Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: Progress and challenges
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59 BASIC BIOLOGICAL SCIENCES↗
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Major impacts of widespread structural variation on sorghum
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.
59 BASIC BIOLOGICAL SCIENCES↗
Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes
The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific noncrop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived single nucleotide polymorphisms for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that noncrop samples from the Caucasus, Siberia, and Italy may be truly wild, whereas those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.
59 BASIC BIOLOGICAL SCIENCES↗
Increased nitrogen use efficiency in crop production can provide economic and environmental benefits
Potential economic and environmental benefits of increasing nitrogen-use efficiency (NUE) are widely recognized but scarcely quantified. This study quantifies the effects of increased NUE on 1) the national agricultural economy using a simulation model of US agriculture and 2) regional water quality effects using a biogeochemical model for the Arkansas-White-Red river basin. Here, national economic effects are reported for NUE improvement scenarios of 10%, 20%, 50%, and 100%, whereas regional water quality effects are estimated for a 20% NUE improvement scenario in the Arkansas-White-Red river basin. Simulating a 20% increase in NUE in row crops is shown to reduce N requirements by 1.4 million tonnes y-1 and increase farmer net profits by 1.6% ($743 million) per year by 2026 over the baseline simulation for the same period. For each 10% increase in NUE, annual farm revenues for commodity crops increased over the baseline by approximately $350 million per year by 2026. Changes in crop prices and land-use relative to the baseline were less than 2%. This suggests a net benefit even though fertilizer cost savings can result in increased cultivation of land, i.e., ‘Jevon's paradox’. Results from the biogeochemical model of the Arkansas-White-Red river basin suggest that a 20% increase in NUE corresponds to a 5.72% reduction in nitrate loadings to freshwaters, with higher reductions in agricultural watersheds. The value of these reductions was estimated as $43 ha-1, for a total of $15.3 to 136.7 million yr-1 in avoided water treatment costs. After estimating the social value of increased NUE, we conclude with a discussion of potential strategies to increase efficiency and the research needed to achieve this goal. These include perennialization of the agricultural landscape, genetic crop improvement, targeted fertilizer application, and manipulation of the plant-root microbiome.
54 ENVIRONMENTAL SCIENCES↗
Targeted DNA insertion in plants
Conventional methods of DNA sequence insertion into plants, using Agrobacterium -mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.
Dong, Oliver Xiaoou↗
Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria
Abstract Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.
59 BASIC BIOLOGICAL SCIENCES↗
Hydrothermal pretreatment for valorization of genetically engineered bioenergy crop for lipid and cellulosic sugar recovery
Lipids accumulated in the vegetative tissues of cellulosic feedstocks can be a potential raw material for biodiesel and bioethanol production. In this work, bagasse of genetically engineered sorghum was subjected to liquid hot-water pretreatment at 170, 180, and 190°C for different reaction time. Under the optimal pretreatment condition (170°C, 20 min), the residue was enriched in glucan (57.39 ± 2.63 % w/w) and xylan (13.38 ± 0.49 % w/w). The total lipid content of the pretreated residue was 6.81% w/w, similar to that observed in untreated bagasse (6.30% w/w). Pretreatment improved the enzymatic digestibility of bagasse, allowing a recovery of 79% w/w and 86% w/w of glucose and xylose, respectively. The pretreatment and enzymatic saccharification resulted in a 2-fold increase in total lipid in enzymatic residue compared to the original bagasse. Furthermore, pretreatment and enzymatic hydrolysis enabled high sugar recovery while concentrating triglycerides and free fatty acids in the residue.
59 BASIC BIOLOGICAL SCIENCES↗
Data for Hydrothermal Pretreatment for Valorization of Genetically Engineered Bioenergy Crop for Lipid and Cellulosic Sugar Recovery
Lipids accumulated in the vegetative tissues of cellulosic feedstocks can be a potential raw material for biodiesel and bioethanol production. In this work, bagasse of genetically engineered sorghum was subjected to liquid hot-water pretreatment at 170, 180, and 190 °C for different reaction time. Under the optimal pretreatment condition (170 °C, 20 min), the residue was enriched in glucan (57.39 ± 2.63 % w/w) and xylan (13.38 ± 0.49 % w/w). The total lipid content of the pretreated residue was 6.81% w/w, similar to that observed in untreated bagasse (6.30% w/w). Pretreatment improved the enzymatic digestibility of bagasse, allowing a recovery of 79% w/w and 86% w/w of glucose and xylose, respectively. The pretreatment and enzymatic saccharification resulted in a 2-fold increase in total lipid in enzymatic residue compared to the original bagasse. Thus, pretreatment and enzymatic hydrolysis enabled high sugar recovery while concentrating triglycerides and free fatty acids in the residue.
Conversion↗
Construct design for precise DNA insertion in plants
Precise insertion of DNA sequences at targeted locations in plant genomes is pivotal for synthetic biology, genetics, and crop improvement. Construct design plays a critical role in achieving precise insertions, yet practical guidance remains limited. This review provides an in-depth overview of construct design principles and targeted DNA insertion (knock-in) strategies in plants. We assess the strengths, limitations, and construct requirements of current knock-in methods for specific applications, including short, large, and multifragment insertions. Additionally, we explore the potential of adopting advanced nonplant technologies to enhance knock-in efficiency and precision in plants. This review provides a valuable resource for facilitating the effective application of knock-in technologies to genetically improve crops with minimal off-target effects.
DNA construct↗
Knockout of ABC transporter gene ABCA2 confers resistance to Bt toxin Cry2Ab in Helicoverpa zea
Evolution of pest resistance reduces the benefits of widely cultivated genetically engineered crops that produce insecticidal proteins derived from Bacillus thuringiensis (Bt). Better understanding of the genetic basis of pest resistance to Bt crops is needed to monitor, manage, and counter resistance. Previous work shows that in several lepidopterans, resistance to Bt toxin Cry2Ab is associated with mutations in the gene encoding the ATP-binding cassette protein ABCA2. The results here show that mutations introduced by CRISPR/Cas9 gene editing in the Helicoverpa zea (corn earworm or bollworm) gene encoding ABCA2 (HzABCA2) can cause resistance to Cry2Ab. Disruptive mutations in HzABCA2 facilitated the creation of two Cry2Ab-resistant strains. A multiple concentration bioassay with one of these strains revealed it had > 200-fold resistance to Cry2Ab relative to its parental susceptible strain. All Cry2Ab-resistant individuals tested had disruptive mutations in HzABCA2. We identified five disruptive mutations in HzABCA2 gDNA. The most common mutation was a 4-bp deletion in the expected Cas9 guide RNA target site. The results here indicate that HzABCA2 is a leading candidate for monitoring Cry2Ab resistance in field populations of H. zea.
60 APPLIED LIFE SCIENCES↗
DEEPER: An Intergrated Platform for Deeper Roots
Crops with deeper roots would have multiple benefits, including better drought tolerance, reduced requirement for nitrogen fertilizer, and better sequestration of atmospheric CO 2 . DEEPER is an integrated platform of phenomic, genomic, and in silico technologies to generate maize lines with deeper roots. DEEPER is: LEADER (Leaf Elemental Accumulation from Deep Roots) is a breakthrough technology to nondestructively measure rooting depth by using the plant itself as a sensor. LEADER uses handheld X-ray Fluorescence spectrometry to quantify foliar accumulation of elements that are differentially distributed in the soil profile. LEADER is nondestructive and is orders of magnitude cheaper, faster, and more precise than any competing assay of rooting depth in the field. LEADER is able to distinguish deep-rooted from shallow-rooted maize lines in the field without the need for costly and noisy soil coring. RootRobot/DIRT3D, to automatically phenotype root architecture in any field, combining RootRobot, a mechatronics platform to excavate, clean, section, and image mature root crowns, with DIRT3D, software to quantify architectural traits in 3D. Anatomics, a high-throughput platform to phenotype root anatomy, combining LAT 2.0, a technology for 3D imaging of root anatomy and composition, with RootScan3D, software to automatically extract 3D anatomical and cell wall composition metrics from LAT 2.0 output. Using this platform we discovered two novel root traits, parenchyma cell wall thickness and multiseriate cortical sclerenchyma, that improve rooting depth and drought tolerance in maize and wheat. OpenSimRoot/Deep, software to simulate root interaction with hard subsoils. Using this platform we discovered novel concepts regarding how to increase crop rooting depth by modulating how individual root axes respond to hard soil. DeepGenes, a toolkit of genes, parent lines, and genomic selection strategies to enable breeding hybrids with deeper roots. We discovered 3 novel root genes that increase rooting depth in maize and wheat. DEEPER discovered novel root phenotypes for deeper rooting, and delivered validated ideotypes for deeper-rooted maize; novel technologies to rapidly assess root depth, root architecture and anatomy in field-grown plants; novel software tools for root modeling and 3D image analysis of root architecture and anatomy; and validated genes and genomic selection models to deploy traits for deeper rooting in maize breeding. Each DEEPER technology is transformative in its own right, and exceeds existing technologies. They are mutually synergistic, deployable for field-grown plants, and are ready for application. The phenotyping and modeling technologies are readily applicable to many crops, and genetic leads in maize may have utility in other grasses. Taken as a whole they represent a transformative platform to develop deeper-rooted crops, with greater drought tolerance, reduced fertilizer requirement, and greater carbon sequestration.
59 BASIC BIOLOGICAL SCIENCES↗
Development of male-sterile lines of Setaria viridis to accelerate C 4 model plant genetics
Setaria viridis is a diploid C 4 grass in the Poaceae family, notable for its rapid life cycle of 6–8 weeks from sowing to seed—much shorter than the 4–5 months required by crops such as Zea mays and Sorghum bicolor . This fast growth makes S. viridis a valuable model for C 4 crop research. Genetic crosses are essential for studying gene function, but manual crossing is labor-intensive and time-consuming. Here, to address this, we developed a male-sterile line by targeting the S. viridis ortholog of Setaria italica NO POLLEN 1 ( SiNP1 ), which encodes a glucose–methanol–choline oxidoreductase required for pollen exine formation. Using Cas9 and TREX2 -mediated genome editing, we generated SiNP1 knockouts in both the S. viridis ME034V and A10.1 backgrounds that were fully male-sterile. Backcrossing T 0 male-sterile plants to ME034V wild-type followed by selfing yielded a stable BC 1 F 2 line homozygous for a 59 bp deletion in the S. viridis NO POLLEN 1 gene, easily genotyped by PCR and maintained by heterozygous siblings. Using this line, we developed a simple and efficient crossing protocol that eliminates the need for emasculation. This method enables a single person to perform up to 100 crosses per day—compared to 15 using traditional methods—and yields 20–32 F 1 hybrid seeds per panicle with 100% genetic purity. We also quantified pollen flow and outcrossing frequencies under greenhouse conditions to develop optimal bagging strategies and prevent unintended pollination. This resource accelerates genetic research in S. viridis , enhancing its utility as a premier C 4 model for mapping and functional genomics.
C4 research↗
TGCM: (T)rait, (G)ene, and (C)rop Growth (M)odel Directed Targeted Gene Characterization in Sorghum (Final Technical Report)
Understanding which genes control important crop traits could help scientists develop better bioenergy and food crops more efficiently. However, plant genomes contain tens of thousands of genes, and testing each one individually is expensive and time-consuming. This project developed computational tools to predict which genes are most likely to matter, allowing researchers to focus their efforts where they will have the greatest impact. This project developed and validated integrated approaches combining machine learning, quantitative genetics, and crop growth modeling to improve the efficiency of functional gene characterization in sorghum (Sorghum bicolor), a critical bioenergy and food security crop. The research addressed a fundamental challenge in plant biology: the majority of genes in plant genomes lack experimentally validated functions, making it difficult to prioritize which genes to study using resource-intensive reverse genetics approaches.
60 APPLIED LIFE SCIENCES↗
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci
Abstract Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet ( Setaria viridis ), a model species for studies of C 4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet ( Setaria italica ). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validated Less Shattering1 ( SvLes1 ) as a gene whose product controls seed shattering. In S. italica , this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.
59 BASIC BIOLOGICAL SCIENCES↗
Novel technologies for emission reduction complement conservation agriculture to achieve negative emissions from row-crop production
Plants remove carbon dioxide from the atmosphere through photosynthesis. Because agriculture’s productivity is based on this process, a combination of technologies to reduce emissions and enhance soil carbon storage can allow this sector to achieve net negative emissions while maintaining high productivity. Unfortunately, current row-crop agricultural practice generates about 5% of greenhouse gas emissions in the United States and European Union. Here, to reduce these emissions, significant effort has been focused on changing farm management practices to maximize soil carbon. In contrast, the potential to reduce emissions has largely been neglected. Through a combination of innovations in digital agriculture, crop and microbial genetics, and electrification, we estimate that a 71% (1,744 kg CO 2 e/ha) reduction in greenhouse gas emissions from row crop agriculture is possible within the next 15 y. Importantly, emission reduction can lower the barrier to broad adoption by proceeding through multiple stages with meaningful improvements that gradually facilitate the transition to net negative practices. Emerging voluntary and regulatory ecosystems services markets will incentivize progress along this transition pathway and guide public and private investments toward technology development. In the difficult quest for net negative emissions, all tools, including emission reduction and soil carbon storage, must be developed to allow agriculture to maintain its critical societal function of provisioning society while, at the same time, generating environmental benefits.
54 ENVIRONMENTAL SCIENCES↗
Data for Miscanthus giganteus Biolistic Transformation Using the Visible RUBY Red Marker Gene to Monitor Transformation Efficiency
Miscanthus × giganteus ( M × g ) is a high- yielding perennial C4 bioenergy crop, but genetic improvement by breeding is constrained by triploid sterility and clonal propagation. Improving genetic transformation methods for M × g would provide opportunities for advantageous trait introgression. Use of an easy to phenotype reporter gene is a promising strategy to improve transformation processes and efficiency. This study presents an efficient novel method for biolistic transformation of inflorescence- derived callus in M × g and demonstrates its efficacy using RUBY, a betalain-based noninvasive reporter that is visible throughout the transformation process. RUBY expression ( Zea mays codon optimized) was visible from callus stage through plantlet development into maturity. RUBY expressing independently transformed plants were confirmed by hygromycin phosphotransferase ELISA and by genomic PCR demonstrating that the RUBY phenotype is sufficient for screening transformants. The Zea mays codon optimized hygromycin selection marker was driven by previously established promoters for Miscanthus, ZmUBI and 2×35S, while the RUBY gene expression was controlled by a known Zea mays C4 promoter, Brachypodium UBI10, newly employed in Miscanthus. The construct containing the 2×35S promoter for hygromycin had a 15.1% transformation efficiency while the ZmUBI promoter had a 20.5% transformation efficiency. This study provides a novel, highly efficient protocol for successful biolistic transformation of M × g for stable expression. This study also demonstrates that RUBY expression can be used as a convenient and powerful monitor of transformation in ongoing and future work to engineer M × g into an improved bioproduct feedstock. **NOTE: in "TableS2_ProtocolComparison.csv", the data from row 665 to 971 should be removed.
Gene Editing↗
Spinning the Facts against Genetically Engineered Foods?
A signaling game is developed in order to derive the equilibrium conditions under which special interest groups (SIGs) involved in the controversial debate over genetically engineered (GE) foods have the incentive to truthfully reveal their information or spin facts regarding the health impact of GE foods. Consumers can choose to inspect information provided by SIGs at a cost. The risk of spinning facts is much higher for pro-GE groups, because if it turns out that a certain GE food is unsafe, the penalty will be severe. However, anti-GE groups can still spin facts at low risk even if consumers choose to inspect. This helps explain why some pro-GE groups, particularly the biotech industry, tend to remain silent. Revealing information regarding the safety of GE foods could be counterproductive given pre-existing public skepticism. Consumers may not make “better” decisions with more information provided because more information increases their inspection costs. When it is costlier for consumers to inspect, it is more likely that anti-GE groups will continue to spin facts about the negative health impact of GE foods.
59 BASIC BIOLOGICAL SCIENCES↗