RESUMEN
Cyanogenic glucosides (CGs) play a key role in host-plant defense to insect feeding; however, the metabolic tradeoffs between synthesis of CGs and plant growth are not well understood. In this study, genetic mutants coupled with nondestructive phenotyping techniques were used to study the impact of the CG dhurrin on fall armyworm [Spodoptera frugiperda (J.E. Smith)] (FAW) feeding and plant growth in sorghum [Sorghum bicolor (L.) Moench]. A genetic mutation in CYP79A1 gene that disrupts dhurrin biosynthesis was used to develop sets of near-isogenic lines (NILs) with contrasting dhurrin contents in the Tx623 bmr6 genetic background. The NILs were evaluated for differences in plant growth and FAW feeding damage in replicated greenhouse and field trials. Greenhouse studies showed that dhurrin-free Tx623 bmr6 cyp79a1 plants grew more quickly than wild-type plants but were more susceptible to insect feeding based on changes in green plant area (GPA), total leaf area, and total dry weight over time. The NILs exhibited similar patterns of growth in field trials with significant differences in leaf area and dry weight of dhurrin-free plants between the infested and non-infested treatments. Taken together, these studies reveal a significant metabolic tradeoff between CG biosynthesis and plant growth in sorghum seedlings. Disruption of dhurrin biosynthesis produces plants with higher growth rates than wild-type plants but these plants have greater susceptibility to FAW feeding.
Asunto(s)
Sorghum , Animales , Nitrilos/metabolismo , Plantones/genética , Plantones/metabolismo , Sorghum/genética , Spodoptera/metabolismoRESUMEN
Advancements in phenotyping techniques capable of rapidly and nondestructively detecting impacts of drought on crops are necessary to meet the 21st-century challenge of food security. Here, we describe the use of hyperspectral reflectance to predict variation in physiological and anatomical leaf traits related with water status under varying water availability in six maize (Zea mays) hybrids that differ in yield stability under drought. We also assessed relationships among traits and collections of traits with yield stability. Measurements were collected in both greenhouse and field environments, with plants exposed to different levels of water stress or to natural water availability, respectively. Leaf spectral measurements were paired with a number of physiological and anatomical reference measurements, and predictive spectral models were constructed using a partial least-squares regression approach. All traits were relatively well predicted by spectroscopic models, with external validation (i.e. by applying partial least-squares regression coefficients on a dataset distinct from the one used for calibration) goodness-of-fit (R 2 ) ranging from 0.37 to 0.89 and normalized error ranging from 12% to 21%. Correlations between reference and predicted data were statistically similar for both greenhouse and field data. Our findings highlight the capability of vegetation spectroscopy to rapidly and nondestructively identify a number of foliar functional traits affected by drought that can be used as indicators of plant water status. Although we did not detect trait coordination with yield stability in the hybrids used in this study, expanding the range of functional traits estimated by hyperspectral data can help improve trait-based breeding approaches.
Asunto(s)
Deshidratación/genética , Deshidratación/fisiopatología , Sequías , Hojas de la Planta/anatomía & histología , Hojas de la Planta/genética , Zea mays/anatomía & histología , Zea mays/genética , Productos Agrícolas/anatomía & histología , Productos Agrícolas/genética , Productos Agrícolas/fisiología , Variación Genética , Genotipo , Fenotipo , Hojas de la Planta/fisiología , Análisis Espectral/métodos , Estrés Fisiológico/genética , Estrés Fisiológico/fisiología , Estados Unidos , Agua/metabolismo , Zea mays/fisiologíaRESUMEN
KEY MESSAGE: Seven novel alleles of SBEIIb and one allele of SSIIa co-segregated with the ASV phenotype and contributed to distinct starch quality traits important for food-processing applications. Sorghum is an important food crop for millions of people in Africa and Asia. Whole-genome re-sequencing of sorghum EMS mutants exhibiting an alkali spreading value (ASV) phenotype revealed candidate SNPs in Sobic.004G163700 and Sobic.010G093400. Comparative genomics identified Sobic.010G093400 as a starch synthase IIa and Sobic.004G163700 as a starch branching enzyme IIb. Segregation analyses showed that mutations in Sobic.010G093400 or Sobic.004G163700 co-segregated with the ASV phenotype. Mutants in SSIIa exhibited no change in amylose content but expressed lower final viscosity and lower starch gelatinization temperature (GT) than starches from non-mutant plants. The sbeIIb mutants exhibited significantly higher amylose levels and starch GT and lower viscosity compared to non-mutant starches and ssIIa mutants. Mutations in SBEIIb had a dosage-dependent effect on amylose content. Double mutants of sbeIIb and ssIIa resembled their sbeIIb parent in amylose content, starch thermal properties and viscosity profiles. These variants will provide opportunities to produce sorghum varieties with modified starch end-use qualities important for the beer brewing and baking industries and specialty foods for humans with diabetes.
Asunto(s)
Amilosa/análisis , Harina/análisis , Sorghum/genética , Almidón/análisis , Enzima Ramificadora de 1,4-alfa-Glucano/genética , Álcalis , Alelos , Análisis Mutacional de ADN , Dosificación de Gen , Mutación , Fenotipo , Proteínas de Plantas/genética , Polimorfismo de Nucleótido Simple , Alineación de Secuencia , Almidón Sintasa/genética , ViscosidadRESUMEN
Sorghum, an ancient old-world cereal grass, is the dietary staple of over 500 million people in more than 30 countries in the tropics and semitropics. Its C4 photosynthesis, drought resistance, wide adaptation, and high nutritional value hold the promise to alleviate hunger in Africa. Not present in other major cereals, such as rice, wheat, and maize, condensed tannins (proanthocyanidins) in the pigmented testa of some sorghum cultivars have been implicated in reducing protein digestibility but recently have been shown to promote human health because of their high antioxidant capacity and ability to fight obesity through reduced digestion. Combining quantitative trait locus mapping, meta-quantitative trait locus fine-mapping, and association mapping, we showed that the nucleotide polymorphisms in the Tan1 gene, coding a WD40 protein, control the tannin biosynthesis in sorghum. A 1-bp G deletion in the coding region, causing a frame shift and a premature stop codon, led to a nonfunctional allele, tan1-a. Likewise, a different 10-bp insertion resulted in a second nonfunctional allele, tan1-b. Transforming the sorghum Tan1 ORF into a nontannin Arabidopsis mutant restored the tannin phenotype. In addition, reduction in nucleotide diversity from wild sorghum accessions to landraces and cultivars was found at the region that codes the highly conserved WD40 repeat domains and the C-terminal region of the protein. Genetic research in crops, coupled with nutritional and medical research, could open the possibility of producing different levels and combinations of phenolic compounds to promote human health.
Asunto(s)
Alelos , Sorghum/metabolismo , Taninos/metabolismo , Secuencia de Bases , Datos de Secuencia Molecular , Filogenia , Polimorfismo Genético , Sitios de Carácter Cuantitativo , Homología de Secuencia de Ácido Nucleico , Sorghum/genética , Taninos/genéticaRESUMEN
In both plant breeding and crop management, interpretability plays a crucial role in instilling trust in AI-driven approaches and enabling the provision of actionable insights. The primary objective of this research is to explore and evaluate the potential contributions of deep learning network architectures that employ stacked LSTM for end-of-season maize grain yield prediction. A secondary aim is to expand the capabilities of these networks by adapting them to better accommodate and leverage the multi-modality properties of remote sensing data. In this study, a multi-modal deep learning architecture that assimilates inputs from heterogeneous data streams, including high-resolution hyperspectral imagery, LiDAR point clouds, and environmental data, is proposed to forecast maize crop yields. The architecture includes attention mechanisms that assign varying levels of importance to different modalities and temporal features that, reflect the dynamics of plant growth and environmental interactions. The interpretability of the attention weights is investigated in multi-modal networks that seek to both improve predictions and attribute crop yield outcomes to genetic and environmental variables. This approach also contributes to increased interpretability of the model's predictions. The temporal attention weight distributions highlighted relevant factors and critical growth stages that contribute to the predictions. The results of this study affirm that the attention weights are consistent with recognized biological growth stages, thereby substantiating the network's capability to learn biologically interpretable features. Accuracies of the model's predictions of yield ranged from 0.82-0.93 R2 ref in this genetics-focused study, further highlighting the potential of attention-based models. Further, this research facilitates understanding of how multi-modality remote sensing aligns with the physiological stages of maize. The proposed architecture shows promise in improving predictions and offering interpretable insights into the factors affecting maize crop yields, while demonstrating the impact of data collection by different modalities through the growing season. By identifying relevant factors and critical growth stages, the model's attention weights provide valuable information that can be used in both plant breeding and crop management. The consistency of attention weights with biological growth stages reinforces the potential of deep learning networks in agricultural applications, particularly in leveraging remote sensing data for yield prediction. To the best of our knowledge, this is the first study that investigates the use of hyperspectral and LiDAR UAV time series data for explaining/interpreting plant growth stages within deep learning networks and forecasting plot-level maize grain yield using late fusion modalities with attention mechanisms.
RESUMEN
Dwarfism is a useful trait in many crop plants because it contributes to improved lodging resistance and harvest index. The mutant allele dw3-ref (dwarf3-reference) of sorghum [Sorghum bicolor (L.) Moench] is characterized by an 882 bp tandem duplication in the fifth exon of the gene that is unstable and reverts to wild-type at a frequency greater than 0.001 in many genetic backgrounds. The goal of this research was to identify stable alleles of dw3 (dwarf3) that could be backcrossed into elite parent lines to improve height stability of the crop. To discover new alleles of dw3, a panel consisting mostly of sorghum conversion lines (SC-lines) was screened by polymerase chain reaction for the 882 bp tandem duplication in the fifth exon of dw3-ref. Sanger sequencing was used to characterize the DNA sequence of this fragment in genotypes that did not contain the 882 bp tandem duplication. Sequence analysis identified three indel mutations, including an 82 bp deletion, a 6 bp duplication, and a 15 bp deletion in this region of the gene. Field trials of the donor genotypes with these new alleles indicated no wild-type revertants of dw3-sd3 (dwarf3-stable dwarf), dw3-sd4, and dw3-sd5. These alleles were backcrossed into Tx430. Field trials of backcross progeny (BC2F4) with the dw3-sd3, dw3-sd4, and dw3-sd5 alleles indicated no revertants. The plant height and flowering time characteristics of the backcross progeny were similar or slightly shorter and earlier than the recurrent parent. These findings demonstrate that dw3-sd3, dw3-sd4, and dw3-sd5 alleles will be useful in breeding for the stable dwarf trait.
Asunto(s)
Alelos , Sorghum , Sorghum/genética , Mutación , Genes de Plantas , Proteínas de Plantas/genética , GenotipoRESUMEN
Yield for biofuel crops is measured in terms of biomass, so measurements throughout the growing season are crucial in breeding programs, yet traditionally time- and labor-consuming since they involve destructive sampling. Modern remote sensing platforms, such as unmanned aerial vehicles (UAVs), can carry multiple sensors and collect numerous phenotypic traits with efficient, non-invasive field surveys. However, modeling the complex relationships between the observed phenotypic traits and biomass remains a challenging task, as the ground reference data are very limited for each genotype in the breeding experiment. In this study, a Long Short-Term Memory (LSTM) based Recurrent Neural Network (RNN) model is proposed for sorghum biomass prediction. The architecture is designed to exploit the time series remote sensing and weather data, as well as static genotypic information. As a large number of features have been derived from the remote sensing data, feature importance analysis is conducted to identify and remove redundant features. A strategy to extract representative information from high-dimensional genetic markers is proposed. To enhance generalization and minimize the need for ground reference data, transfer learning strategies are proposed for selecting the most informative training samples from the target domain. Consequently, a pre-trained model can be refined with limited training samples. Field experiments were conducted over a sorghum breeding trial planted in multiple years with more than 600 testcross hybrids. The results show that the proposed LSTM-based RNN model can achieve high accuracies for single year prediction. Further, with the proposed transfer learning strategies, a pre-trained model can be refined with limited training samples from the target domain and predict biomass with an accuracy comparable to that from a trained-from-scratch model for both multiple experiments within a given year and across multiple years.
RESUMEN
Genotype-by-environment interaction (GEI) is among the greatest challenges for maize breeding programs. Strong GEI limits both the prediction of genotype performance across variable environmental conditions and the identification of genomic regions associated with grain yield. Incorporating GEI into yield prediction models has been shown to improve prediction accuracy of yield; nevertheless, more work is needed to further understand this complex interaction across populations and environments. The main objectives of this study were to: 1) assess GEI in maize grain yield based on reaction norm models and predict hybrid performance across a gradient of environmental (EG) conditions and 2) perform a genome-wide association study (GWAS) and post-GWAS analyses for maize grain yield using data from 2014 to 2017 of the Genomes to Fields initiative hybrid trial. After quality control, 2,126 hybrids with genotypic and phenotypic data were assessed across 86 environments representing combinations of locations and years, although not all hybrids were evaluated in all environments. Heritability was greater in higher-yielding environments due to an increase in genetic variability in these environments in comparison to the low-yielding environments. GWAS was carried out for yield and five single nucleotide polymorphisms (SNPs) with the highest magnitude of effect were selected in each environment for follow-up analyses. Many candidate genes in proximity of selected SNPs have been previously reported with roles in stress response. Genomic prediction was performed to assess prediction accuracy of previously tested or untested hybrids in environments from a new growing season. Prediction accuracy was 0.34 for cross validation across years (CV0-Predicted EG) and 0.21 for cross validation across years with only untested hybrids (CV00-Predicted EG) when compared to Best Linear Unbiased Prediction (BLUPs) that did not utilize genotypic or environmental relationships. Prediction accuracy improved to 0.80 (CV0-Predicted EG) and 0.60 (CV00-Predicted EG) when compared to the whole-dataset model that used the genomic relationships and the environmental gradient of all environments in the study. These results identify regions of the genome for future selection to improve yield and a methodology to increase the number of hybrids evaluated across locations of a multi-environment trial through genomic prediction.
RESUMEN
Remote sensing enables the rapid assessment of many traits that provide valuable information to plant breeders throughout the growing season to improve genetic gain. These traits are often extracted from remote sensing data on a row segment (rows within a plot) basis enabling the quantitative assessment of any row-wise subset of plants in a plot, rather than a few individual representative plants, as is commonly done in field-based phenotyping. Nevertheless, which rows to include in analysis is still a matter of debate. The objective of this experiment was to evaluate row selection and plot trimming in field trials conducted using four-row plots with remote sensing traits extracted from RGB (red-green-blue), LiDAR (light detection and ranging), and VNIR (visible near infrared) hyperspectral data. Uncrewed aerial vehicle flights were conducted throughout the growing seasons of 2018 to 2021 with data collected on three years of a sorghum experiment and two years of a maize experiment. Traits were extracted from each plot based on all four row segments (RS) (RS1234), inner rows (RS23), outer rows (RS14), and individual rows (RS1, RS2, RS3, and RS4). Plot end trimming of 40 cm was an additional factor tested. Repeatability and predictive modeling of end-season yield were used to evaluate performance of these methodologies. Plot trimming was never shown to result in significantly different outcomes from non-trimmed plots. Significant differences were often observed based on differences in row selection. Plots with more row segments were often favorable for increasing repeatability, and excluding outer rows improved predictive modeling. These results support long-standing principles of experimental design in agronomy and should be considered in breeding programs that incorporate remote sensing.
RESUMEN
Quantifying the digestibility of proteins in cereal grain is important for assessing and improving the nutritional quality of the grain after ingestion. This trait is particularly important for sorghum since the grain protein is known to be less digestible after wet cooking compared to other cereals. The reduced digestibility contributes to malnutrition in regions where sorghum is consumed as a staple food. We describe here a modified, high-throughput protocol to quantify pepsin-digestible proteins in sorghum grain before and after cooking. The protocol includes three basic steps: â¢grinding and cooking the sorghum into a small porridge for 20 min,â¢digesting the porridge with pepsin for at least 2 h,â¢extracting and assaying the protein extract. This method closely resembles the reality of sorghum usage as food and feed, can be scaled to process large numbers of samples and can be adapted for use with other cereal crops. This protocol requires only basic lab equipment and expertise, and one person can easily process 280 samples (140 accessions) in 7-8 h.
RESUMEN
Field crop traits have and are experiencing significant changes due to genetic and agronomic improvements. How these changes affect regional water quantity and quality processes has not been clarified. The St. Joseph River Watershed (SJRW) located in the U.S. Corn Belt was selected as a case study area. Crop (corn and soybean) trait improvements in the past decades were reviewed and summarized and include changes of growing degree days (GDD), leaf area index (LAI), light utilization (LU), drought tolerance (DT), nutrient content (NC), and harvest index (HI). Based on a calibrated 9-year (from 2011 to 2019) SWAT (Soil and Water Assessment Tool) simulation in SJRW, sensitivities of the above crop traits to yield, ETa, stream flow, tile flow, surface runoff, and nutrient loads (NO3N, TN, soluble-P, and TP) were analyzed. Crop traits and their corresponding SWAT parameters for the 2010s were obtained from model calibration and used as the baseline/current scenario; for the 1980s, they were summarized from literature review and used as an historical scenario, while those for the 2040s were determined by assuming crop traits are changing linearly with time and projected as the future scenario. Water quantity and quality changes under the historical and future crop scenarios were compared with the baseline/current simulation. Results showed LU and DT were the most sensitive crop traits to water quantity (i.e., ETa, stream flow, tile flow, and surface runoff), while HI was the most sensitive to nutrient loads. The impacts of crop improvements on nutrient loads were more significant than on water budgets. Compared with the baseline, the historical and future scenarios resulted in 1.5 - 2.0% changes of stream flow, 6.8 - 18.6% changes of nitrogen loads (NO3N and TN) and 2.6 - 3.9% changes of phosphorus loads (soluble-P, and TP) in the stream flow, annually. Moreover, in certain months, these changes can reach about 12% for stream flow, 42% for nitrogen loads, and 12% for phosphorus loads. Nitrogen losses by tile drainage and percolation, and phosphorus losses by surface runoff and tile drainage were most significantly affected by the crop improvements. Future work should consider expected crop improvements when studying long-term hydrology and nutrient cycles in agricultural watersheds.
Asunto(s)
Agricultura , Agua , Nitrógeno/análisis , Fósforo/análisis , Ríos/química , Calidad del Agua , Zea maysRESUMEN
Leaf area index (LAI) is an important variable for characterizing plant canopy in crop models. It is traditionally defined as the total one-sided leaf area per unit ground area and is estimated by both direct and indirect methods. This paper explores the effectiveness of using light detection and ranging (LiDAR) data to estimate LAI for sorghum and maize with different treatments at multiple times during the growing season from both a wheeled vehicle and Unmanned Aerial Vehicles. Linear and nonlinear regression models are investigated for prediction utilizing statistical and plant structure-based features extracted from the LiDAR point cloud data with ground reference obtained from an in-field plant canopy analyzer (indirect method). Results based on the value of the coefficient of determination (R 2) and root mean squared error for predictive models ranged from â¼0.4 in the early season to â¼0.6 for sorghum and â¼0.5 to 0.80 for maize from 40 Days after Sowing to harvest.
RESUMEN
As the plant variety protection (PVP) of commercial inbred lines expire, public breeding programs gain a wealth of genetic materials that have undergone many years of intense selection; however, the value of these inbred lines is only fully realized when they have been well characterized and are used in hybrid combinations. Additionally, while yield is the primary trait by which hybrids are evaluated, new phenotyping technologies, such as ear photometry (EP), may provide an assessment of yield components that can be scaled to breeding programs. The objective of this experiment was to use EP to describe the testcross performance of inbred lines from temperate and tropical origins. We evaluated the performance of 298 public and ex-PVP inbred lines and 274 Drought Tolerant Maize for Africa (DTMA) inbred lines when crossed to Iodent (PHP02) and/or Stiff Stalk (2FACC) testers for 25 yield-related traits. Kernel weight, kernels per ear, and grain yield predicted by EP were correlated with their reference traits with r = 0.49, r = 0.88, and r = 0.75, respectively. The testcross performance of each maize inbred line was tester dependent. When lines were crossed to a tester within the heterotic group, many yield components related to ear size and kernels per ear were significantly reduced, but kernel size was rarely impacted. Thus, the effect of heterosis was more noticeable on traits that increased kernels per ear rather than kernel size. Hybrids of DTMA inbred lines crossed to PHP02 exhibited phenotypes similar to testcrosses of Stiff Stalk and Non-Stiff Stalk heterotic groups for yield due to significant increases in kernel size to compensate for a reduction in kernels per ear. Kernels per ear and ear length were correlated (r = 0.89 and r = 0.84, respectively) with and more heritable than yield, suggesting these traits could be useful for inbred selection.
RESUMEN
Sorghum is an important food crop in many parts of Africa and Asia. Landraces of sorghum are known to exhibit variation in food quality traits including starch and protein content and composition. In this study, a panel of diverse sorghum breeding lines and 788 sorghum conversion (SC) lines representing the global germplasm diversity of the crop were evaluated for variation in starch quality based on alkali spreading value (ASV). A small number of genotypes with stable expression of the ASV+ phenotype across seasons were identified; mostly representing Nandyal types from India. Genetic studies showed the ASV+ phenotype was inherited as a recessive trait. Whole genome resequencing of ASV+ donor lines revealed SNPs in genes involved in starch biosynthesis. A genome wide association study (GWAS) identified a significant SNP associated with ASV near Sobic.010G273800, a starch branching enzyme I precursor, and Sobic.010G274800 and Sobic.010G275001, both annotated as glucosyltransferases. Physiochemical analyses of accessions with contrasting ASV phenotypes demonstrated an environment dependent lower starch gelatinization temperature (GT), amylose content of approximately 22%, and good gel consistency. The starch quality attributes of these lines could be valuable in food products that require good gel consistency and viscosity.
Asunto(s)
Sorghum , África , Álcalis , Asia , Estudio de Asociación del Genoma Completo , India , Fitomejoramiento , Sorghum/genética , AlmidónRESUMEN
BACKGROUND: Breakthrough imaging technologies may challenge the plant phenotyping bottleneck regarding marker-assisted breeding and genetic mapping. In this context, X-Ray CT (computed tomography) technology can accurately obtain the digital twin of root system architecture (RSA) but computational methods to quantify RSA traits and analyze their changes over time are limited. RSA traits extremely affect agricultural productivity. We develop a spatial-temporal root architectural modeling method based on 4D data from X-ray CT. This novel approach is optimized for high-throughput phenotyping considering the cost-effective time to process the data and the accuracy and robustness of the results. Significant root architectural traits, including root elongation rate, number, length, growth angle, height, diameter, branching map, and volume of axial and lateral roots are extracted from the model based on the digital twin. Our pipeline is divided into two major steps: (i) first, we compute the curve-skeleton based on a constrained Laplacian smoothing algorithm. This skeletal structure determines the registration of the roots over time; (ii) subsequently, the RSA is robustly modeled by a cylindrical fitting to spatially quantify several traits. The experiment was carried out at the Ag Alumni Seed Phenotyping Facility (AAPF) from Purdue University in West Lafayette (IN, USA). RESULTS: Roots from three samples of tomato plants at two different times and three samples of corn plants at three different times were scanned. Regarding the first step, the PCA analysis of the skeleton is able to accurately and robustly register temporal roots. From the second step, several traits were computed. Two of them were accurately validated using the root digital twin as a ground truth against the cylindrical model: number of branches (RRMSE better than 9%) and volume, reaching a coefficient of determination (R2) of 0.84 and a P < 0.001. CONCLUSIONS: The experimental results support the viability of the developed methodology, being able to provide scalability to a comprehensive analysis in order to perform high throughput root phenotyping.
RESUMEN
While gut bacteria have different abilities to utilize dietary fibers, the degree of fiber structural alignment to bacteria species is not well understood. Corn bran arabinoxylan (CAX) was used to investigate how minor polymer fine structural differences at the genotype × environment level influences the human gut microbiota. CAXs were extracted from 4 corn genotypes × 3 growing years and used in in vitro fecal fermentations. CAXs from different genotypes had varied contents of arabinose/xylose ratio (0.46-0.54), galactose (58-101 mg/g), glucuronic acid (18-32 mg/g). There was genotype- but not environment-specific differences in fine structures. After 24 h fermentation, CAX showed different acetate (71-86 mM), propionate (35-44 mM), butyrate (7-10 mM), and total short chain fatty acid (SCFA) (117-137 mM) production. SCFA profiles and gut microbiota both shifted in a genotype-specific way. In conclusion, the study reveals a very high specificity of fiber structure to gut bacteria use and SCFA production.
Asunto(s)
Microbioma Gastrointestinal/efectos de los fármacos , Xilanos/química , Zea mays/genética , Acetatos/química , Arabinosa/química , Butiratos/química , Fibras de la Dieta/análisis , Ácidos Grasos Volátiles/química , Heces , Fermentación , Galactosa/química , Genotipo , Ácido Glucurónico/química , Humanos , Polímeros/química , Propionatos/química , Xilosa/químicaRESUMEN
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.
Asunto(s)
Grano Comestible/genética , Genes Dominantes , Hibridación Genética , Modelos Genéticos , Fitomejoramiento/métodos , Carácter Cuantitativo Heredable , Zea mays/genética , Grano Comestible/crecimiento & desarrollo , Epistasis Genética , Evolución Molecular , Interacción Gen-Ambiente , Zea mays/crecimiento & desarrolloRESUMEN
Sweet sorghum has the potential to become a versatile feedstock for large-scale bioenergy production given its sugar from stem juice, cellulose/hemicellulose from stalks, and starch from grain. However, for researchers to maximize its feedstock potential a first step includes additional evaluations of the 2,180 accessions with varied origins in the US historic sweet sorghum collection. To assess genetic diversity of this collection for bioenergy breeding and population structure for association mapping, we selected 96 accessions and genotyped them with 95 simple sequence repeat markers. Subsequent genetic diversity and population structure analysis methods identified four subpopulations in this panel, which correlated well with the geographic locations where these accessions originated or were collected. Model comparisons for three quantitative traits revealed different levels of population structure effects on flowering time, plant height, and brix. Our results suggest that diverse germplasm accessions curated from different geographical regions should be considered for plant breeding programs to develop sweet sorghum cultivars or hybrids, and that this sweet sorghum panel can be further explored for association mapping.
Asunto(s)
Variación Genética , Genética de Población , Sorghum/genética , Biocombustibles , Productos Agrícolas/genética , Cruzamientos Genéticos , ADN de Plantas/genética , Marcadores Genéticos , Genotipo , Humanos , Modelos Genéticos , Secuencias Repetitivas de Ácidos Nucleicos/genética , Estados UnidosRESUMEN
Among major cereals domesticated as staple food, only sorghum has a high proportion of cultivars with condensed tannins in grain, which can trigger bitter taste perception in animals by binding to type 2 taste receptors (TAS2Rs). Here, we report the completion of uncovering of a pair of duplicate recessive genes (Tannin1 and Tannin2) underlying tannin presence. Three loss-of-function alleles from each gene were identified in non-tannin sorghum desired as palatable food. Condensed tannins effectively prevented sparrows from consuming sorghum grain. Parallel geographic distributions between tannin sorghum and Quelea quelea supported the role of tannins in fighting against this major herbivore threat. Association between geographic distributions of human TAS2R variants and tannin sorghum across Africa suggested that different causes had probably driven this bidirectional selection according to varied local herbivore threats and human taste sensitivity. Our investigation uncovered coevolution among humans, plants and environments linked by allelochemicals.
Asunto(s)
Feromonas/metabolismo , Sorghum/metabolismo , Taninos/metabolismo , África , Alcadienos , Animales , Conducta Alimentaria , Humanos , Feromonas/análisis , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Selección Genética , Sorghum/química , Sorghum/genética , Sorghum/parasitología , Gorriones/fisiología , Taninos/análisis , GustoRESUMEN
Genetic linkage maps are fundamental for the localization of genes conferring tolerance to greenbug, Schizaphis graminum (Rondani), feeding damage in sorghum, Sorghum bicolor (L.) Moench. Thirteen linkage groups (LGs) containing 60 simple sequence repeat (SSR) loci were mapped by using a set of sorghum recombinant inbred lines (RILs) obtained from the cross '96-4121' (greenbug-tolerant parent) x Redlan (greenbug-susceptible parent). The LG spanned a distance of 603.5 cM, with the number of loci per LG varying from 2 to 14. Seventeen additional SSR loci were unlinked at a log of odds value of 3.0. Based on chlorophyll loss occurring after greenbug feeding, visual damage ratings, and soil plant analysis development (SPAD), chlorophyll-loss indices were recorded for each RIL and for the parents used in the cross. Composite-interval mapping identified three quantitative trait loci (QTLs) associated with biotype I and five QTLs associated with biotype K. The amount of phenotypic variation explained by these QTLs ranged from 9 to 19.6%. The identification of QTLs that influence greenbug tolerance will not only facilitate the use of marker-assisted selection in sorghum breeding programs but also will provide a solid foundation for detailed characterization of individual loci implicated in greenbug tolerance in sorghum.