Genotype by environment interaction, correlation, AMMI, GGE biplot and cluster analysis for grain yield and other agronomic traits in sorghum (Sorghum bicolor L. Moench).

Genotype by environment (G×E) interaction is a major factor limiting the success of germplasm selection and identification of superior genotypes for use in plant breeding programs. Similar to the case in other crops, G×E complicates the improvement of sorghum, and hence it should be determined and used in decision-making programs. The present study aimed at assessing the G×E interaction, and the correlation between traits for superior sorghum genotypes. Three hundred twenty sorghum landraces and four improved varieties were used in alpha lattice experimental design-based field trial across three environments (Melkassa, Mieso and Mehoni) in Ethiopia. Phenotypic data were collected for days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT) and grain yield (GY). The results revealed that the variance due to genotype, environment and G×E interaction were highly significant (P < 0.001) for all traits. GY and PAWT were highly affected by environments and G×E whereas DTF, PALH, PAWD and PH were mainly affected by genotypic variation. Therefore, multi-environment testing is needed for taking care of G × E interaction to identify high yielding and stable sorghum landraces. GY and PAWT revealed highly significant positive correlations indicating the possibility of effective selection of the two traits simultaneously. Among the studied populations, South Wello, West Hararghe and Shewa zones had highly diverse genotypes that were distributed across all clusters. Hence, these areas can be considered as hotspots for identifying divergent sorghum landraces that could be used in breeding programs. Melkassa was the most representative environment whereas Mieso was the most discriminating. Five genotypes (G148, G123, G110, G203 and G73) were identified as superior across the test environments for grain yield with farmer-preferred trait, such as plant height. The identified stable and high yielding genotypes are valuable genetic resources that should be used in sorghum breeding programs.

Gene duplication drove the loss of awn in sorghum.

Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with "noncoding DNA" and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.

Formation of Proto-Kranz in C3 Rice Induced by Spike-Stalk Injection Method.

Introduction of C4 photosynthetic traits into C3 crops is an important strategy for improving photosynthetic capacity and productivity. Here, we report the research results of a variant line of sorghum-rice (SR) plant with big panicle and high spikelet density by introducing sorghum genome DNA into rice by spike-stalk injection. The whole-genome resequencing showed that a few sorghum genes could be integrated into the rice genome. Gene expression was confirmed for two C4 photosynthetic enzymes containing pyruvate, orthophosphate dikinase and phosphoenolpyruvate carboxykinase. Exogenous sorghum DNA integration induced a series of key traits associated with the C4 pathway called "proto-Kranz" anatomy, including leaf thickness, bundle sheath number and size, and chloroplast size in bundle sheath cells. Significantly, transgenic plants exhibited enhanced photosynthetic capacity resulting from both photosynthetic CO2-concentrating effect and improved energy balance, which led to an increase in carbohydrate levels and productivity. Furthermore, such rice plant exhibited delayed leaf senescence. In summary, this study provides a proof for the feasibility of inducing the transition from C3 leaf anatomy to proto-Kranz by spike-stalk injection to achieve efficient photosynthesis and increase productivity.

Differential responses of sorghum genotypes to drought stress revealed by physio-chemical and transcriptional analysis.

Sorghum is an essential food crop for millions of people in the semi-arid regions of the world, where its production is severely limited by drought stress. Drought in the early stages of crop growth and development irreversibly interferes, which leads to poor yield. The effect of drought stress in sorghum was studied at physiological, biochemical, and molecular levels in a set of two genotypes differing in their tolerance to drought. Drought stress was imposed by restraining water for 10 days on 25 days old seedlings. A significant influence of water stress was observed on the considered morpho-physiological and biochemical traits. The genotype DRT1019 exhibited physiological and biochemical indicators of drought avoidance through delayed leaf rolling, osmotic adjustment, ideal gas-exchange system, solute accumulation, an increased level of enzyme synthesis and root trait expression as compared to the ICSV95022 genotype. Furthermore, differences in the metabolite changes viz. total carbohydrate, total amides, and lipids were found between the two genotypes under drought stress. In addition, transcript profiling of potential candidate drought genes such as SbTIP3-1, SbDHN1, SbTPS, and SbDREB1A revealed up-regulation in DRT1019, which corresponded with other important physiological and biochemical parameters exhibited in the genotype. In conclusion, this study provides an improved understanding of whole plant response to drought stress in sorghum. Additionally, our results provide promising candidate genes for drought tolerance in sorghum that can be used as potential markers for drought tolerance breeding programs.

Leaf angle distribution in Johnsongrass, leaf thickness in sorghum and Johnsongrass, and association with response to Colletotrichum sublineola.

Basal leaf angle distribution was surveyed in twenty-one Johnsongrass cultivars near the end of the vegetative stage. The angles increased from the top to the bottom leaves, and compared to cultivated grain sorghums, the average angle was larger in Johnsongrass. When basal leaf angle distribution data were correlated with pathogenicity test data from excised-leaf assays for three isolates of Colletotrichum sublineola, the results showed a weak positive correlation between basal leaf angle and pathogenicity level in Johnsongrass. In order to investigate a protective role of leaf thickness to C. sublineola, leaf thickness was measured in three sorghum cultivars and one Johnsongrass cultivar at the 8-leaf-stage. Leaf thickness near the apex, near the base, and half-way between the two points were measured in the top four leaves of each plant. Thickness of leaf blade and midrib were recorded separately. Using an excised-leaf-assay, the three points were inoculated with C. sublineola, and pathogenicity level was recorded 4-days-post-inoculation. Results showed strong negative correlations between leaf midrib thickness and pathogenicity level in sorghum and Johnsongrass but not in leaf blades.

Toward "Smart Canopy" Sorghum: Discovery of the Genetic Control of Leaf Angle Across Layers.

A "smart canopy" ideotype has been proposed with leaves being upright at the top and more horizontal toward the bottom of the plant to maximize light interception and conversion efficiencies, and thus increasing yield. The genetic control of leaf angle has, to date, been studied on one or two leaves, or data have been merged from multiple leaves to generate average values. This approach has limited our understanding of the diversity of leaf angles across layers and their genetic control. Genome-wide association studies and quantitative trait loci mapping studies in sorghum (Sorghum bicolor) were performed using layer-specific angle data collected manually and via high-throughput phenotyping strategies. The observed distribution of angles in indoor and field settings is opposite to the ideotype. Several genomic regions were associated with leaf angle within layers or across the canopy. The expression of the brassinosteroid-related transcription factor BZR1/BES1 and the auxin-transporter Dwarf3 were found to be highly correlated with the distribution of angles at different layers. The application of a brassinosteroid biosynthesis inhibitor could not revert the undesirable overall angle distribution. These discoveries demonstrate that the exploitation of layer-specific quantitative trait loci/genes will be instrumental to reversing the natural angle distribution in sorghum according to the "smart canopy" ideotype.

Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor.

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology.

Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.

Morphological changes during juvenile-to-adult phase transition in sorghum.

MAIN CONCLUSION: Morphological and genetic markers indicate that in sorghum, the juvenile-to-adult phase transition occurs during the fourth and fifth leaf stages. This timing differs from those reported for other plants. The juvenile-to-adult (JA) phase transition is an important event for optimizing vegetative growth and reproductive success in plants. Among the Poaceae crops, which are a vital food source for humans, studies of the JA phase transition have been restricted to rice and maize. We studied the morphological and genetic changes that occur during the early development of sorghum and found that dramatic changes occur in shoot architecture during the early vegetative stages. Changes were observed in leaf size, leaf shape, numbers of trichomes, and size of the shoot apical meristem. In particular, the length/width ratios of the leaf blades in the fifth and upper leaves were completely different from those of the second to fourth leaves. The fifth and upper leaves have trichomes on their adaxial sides, which were absent on the lower leaves. We also analyzed expression of two microRNAs that are known to be molecular markers of the JA phase transition and found that expression of miR156 was highest in the second to fourth leaves and then was gradually down-regulated, whereas miR172 expression followed the opposite pattern. These results suggest that in sorghum, the second and third leaves represent the juvenile phase, the fourth and fifth leaves are in the transition stage, and the sixth and upper leaves are in the adult phase. Thus, the JA phase transition occurs during the fourth and fifth leaf stages. These findings are expected to be useful for understanding the early development of sorghum.

Genetic Architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor.

The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.

Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS.

Because structural variation in the inflorescence architecture of cereal crops can influence yield, it is of interest to identify the genes responsible for this variation. However, the manual collection of inflorescence phenotypes can be time consuming for the large populations needed to conduct genome-wide association studies (GWAS) and is difficult for multidimensional traits such as volume. A semiautomated phenotyping pipeline, TIM (Toolkit for Inflorescence Measurement), was developed and used to extract unidimensional and multidimensional features from images of 1,064 sorghum (Sorghum bicolor) panicles from 272 genotypes comprising a subset of the Sorghum Association Panel. GWAS detected 35 unique single-nucleotide polymorphisms associated with variation in inflorescence architecture. The accuracy of the TIM pipeline is supported by the fact that several of these trait-associated single-nucleotide polymorphisms (TASs) are located within chromosomal regions associated with similar traits in previously published quantitative trait locus and GWAS analyses of sorghum. Additionally, sorghum homologs of maize (Zea mays) and rice (Oryza sativa) genes known to affect inflorescence architecture are enriched in the vicinities of TASs. Finally, our TASs are enriched within genomic regions that exhibit high levels of divergence between converted tropical lines and cultivars, consistent with the hypothesis that these chromosomal intervals were targets of selection during modern breeding.

Evaluation of a miniaturized NIR spectrometer for cultivar identification: The case of barley, chickpea and sorghum in Ethiopia.

Crop cultivar identification is fundamental for agricultural research, industry and policies. This paper investigates the feasibility of using visible/near infrared hyperspectral data collected with a miniaturized NIR spectrometer to identify cultivars of barley, chickpea and sorghum in the context of Ethiopia. A total of 2650 grains of barley, chickpea and sorghum cultivars were scanned using the SCIO, a recently released miniaturized NIR spectrometer. The effects of data preprocessing techniques and choosing a machine learning algorithm on distinguishing cultivars are further evaluated. Predictive multiclass models of 24 barley cultivars, 19 chickpea cultivars and 10 sorghum cultivars delivered an accuracy of 89%, 96% and 87% on hold-out sample. The Support Vector Machine (SVM) and Partial least squares discriminant analysis (PLS-DA) algorithms consistently outperformed other algorithms. Several cultivars, believed to be widely adopted in Ethiopia, were identified with perfect accuracy. These results advance the discussion on cultivar identification survey methods by demonstrating that miniaturized NIR spectrometers represent a low-cost, rapid and viable tool. We further discuss the potential utility of the method for adoption surveys, field-scale agronomic studies, socio-economic impact assessments and value chain quality control. Finally, we provide a free tool for R to easily carry out crop cultivar identification and measure uncertainty based on spectral data.

Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker-trait associations.

Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. Methods: In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. Key Results: Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P < 2.9 × 10-6) on chromosomes SBI-02, SBI-03, SBI-05 and SBI-09. Co-localization of significant and suggestive (P < 5.7 × 10-5) associations for several traits indicated hotspots controlling root-system development on chromosomes SBI-02 and SBI-03. Conclusions: Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions of the present study.

Variáveis morfogênicas e estruturais de sorgo forrageiro implantado com diferentes arranjos populacionais sob pastoreio contínuo / Morphogenetic and structural variables of sorghum implanted with different population arrangements under continuous grazing

O objetivo do estudo foi avaliar os efeitos da utilização de diferentes arranjos populacionais na implantação de sorgo forrageiro nas características morfogênicas e estruturais do pasto. Os tratamentos foram 22 ou 44cm entrelinhas e 12 ou 24kg de sementes ha-1. O método de pastoreio foi contínuo. Foram utilizadas 36 novilhas, com idade e peso corporal médios de 15 meses de 262kg. As variáveis morfogênicas não foram influenciadas significativamente (P>0,05) pelos arranjos populacionais e pelos períodos de avaliação, sendo obtidos taxa de alongamento e senescência foliar de 1,43 e 1,11cm dia-1afilho-1, respectivamente, taxa de aparecimento foliar e intervalo de surgimento de folhas de 0,28 folhas dia-1afilho-1 e 3,81 dias, filocrono e duração de vida foliar de 72,99 e 351,68 graus dia, nessa ordem. As características estruturais do pasto foram influenciadas pelos períodos de avaliação. Do primeiro para o terceiro período de avaliação, foi verificada uma redução de 65,53% no número de folhas em alongamento e de 47,79% no número de folhas vivas.(AU)

The objective of the study was to evaluate the effects of using different population arrangements in the implementation of sorghum in the morphogenetic and structural characteristics of the pasture. The treatments were 22 or 44cm between rows and 12 or 24kg ha-1 of seed. The grazing method was continuous. The sample consisted of 36 heifers with an average age of 15 months and average body weight of 262kg. Morphogenic variables were not significantly influenced (P>0.05) by population arrangements and evaluation periods, elongation rate and leaf senescence of 1.43 and 1.11cm afilho-1 day-1 being obtained, respectively, and leaf appearance rate of leaf appearance leaves the range of 0.28 day-1 and 1afilho 3.81 days, phyllochron and leaf duration of life of 72.99 and 351.68 degree day, in that order. The structural characteristics of the pasture were influenced by evaluation periods. From the first to the third evaluation period, a reduction of 65.53% in the number of leaves in stretching and 47.79% in the number of living leaves was verified.(AU)

High-Resolution Laser Scanning Reveals Plant Architectures that Reflect Universal Network Design Principles.

Transport networks serve critical functions in biological and engineered systems, and yet their design requires trade-offs between competing objectives. Due to their sessile lifestyle, plants need to optimize their architecture to efficiently acquire and distribute resources while also minimizing costs in building infrastructure. To understand how plants resolve this design trade-off, we used high-precision three-dimensional laser scanning to map the architectures of tomato, tobacco, or sorghum plants grown in several environmental conditions and through multiple developmental time points, scanning in total 505 architectures from 37 plants. Using a graph-theoretic algorithm that we developed to evaluate design strategies, we find that plant architectures lie along the Pareto front between two simple length-based objectives-minimizing total branch length and minimizing nutrient transport distance-thereby conferring a selective fitness advantage for plant transport processes. The location along the Pareto front can distinguish among species and conditions, suggesting that during evolution, natural selection may employ common network design principles despite different optimization trade-offs.

A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops.

Recent advances in omics technologies have not been accompanied by equally efficient, cost-effective, and accurate phenotyping methods required to dissect the genetic architecture of complex traits. Even though high-throughput phenotyping platforms have been developed for controlled environments, field-based aerial and ground technologies have only been designed and deployed for short-stature crops. Therefore, we developed and tested Phenobot 1.0, an auto-steered and self-propelled field-based high-throughput phenotyping platform for tall dense canopy crops, such as sorghum (Sorghum bicolor). Phenobot 1.0 was equipped with laterally positioned and vertically stacked stereo RGB cameras. Images collected from 307 diverse sorghum lines were reconstructed in 3D for feature extraction. User interfaces were developed, and multiple algorithms were evaluated for their accuracy in estimating plant height and stem diameter. Tested feature extraction methods included the following: (1) User-interactive Individual Plant Height Extraction (UsIn-PHe) based on dense stereo three-dimensional reconstruction; (2) Automatic Hedge-based Plant Height Extraction (Auto-PHe) based on dense stereo 3D reconstruction; (3) User-interactive Dense Stereo Matching Stem Diameter Extraction; and (4) User-interactive Image Patch Stereo Matching Stem Diameter Extraction (IPaS-Di). Comparative genome-wide association analysis and ground-truth validation demonstrated that both UsIn-PHe and Auto-PHe were accurate methods to estimate plant height, while Auto-PHe had the additional advantage of being a completely automated process. For stem diameter, IPaS-Di generated the most accurate estimates of this biomass-related architectural trait. In summary, our technology was proven robust to obtain ground-based high-throughput plant architecture parameters of sorghum, a tall and densely planted crop species.

Morphological Characterization of a New and Easily Recognizable Nuclear Male Sterile Mutant of Sorghum (Sorghum bicolor).

Sorghum (Sorghum bicolor L. Moench) is one of the most important grain crops in the world. The nuclear male sterility (NMS) trait, which is caused by mutations on the nuclear gene, is valuable for hybrid breeding and genetic studies. Several NMS mutants have been reported previously, but none of them were well characterized. Here, we present our detailed morphological characterization of a new and easily recognizable NMS sorghum mutant male sterile 8 (ms8) isolated from an elite inbred BTx623 mutagenized by ethyl methane sulfonate (EMS). Our results show that the ms8 mutant phenotype was caused by a mutation on a single recessive nuclear gene that is different from all available NMS loci reported in sorghum. In fertile sorghum plants, yellow anthers appeared first during anthesis, while in the ms8 mutant, white hairy stigma emerged first and only small white anthers were observed, making ms8 plants easily recognizable when flowering. The ovary development and seed production after manual pollination are normal in the ms8 mutant, indicating it is female fertile and male sterile only. We found that ms8 anthers did not produce pollen grains. Further analysis revealed that ms8 anthers were defective in tapetum development, which led to the arrest of pollen formation. As a stable male sterile mutant across different environments, greenhouses, and fields in different locations, the ms8 mutant could be a useful breeding tool. Moreover, ms8 might be an important for elucidating male gametophyte development in sorghum and other plants.

Genome-Wide Association Study for Nine Plant Architecture Traits in Sorghum.

Sorghum [ (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes. A total of 101 single-nucleotide polymorphism (SNP) representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, () and (), affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL) for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation () and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs.

3D Sorghum Reconstructions from Depth Images Identify QTL Regulating Shoot Architecture.

Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.

Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis.

Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.