Benthic diversity of River Gomti in relation to the prevailing environmental conditions in Lucknow

To evaluate the benthic diversity of River Gomti in relation to the prevailing environmental conditions, four stations, viz., Maa Chandrika Devi, Daliganj, Ambedkar Park and Aquaduct, were identified from upstream to downstream along the course of the river in Lucknow. Dissolved oxygen was low on many occasions at all the stations except Maa Chandrika Devi and chemical oxygen demand values were high. There was a gradual increase in mean nitrite and phosphate values from up to downstream. Benthic fauna was dominated by oligochaetes and chironomus larvae. Other groups reported were leeches, nematodes, sponges, crustaceans, pelycypodes, gastropods and fish fry. Population density was exceptionally high at Daliganj (20,135 m sub(-1) ) followed by Ambedkar Park (5,199 m sub(-1)) and Aquaduct (3,287 m sub(-1)), and low at Maa Chandrika Devi (264 m sub(-1)). Oligochaete genera common at all the four stations were Lumbricillus, Limnodrillus, Branchiura, Chaetogaster, Nais and Tubifex. Odonates were reported only from Maa Chandrika Devi while sponges were encountered at Daliganj and Aquaduct. On some occasions, fish fry were also found at Ambedkar Park and Aquaduct. Seasonally, maxima for population density were observed during pre-monsoon and minima during monsoon. The organic pollution indicator benthic species reported were tubificids, chironomids, culicoid larvae, Lamellidens sp., Corbicula sp., Lymnaea sp. and leech. Branchiurans, Tubifex sp. and Chironomus larvae were reported at all the stations. Filthy condition with foul smell throughout the length of the river coupled with poor water quality and appearance of indicator organisms at all the stations indicate that the river is under severe pollution stress due to anthropogenic discharges and it has reached an alarming stage

New challenges in breeding chickpea under changing climate

Climate change is a continuous natural process leading to evolution of diverse flora and fauna. The variability thus created during process of evolution followed by selection of most fit by nature itself forms primary base for crop improvement programs. However, the industrialization led climate change in the present era has been witnessed in form of abrupt rise or drop in temperature, erratic or uneven and untimely rainfall resulting in floods and drought situations. This is a cause of concern as such changes have direct impact on food production. Since most of the pulse crops including chickpea is sensitive to such climate changes, there is need to define likely effects of climate change on chickpea crop and strategies to mitigate its impact on chickpea production and productivity. Among various abiotic and biotic stresses likely to emerge are deficient or high soil moisture, frequent and untimely rains leading to unseasonal flood like situations during winter season, extreme temperatures during different crop growth stages such as frost during vegetative stage, low or high temperature at reproductive stage leading to flower/pod drop and abrupt rise in temperature during vegetative stage leading to initiation of early flowering followed by sudden drop in temperature leading to flower or pod drop; excessive crop growth due to frequent untimely winter rains, higher incidence of root diseases (collar rot and wet root rot) due to high temperature and high soil moisture at early stage of crop growth, increased incidence of foliar diseases (botrytis gray mould, Ascochyta blight, Alternaria blight, stem rot etc.) due to excessive vegetative growth, and more aggression of weak pathogens causing dry root rot and collar rot are likely to cause huge damage to chickpea crop. Similarly, rise in atmospheric humidity at the time of flowering and podding stage may lead to higher activities of insect pests like gram pod borer, cut worm etc. Among various strategies to combat these challenges, strategies like screening of germplasm accessions to identify donors possessing traits of economic importance, diseases and insect pest resistance, tolerance to temperature extremities (cold and heat stress), frost, high or low soil moisture stress etc. will be of paramount importance. Careful screening of genetic resources (core or mini-core sets) including wild relatives and primitive landraces will become imperative. The mapping and tagging of gene(s) or quantitative trait loci (QTLs) responsible for imparting resistance/tolerance to abiotic and biotic stresses and yield attributes will be desirable for targeted transfer of the required traits. Further, rapid generation advancement and integration of molecular markers in enhancing efficiency of selection methods will ensure desired improvement in chickpea

Pangenomics in microbial and crop research: Progress, applications, and perspectives

Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems

Does improved oleic acid content due to marker-assisted introgression of ahFAD2 mutant alleles in peanuts alter its mineral and vitamin composition?

Peanuts (Arachis hypogaea L.) with high oleic acid content have extended shelf life and several health benefits. Oleic, linoleic, and palmitic acid contents in peanuts are regulated by ahFAD2A and ahFAD2B mutant alleles. In the present study, ahFAD2A and ahFAD2B mutant alleles from SunOleic 95R were introgressed into two popular peanut cultivars, GG-7 and TKG19A, followed by markers-assisted selection (MAS) and backcrossing (MABC). A total of 22 MAS and three MABC derived lines were developed with increased oleic acid (78–80%) compared to those of GG 7 (40%) and TKG 19A (50%). Peanut kernel mineral and vitamin composition remained unchanged, while potassium content was altered in high oleic ingression lines. Two introgression lines, HOMS Nos. 37 and 113 had over 10% higher pooled pod yield than respective best check varieties. More than 70% recurrent parent genome recovery was observed in HOMS-37 and HOMS-113 through recombination breeding. However, the absence of recombination in the vicinity of the target locus resulted in its precise introgression along with ample background genome recovery. Selected introgression lines could be released for commercial cultivation based on potential pod yield and oleic acid content

Genetic resources conservation and strategies for enhanced utilization in crop improvement

Global food production will need to double to feed the more than 9 billion people by 2050..

Regulatory non-coding RNAs: A new frontier in regulation of plant biology

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed

Super Annigeri 1 and improved JG 74: Two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.)

Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76–87% and 90–95% recurrent parent genome recovery, respectively. On the other hand, 90–97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea

Design and fabrication of an intrinsically gain flattened Erbium doped fiber amplifier

We report design and subsequent fabrication of an intrinsically gain flattened Erbium doped fiber amplifier (EDFA) based on a highly asymmetrical and concentric dual-core fiber, inner core of which was only partially doped. Phase-resonant optical coupling between the two cores was so tailored through optimization of its refractive index profile parameters that the longer wavelengths within the C-band experience relatively higher amplification compared to the shorter wavelengths thereby reducing the difference in the well-known tilt in the gains between the shorter and longer wavelength regions. The fabricated EDFA exhibited a median gain ?28 dB (gain excursion below $\pm$2.2 dB within the C-band) when 16 simultaneous standard signal channels were launched by keeping the I/P level for each at ?20 dBm/ channel. Such EDFAs should be attractive for deployment in metro networks, where economics is a premium, because it would cut down the cost on gain flattening filter head

InDel markers: An extended marker resource for molecular breeding in chickpea

Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)

Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety “Asha” (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits