Translational genomics for improving dryland crops

Although crop improvement programs have made excellent progress in enhancing crop productivity and production, there is still a huge scope to fill the yield gap for majority of crops in dryland areas. Genomics-assisted breeding can help enhancing crop productivity as well as nutrition in these crops. However, until recently, majority of the dryland crops have remained untouched with genomics revolution. Two key reasons for this situation include engagement of only few institutes and availability of limited resources at international level for research and development in these crops. With an objective to address these issues, the Center of Excellence in Genomics and Systems Biology (CEGSB) at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) floated several multi-institutional consortia. As a result of collaborative efforts from such strong partnership, a large number of genomic resources including genome assemblies for 9 crops have been developed and several improved lines have been developed through molecular breeding. In summary, translational genomics approach has transformed the so-called ‘orphan crops’ to ‘genomic resources-rich crops’ and contributed to develop several improved lines in some dryland crops

Seven seasons of learning and engaging smallholder farmers in the drought-prone areas of sub-Saharan Africa and South Asia through Tropical Legumes, 2007–2014

Tropical Legumes II (TL II) is a Bill & Melinda Gates Foundation sponsored project implemented by three International Agricultural Research Centers – International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), International Centre for Tropical Agriculture (CIAT) and International Institute for Tropical Agriculture (IITA). The project aims to improve the livelihoods of smallholder farmers in the drought-prone areas of Sub-Saharan Africa (SSA) and South Asia (SA) through improved productivity and production of six major grain legumes – chickpea, common bean, cowpea, groundnut, pigeonpea and soybean. The project activities were implemented in Burkina Faso, Ghana, Mali, Niger, Nigeria, Senegal, Ethiopia, Kenya, Malawi, Mozambique, Tanzania, Uganda and Zimbabwe in SSA, and India and Bangladesh in SA. The project has been running for the past two phases: Phase I (2007 – 2011) and Phase II (2012 – 2014). The project is designed to help the smallholder farmers to overcome constraints, such as drought, pests, diseases and lack of improved seed varieties. TL II is expected to enhance the productivity by at least 20% through increased adoption covering 30% of legume area, strengthening national breeding programs and generating at least $1.3 billion in added value. This has resulted in significant achievements. The active breeding programs are now in place in all 15 countries. New seed varieties (163) have been released and are fast replacing the old ruling seed varieties. Thirty seven national partners were trained at MSc and PhD levels. As a result of the enhanced skills and knowledge of seed value chain actors, seed production significantly increased by 221$448 million has been generated from the project funding and nearly $976 million from the project and investment partners. Even when using the adoption rates data from adoption and expert opinion surveys, the aggregate gross benefits from TL II-related modern legume varieties is estimated at about$978 million, which is still far above the total TL II investment grossly compounded at $48 million. In effect, for each dollar invested, the project generated$9 with direct project investment or $20 with partnership’s investment and again$20 when using adoption rate based estimate. These successes and associated challenges will be discussed in detail in subsequent chapters of this book

Analysis of Small RNA Sequencing Data in Plants

Over the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies

Genomic resources in chickpea

Chickpea has considerably increased the genomic resources in recent years providing highly saturated genetic maps including anonymous or gene-specific markers targeting some agronomic traits of interest. In addition, the publication of the two draft genome sequences of Kabuli and Desi chickpea types opens a new era in genomic tools. Furthering in our understanding of the association between phenotypic traits (Quantitative Trait loci-QTL-or genes) with the transcriptome and gene annotation provided by genome sequencing data will be the future challenge to be able to exploit with success marker-assisted Selection(MAS)

Harvesting the promising fruits of genomics: Applying genome sequencing technologies to crop breeding

Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population

Improving crop performance under drought - cross-fertilization of disciplines

Better crop performance in dry environments is imperative for food security in the face of climate change. This has never been as true as in 2017, but the concern has existed for decades. The four InterDrought conferences held since 1995 have addressed issues associated with crop performance under drought with a clear multi-disciplinary approach. During this time Journal of Experimental Botany has been at the forefront in publishing the underlying experimental science encompassing the disciplines and scales of organization required in drought research. We hope that the papers highlighted here will be useful to, and instrumental for, broadening interdisciplinary understanding of drought tolerance

Progress in understanding drought tolerance: From alleles to cropping systems

Improving crop yields under rainfed environments is key to meeting the food security demands of an everincreasing population, but climate change-associated expansion of drought-affected arable land means that resilient crops and agronomic practices are critical. High-throughput plant phenomics and modern genetic approaches must be directed towards precise understanding of factors controlling crop yield. This special issue covers root dynamics, turgor management under desiccation, molecular responses to dehydration, impact of drought on plant development and seed abortion, and adjustment of traits to the most frequent patterns of drought. It also addresses interdisciplinary views for enhancing genetic gains and achieving a more sustainable climate-resilient agronomy

Strategies for pigeonpea improvement

In order to feed an ever-increasing population, it is essential to deal yield reducing factors. Climate smart crop varieties that yield more with fewer inputs will be required to achieve the success. In this scenario pigeonpea plays an important role as it can stand in relatively harsh environmental conditions. Hybrid breeding along with the pure line breeding, genetic resources and genomics advances are enriching this crop. However, the pigeonpea improvement program must be re-oriented in order to deal with the yield-reducing factors and to break the yield plateau

Carp seed production during drought year 1987 under controlled hatchery system

The introduction of the controlled hatchery system "Model CIFE D-81" resulted in a production of 60 lakhs Indian major carp seed in the drought area of eastern Uttar Pradesh. The hatchery system provided optimum temperature, dissolved oxygen and pH for breeding and hatching and also removed the metabolites generated. The technology is simple and the success of the program attracts pisciculturists

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