Uday C. Jha

Bio: Uday C. Jha is an academic researcher from Indian Institute of Pulses Research. The author has contributed to research in topics: Abiotic component & Molecular breeding. The author has an hindex of 3, co-authored 7 publications receiving 272 citations.

Cytoplasmic male sterility (CMS) in hybrid breeding in field crops

Abstract: A comprehensive understanding of CMS/Rf system enabled by modern omics tools and technologies considerably improves our ability to harness hybrid technology for enhancing the productivity of field crops. Harnessing hybrid vigor or heterosis is a promising approach to tackle the current challenge of sustaining enhanced yield gains of field crops. In the context, cytoplasmic male sterility (CMS) owing to its heritable nature to manifest non-functional male gametophyte remains a cost-effective system to promote efficient hybrid seed production. The phenomenon of CMS stems from a complex interplay between maternally-inherited (mitochondrion) and bi-parental (nucleus) genomic elements. In recent years, attempts aimed to comprehend the sterility-inducing factors (orfs) and corresponding fertility determinants (Rf) in plants have greatly increased our access to candidate genomic segments and the cloned genes. To this end, novel insights obtained by applying state-of-the-art omics platforms have substantially enriched our understanding of cytoplasmic-nuclear communication. Concomitantly, molecular tools including DNA markers have been implicated in crop hybrid breeding in order to greatly expedite the progress. Here, we review the status of diverse sterility-inducing cytoplasms and associated Rf factors reported across different field crops along with exploring opportunities for integrating modern omics tools with CMS-based hybrid breeding.

Genomics‑assisted breeding in four major pulse crops of developing countries: present status and prospects

Abstract: Key message Given recent advances in pulse molecu‑ lar biology, genomics‑driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops. Abstract The global population is continuously increas- ing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situa- tion is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutri- ent deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood genera- tion for millions of resource-poor farmers practising agri- culture in the semi-arid and sub-tropical regions. Limited

Abiotic stresses, constraints and improvement strategies in chickpea

Abstract: Chickpea (Cicer arietinum L.) is cultivated mostly in the arid and semi-arid regions of the world. Climate change will bring new production scenarios as the entire growing area in Indo–Pak subcontinent, major producing area of chickpea, is expected to undergo ecological change, warranting strategic planning for crop breeding and husbandry. Conventional breeding has produced several high-yielding chickpea genotypes without exploiting its potential yield owing to a number of constraints. Among these, abiotic stresses include drought, salinity, water logging, high temperature and chilling frequently limit growth and productivity of chickpea. The genetic complexity of these abiotic stresses and lack of proper screening techniques and phenotyping techniques and genotype-by-environment interaction have further jeopardized the breeding programme of chickpea. Therefore, considering all dispiriting aspects of abiotic stresses, the scientists have to understand the knowledge gap involving the physiological, biochemical and molecular complex network of abiotic stresses mechanism. Above all emerging ‘omics’ approaches will lead the breeders to mine the ‘treasuring genes’ from wild donors and tailor a genotype harbouring ‘climate resilient’ genes to mitigate the challenges in chickpea production.

Breeding and Genomics Approaches for Improving Productivity Gains in Chickpea Under Changing Climate

Abstract: Chickpea is a well-recognized global grain legume that plays an important role for providing plant-based protein security to global human population. Given the rising uncertainties in global climate coupled with growing occurrence of various pests and diseases and a range of abiotic stresses, global chickpea production is seriously challenged. Therefore, conventional breeding approaches are not adequate to meet the rising demand for chickpea. Evolving genomic technologies have yielded considerable success in accelerating molecular breeding program in various crops. To this end, unprecedented advances in genome sequencing technologies facilitated largely by next-generation sequencing (NGS) technologies have allowed decoding of whole genome sequences of both cultivated and wild species of chickpea. These developments have opened up great opportunity to improve the efficiency of chickpea breeding programs through deployment of large-scale genomic tools. Efforts are underway to re-sequence multiple genomes for identifying new haplotypes of traits of breeding importance in the crop from wider germplasm resources such as the core collection and reference sets. Taken together, these massive genomic resources including the high-density genotyping assays have allowed chickpea breeders to embrace modern breeding techniques like genomic selection (GS) for enhancing genetic gain. This chapter focuses on the genomics-assisted improvement of chickpea, with an emphasis on the traits that impart resilience to changing climate. In addition to genomics, we highlight progress and possibilities of transgenic research for improving tolerance against biotic and abiotic stress resistance in chickpea. Moreover, the introduction of novel breeding schemes such as “speed breeding”, CRISPR/Cas9-based genome editing holds great promise for accelerating the genetic gains projected to meet the ever-increasing demand for plant-based proteins.

Mapping QTL for important seed traits in an interspecific F2 population of pigeonpea

Abstract: Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus scarabaeoides (L.) Thouars acc. ICP 15739 and an F2 population derived from this interspecific cross. Maximum phenotypic values recorded for the F2 population were higher than observed in the parent ICPL 20340 [F2 max vs ICPL 20340: SW (7.05 vs 5.38), ST (4.63 vs 4.51), EC (65.17 vs 9.72), WU (213.17 vs 109.5)], which suggested contribution of positive alleles from the wild parent, ICP 15739. Concurrently, to identify the QTL controlling these seed traits, we assayed two parents and 94 F2 individuals with 113 polymorphic simple sequence repeat (SSR) markers. In the F2 population, 98 of the 113 SSRs showed Mendelian segregation ratio 1:2:1, whereas significant deviations were observed for 15 SSRs with their χ2 values ranging between 6.26 and 20.62. A partial genetic linkage map comprising 83 SSR loci was constructed. QTL analysis identified 15 marker-trait associations (MTAs) for seed traits on four linkage groups i.e. LG01, LG02, LG04 and LG05. Phenotypic variations (PVs) explained by these QTL ranged from 4.4 (WU) to 19.91% (EC). These genomic regions contributing significantly towards observed variability of seed traits would serve as potential candidates for future research that aims to improve seed traits in pigeonpea.

Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions

Abstract: Increasing vulnerability of plants to a variety of stresses such as drought, salt and extreme temperatures poses a global threat to sustained growth and productivity of major crops. Of these stresses, drought represents a considerable threat to plant growth and development. In view of this, developing staple food cultivars with improved drought tolerance emerges as the most sustainable solution towards improving crop productivity in a scenario of climate change. In parallel, unraveling the genetic architecture and the targeted identification of molecular networks using modern “OMICS” analyses, that can underpin drought tolerance mechanisms, is urgently required. Importantly, integrated studies intending to elucidate complex mechanisms can bridge the gap existing in our current knowledge about drought stress tolerance in plants. It is now well established that drought tolerance is regulated by several genes, including transcription factors (TFs) that enable plants to withstand unfavorable conditions, and these remain potential genomic candidates for their wide application in crop breeding. These TFs represent the key molecular switches orchestrating the regulation of plant developmental processes in response to a variety of stresses. The current review aims to offer a deeper understanding of TFs engaged in regulating plant’s response under drought stress and to devise potential strategies to improve plant tolerance against drought.

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

Abstract: Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gain is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last five years. The availability of draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seem appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.