Identification of New Drug Candidates Against \u3cem\u3eBorrelia burgdorferi\u3c/em\u3e Using High-Throughput Screening

Lyme disease is the most common zoonotic bacterial disease in North America. It is estimated that .300,000 cases per annum are reported in USA alone. A total of 10%–20% of patients who have been treated with antibiotic therapy report the recrudescence of symptoms, such as muscle and joint pain, psychosocial and cognitive difficulties, and generalized fatigue. This condition is referred to as posttreatment Lyme disease syndrome. While there is no evidence for the presence of viable infectious organisms in individuals with posttreatment Lyme disease syndrome, some researchers found surviving Borrelia burgdorferi population in rodents and primates even after antibiotic treatment. Although such observations need more ratification, there is unmet need for developing the therapeutic agents that focus on removing the persisting bacterial form of B. burgdorferi in rodent and nonhuman primates. For this purpose, high-throughput screening was done using BacTiter-Glo assay for four compound libraries to identify candidates that stop the growth of B. burgdorferi in vitro. The four chemical libraries containing 4,366 compounds (80% Food and Drug Administration [FDA] approved) that were screened are Library of Pharmacologically Active Compounds (LOPAC1280), the National Institutes of Health Clinical Collection, the Microsource Spectrum, and the Biomol FDA. We subsequently identified 150 unique compounds, which inhibited .90% of B. burgdorferi growth at a concentration of ,25 µM. These 150 unique compounds comprise many safe antibiotics, chemical compounds, and also small molecules from plant sources. Of the 150 unique compounds, 101 compounds are FDA approved. We selected the top 20 FDA-approved molecules based on safety and potency and studied their minimum inhibitory concentration and minimum bactericidal concentration. The promising safe FDA-approved candidates that show low minimum inhibitory concentration and minimum bactericidal concentration values can be chosen as lead molecules for further advanced studies

Influence of diazotrophic bacteria on nodulation, nitrogen fixation, growth promotion and yield traits in five cultivars of chickpea

Three bacteria, IC-59, IC-76A and IC-2002, isolated from the nodules of chickpea, were characterized for nodulation, nitrogen fixation, plant growth-promoting (PGP) and yield traits in five cultivars of chickpea such as BG256, RSG888, Subhra, K850 and ICCV2. All the bacteria produced cellulase, protease, β-1,3-glucanase, indole acetic acid, siderophore, hydro cyanic acid and 1-aminocyclopropane-1-carboxylate deaminase while none produced lipase and chitinase. The 16 S rDNA gene sequences of IC-59, IC-76A and IC-2002 were found to match closely with Rhizobium pusense, Paraburkholderia kururiensis and Stenotrophomonas maltophilia, respectively. The three bacteria nodulated all the cultivars of chickpea well, amplified nifH gene and fixed nitrogen. Under greenhouse conditions at 30 and 45 days after sowing, treatment of five cultivars of chickpea with bacterial cultures IC-59, IC-76A and IC-2002, enhanced the nodule number (up to 45%, 38% and 43%), nodule weight (up to 31%, 15% and 39%), shoot weight (11%, 16% and 14%) and root weight (37%, 48% and 62%), respectively, over the un-inoculated control. At crop maturity, IC-59, IC-76A and IC-2002 were found to enhance the shoot weight (16%, 40% and 26%), pod number (37%, 69% and 81%), pod weight (17%, 45% and 49%), seed number (21%, 31% and 39%) and seed weight (14%, 56% and 65%), respectively, over the un-inoculated control. Among the five cultivars, Subhra was found to enhance most of the PGP traits when treated with the three diazotrophic bacteria. It is concluded that the three diazotrophic bacteria could be potentially exploited for improving nodulation, nitrogen fixation, PGP and yields of chickpea

Effect of post-emergence herbicide imazethapyr on phenological and agronomic traits in chickpea breeding lines

Chickpea is sensitive to herbicides and manual weeding is currently the only option for weed control in many developing countries in arid and semi-arid regions of the world. The farmers in these countries need herbicide-tolerant varieties to use post-emergence herbicides to control weeds. In this direction, a study was conducted with 21 breeding lines at four locations in India (Patancheru, Bijapur, Nandyal and Sehore) during postrainy season of 2014-15. The trial was conducted under field conditions in RBD with four replications in both control (hand weeding) and sprayed (herbicide: Imazethapyr @ 750 ml/ha) treatments. The herbicide was sprayed 30 days after sowing. Herbicide effect was studied on phenological (days to flowering and maturity) and agronomic (number of primary and secondary branches, plant height, seed yield, 100-seed weight and harvest index) traits. The results indicated that time to flowering and maturity was delayed up to 16.5 and 18.5 days, respectively. Herbicide had no effect on primary branches, while the number of secondary branches was increased up to 12. Plant height was severely reduced by 18cm. The reduction in seed yield was observed up to 49%, whereas 100-seed weight was increased across locations. Location-specific superior lines (Nandyal: ICCIL 04016, ICCIL 04004, ICCV 10114; Patancheru: ICCIL 04007; Bijapur: ICCV 04516, ICCV 10, ICCV 97105, ICCIL 01026, ICCV 09106; Sehore: ICCV 08102) were identified. These lines can be used as potential sources for developing herbicide tolerant varieties in chickpea. Weed management through herbicides is economical and facilitates minimum tillage methods, which help preserve topsoil

High yielding and drought tolerant genotypes developed through marker-assisted back crossing (MBAC) in chickpea

Chickpea (Cicer arietinum L.) is the second largest grown food legume crop in the world after common bean. This crop is largely grown under rainfed conditions in Asia and sub-Saharan Africa where terminal drought is the major production constraint. Generation of large scale genomic resources in chickpea during the recent years has made it possible to improve the complex traits like drought tolerance. A “QTL-hotspot” harbouring QTLs for several root and drought tolerance traits was transferred from the drought tolerant line ICC 4958 to a leading chickpea cultivar JG 11 (ICCV 93954), and a widely adapted cultivar Bharati (ICCV 10) in India. A set of 20 BC3F4/ BC3F5 introgression lines (ILs) of JG 11 and 22 of Bharati were evaluated at three to four locations (Patancheru, Nandyal, Gulbarga and Dharwad) in Southern India over two years during 2011-12 to 2014-15. Many lines giving at least 10% higher yield than the recurrent parents JG 11 and Bharati were identified at each location and in each growing condition (rainfed/irrigated). As the introgressed genomic region also influences seed size, most ILs had bigger seed than the recurrent parents. These results are very encouraging and demonstrate the effectiveness of marker-assisted breeding in improving terminal drought stress tolerance in chickpea

Prospects of new chickpea varieties in Andhra Pradesh

Andhra Pradesh is an important chickpea growing state in southern India, with spectacular increase in chickpea area from 120,000 ha in 1997/98 to 638,000 ha in 2007/08. The chickpea revolution in Andhra Pradesh has improved the prospects of many resource-poor, small land holding and rainfed farmers of Andhra Pradesh. However, the growing season of chickpea in Andhra Pradesh is warm and short (90-110 days), and drought is the foremost factor responsible for significant yield losses. Rainfall in major chickpea-growing regions is quite uncertain and erratic, resulting in poor yields. The Regional Agricultural Research Station of Acharya N G Ranga Agricultural University, Nandyal, Andhra Pradesh, India is the lead centre responsible for location-specific research in chickpea in Andhra Pradesh. With support from ICRISAT and ICAR, the centre has initiated crop improvement programmes during 2004 and has released four promising chickpea varieties for commercial cultivation. Three desi varieties viz., Nandyal Sanaga 1(NBeG 3), Dheera (NBeG 47), and Nandyal Gram 49 (NBeG 49) released for Andhra Pradesh and one large-seeded kabuli Nandyal Gram 119 (NBeG 119) released for the southern zone comprising Andhra Pradesh, Karnataka and Tamil Nadu, are cutting across chickpea growing regions of Andhra Pradesh. Nandyal Sanaga 1, released in 2012, is a bold-seeded desi variety tolerant to drought and heat; Dheera released during 2015 is also a desi variety and the first of its kind in India, suitable for mechanical harvesting. Nandyal Gram 49 released during 2016 is a highyielding desi variety with attractive seeds; whereas Nandyal Gram 119 is early bold-seeded kabuli variety released during 2015. These varieties have clearly demonstrated their advantage (10%-15 % increase over popular varieties of the tract) in farmers’ holdings in large-scale demonstrations and are being preferred by farmers of not only Andhra Pradesh, but also Karnataka, Tamil Nadu, Odisha and Maharastra. Efforts are underway to promote large-scale adoption of these varieties to maximize long term productivity of chickpeas in rainfed vertisols

Climate Change and Heat Stress Tolerance in Chickpea

Chickpea (Cicer arietinum L.) is a cool-season food legume and suffers heavy yield losses when exposed to heat stress at the reproductive (flowering and podding) stage. Heat stress is increasingly becoming a severe constraint to chickpea production due to the changing scenario of chickpea cultivation and expected overall increase in global temperatures due to climate change. A temperature of 35 °C was found to be critical in differentiating heat-tolerant and heat-sensitive genotypes in chickpea under field conditions. Large genetic variations exist in chickpea for reproductive-stage heat tolerance. Many heat-tolerant genotypes have been identified through screening of germplasm/breeding lines under heat stress conditions in the field. A heat-tolerant breeding line ICCV 92944 has been released in two countries (as Yezin 6 in Myanmar and JG 14 in India) and is performing well under late-sown conditions. Heat stress during the reproductive phase adversely affects pollen viability, fertilization, pod set, and seed development, leading to abscission of flowers and pods, and substantial losses in grain yield. Studies on physiological mechanisms and genetics of heat tolerance, and identification of molecular markers and candidate genes for heat tolerance, are in progress. The information generated from these studies will help in developing effective and efficient breeding strategies for heat tolerance. The precision and efficiency of breeding programs for improving heat tolerance can be enhanced by integrating novel approaches, such as marker-assisted selection, rapid generation turnover, and gametophytic selection. Chickpea cultivars with enhanced heat tolerance will minimize yield losses in cropping systems/growing conditions where the crop is exposed to heat stress at the reproductive stage

Genomic-enabled prediction model with genotype × environment interaction in elite chickpea lines

Genomic selection (GS) allows safe phenotyping and reduces cost and shortening selection cycles. Incorporating of genotype × environment (G×E) interactions in genomic prediction models improves the predictive ability of lines performance across environments and in target environments. Phenotyping data on a set of 320 elite chickpea breeding lines on different traits (e.g., plant height, days to maturity, and seed yield), from three consecutive years for two different treatments at two locations were recorded. These lines were genotyped on DArTseq(1.6K) and Genotyping- by-Sequencing (GBS; 89K SNPs) platforms. Five different models were fitted, four of which included genomic information as main effects (baseline model) and/or G×E interactions. Three different cross-validation schemes that mimic real scenarios that breeders might face on fields were considered to assess the predictive ability of the models (CV2: incomplete field trials; CV1: newly developed lines; and CV0: new previously untested environments). Different prediction models gave different results for the different traits; however, some interesting patterns were observed. For CV1, analyzing yield seed interaction models improved baseline counterparts on an average between 55 and 92% using DArT and DArT combined with GBS data, respectively [between 9 and 112% for all traits]. While for CV2 these improvements varied b tween 65 and 102% [between 8 and 130% remaining traits]. In CV0, no clear advantage was observed considering the interaction term. These results suggest that GS models hold potential for breeder’s applications on chickpea cultivar improvements

High temperature tolerance in grain legumes

High temperature stress (or heat stress) during reproductive stages is becoming aserious constraint toproductivity of grain legumes as their cultivation is expanding to warmer environments and temperature variability is increasing due to climate change.Large genetic variations exist ingrainlegumesforheat tolerance whichcan be exploited for development of locally adapted heat tolerant cultivars. Heat tolerant cultivars will be more resilient to the impacts of climate change, allow flexibility in sowing dates and enhance opportunities for expanding area of grain legumes to new nichesand croppingsystems

Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013–14 and 2014–15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas

Integrated breeding approaches for improving drought and heat adaptation in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is a dry season food legume largely grown on residual soil moisture after the rainy season. The crop often experiences moisture stress towards end of the crop season (terminal drought). The crop may also face heat stress at the reproductive stage if sowing is delayed. The breeding approaches for improving adaptation to these stresses include the development of varieties with early maturity and enhanced abiotic stress tolerance. Several varieties with improved drought tolerance have been developed by selecting for grain yield under moisture stress conditions. Similarly, selection for pod set in the crop subjected to heat stress during reproductive stage has helped in the development of heat‐tolerant varieties. A genomic region, called QTL‐hotspot, controlling several drought tolerance‐related traits has been introgressed into several popular cultivars using marker‐assisted backcrossing (MABC), and introgression lines giving significantly higher yield than the popular cultivars have been identified. Multiparent advanced generation intercross (MAGIC) approach has been found promising in enhancing genetic recombination and developing lines with enhanced tolerance to terminal drought and heat stresses