Whole-Genome Sequencing of Pigeonpea: Requirement, Background History, Current Status and Future Prospects for Crop Improvement

Despite of being a very important crop, pigeonpea did not have genomic resources until 2005. Pigeonpea Genomics Initiative (PGI) supported by Indian Council of Agricultural Research (ICAR) under Indo-US Agriculture Knowledge Initiative was the first major initiative that delivered first set of molecular markers in large numbers, first set of mapping populations, first set of transcriptome assemblies, etc. Subsequently, two consortia—1) International Initiative for Pigeonpea Genomics (IIPG), led by International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and 2) Led by National Research Centre on Plant Biotechnology (NRCPB)—delivered two draft genome assemblies for Asha (ICPL 87119) variety. In summary, all these genomic resources transformed pigeonpea from an ‘orphan crop’ to ‘genomics resources-rich crop’. After publication of draft genome sequences, a detailed plan was developed to utilize draft genome information for pigeonpea improvement. This plan in the form of a proposal was approved by Ministry of Agriculture, Government of India and United States Agency for International Development (USAID)—India. In addition to this major project, two additional projects were funded by Department of Biotechnology, Government of India. All these efforts have established high-density genotyping platforms such as genotyping by sequencing (GBS) and ​‘Axiom® CajanusSNP Array’, produced the first generation HapMap, generated whole-genome re-sequencing data of >400 pigeonpea lines, evaluated several mapping populations for desired traits, established marker–trait association for several traits of interest to breeders and also identified best-performing lines. Additionally, multi-parent advance generation inter-cross (MAGIC) and nested association mapping (NAM) populations are being developed. With the availability of above-mentioned information, next few years will be witnessing application of genomics-assisted breeding for pigeonpea improvement. It is anticipated that improved pigeonpea lines developed through genomics interventions will reach to farmers’ fields and elevate the game towards pulse sufficiency for poor farmers in arid and semi-arid regions of the world in near future

Modern Genomic Tools for Pigeonpea Improvement: Status and Prospects

Pigeonpea owing to its ability to sustain harsh environment and limited input/water requirement remains an excellent remunerative crop in the face of increasing climatic adversities. With nearly 70% share in global pigeonpea production, India is the leading pigeonpea producing country. Since the mid-1900s, constant research efforts directed to improve yield and resistance levels of pigeonpea have resulted in the development and deployment of several commercially accepted cultivars in India, accommodating into diverse agro-climatic zones. However, the crop productivity needs incremental improvements in order to meet the growing nutritional demands, especially in developing countries like India where pigeonpea forms a dominant part of vegetarian diet. Empowering crop improvement strategies with genomic tool kit is imperative to attain the project gains in crop yield. In the context, adoption of next-generation sequencing (NGS) technology has helped establish a wide range of genomic resources to support pigeonpea breeding, and the existing molecular tool kit includes genome-wide genetic markers, transcriptome/genome assemblies, and candidate genes/QTLs for target traits. Similarly, availability of whole mitochondrial genome sequence and derived DNA markers is immensely relevant in order to furthering the understanding of cytoplasmic male sterility (CMS) system and hybrid breeding. This chapter covers the progress of developing modern genomic resources in pigeonpea and highlights their vital role in designing future crop breeding schemes

Influence of hydride orientation on fracture toughness of CWSR Zr-2.5%Nb pressure tube material between RT and 300 degrees C

An experimental setup was designed, fabricated and used to form radial hydrides in Zr-2.5%Nb alloy pressure tube spool. The design of setup was based on ensuring a hoop stress in the spool greater than threshold stress for reorientation of hydrides in this alloy, which was achieved by manipulating the thermal expansion coefficient of the plunger and pressure tube material and diametral interference between them. The experimental setup was loaded on a universal testing machine (UTM) fitted with an environmental chamber and subjected to a temperature cycle for the stress reorientation treatment. The metallographic examination of the hydrogen charged spools subjected to stress re-orientation treatment using this set up revealed formation of predominantly radial hydrides. The variation of fracture toughness of material containing radial hydride with test temperature showed typical 'S' curve behavior with transition temperatures more than that of the material containing circumferential hydride. (C) 2017 Elsevier B.V. All rights reserved

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Not AvailableCarvacrol is a herbal antimicrobial agent with in vitro activity against several bacterial pathogens. However, multidrug resistant strains of Pseudomonas aeruginosa are resistant to herbal antimicrobial compounds including carvacrol. Resistance of P. aeruginosa to carvacrol is not well studied. This study was aimed to identify the gene(s) associated with carvacrol resistance, thus to understand its mechanisms in P. aeruginosa. A herbal drug resistant strain was isolated from a hospital environment. Carvacrol sensitive mutant was generated using transposon mutagenesis. The inactivated gene in the mutant was identified as mexA, which is part of the mexAB-oprM operon. Inactivation of the mexA gene resulted in a >31-fold reduction in MIC of carvacrol, whereas a >80-fold reduction was observed in the presence of drug efflux inhibitor phenylalanine-arginine β-naphthylamide (PAβN). The parental herbal-resistant strain was completely killed within 3 h of incubation in the presence of carvacrol and PAβN. The mexA inactivation did not affect the resistance to other herbal compounds used. The results demonstrate that resistance to carvacrol in P. aeruginosa is mediated by the MexAB-OprM efflux pump.Not Availabl

Molecular Mapping of Genes and QTLs in Pigeonpea

Pigeonpea is one of the most important grain legume crops grown in arid and semiarid regions of the world. There is an increasing demand for the development of new cultivars with high yield potential and better adaptability to adverse environmental conditions. Recent advances in genomics tools and techniques have helped to develop large repertoire of molecular markers and genotypic platforms. The availability of molecular markers facilitated the development of high-density genetic maps that have been used in discovery of important/major QTLs for targeted traits in pigeonpea. In addition, the availability of high-throughput genotypic platforms helped to generate whole genome genotypic data in high-throughput manner necessary for whole genome scanning/genome-wide association mapping of economically important traits. The advances in comparative genomics, transcriptomics, and whole genome sequencing have uncovered thousands of useful genes including some genes unique to pigeonpea crop. The availability of wealth of genomics resources/information will facilitate molecular breeding aimed at improving production and productivity of pigeonpea in extreme environments of arid and semiarid regions of the world

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Not AvailableBackground In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.Not Availabl