Search

Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51–356 µg ml-1), indole-3 acetic acid (IAA) production (14.3–46.2 µg ml-1), and production of organic acids (72–178 µg ml-1). Inoculation of bacterial consortium (Bacillus subtilis NM-2, Brucella haematophilum NM-4, and Bacillus cereus NM-6) significantly improved seedling growth and vigor index (1009.2-1100) as compared to non-inoculated stressed plants (630-957). Through rhizoscanning, efficiency of the consortium was validated by improved root parameters such as root length (17%), diameter, and surface area (18%) of all tested genotypes as compared with respective non-inoculated stressed treatments. Furthermore, the response of consortium inoculation on three rice genotypes was positively correlated with improved plant growth and drought stress ameliorating traits by the accumulation of osmoprotectant, i.e., proline (85.8%–122%), relative water content (51%), membrane stability index (64%), and production of antioxidant enzymes to reduce oxidative damage by reactive oxygen species. A decrease in temperature and improved chlorophyll content of inoculated plants were found using infrared thermal imaging and soil plant analyzer development (SPAD), respectively. The key supporting role of inoculation toward stress responses was validated using robust techniques like infrared thermal imaging and an infrared gas analyzer. Furthermore, principal component analysis depicts the contribution of inoculation on stress responses and yield of tested rice genotypes under water stress. The integration of drought-tolerant rice genotype (NIBGE-DT02) and potential bacterial strains, i.e., NM-2, NM-4, and NM-6, can serve as an effective bioinoculant to cope with water scarcity under current alarming issues related to food security in fluctuating climate.

Sustainable wheat production in drought prone areas can be achieved by developing resilient wheat varieties. In the present study, chemical mutagenesis was used to induce mutations in a cultivated wheat variety ‘NN-Gandum-1’. In total, 44 mutants were selected based on their high yield potential for exposing to well-watered (W 1) and rainfed (W 2) conditions for one season. Then, 24 mutants were selected and were exposed to W 1 and W 2 regimes. On the basis of least relative reduction in physiological parameters under W 2 regime, five mutants were selected for conducting exome capturing assays. In total, 184 SNPs were identified in nine genes (ABC transporter type 1, aspartic peptidase, cytochrome P450, transmembrane domain, heavy metal-associated domain, HMA, NAC domain, NAD (P)-binding domain, S-type anion channel, Ubiquitin-conjugating enzyme E2 and UDP-glucuronosyl/UDP-glucosyltransferase). Maximum number of mutations were observed in chr.2D, which contained mutations in three genes, i.e. ABC transporter type 1, NAD (P)-binding domain and UDP-glucuronosyl/UDP-glucosyltransferase which may have a role in conferring drought tolerance. The selected mutants were further tested for studying their biochemical responses under both the regimes for 2 years. The extent of membrane damage was estimated through malondialdehyde and hydrogen per oxidase, and tolerance to drought stress was assessed via antioxidant enzymes in leaves. The selected mutants under drought stress increased the accumulation of proline content, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids and total soluble protein. These mutants can further be explored to understand the genetic circuits of drought tolerance in wheat.

Virus-induced gene silencing (VIGS) by deploying viral-based vectors such as tobacco rattle virus (TRV) is a homology-based gene silencing technique in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) to validate the function of particular genes. The study presented here showed the induction of DNA methylation in the promoter regions of three phenotypic marker genes in different cotton accessions, including two endogenous genes such as phytoene desaturase (PDS) and phytoene synthase (PSY), and an exogenous gene, such as green fluorescent protein (GFP). First, DNA methylation was established in transgenic GFP cotton where methylation persisted up to S

Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each generation under disease pressure in a country where the disease is endemic. We utilized quantitative trait loci (QTL) mapping in four crosses with different sources of resistance to identify single nucleotide polymorphism (SNP) markers associated with the resistance trait to allow development of varieties without the need for field screening every generation. To assist in the analysis of multiple populations, a new publicly available R/Shiny App was developed to streamline genetic mapping using SNP arrays and to also provide an easy method to convert and deposit genetic data into the CottonGen database. Results identified several QTL from each cross, indicating possible multiple modes of resistance. Multiple sources of resistance would provide several genetic routes to combat the virus as it evolves over time. Kompetitive allele specific PCR (KASP) markers were developed and validated for a subset of QTL, which can be used in further development of CLCuV-resistant cotton lines.

Exploiting new genetic resources is an effective way to achieve sustainable wheat production. To this end, we exposed wheat seeds of the “Punjab-11” cultivar to gamma rays. A total of 32 stable mutants (M7) were developed, followed by characterization by conducting multilocation trials over two seasons. Principal component analysis (PCA) showed that the first six components accounted for 90.28% of the total variation among the plant height, tillers per plant, 1000-kernel weight, grain yield, and quality traits. All mutants were grouped into three clusters based on high yield index values. The genotype by trait (GT) bi-plot revealed significant associations between yield and its components among the mutants. Positive correlations were estimated for tillers per plant, plant height, 1000-kernel weight, and grain yield, however, yield components showed negative associations with protein, moisture, and gluten contents. The mutant lines Pb-M-59 waxy, Pb-M-1272 waxy, Pb-M-2260, Pb-M-1027 waxy, Pb-M-1323 waxy, and Pb-M-1854 exhibited maximum grain yield, 1000-grain weight, and tillers per plant values. Likewise, Pb-M-2725, Pb-M-2550, and Pb-M-2728 were found to be the best mutant lines in terms of grain quality, thus, the use of gamma radiation is effective in improving the desirable traits, including yield and grain quality. It is suggested that these traits can be improved beyond the performance of corresponding traits in their parent genotypes. The newly produced mutants can also be used to explore the genetic mechanisms of complex traits in the future.

Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants—similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.

Sustainable production and improved genetic gains can be achieved by broadening the genetic window of elite wheat germplasm. Here, we induced mutations in two spring wheat varieties, viz., NN-Gandum-1 (NN-1) and Punjab-11 (Pb-11), by exposing their seeds to ethyl methane sulfonate (EMS) and γ-rays, respectively. We characterized &gt, 3500 lines of each NN-1 and Pb-11 derived population in three consecutive generations, viz., M5, M6, and M7, for important traits, e.g., plant height, heading date, spike morphology and rust resistance. We observed significant genetic variation and correlations in both populations for all investigated traits. We observed differences in terms of number of mutants between NN-1 (22.76%) and Pb-11 (26.18%) which could be ascribed to the genotype-by-mutagen interaction. High broad-sense heritability (H2) estimates, that are vital for higher genetic gains, were observed for all of the investigated traits in both populations (H2 = 0.69–0.91 in NN-1 and 0.84–0.98 in Pb-11). Particularly, to breed for rust resistance, we selected a subset (n = 239) of M7 lines that also showed phenotypic variation for other traits. Our studies (1) show the relevance to artificial mutagenesis to create genetic variation in elite germplasm for their immediate use in current breeding programs, and (2) provide material for downstream identification of genes associated with traits of high agronomic importance.

Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing, derived from prokaryotic immunity system, is rapidly emerging as an alternative platform for introducing targeted alterations in genomes. The CRISPR-based tools have been deployed for several other applications including gene expression studies, detection of mutation patterns in genomes, epigenetic regulation, chromatin imaging, etc. Unlike the traditional genetic engineering approaches, it is simple, cost-effective, and highly specific in inducing genetic variations. Despite its popularity, the technology has limitations such as off-targets, low mutagenesis efficiency, and its dependency on in-vitro regeneration protocols for the recovery of stable plant lines. Several other issues such as persisted CRISPR activity in subsequent generations, the potential for transferring to its wild type population, the risk of reversion of edited version to its original phenotype particularly in cross-pollinated plant species when released into the environment and the scarcity of validated targets have been overlooked. This article briefly highlights these undermined aspects, which may challenge the wider applications of this platform for improving crop genetics.

Improved fiber yield is considered a constant goal of upland cotton (Gossypium hirsutum) breeding worldwide, but the understanding of the genetic basis controlling yield-related traits remains limited. Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information with the development of high-throughput genotyping, phenotyping will be a major challenge for genetic mapping studies. We believe that high-quality phenotyping and appropriate experimental design coupled with new statistical models will accelerate progress in dissecting the genetic architecture of complex traits.

Sustainable wheat production in drought prone areas can be achieved by developing resilient wheat varieties. In the present study, chemical mutagenesis was used to induce mutations in a cultivated wheat variety ‘NN-Gandum-1’. In total, 44 mutants were selected based on their high yield potential for exposing to well-watered (W1) and rainfed (W2) conditions for one season. Then 24 mutants were selected, and were exposed to W1 and W2 regimes. On the basis of least relative reduction in physiological parameters under W2 regime, five mutants were selected for conducting exome capturing assays. In total, 184 SNPs were identified in nine genes (ABC transporter type 1, Aspartic peptidase, Cytochrome P450, transmembrane domain, Heavy metal-associated domain, HMA, NAC domain, NAD (P)-binding domain, S-type anion channel, Ubiquitin-conjugating enzyme E2 and UDP-glucuronosyl/UDP-glucosyltransferase). Maximum number of mutations were observed in chr.2D, which contained mutations in three genes i.e. ABC transporter type 1, NAD (P)-binding domain and UDP-glucuronosyl/UDP-glucosyltransferase which may have a role in conferring drought tolerance. The selected mutants were further tested for studying their biochemical responses under both the regimes for two years. The extent of membrane damage was estimated through malondialdehydeand hydrogen per oxidase and tolerance to drought stress was assessed via antioxidant enzymes in leaves. The selected mutants under drought stress increased the accumulation of proline content, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids and total soluble protein. Finally, the procedure of narrowing down the number of developed mutants from a large mutation population (>4000) is found useful for exploring the complex trait like drought without compromising yield potential. These mutants can further be explored to understand the genetic circuits of drought tolerance in wheat which will pave the way towards improving livelihood of resource poor farming community mostly relying on cereal food.

Traditional breeding has made significant progress toward improving cotton adaptation in prevailing environments for increased yield and quality. The conventional breeding systems are handicapped owing to lengthy breeding process, random insertion of genes, and phenotype-based selections which are often misleading. Recently developed CRISPR/Cas9 genome editing technology opens a new era for acquiring precision cotton breeding. CRISPR/Cas9 is a naturally occurred genome editing tool adopted from prokaryotic adoptive immune defense system. Due to its simplicity and robustness, CRISPR/Cas9 has been quickly adopted to use in multiple fields, including gene function study and precise breeding. Since it was adopted in cotton for the first time in 2017, in which Li and colleagues edited an endogenous functional gene MYB-15 like in cotton, CRISPR/Cas9 has been quickly adopted by several cotton research laboratories and biotechnological industries worldwide. Currently, CRISPR/Cas9 has been widely used to study gene function and cotton improvement, including fiber development, resistance to abiotic and biotic stress, modification of cotton morphology, and secondary metabolism. In the next decade, CRISPR/Cas9-based precise breeding will significantly enhance cotton breeding and production.

Cotton is an important natural fiber crop and is known as “white gold” due to its economic importance. Its seed is also a source of oil, proteins, and feed for the livestock. Sustaining cotton production has been a major challenge owing to the multitude of biotic and abiotic stresses. Among these, the infestation of insect pests and diseases are the most devastating yield depressing factors. Keeping insect population under control heavily relies on the application of chemicals (pesticides) which may raise serious environmental concerns. Production of insecticidal proteins in the cotton plants through different genetic means opened a new era of insect-pest management. On the basis of number of transgenes introduced, three different generations of the Bt-cotton (cotton expressing genes coding for different insect toxins from the soil bacterium Bacillus thuringiensis) have been developed. The first generation of Bt cotton carried a single Bt gene, while the second- and third-generation Bt cottons contained double and triple genes for a better control over lepidopteran insects. In addition to Bt genes, genes conferring tolerance to different herbicides have also been introduced in cotton for controling weeds more effectively. Cultivation of Bt cotton has been instrumental in controlling bollworms; however, the emergence of resistance in insects against the Bt toxins has been reported in few regions worldwide. In this chapter, current state of the art knowledge on transgenic cotton including generations of Bt cotton, mechanism of action, risk assessment, and prospects has been discussed.

Cotton plant achieved two remarkable milestones recently. It was the first ever plant grown on lunar surface in 2019. Secondly, construction of high-quality contagious genome assemblies of tetraploid cultivated cottons in 2019 and then five tetraploids in 2020 remained instrumental in elucidating the evolution and adaptation and redesigning the genetic circuits of high-quality fiber as well as other agronomic traits. The generated information can be utilized for the identification of DNA markers associated with desirable traits as well as designing new genome editing experiments for altering the expression of genes. These findings will be instrumental in transforming the current trajectory of developing cotton varieties into precision breeding for achieving sustained enhanced cotton production in the future.

Like many other crops, cultivated cotton species specifically tetraploids are vulnerable to changing environmental conditions. These environmental adversities synergistically act with the prevailing stresses such as drought, salinity, water logging, and excessive heat, thus depressing the cotton yield by 50% and deteriorating lint quality substantially. Genetics of tolerance to these stresses is largely complex, making selections of tolerant cotton plants in early generation fairly difficult for the breeders. The emerging selection procedures particularly deployment of DNA markers or genomic selection may help to select cotton plants with true-to-type resilient genetics. Genome-wide association studies (GWAS) complemented by resequencing of cotton germplasm led to the discovery of SNPs associated with tolerance to abiotic stresses. Till now, about 30 QTLs linked with drought tolerance and yield and 66 QTLs for salt tolerance have been discovered. In the future, resequencing of cotton germplasm (>1000 accessions) would lead to the discovery of new SNPs for establishing high-density SNP arrays—will strengthen the capabilities of warranting precision breeding in cotton, a way to develop climate-smart cotton cultivars.

Genetically modified (GM) cotton is one of the three biotech crops which together occupy ~95% of the total area on which GM crops are currently grown. Being a nonfood crop, GM cotton is also cultivated in those countries which have a strict policy for the cultivation of GM crops. Cotton, therefore, has been the target of various genetic improvement programs such as insect resistance, biotic and abiotic stress tolerance traits, herbicide tolerance, and reduction of antinutrient contents such as gossypol, expressing different genes conferring these traits or sometimes stacked with other traits. As a result, different classes of GM cotton have been evolved, which can be referred to as first, second, and third. In this chapter, we will briefly discuss these generations of the GM cotton and provide our point of view for future engineering of GM traits in cotton.

Development of naturally colored cotton varieties has remained one of the major breeding objectives which will help in avoiding the use of dyes and chemicals for providing color to lint. In genetic stocks, only green- and brown-colored producing lint genotypes are available, thus restricting the development of naturally colored cotton related textile market. Further, little information about the inheritance and development of lint color formation as well as its association with fiber quality is the main obstacle in availability of elite naturally colored cotton germplasm. In this chapter, information regarding the inheritance of fiber color and its quality and the course of fiber color development are elaborated. In silico analyses have unraveled the structural difference, chromosomal location, and expression of genes related to flavonoid biosynthesis pathways in colored cotton. These genes are nonrandomly distributed in all chromosomes with a greater number of genes found in the At sub-genome. Gene structure revealed that closely related genes are similar in length and number of exon and intron, like all genes in PAL family having one intron. Expression analysis indicated that 24 genes are downregulated in both colored and white cotton fiber and generated separate group in heat map. In addition to this, it is concluded that the role of major flavonoid biosynthesis-related pathway genes GhC4H, GhCHS, GhCHI, GhF3H, GhDFR, and GhANR cannot be neglected to engineer different fiber colors. The generated information can be used to initiate precision breeding for introducing colored lint genes and/or inserting mutations in these genes using CRISPR-Cas in cultivated cotton species.

Rice, a staple cereal crop in many parts of the world, has been confronted with multiple environmental stresses including high temperature, negatively impacts the booting as well as anthesis growth stages. The situation is further complicated by the changing climatic conditions, resulting in gradual escalation of temperature as well as changing the rainfall pattern and frequency, thus raising a concern of food security worldwide. The situation can be combat by developing rice varieties with excellent genetics with improved morpho-physiological, biochemical, and molecular mechanisms, together can minimize the adverse effects of heat stress. Here, several strategies (encompassing genetic and genomic, and mechanisms involved) for mitigating the impact of high temperature on rice have been discussed. Finally, the utilization of genomic knowledge in augmenting the conventional breeding approaches have been comprehensively elaborated to develop heat tolerant germplasm.