Crop Genetics Research Articles

Research Progress and Application of Miniature CRISPR-Cas12 System in Gene Editing

CRISPR-Cas system, a natural acquired immune system in prokaryotes that defends against exogenous DNA invasion because of its simple structure and easy operation, has been widely used in many research fields such as synthetic biology, crop genetics and breeding, precision medicine, and so on. The miniature CRISPR-Cas12 system has been an emerging genome editing tool in recent years. Compared to the commonly used CRISPR-Cas9 and CRISPR-Cas12a, the miniature CRISPR-Cas12 system has unique advantages, such as rich PAM sites, higher specificity, smaller volume, and cytotoxicity. However, the application of miniature Cas12 proteins and the methods to improve its editing efficiency have not been systematically summarized. In this review, we introduce the classification of CRISPR-Cas system and summarize the structural characteristics of type V CRISPR-Cas system and the cleavage mechanism of five miniature Cas12 proteins. The application of a miniature CRISPR-Cas12 system in the gene editing of animals, plants, and microorganisms is summarized, and the strategies to improve the editing efficiency of the miniature CRISPR-Cas12 system are discussed, aiming to provide reference for further understanding the functional mechanism and engineering modification of the miniature CRISPR-Cas12 system.

Soybean Yield Losses Related to Drought Events in Brazil: Spatial–Temporal Trends over Five Decades and Management Strategies

By the end of the decade, the world population is expected to increase by nearly one billion people, posing challenges to meeting global food demand. In this scenario, soybean production is projected to increase by 18% within this decade. Despite being the largest soybean producer, responsible for over 40% of soybeans produced worldwide, drought events often impair Brazilian production. The goals of the present research were to quantify soybean yield losses related to drought in Brazil from 1973 to 2023 at national, state, and municipal levels and to assess the spatial distribution of losses across the production areas. The hypothesis investigated is that year-to-year variations in soybean yield are closely related to water availability, considering that crop management practices are constant from year to year, while increments in soybean yield across time (more than five years) relate tightly to better crop management practices and breeding improvements. Thus, quantifying year-to-year yield losses might demonstrate the effects of water availability on soybean yield. Yield data from the 1976/1977 to 2022/2023 crop seasons from the 26 states and the Federal District came from the National Supply Company, while the Brazilian Institute of Geography and Statistics supplied yield data for the 1973/1974 to 2020/2021 crop seasons from 1998 municipalities with more than 14 crop seasons. Soybean drought yield losses were calculated for each cropping season individually at the municipal, state, and national levels, based on the deviation in the observed yield to the corresponding maximum yield in the five-year window, considering that crop management practices and genetics represent a regular increment in soybean yield, which means that production practices improved over time and deviations from year to year are mainly related to drought occurrence. Annual soybean yield loss (expressed in tons, USD, and percentage), frequency of yield loss, and severity of yield loss were calculated at national, state, and municipal levels for each cropping season. The Standardized Precipitation Index (SPI), acquired from the Brazilian Weather Forecast and Climate Studies Center at the National Space Research Institute, was used as a qualitative indicator to corroborate the assessed soybean yield losses related to drought. The results demonstrate yield losses in more than 50% of crop seasons at the national level, with a similar frequency across the five decades, albeit with lower severities in the last 30 years. The Central–West region was more stable than the South region, with yield losses of up to 74%. In five decades, yield losses related to drought events stand at 11.65%, corresponding to 280 million tons or USD 152 billion (considering the average soybean price in 2022 at the Chicago Board of Trade). At the municipal level, analogous behavior was observed across time and space. The outcomes from the present research might subsidize public and corporative policies related to agricultural zoning, farm loan programs, crop insurance contracts, and food security, contributing to higher agricultural, environmental, economic, and social sustainability.

Non-additive expression genes play a critical role in leaf vein ratio heterosis in Nicotiana tabacum L.

Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies.

School of ecological selection of academician of the Russian academy of sciences V.F. Pivovarova

The article outlines the main milestones in the formation of the scientific school of Academician of the Russian Academy of Sciences Viktor Fedorovich Pivovarov – a talented organizer of scientific research on vegetable growing, a leading scientist in the field of ecology, introduction, selection and seed production of vegetable crops, Honored Scientist of the Russian Federation, laureate of the State Prize and Government Prizes of the Russian Federation V. Pivovarov. F. has extensive experience both in Russia and abroad in solving theoretical and practical problems in the industry. He developed a new scientific direction of research on ecological selection and genetics of vegetable crops. The article presents the directions of the ecological selection scientific school: increasing the adaptability of agricultural crops to various environmental factors; identifying the peculiarities of the genotype-environment interaction; development of methods for accelerating the breeding process to create highly productive varieties and hybrids resistant to abiotic and biotic stressors; ecological selection for low levels of radionuclides and technologies that reduce the amount of pollutants in vegetable products. School of V.F. Pivovarov Academician of the Russian Academy of Sciences was organized on the basis of common scientific interests, the importance of environmental research for breeding, a high level of scientific results, continuity and great development prospects.

3D Morphological Feature Quantification and Analysis of Corn Leaves.

Marked variations in the 3-dimensional (3D) shape of corn leaves can be discerned as a function of various influences, including genetics, environmental factors, and the management of cultivation processes. However, the causes of these variations remain unclear, primarily due to the absence of quantitative methods to describe the 3D spatial morphology of leaves. To address this issue, this study acquired 3D digitized data of ear-position leaves from 478 corn inbred lines during the grain-filling stage. We propose quantitative calculation methods for 13 3D leaf shape features, such as the leaf length, 3D leaf area, leaf inclination angle, blade-included angle, blade self-twisting, blade planarity, and margin amplitude. Correlation analysis, cluster analysis, and heritability analysis were conducted among the 13 leaf traits. Leaf morphology differences among subpopulations of the inbred lines were also analyzed. The results revealed that the 3D leaf traits are capable of revealing the morphological differences among different leaf surfaces, and the genetic analysis revealed that 84.62% of the 3D phenotypic traits of ear-position leaves had a heritability greater than 0.3. However, the majority of 3D leaf shape traits were strongly affected by environmental conditions. Overall, this study quantitatively investigated 3D leaf shape in corn, providing a reliable basis for further research on the genetic regulation of corn leaf morphology and advancing the understanding of the complex interplay among crop genetics, phenotypes, and the environment.

Long‐term crop yield benefits of subsurface drainage on poorly drained soils

AbstractSubsurface drainage is an important agricultural practice that has been widely utilized in the US Midwest to improve the productivity of poorly drained soils. Although widely adopted, long‐term yield benefits of drainage, particularly with varying spacings, in an ever‐changing climate are largely unknown. The goals of this study were to assess how various drainage spacings (5, 10, and 20 m) impacted crop yields compared to the undrained control in a long‐term trial (started in 1984) in southeastern Indiana and how these effects were influenced by the amount of rainfall of specific periods of the growing season. Drainage treatments led to an increase in corn (Zea mays) yields (by 12%–17%) but did not significantly affect soybean (Glycine max) yields compared to the control. In the initial 10 years of the experiment, drainage benefits were subtle and corn yields did not vary significantly across spacing treatments, whereas in the most recent 10 corn years, the drainage treatment effects became more pronounced, likely due to the combined effects of long‐term drainage system and conservation practices of no‐till and cover crops. Over 37 years, corn yields remained stagnant in the undrained plots but progressively increased in the drained treatments. Both corn and soybean yields showed a negative correlation with rainfall 14 days post‐planting, while drainage spacing treatments partially mitigated this negative effect. Our findings underscore the importance of effective drainage as a necessary prerequisite for realizing the potential benefits of conservation practices and improved crop genetics for increased crop productivity.

Role of Nitrogen in Wheat Production System and Nitrogen for Improving Wheat Yield and Quality: A Review

Wheat is the staple food across the different parts of the world. To increase the wheat productivity by utilizing the fertilizers. Nitrogen plays a key role in increasing productivity and the quality of the crops. In this review article, we studied the relationship between nitrogen and wheat parameters, the impact of excessive nitrogen used in wheat, NUE (Nitrogen use efficiency) in wheat production, and examined various nitrogen management strategies aimed at enhancing both yield and quality. Different nitrogen application techniques, such as broadcast and side-dressing, have been evaluated, with the rate of nitrogen showing a significant influence on wheat parameters. Key components influencing NUE in wheat farming, including soil characteristics, nitrogen application timing and rate, environmental factors, and crop genetics, are discussed. Furthermore, innovative nitrogen management practices such as precision farming techniques, cover cropping, and the use of biofertilizers as effective strategies for improving NUE and promoting sustainable wheat production. The abstract underscores the importance of balancing nitrogen application to meet crop demands at different growth stages while minimizing nitrogen losses and environmental risks. By integrating advanced technologies, agronomic practices, and scientific insights, farmers can optimize nitrogen use efficiency in wheat production systems, thereby enhancing both yield and quality outcomes.

Study on the mechanism of peanut resistance to Fusarium oxysporum infection induced by Bacillus thuringiensis TG5.

Peanut root rot, commonly referred to as rat tail or root rot, is caused by a range of Fusarium species. A strain of bacteria (named TG5) was isolated from crop rhizosphere soil in Mount Taishan, Shandong Province, China, through whole genome sequencing that TG5 was identified as Bacillus thuringiensis, which can specifically produce chloramphenicol, bacitracin, clarithromycin, lichen VK21A1 and bacitracin, with good biological control potential. Based on liquid chromatography tandem mass spectrometry metabonomics analysis and transcriptome conjoint analysis, the mechanism of TG5 and carbendazim inducing peanut plants to resist F. oxysporum stress was studied. In general, for peanut root rot caused by F. oxysporum, B. thuringiensis TG5 has greater advantages than carbendazim and is environmentally friendly. These findings provide new insights for peanut crop genetics and breeding, and for microbial pesticides to replace traditional highly toxic and highly polluting chemical pesticides. Based on the current background of agricultural green cycle and sustainable development, it has significant practical significance and broad application prospects.

Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits.

Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.

Streamlined Agrobacterium rhizogenes-mediated hairy root transformation for efficient CRISPR/Cas9-based gene editing evaluation in diverse Citrullus varieties

The CRISPR/Cas9 genome-editing system serves as a pivotal tool for enhancing crop genetics. Within this system, single guide RNAs (sgRNAs) are instrumental in the precise cleavage of DNA double strands. However, the efficiency of gene editing varies among sgRNAs, emphasizing the need to meticulously select target sites, especially in the context of Citrullus lanatus, a species notorious for its challenging and inefficient generation of transgenic plants through stable transformation. This study employed an Agrobacterium rhizogenes-mediated hairy root method to assess effective target sites for gene editing of ClCIPK17 across various Citrullus species. Hairy roots were successfully induced in different plant tissues at diverse growth stages of Citrullus lanatus, Citrullus mucosospermus, and Citrullus amarus. Employing a vector with two sgRNAs (sgRNA1 and sgRNA5) positioned within conserved regions of exon 1 and exon 5 of ClCIPK17 in the CRISPR/Cas9 system, targeted mutations were detected in 90.9% of accessions across the four Citrullus species. Notably, 73.94% of all examined hairy roots exhibited mutations at the sgRNA1 site, while the sgRNA5 site showed no mutations. Among the 31 different mutation types identified at the sgRNA1 site, base deletion was the most prevalent. Using the sgRNA1 site of ClCIPK17, stable transgenic watermelon buds were obtained from explants, and the targeted mutations of the sgRNA1 site were confirmed. These findings underscore the viability of the hairy root transformation system in assessing the editing efficiency of sgRNA targets in diverse Citrullus species.

Communicating trust and trustworthiness through scientists' biographies: Benevolence beliefs.

A goal of many science communicators is to foster trust in scientists and their work. This study investigates if existing textual resources that scientists create in the course of their regular activities can be improved to enhance perceptions of scientists as trustworthy. Building on Mayer et al.'s integrative model of organizational trust, we examine how communicating benevolence through short biographies can affect trustworthiness perceptions using a 3 (degree of benevolence information: high, unspecified, low) × 3 (research area: crop genetics, corn and soy genetics, biotechnology use) survey design. We find that the degree of benevolence information significantly influences perceptions of benevolence and integrity, as well as willingness to trust, with these effects being consistent across different research areas. However, the degree of benevolence communicated had no significant effect on the perceived competence of the scientists. These findings underscore the importance of highlighting benevolence in communication to positively influence trustworthiness perceptions, thus offering insights for science communication practices.

Benefitting productivity and the environment: Current and future maize cropping systems improve yield while reducing nitrate load.

Increases in cereal crop yield per area have increased global food security. "Era" studies compare historical and modern crop varieties in controlled experimental settings and are routinely used to understand how advances in crop genetics and management affect crop yield. However, to date, no era study has explored how advances in maize (Zea mays L.) genetics and management (i.e., cropping systems) have affected environmental outcomes. Here, we developed a cropping systems era study in Iowa, USA, to examine how yield and nitrate losses have changed from "Old" systems common in the 1990s to "Current" systems common in the 2010s, and to "Future" systems projected to be common in the 2030s. We tested the following hypothesis: If maize yield and nitrogen use efficiency have improved over previous decades, Current and Future maize systems will have benefits to water quality compared to Old systems. We show that not only have maize yield and nitrogen use efficiency (kg grain kg-1 N), on average, improved over time but also yield-scaled nitrate load + soil nitrate was reduced by 74% and 91% from Old to Current and Future systems, respectively. Continuing these trajectories of improvement will be critical to meet the needs of a growing and more affluent population while reducing deleterious effects of agricultural systems on ecosystem services.

Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society.

Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground-breaking work, especially his effort to list orphan tropical crops to genomic resource-rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agriculturallandscape.

Кафедре генетики , селекции и семеноводства - 100 лет

The year 2023 is a special year for domestic selection: this year marks the 100th anniversary of the establishment of the Department of Plant Breeding and Seed Production at Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, the first department of this profile in Russia. Among the rapid changes in everyday life in post-revolutionary Russia, much was possible even in such a conservative environment as education. In 1923, thanks to the efforts of the Russian geneticist and breeder Sergey I. Zhegalov, this department was organised on the basis of the Breeding Station. The activities of the Department of Genetics, Plant Breeding and Seed Production are based on a solid academic foundation laid by Sergei I. Zhegalov and developed by his followers who have headed and worked at the department. The Department of Genetics, Plant Breeding and Seed Production was and is a methodological center for the training of genetic breeders. The textbooks and training manuals written by its staff from Zhegalov’s time to the present day have been fundamental for all universities in the country. In 1988, on the initiative of Professor Yuri B. Konovalov, a new specialty “Breeding and Genetics of Agricultural Crops” was started at Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, which was supervised nationally by the Department of Genetics, Plant Breeding and Seed Production. During the existence of the department, more than 100 doctors and candidates of sciences have been trained. Graduates of the department can be found in in almost all major agricultural universities and research institutes in neighbouring countries, Eastern Europe, the Middle East, Vietnam, Syria, Egypt, China and many other countries.

Population genetics of horticultural crops aided by multi-omics technology and its implications for ornamental plants

Population genetics of horticultural crops aided by multi-omics technology and its implications for ornamental plants

Impact of Chemical Spray on Seed Longevity for Induction of Seed Dormancy in Mungbean (Vigna radiata L.)

The present investigation was conducted during Kharif, 2022 season at the field of Crop Research Centre (CRC) and Genetics and Plant Breeding Research Lab, School of Agriculture, ITM University, Gwalior, Madhya Pradesh to study the effect of chemical spray on longevity of seed. The experimental material consisted of ten mungbean genotype namely, IPM 2-3, IPM 2-14, Meha, Soorya, Virat, Varsha, Kanika, Vashudha, Heena and Shikha and seven treatments namely, control (water spray), GA3 @ 80 ppm, ABA @ 50 ppm, H2 O2 @ 10 mM, MH @ 1000 ppm, KNO3 @ 1 mM and IAA @ 100 ppm applied as foliar spray at 45 and 60 DAS. Longevity of seed observed after storage of 2 months intervals on different parameters like seed viability (TZ test) and electrical conductivity (dS/m). Electrical conductivity (EC) revealed that there was significant difference between the varieties, treatment and their interaction for all the testing months of storage. Numerically lower values were recorded in H2 O2 @ 10 mm (T3 ), irrespective of varieties. In general, higher EC was recorded in MH @ 1000 ppm (T4 ). It was found that the EC of the varieties were influenced by their interaction with treatments during all the testing months of storage. Seed viability (TZ test) revealed that there was significant difference between the varieties, treatment and their interaction for all months in storage. Numerically lower values were recorded in MH @ 1000 ppm (T4 ), irrespective of varieties. In general, higher seed viability was recorded in control (T0 ) in all varieties. There exists a close relationship between induced dormancy on various biochemical parameters which thereby plays a vital role in enhancing longevity of mungbean seeds.

Update on functional analysis of long non-coding RNAs in common crops.

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.

In this chapter, we explore the application of high-throughput crop phenotyping facilities for phenotype data acquisition and the extraction of significant information from the collected data through image processing and data mining methods. Additionally, the construction and outlook of crop phenotype databases are introduced and the need for global cooperation and data sharing is emphasized. High-throughput crop phenotyping significantly improves accuracy and efficiency compared to traditional measurements, making significant contributions to overcoming bottlenecks in the phenotyping field and advancing crop genetics.

Elementary and Advanced Mechanisms for Genetic Engineering in Crops

Presently, the field of plant breeding is in the genomics era, where innovative techniques are being integrated to accelerate and enhance the efficiency of breeding. Traditional plant breeding methods rely on maintaining plant germplasm with desirable agronomic traits from distinct plants produced through crosses or mutagenesis. However, advancements in genetic engineering encompass all forms of genetic modification through recombinant DNA technology (RDT) and cell fusion mechanisms. These approaches shed light on areas involving mutant organisms, DNA replication, genetic linkage resolution, genetically modified organisms (GMOs), protein sequencing, functional genomics, and computational genomics alterations in genetic engineering. The integration of structural genomics into breeding and eugenics analysis has resulted in a vast knowledge base on crop genetics, species divergence, and molecular origin of traits, as well as the evolutionary history of crop lineage from ancient ancestral species. The genomic data and advancements have proven essential in identifying rare genes, alleles, or local lesions crucial to significant agronomic traits, thereby expediting breeding cycles. This article aims to explore the potential of emerging genetic engineering technologies, including synthetic biology and genome editing, to further advance crop genetics and plant breeding.

Virtual Special Issue: Vegetable Crop Breeding and Genetics—Addressing Global Needs

Virtual Special Issue: Vegetable Crop Breeding and Genetics—Addressing Global Needs