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Abstract The study was designed to validate the previously reported 34 SSR markers using 78 chilli genotypes to detect significant trait specific markers as well as superior genotypes resistant to Phytophthora capsici root rot (PcRR). In this context, the identification of germplasm with higher yield per plant (YPP) leads to hype in stress tolerance index (STI) in genotypes, Chakwal3 (11.98), Greenfire (10.14), Advanta5017 (9.94) and Chakwal4 (7.8). The identified genotypes were also found as resistant and moderately resistant due to existence of below 50% of disease incidence. Moreover, biplot showed the interrelation of STI with YPP through the formation of acute angle by their respective vectors. In the current study, the markers Hpms1172 and CAMS177 was found significant for STI. However, the marker CAMS066 was found associated with relative cell injury, CA06g27450 with disease incidence and CAMS173 with relative leaf damage. The bright bands on gel pictures of significant markers showed the association of these markers with resistant genotypes i.e. Chakwal3, Advanta-5017 and Chakwal4 as well as with a single moderately resistant genotype i.e. Greenfire. The markerstudes confirmed the phenotypic data by showing association of markers i.e. Hpms1172 and CAMS177, r with stress tolerance index. The principal coordinate analysis aligned with the results obtained from marker-assisted selection. Thus, currently practiced marker assisted selection detected high yielding genotypes in PcRR disease stress condition that will be helpful in progressing breeding programs in chilli.

Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world’s agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.

Abstract Cotton is one of the most important fiber crops that plays a vital role in the textile industry. Its production has been unstable over the years due to climate change induced biotic stresses such as insects, diseases, and weeds, as well as abiotic stresses including drought, salinity, heat, and cold. Traditional breeding methods have been used to breed climate resilient cotton, but it requires a considerable amount of time to enhance crop tolerance to insect pests and changing climatic conditions. A promising strategy for improving tolerance against these stresses is genetic engineering. This review article discusses the role of genetic engineering in cotton improvement. The essential concepts and techniques include genome editing via clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated protein 9 (CRISPR-Cas9), overexpression of target genes, downregulation using RNA interference (RNAi), and virus-induced gene silencing (VIGS). Notably, the Agrobacterium-mediated transformation has made significant contributions to using these techniques for obtaining stable transgenic plants.

Climate change poses emerging threats to wheat growth in coming future. These threats need to be explored to ensure sustainable wheat production. To do this, the SALTMED model was calibrated using data from experiments conducted on different levels of irrigation and nitrogen doses. The performance of the SALTMED model was assessed based on values of the root mean square error (RMSE), normalized root mean square error (NRMSE), coefficient of determination (R2) and coefficient of residual mass (CRM) that ranged from 0.23–1.82, 0.09–0.17, 0.91–0.93 and −0.01–0.02, respectively for calibration and 0.31–1.89, 0.11–0.31, 0.87–0.90 and −0.02–0.01, respectively for validation. Projections for future climate scenarios for wheat growth indicated that by the end of the century, sowing dates advanced by nine days under the RCP4.5 scenario and eleven days under the RCP8.5 scenario, while harvesting dates shifted earlier by twenty-four days under RCP4.5 and twenty-eight days under RCP8.5. Consequently, the overall crop duration was shortened by fifteen days under RCP4.5 and eighteen days under RCP8.5. Further simulations revealed that the wheat yield was reduced by 14.2% under RCP4.5 and 21.0% under RCP8.5; the dry matter was reduced by 14.9% under RCP4.5 and 23.3% under RCP8.5; the irrigation amount was expected to increase by 14.9% under RCP4.5 and 18.0% under RCP8.5; and water productivity was expected to be reduced by 25.3% under RCP4.5 and 33.0% under RCP8.5 until the end of century. The hypothetical scenarios showed that adding an extra 20–40% more nitrogen can enhance wheat yield and dry matter by 10.2–23.0% and 11.5–24.6%, respectively, under RCP4.5, and by 12.0–23.4% and 12.9–29.6%, respectively, under RCP8.5. This study offers valuable insights into the effects of climate change on future wheat production so that effective contingency plans could be made by policymakers and adopted by stakeholders for higher wheat productivity.

This study aimed to investigate the impact of individual drought, heat, and combined drought and heat stress on twelve cotton genotypes, including eight tolerant and four susceptible genotypes. A field experiment was carried out by employing a randomized complete block split-plot design, with treatments (control, drought, heat, drought + heat), and cotton genotypes assigned to the main plots and sub-plots respectively. The results showed that the combined stress had a more severe impact on the yield and fiber quality of cotton genotypes compared to individual stresses. Among the studied genotypes, FB-Shaheen, FH-207, MNH-886, and White Gold exhibited superior performance in regard to agronomic and fiber quality characters under combined stress environments. Physiological parameters, including transpiration rate, stomatal conductance, relative water contents, and photosynthetic rate, were significantly reduced under combined stress. However, specific genotypes, MNH-886, FH-207, White Gold, and FB-Shaheen, demonstrated better maintenance of these parameters, indicating their enhanced tolerance to the combined stress. Furthermore, the accumulation of reactive oxygen species was more pronounced under combined stress compared to individual stressors. Tolerant genotypes showed lower levels of H2O2 and MDA accumulation, while susceptible genotypes exhibited higher levels of oxidative damage. Antioxidant enzyme activities, such as superoxide dismutase, peroxidase, and catalase, increased under combined stress, with tolerant genotypes displaying higher enzyme activities. Conversely, susceptible genotypes (AA-703, KZ 191, IR-6, and S-15) demonstrated lower increases in enzymatic activities under combined stress conditions. Biochemical traits, including proline, total phenolic content, flavonoids, and ascorbic acid, exhibited higher levels in resistant genotypes under combined stress, while sensitive genotypes displayed decreased levels of these traits. Additionally, chlorophyll a & b, and carotenoid levels were notably decreased under combined stress, with tolerant genotypes experiencing a lesser decrease compared to susceptible genotypes.

Abstract The introduction of genetically modified (GM) cotton in 1996 in the US and its worldwide spread later rejuvenated cotton production in many parts of the world. The evolution is continued since then and currently, the 3rd and fourth generation of same GM cotton is grown in many parts of the world. The GM cotton introduced in 1996 was simple Bt cotton that expressed a single Cry1Ac gene, the later generation carried multiple Cry genes along with the genes controlling herbicide tolerance. Current day GM cotton does not only give stable resistance against lepidopteran insects but also facilitates the farmers to spray broad-spectrum herbicides without harming the crop. The evolution of GM cotton is continued both on the basic and applied side and interventions have been introduced during the last decade. Earlier the cotton transformation was limited to Cocker strains which are getting possible in many other varieties, too. It is successful with both gene gun, and Agrobacterium and inplanta transformation has made it a routine activity. Apart from overexpression studies for various purposes including biotic, abiotic, and quality traits, RNAi and genome editing are explored vigorously. Through this review, we have tried to explore and discuss various interventions for improving transformation protocols, the applications of cotton transformation, and future strategies being developed to get maximum benefits from this technology during the last decade.

Carrot (Daucus carota L.) seed quality is affected by umbel position due to uneven maturation of carrot seeds produced in different umbel orders. However, keeping this in view, we tested whether seed quality could be improved with the suppression of tertiary umbels under exogenous auxin application. Using auxin-producing bacterial isolates, i.e., Bacillus sp. MN54, Enterobacter sp. MN17, Pantoea sp. MN34, and Burkholderia phytofirmans PsJN, the arrangements of carrot umbel order were evaluated in terms of quality carrot seed production. The results revealed that auxin production by plant-growth-promoting rhizobacteria showed significant differences among measured growth indices, yield, and seed quality attributes. The selected endophytic strains co-applied with auxin via foliar application improved all growth- and yield-related traits, as well as the enzymatic activities of carrots. Noticeably, MN17+L-tryptophan and MN34+L-tryptophan effectively minimized the number of tertiary umbels by increasing the number of secondary umbels. Furthermore, treating with PsJN+L-tryptophan and MN34+L-tryptophan resulted in reduced conductivity of seed leachates and malondialdehyde levels in primary, secondary, and tertiary umbel seeds. These findings collectively indicate the potential of the foliar application of PsJN+L-tryptophan and MN34+L-tryptophan to effectively alter umbel arrangement, leading to improved yield and seed quality. This study implies that carrot seed producers can consider employing specific PGPB strains, particularly MN34+L-tryptophan, to suppress tertiary umbels and achieve higher yields of high-quality carrot seeds.

Stripe rust is a continuous threat to wheat crop all over the world. It causes considerable yield losses in wheat crop every year. Continuous deployment of adult plant resistance (APR) genes in newly developing wheat cultivars is the most judicious strategy to combat this disease. Herein, we dissected the genetics underpinning stripe rust resistance in Pakistani wheat germplasm. An association panel of 94 spring wheat genotypes was phenotyped for two years to score the infestation of stripe rust on each accession and was scanned with 203 polymorphic SSRs. Based on D´ measure, linkage disequilibrium (LD) exhibited between loci distant up to 45 cM. Marker-trait associations (MTAs) were determined using mixed linear model (MLM). Total 31 quantitative trait loci (QTLs) were observed on all 21 wheat chromosomes. Twelve QTLs were newly discovered as well as 19 QTLs and 35 previously reported Yr genes were validated in Pakistani wheat germplasm. The major QTLs were QYr.uaf.2AL and QYr.uaf.3BS (PVE, 11.9%). Dissection of genes from the newly observed QTLs can provide new APR genes to improve genetic resources for APR resistance in wheat crop.

Food security is directly coupled with enhanced production under optimized cropping intensity. Intercropping is a diversified and sustainable agricultural technique with optimized cropping intensity. Intercropping is used to obtain a higher yield and more balanced products per unit area. This study was performed at Aidyn Research Institute, Nur Sultan, Kazakhstan, in 2018 and 2019 to identify the effects of different sowing patterns on maize-white bean (Zea mays–Phaseolus vulgaris) sowing systems. The field experiment was arranged in a randomized complete block design with three replications. Göynük-98 was used for white beans, and SY Miami was used for maize, with 20 cm and 40 cm row spaces for maize, and 10 cm and 20 cm row spaces for white bean and sole maize, sole white bean, maize-white bean-maize-white bean, maize-white bean-white bean-maize and white bean-maize-maize-white bean sowing systems. The results showed that wide row spacing was better than narrow row spacing in terms of land equivalent ratio (LER) for both maize and white beans, but grain yield was higher in narrow row spacing. Yield items for both maize and white beans showed higher values in intercropping. Grain yield was higher in sole sowing. The maize-white bean-white bean-maize sowing system for maize and the white bean-maize-maize-white bean sowing system for white beans were determined as the best sowing systems according to the yield components.

The development of high-yielding heat-tolerant cotton cultivars harboring plastic phenotypes across warming climatic regions is prime objectives of today’s cotton breeding programs. We evaluated eight parents and 15 F1 hybrids under normal and heat stress conditions. Agronomic and biochemical characters were analyzed using standard least square, correlation, principal component analysis (PCA), and hierarchical clustering. The results explained a significant reduction in all traits except hydrogen peroxide contents, catalase, and peroxidase activities with a prominent increase under heat stress. A significant positive correlation was observed among all agronomic and biochemical traits. POD was found to have a maximum positive correlation with CAT (0.947) and minimum with boll weight (0.050). PCA showed first two components accounting for 78.64% of the total variation, with 55.83% and 22.80% of the total variation, respectively. Based on multivariate analyses methods 23 genotypes have been placed in 3 groups: tolerant (cluster-3), moderately tolerant (cluster-2), and susceptible (cluster-1). In a general perspective hybrids have better performance across normal and heat stress supports the idea of hybrid adaptability across stress environments. In specific FH-458 × FH-313 cross performed best across both conditions for yield and physiological traits. Hence, the generated information from the present study would support breeders in developing heat-resilient cultivars to endure the prevailing extreme environmental conditions.

Genetic diversity present in gene pool is an important determination for breeding programs, and characterization is useful of building crop plant collections primarily based on the knowledge of the presence of valuable genes and traits. Developing successful varieties for increasing the future yield and quality of tomato depend mainly on the genetic diversity of parents used in the breeding program. Molecular characterization of 21 tomato genotypes used in in Pakistani breeding program was studied using random amplified polymorphic DNA (RAPD) markers. Total 102 bands were amplified among 21 genotypes using 20 RAPD primers. Overall 73.5% polymorphism was shown as 75 out of 102 loci were polymorphic. High degree of divergence between varieties was indicated by low level of monomorphic bands. The number of PCR products per primer varied from 2-8 with an average of 5.1 bands per primer. Primer GL J-20 and GL C-09 produced maximum number of bands whereas the primers GL A-09 produced the lowest. The polymorphism per RAPD primer ranged from 50% to 100% with an average of 73.5%. The accumulative analysis of amplified products generated by RAPD’s was enough to assess the genetic diversity among the genotypes. The information would be helpful for formulating future breeding and genome mapping programs. This study will also work as an indicator for tomato breeders to evolve varieties with genetic diverse back ground to achieve sustainability in tomato production in the country.

Resistance to Cotton leaf curl virus (CLCuV) in three cultivars of cotton was investigated in crosses with a susceptible cultivar using generation mean analysis. No single gene of major effect controlled resistance to Cotton leaf curl virus in the three crosses. The mean number of effective factors controlling resistance in cross LRA-5166 × S-12 was estimated to be at least five. Estimates of broad and narrow sense heritability indicate that effects by the environment were larger than those of genetic components. Epistasis was significant in two crosses. Additive gene effects contributed more to resistance than to susceptibility in contrast with dominance gene effect. Reciprocal differences were detected in the cross with LRA-5166. Estimates of genetic gain ranged form low to moderate. Thus, a breeding method that makes use of additive variance should be used because much of the variances for resistance are additive, whereas dominance effects, at least in these crosses, tended to contribute to susceptibility.