International Crops Research Institute for the Semi-Arid Tropics
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Potential environmental and human health implications of nanomaterials used in sustainable agriculture and soil improvement
No full textAgriculture is an important component of the ecosystem, and every human being is directly or indirectly associated with it. The use of tools and technology in agriculture has improved over time and has also contributed to increasing food production. However, the bulge in a global population at a frightening rate and the yield plateau in most of the crops has added more concern to the subject. Nanomaterials might play a remarkable role in breaking the yield plateau and have proved to be significant in enhancing the shelf life of processed foods. Although the history of nanotechnological interventions can be traced back to the previous few decades, the employment of nanomaterials is still restricted in agricultural systems. The research in the field of agricultural nanotechnology is growing at a very faster pace, but there still exists a significant difference in the research and its practical applications. A plethora of reports are available that claim the several beneficial effects of introducing nanomaterials in agroecosystems; however, several few reports have also warned about their postapplication effects in the soil, human, and environment. This provokes a dire need for evaluation of interactions existing between nanomaterials concerning soil, plants, soil microflora, and the environment before their field applications. The present chapter, therefore, highlights the fate, advantages, and issues related to nanomaterials and their interaction with the components of agroecosystems
Receptor-like kinases induced by abscisic acid in plants
No full textReceptors are core elements of every biochemical signaling. It is the starting point from where signal transduction comes into action inside the cell. Receptor-like kinases (RLKs) are either membrane-localized or cytosolic receptors, having a characteristic kinase catalytic activity. They function to transduce information from extracellular stimuli or elicitors to the nucleus of plant cells, eventually activating specific genes responsible for plant growth, development, and stress tolerance, depending on the type of signal received. Abscisic acid (ABA), a phytohormone, regulates plant growth by modulating reproductive and vegetative growth, seed maturation, and development. Apart from normal physiological functions, ABA enables the plant to tolerate abiotic stress by accelerating stress tolerance responses. ABA also acts as an inducer for several RLKs indicating the potential role of RLKs in stress signaling pathways and responses. ABA induces RLKs for modulating various types of physiological roles via diverse signaling routes
Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9
Get PDFCRISPR-mediated genome editing has become a powerful tool for the genetic modification of biological traits. However, developing an efficient, site-specific, gene knock-in system based on homology-directed DNA repair (HDR) remains a significant challenge in plants, especially in woody species like poplar. Here, we show that simultaneous inhibition of non-homologous end joining (NHEJ) recombination cofactor XRCC4 and overexpression of HDR enhancer factors CtIP and MRE11 can improve HDR efficiency for gene knock-in. Using this approach, the BleoR gene was integrated onto the 3′ end of the MKK2 MAP kinase gene to generate a BleoR-MKK2 fusion protein. Based on fully edited nucleotides evaluated by TaqMan real-time PCR, the HDR-mediated knock-in efficiency was up to 48% when using XRCC4 silencing incorporated with a combination of CtIP and MRE11 overexpression compared with no HDR enhancement or NHEJ silencing. Furthermore, this combination of HDR enhancer overexpression and NHEJ repression also increased genome targeting efficiency and gave 7-fold fewer CRISPR-induced insertions and deletions (InDels), resulting in no functional effects on MKK2-based salt stress responses in poplar. Therefore, this approach may be useful not only in poplar and plants or crops but also in mammals for improving CRISPR-mediated gene knock-in efficiency
Cytogenetics to functional genomics: six decades journey of Professor P.K. Gupta
Get PDFWe had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome-wide association mapping and molecular breeding including marker-assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium, interspecific/intergeneric relationships involving the genus Hordeum and re-examining taxonomy of the tribe Triticeae
QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
Get PDFTo identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement
Genome-wide association mapping for identification of sheath blight resistance loci from wild rice Oryza rufipogon
Get PDFSheath blight (ShB) caused by Rhizoctonia solani is one of the serious constraints that hamper global rice production. It causes severe yield loss of up to 69% under favorable environmental conditions. The application of chemical fungicides remains the primary approach for the management of this disease. But, overuse of chemical fungicides causes potential health and environmental risk. The use of host plant resistance is a very effective, economic, and sustainable strategy to control sheath blight disease in rice. In this report, we have evaluated 405 accessions of Oryza rufipogon for four ShB-related traits i.e. lesion height (LH), plant height (PH), relative lesion length (RLH), and disease score (DS) during the years 2015, 2016, and 2017. A total of 44,109 high-quality SNP markers on 301 accessions were employed to identify significant marker-trait associations using a genome-wide association study (GWAS). The GWAS analysis revealed a total of 22 significant SNPs associated with the ShB-related traits distributed on all the rice chromosomes except 10 and 12. Among them, eleven were associated with RLH, seven with PH, and one each with LH and DS. The SNPs on chromosomes 3 and 9 were associated with multiple traits. Furthermore, seven ShB resistance loci were also found to be co-localized with previously reported ShB resistance genes/QTLs. These findings provide valuable information to identify key SNPs associated with ShB resistance. Significantly associated SNPs could be used for introgression of ShB resistance traits into rice cultivars using marker-assisted selection
Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes
Get PDFLivestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL
Validity and validation in archetype analysis: practical assessment framework and guidelines
Get PDFArchetype analysis is a promising approach in sustainability science to identify patterns and explain mechanisms shaping the sustainability of social-ecological systems. Although considerable efforts have been devoted to developing quality standards and methodological advances for archetype analysis, archetype validation remains a major challenge. Drawing on the insights from two international workshops on archetype analysis and on broader literature on validity, we propose a framework that identifies and describes six dimensions of validity: conceptual; construct; internal; external; empirical; and application validity. We first discuss the six dimensions in relation to different methodological approaches and purposes of archetype analysis. We then present an operational use of the framework for researchers to assess the validity of archetype analysis and to support sound archetype identification and policy-relevant applications. Finally, we apply our assessment to 18 published archetype analyses, which we use to describe the challenges and insights in validating the different dimensions and suggest ways to holistically improve the validity of identified archetypes. With this, we contribute to more rigorous archetype analyses, helping to develop the potential of the approach for guiding sustainability solutions
Phenotyping RIL Population to Identify Water Deficit Tolerant Lines in Groundnut (Arachis hypogaea L.)
Get PDFBackground: Genotype sensitivity to mid-season drought suggests the possibility of identifying genotypes with high yield potential and low sensitivity to mid-season droughts. The overall objective of the present research was to select genotypes with high tolerance to mid-season moisture stress. This effort includes assessing the variation of physiological and productive traits among RIL population lines, assessing the range of correlation for physiological and productive traits across two seasons and identifying a set of contrasting material under drought stress conditions.
Methods: To assess the recombinant inbred lines (RIL) under moisture stress, we screened RIL population of groundnut with 432 lines and parents under mid-season drought stress conditions in rabi for two years. During the drought stress period, soil moisture content (SMC) and temperatures were measured. SPAD chlorophyll meter reading (SCMR), specific leaf area (SLA), relative water content (RWC), visual wilting rate (VWR) and canopy temperature (CT) were recorded at the end of the stress period. Pod yield per plant (PYPP), kernel yield per plant (KYPP) and shelling percent (SP) were recorded at harvest.
Result: Physiological traits and yield attributes varied significantly among the RIL population. The Genotype by Trait biplot (GT biplot) revealed that the yield attributes showed a positive association with RWC, SCMR and a negative association with SLA, VWR and CT. The inbred lines were classified as visually healthy with high physiological and high or moderate yield traits; visually wilting with low physiological and low yield traits under a drought environment. The identified superior and inferior lines werefurther utilized to analyze genomic regions and genes for drought tolerance in groundnut
Integrated analysis of carotenoid metabolites and transcriptome identifies key genes controlling carotenoid compositions and content in sweetpotato tuberous roots (Ipomoea batatas L.)
Get PDFSweetpotato (Ipomoea batatas L.) with different depths of yellow color contains different compositions of carotenoids, which are beneficial for human health. In this study, we performed an integrated analysis of metabolomic and transcriptomic to identify key genes playing a major role in carotenoid coloration in sweetpotato tuberous roots. Herein, 14 carotenoids were identified in five sweetpotatoes. Orange-red and orange cultivars were dominated by β-carotene (385.33 μg/g and 85.07 μg/g), yellow cultivar had a high β-cryptoxanthin (11.23 μg/g), light-yellow cultivar was rich in zeaxanthin (5.12 μg/g), whereas lutein (3.34 μg/g) was the main carotenoid in white cultivar. Furthermore, 27 differentially expressed genes involved in carotenoid metabolism were identified based on comparative transcriptome. Weighted gene co-expression network analysis identified 15 transcription factors highly associated with carotenoid content in sweetpotatoes. These results provide valuable information for revealing the regulatory mechanism of carotenoid metabolism in different-colored sweetpotato tuberous roots