Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice

A comprehensive review on rice responses and tolerance to salt stress

The challenge of salinity stress significantly impacts global rice production, especially in coastal and arid regions where the salinization of agricultural soils is on the rise. This review explores the complex physiological, biochemical, and genetic mechanisms contributing to salinity tolerance in rice (Oryza sativa L.) while examining agronomic and multidisciplinary strategies to bolster resilience. Essential adaptations encompass the regulation of ionic balance, the management of antioxidants, and the adjustments to osmotic pressure, all driven by genes such as OsHKT1;5 and transcription factors like OsbZIP73. The evolution of breeding strategies, encompassing traditional methods and cutting-edge innovations, has produced remarkable salt-tolerant varieties such as FL478 and BRRI dhan47. The advancements in this field are enhanced by agronomic innovations, including integrated soil management, crop rotation, and chemical treatments like spermidine, which bolster stress tolerance through antioxidant activity and transcriptional regulation mechanisms. Case studies from South Asia, Sub-Saharan Africa, the Middle East and, Australia demonstrate the transformative potential of utilizing salt-tolerant rice varieties; however, challenges persist, such as the polygenic nature of salinity tolerance, environmental variability, and socioeconomic barriers. The review highlights the importance of collaborative efforts across various disciplines, merging genomic technologies, sophisticated phenotyping, and inclusive breeding practices to foster climate-resilient and sustainable rice cultivation. This work seeks to navigate the complexities of salinity stress and its implications for global food security, employing inventive and cohesive strategies to confront the challenges posed by climate change.

Harnessing the power of genomics to develop climate-smart crop varieties: A comprehensive review

Abiotic stresses arising as consequences of climate change pose a serious threat to agricultural productivity on a global scale. Most cultivated crop varieties exhibit susceptibility to such environmental pressures as drought, salinity, and waterlogging. Addressing these abiotic stresses through agronomic means is not only financially burdensome but also often impractical, particularly in the case of abiotic stresses like heat stress. Cultivating resilient varieties that can withstand such pressures emerges as an economically feasible strategy to mitigate these challenges. Nevertheless, the development of stress-tolerant cultivars is hindered by the intricate nature of abiotic stress tolerance, often characterized by low heritability values. Compounding this complexity is the dynamic and multifaceted nature of these stresses, which impede conventional breeding efforts, rendering them painstakingly slow. The identification of molecular markers has emerged as a pivotal advancement in this arena. By pinpointing genomic regions associated with tolerance to abiotic stresses, these markers serve as effective tools for selection and trait introgression. In the post-genomic era, the proliferation of high-density SNP markers has revolutionized breeding strategies. Genomic selection, leveraging these markers, has become the method of choice for addressing polygenic traits with low heritability, such as abiotic stress tolerance. With the functional characterization of many genes being done, precise manipulation through genome editing techniques is gaining significant traction. This review delves into the application of molecular markers in breeding stress-tolerant crop varieties, alongside role of recent genomic techniques in enhancing abiotic stress tolerance. It also explores success stories and identifies potential targets for marker-assisted selection.

Identification of powdery mildew resistance quantitative trait loci in melon and development of resistant near-isogenic lines through marker-assisted backcrossing

BACKGROUND

Melon (Cucumis melo L.), an important cucurbit crop, faces production limitations due to powdery mildew (PM). Developing resistant varieties offers a sustainable, genetics-based alternative to chemical treatments. Therefore, identifying PM resistance quantitative trait loci (QTL) and creating trait-associated markers are essential for efficient melon PM resistance improvement through marker-assisted backcrossing (MABC).

RESULTS

Three F2 populations, A6, B2, and C4, were generated for QTL mapping of PM resistance. Major QTL were identified on chromosome 2 in A6, chromosome 5 in B2, and chromosomes 5 and 12 in C4. A series of TaqMan® assays targeting regions on chromosomes 2, 5, and 12 were developed and validated for foreground and recombinant selection, complemented by the double digest restriction-site associated DNA genotyping system to evaluate the recurrent parent genome recovery. Three MABC programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six PM resistance lines in each green- and orange-fleshed background. PM inoculation on the twelve near-isogenic lines confirmed their resistance to PM.

CONCLUSIONS

We have identified major PM resistance QTL for melon on chromosomes 2, 5, and 12 and have introgressed individual QTL to elite genetic backgrounds using MABC in three and a half years. This study demonstrates the power of combining high-throughput genotyping with breeding efforts and showcases the efficiency of molecular breeding.

QTL-Seq identified a genomic region on chromosome 1 for soil-salinity tolerance in F2 progeny of Thai salt-tolerant rice donor line "Jao Khao"

Introduction

Owing to advances in high-throughput genome sequencing, QTL-Seq mapping of salt tolerance traits is a major platform for identifying soil-salinity tolerance QTLs to accelerate marker-assisted selection for salt-tolerant rice varieties. We performed QTL-BSA-Seq in the seedling stage of rice from a genetic cross of the extreme salt-sensitive variety, IR29, and "Jao Khao" (JK), a Thai salt-tolerant variety.

Methods

A total of 462 F2 progeny grown in soil and treated with 160 mM NaCl were used as the QTL mapping population. Two high- and low-bulk sets, based on cell membrane stability (CMS) and tiller number at the recovery stage (TN), were equally sampled. The genomes of each pool were sequenced, and statistical significance of QTL was calculated using QTLseq and G prime (G') analysis, which is based on calculating the allele frequency differences or Δ(SNP index).

Results

Both methods detected the overlapping interval region, wherein CMS-bulk was mapped at two loci in the 38.41-38.85 Mb region with 336 SNPs on chromosome 1 (qCMS1) and the 26.13-26.80 Mb region with 1,011 SNPs on chromosome 3 (qCMS3); the Δ(SNP index) peaks were -0.2709 and 0.3127, respectively. TN-bulk was mapped at only one locus in the overlapping 38.26-38.95 Mb region on chromosome 1 with 575 SNPs (qTN1) and a Δ(SNP index) peak of -0.3544. These identified QTLs in two different genetic backgrounds of segregating populations derived from JK were validated. The results confirmed the colocalization of the qCMS1 and qTN1 traits on chromosome 1. Based on the CMS trait, qCMS1/qTN1 stably expressed 6%-18% of the phenotypic variance in the two validation populations, while qCMS1/qTN1 accounted for 16%-20% of the phenotypic variance in one validation population based on the TN trait.

Conclusion

The findings confirm that the CMS and TN traits are tightly linked to the long arm of chromosome 1 rather than to chromosome 3. The validated qCMS-TN1 QTL can be used for gene/QTL pyramiding in marker-assisted selection to expedite breeding for salt resistance in rice at the seedling stage.

KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance

Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.

QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued

Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.

Physiological Responses to Salt Stress at the Seedling Stage in Wild (Oryza rufipogon Griff.) and Cultivated (Oryza sativa L.) Rice

Domesticated rice Oryza sativa L. is a major staple food worldwide, and the cereal most sensitive to salinity. It originated from the wild ancestor Oryza rufipogon Griff., which was reported to possess superior salinity tolerance. Here, we examined the morpho-physiological responses to salinity stress (80 mM NaCl for 7 days) in seedlings of an O. rufipogon accession and two Italian O. sativa genotypes, Baldo (mildly tolerant) and Vialone Nano (sensitive). Under salt treatment, O. rufipogon showed the highest percentage of plants with no to moderate stress symptoms, displaying an unchanged shoot/root biomass ratio, the highest Na+ accumulation in roots, the lowest root and leaf Na+/K+ ratio, and highest leaf relative water content, leading to a better preservation of the plant architecture, ion homeostasis, and water status. Moreover, O. rufipogon preserved the overall leaf carbon to nitrogen balance and photosynthetic apparatus integrity. Conversely, Vialone Nano showed the lowest percentage of plants surviving after treatment, and displayed a higher reduction in the growth of shoots rather than roots, with leaves compromised in water and ionic balance, negatively affecting the photosynthetic performance (lowest performance index by JIP-test) and apparatus integrity. Baldo showed intermediate salt tolerance. Being O. rufipogon interfertile with O. sativa, it resulted a good candidate for pre-breeding towards salt-tolerant lines.