Abiotic stress enhancement tools for improving crop tolerance

Abiotic stresses create an unfavourable environment for plant growth, increasing the possibilities of low yield and associated economic loss. Several steps have been taken to address this problem. During the last twenty years, techniques of genetic engineering/transgenic breeding have made significant advances in gene manipulation for inciting desirable traits in transgenic plants. Transgenic techniques allow us to identify potential genes, transcription factors (TFs) and miRNAs, engaged in certain processes in plants, allowing us to gain a comprehensive understanding of the processes at molecular and physiological levels which determine plant resilience and production. The reliability and specificity of this approach ensure that future plant enhancements will be a huge success. As a result, transgenic breeding has determined to be a viable strategy in improving crop abiotic stress tolerance. The approach of CRISPR/Cas gene-editing technique to create stress-tolerant plant variants is gaining popularity right now. The researchers like this user-friendly technology because of its versatility. In the gene-editing process, the DNA sequence "CRISPR" and the endonuclease "Cas" collaborate under the supervision of specific guide RNA. In a variety of plant species, the CRISPR/Cas system is being utilized. In the majority of situations, Cas9 is employed. Various reports have surfaced which demonstrate the utilization of CRISPR/Cas9 technology to improve abiotic stress tolerance of plants. The focus of this review is on the promising and effective applications of transgenic plant breeding for enhancing environmental stress tolerance and crop productivity, as well as its recent developments

Melatonin Induced Cold Tolerance in Plants: Physiological and Molecular Responses

Cold stress is one of the most limiting factors for plant growth and development. Cold stress adversely affects plant physiology, molecular and biochemical processes by determining oxidative stress, poor nutrient and water uptake, disorganization of cellular membranes and reduced photosynthetic efficiency. Therefore, to recover impaired plant functions under cold stress, the application of bio-stimulants can be considered a suitable approach. Melatonin (MT) is a critical bio-stimulant that has often shown to enhance plant performance under cold stress. Melatonin application improved plant growth and tolerance to cold stress by maintaining membrane integrity, plant water content, stomatal opening, photosynthetic efficiency, nutrient and water uptake, redox homeostasis, accumulation of osmolytes, hormones and secondary metabolites, and the scavenging of reactive oxygen species (ROS) through improved antioxidant activities and increase in expression of stress-responsive genes. Thus, it is essential to understand the mechanisms of MT induced cold tolerance and identify the diverse research gaps necessitating to be addressed in future research programs. This review discusses MT involvement in the control of various physiological and molecular responses for inducing cold tolerance. We also shed light on engineering MT biosynthesis for improving the cold tolerance in plants. Moreover, we highlighted areas where future research is needed to make MT a vital antioxidant conferring cold tolerance to plants

High-density SNP-based association mapping of seed traits in fenugreek reveals homology with clover

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs

Genome-Wide Association Mapping of Grain Metal Accumulation in Wheat

Increasing wheat grain yield while ignoring grain quality and metal accumulation can result in metal deficiencies, particularly in countries where bread wheat accounts for the majority of daily dietary regimes. When the accumulation level exceeds a certain threshold, it becomes toxic and causes various diseases. Biofortification is an effective method of ensuring nutritional security. We screened 200 spring wheat advanced lines from the wheat association mapping initiative for Mn, Fe, Cu, Zn, Ni, and Cd concentrations. Interestingly, high-yielding genotypes had high essential metals, such as Mn, Fe, Cu, and Zn, but low levels of toxic metals, such as Ni and Cd. Positive correlations were found between all metals except Ni and Cd, where no correlation was found. We identified 142 significant SNPs, 26 of which had possible pleiotropic effects on two or more metals. Several QTLs co-located with previously mapped QTL for the same or other metals, whereas others were new. Our findings contribute to wheat genetic biofortification through marker-assisted selection, ensuring nutritional security in the long run

Identifying SNP markers associated with distinctness, uniformity, and stability testing in Egyptian fenugreek genotypes.

Distinctness, uniformity, and stability (DUS) test is the legal requirement in crop breeding to grant the intellectual property right for new varieties by evaluating their morphological characteristics across environments. On the other hand, molecular markers accurately identify genetic variations and validate the purity of the cultivars. Therefore, genomic DUS can improve the efficiency of traditional DUS testing. In this study, 112 Egyptian fenugreek genotypes were grown in Egypt at two locations: Wadi El-Natrun (Wadi), El-Beheira Governorate, with salty and sandy soil, and Giza, Giza governorate, with loamy clay soil. Twelve traits were measured, of which four showed a high correlation above 0.94 over the two locations. We observed significant genotype-by-location interactions (GxL) for seed yield, as it was superior in Wadi, with few overlapping genotypes with Giza. We attribute this superiority in Wadi to the maternal habitat, as most genotypes grew in governorates with newly reclaimed salty and sandy soil. As a first step toward genomic DUS, we performed an association study, and out of 38,142 SNPs, we identified 39 SNPs demonstrating conditional neutrality and four showing pleiotropic effects. Forty additional SNPs overlapped between both locations, each showing a similar impact on the associated trait. Our findings highlight the importance of GxL in validating the effect of each SNP to make better decisions about its suitability in the marker-assisted breeding program and demonstrate its potential use in registering new plant varieties

Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program

Manhattan plots for the measured traits.

Significant SNPs associated with the measured traits for the 112 fenugreek genotypes using 38,142 SNPs arranged randomly on the x-axis. The y-axis represents the–log10 (P) values. Thresholds defined by a green horizontal line at 5.2 represent FDR, and a blue horizontal line represents an arbitrary threshold = 3. Manhattan plots represent the size of the prophyll measured at Giza (a), the apex shape of the cotyledonary leaf measured at Wadi (b), and the size of the prophyll measured at Wadi (c).</p

Overlapping significant SNPs between Wadi and Giza.

Overlapping significant SNPs between Wadi and Giza.</p