TILLING by Sequencing (TbyS) for targeted genome mutagenesis in crops

Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding

The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.

Allele mining through TILLING and EcoTILLING approaches in vegetable crops

MAIN CONCLUSION

The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.

Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.

Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes

Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.

Sorghum-Phosphate Solubilizers Interactions: Crop Nutrition, Biotic Stress Alleviation, and Yield Optimization

Sweet sorghum [Sorghum bicolor (L.) Moench] is a highly productive, gluten-free cereal crop plant that can be used as an alternative energy resource, human food, and livestock feed or for biofuel-ethanol production. Phosphate fertilization is a common practice to optimize sorghum yield but because of high cost, environmental hazards, and soil fertility reduction, the use of chemical P fertilizer is discouraged. Due to this, the impetus to search for an inexpensive and eco-friendly microbiome as an alternative to chemical P biofertilizer has been increased. Microbial formulations, especially phosphate solubilizing microbiome (PSM) either alone or in synergism with other rhizobacteria, modify the soil nutrient pool and augment the growth, P nutrition, and yield of sorghum. The use of PSM in sorghum disease management reduces the dependence on pesticides employed to control the phytopathogens damage. The role of PSM in the sorghum cultivation system is, however, relatively unresearched. In this manuscript, the diversity and the strategies adopted by PSM to expedite sorghum yield are reviewed, including the nutritional importance of sorghum in human health and the mechanism of P solubilization by PSM. Also, the impact of solo or composite inoculations of biological enhancers (PSM) with nitrogen fixers or arbuscular mycorrhizal fungi is explained. The approaches employed by PSM to control sorghum phytopathogens are highlighted. The simultaneous bio-enhancing and biocontrol activity of the PS microbiome provides better options for the replacement of chemical P fertilizers and pesticide application in sustainable sorghum production practices.

Fifty years of a public cassava breeding program: evolution of breeding objectives, methods, and decision-making processes

This paper reviews and analyzes key features from cassava breeding at the International Center for Tropical Agriculture (CIAT) over 50 years and draws lessons for public breeding efforts broadly. The breeding team, jointly with national program partners and the private processing sector, defined breeding objectives and guiding business plans. These have evolved through the decades and currently focus on four global product profiles. The recurrent selection method also evolved and included innovations such as estimation of phenotypic breeding values, increasing the number of locations in the first stage of agronomic evaluations, gradual reduction of the duration of breeding cycles (including rapid cycling for high-heritability traits), the development of protocols for the induction of flowering, and the introduction of genome-wide predictions. The impact of cassava breeding depends significantly on the type of target markets. When roots are used for large processing facilities for starch, animal feeding or ethanol production (such as in SE Asia), the adoption of improved varieties is nearly universal and productivity at the regional scale increases significantly. When markets and relevant infrastructure are weak or considerable proportion of the production goes for local artisanal processing and on-farm consumption, the impact has been lower. The potential of novel breeding tools needs to be properly assessed for the most effective allocation of resources. Finally, a brief summary of challenges and opportunities for the future of cassava breeding is presented. The paper describes multiple ways that public and private sector breeding programs can learn from each other to optimize success.

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.

Nitroxin and arbuscular mycorrhizal fungi alleviate negative effects of drought stress on Sorghum bicolor yield through improving physiological and biochemical characteristics

Soil microorganisms play an important role in enhancing soil fertility and plant health. Nitroxin is a bio-fertilizer that is a combination of Azospirilium and Azotobacter rhizobacteria. Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria can enhance biotic and abiotic stress tolerance in plants, whereas little is known regarding their roles in sorghum (Sorghum bicolor L.) growth under drought stress conditions. Therefore, this experiment was conducted to investigate the inoculation of grain sorghum with the bio-fertilizers of Nitroxin and Glomus mosseae effects on some physiological and biochemical traits and yield of grain sorghum under drought stress conditions in the region of Saravan, Iran, in 2017 and 2018. The results of this experiment showed that severe and moderate drought stress conditions decreased the amounts of grain protein percentage, auxin (IAA) content, root colonization, grain yield, and protein yield of grain, whereas grain starch percentage, the activity of catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX) enzymes and content of total carotenoid, total anthocyanin, total flavonoid, electrolyte leakage, and malondialdehyde (MDA) were increased. Inoculation of sorghum plants with bio-fertilizers improved these traits (except starch content, electrolyte leakage, and MDA) under drought stress conditions as well as non-stress conditions. As a result, grain yield and protein yield of sorghum decreased by 43.77 and 43.99%, respectively, under severe drought stress conditions but co-inoculation with Nitroxin and AMF under severe drought stress conditions increased grain yield and protein yield of sorghum by 27 and 19.63%, respectively, compared to non-application of these bio-fertilizers. Thus, Nitroxin and AMF can be recommended for profitable sorghum production under drought stress conditions.

Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity

To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.

Mutagenesis in Rice: The Basis for Breeding a New Super Plant

The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.

High-resolution melting-based TILLING of γ ray-induced mutations in rice

Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics strategy for the high-throughput screening of induced mutations. γ radiation, which often induces both insertion/deletion (Indel) and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting (HRM) analysis. Pooled rice (Oryza sativa) samples mixed at a 1:7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M₂ plants is recommended for screening γ ray-induced mutants in rice. For demonstration, a γ ray-mutagenized M₂ rice population (n=4560) was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution (G→A) and one single nucleotide insertion (A) were identified in OsLCT1, and one trinucleotide (TTC) deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ ray mutagenesis to the breeding of rice and other seed crops.

Identification of Nutritional Components in Black Sesame Determined by Widely Targeted Metabolomics and Traditional Chinese Medicines

Chemical composition of secondary metabolites is of great importance for quality control of agricultural products. Black sesame seeds are significantly more expensive than white sesame seeds, because it is thought that black sesame seeds are more beneficial to human health than white sesame seeds. However, the differences in nutrient composition between black sesame seeds and white sesame seeds are still unknown. The current study examined the levels of different metabolites in black and white sesame seeds via the use of a novel metabolomics strategy. Using widely targeted metabolomics data, we obtained the structure and content of 557 metabolites, out of which 217 metabolites were identified, and discovered 30 metabolic pathways activated by the secondary metabolites in both black and white sesame seeds. Our results demonstrated that the main pathways that were differentially activated included: phenylpropanoid biosynthesis, tyrosine metabolism, and riboflavin metabolism. More importantly, the biomarkers that were significantly different between black seeds and white sesame seeds are highly related to the functions recorded in traditional Chinese medicine. The results of this study may serve as a new theoretical reference for breeding experts to promote the genetic improvement of sesame seeds, and therefore the cultivation of higher quality sesame varieties.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.

Enhancing genetic gain in the era of molecular breeding

As one of the important concepts in conventional quantitative genetics and breeding, genetic gain can be defined as the amount of increase in performance that is achieved annually through artificial selection. To develop pro ducts that meet the increasing demand of mankind, especially for food and feed, in addition to various industrial uses, breeders are challenged to enhance the potential of genetic gain continuously, at ever higher rates, while they close the gaps that remain between the yield potential in breeders' demonstration trials and the actual yield in farmers' fields. Factors affecting genetic gain include genetic variation available in breeding materials, heritability for traits of interest, selection intensity, and the time required to complete a breeding cycle. Genetic gain can be improved through enhancing the potential and closing the gaps, which has been evolving and complemented with modern breeding techniques and platforms, mainly driven by molecular and genomic tools, combined with improved agronomic practice. Several key strategies are reviewed in this article. Favorable genetic variation can be unlocked and created through molecular and genomic approaches including mutation, gene mapping and discovery, and transgene and genome editing. Estimation of heritability can be improved by refining field experiments through well-controlled and precisely assayed environmental factors or envirotyping, particularly for understanding and controlling spatial heterogeneity at the field level. Selection intensity can be significantly heightened through improvements in the scale and precision of genotyping and phenotyping. The breeding cycle time can be shortened by accelerating breeding procedures through integrated breeding approaches such as marker-assisted selection and doubled haploid development. All the strategies can be integrated with other widely used conventional approaches in breeding programs to enhance genetic gain. More transdisciplinary approaches, team breeding, will be required to address the challenge of maintaining a plentiful and safe food supply for future generations. New opportunities for enhancing genetic gain, a high efficiency breeding pipeline, and broad-sense genetic gain are also discussed prospectively.