used in marker-assisted selection to develop resistant elite cultivars.     

Chloroplast derived SSRs reveals genetic relationships in domesticated alliums and wild relatives

Genetic Resources and Crop Evolution - Alliums comprise of popular spices and used for various culinary purposes and nutraceuticals. Poor genetic characterization and scarce information regarding...     

Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)

Fusarium wilt (FW) and Ascochyta blight (AB) are two important diseases of chickpea which cause 100 % yield losses under favorable conditions. With an objective to validate and/or to identify novel quantitative trait loci (QTLs) for resistance to race 1 of FW caused by Fusarium oxysporum f. sp. ciceris and AB caused by Ascochyta rabiei in chickpea, two new mapping populations (F_2:3) namely ‘C 214’ (FW susceptible) × ‘WR 315’ (FW resistant) and ‘C 214’ (AB susceptible) × ‘ILC 3279’ (AB resistant) were developed. After screening 371 SSR markers on parental lines and genotyping the mapping populations with polymorphic markers, two new genetic maps comprising 57 (C 214 × WR 315) and 58 (C 214 × ILC 3279) loci were developed. Analysis of genotyping data together with phenotyping data collected on mapping population for resistance to FW in field conditions identified two novel QTLs which explained 10.4–18.8 % of phenotypic variation. Similarly, analysis of phenotyping data for resistance to seedling resistance and adult plant resistance for AB under controlled and field conditions together with genotyping data identified a total of 6 QTLs explaining up to 31.9 % of phenotypic variation. One major QTL, explaining 31.9 % phenotypic variation for AB resistance was identified in both field and controlled conditions and was also reported from different resistant lines in many earlier studies. This major QTL for AB resistance and two novel QTLs identified for FW resistance are the most promising QTLs for molecular breeding separately or pyramiding for resistance to FW and AB for chickpea improvement.