Variation in shoot architecture traits and their relationship to canopy coverage and light interception in soybean (Glycine max).

BACKGROUND: In soybeans, faster canopy coverage (CC) is a highly desirable trait but a fully covered canopy is unfavorable to light interception at lower levels in the canopy with most of the incident radiation intercepted at the top of the canopy. Shoot architecture that influences CC is well studied in crops such as maize and wheat, and altering architectural traits has resulted in enhanced yield. However, in soybeans the study of shoot architecture has not been as extensive. RESULTS: This study revealed significant differences in CC among the selected soybean accessions. The rate of CC was found to decrease at the beginning of the reproductive stage (R1) followed by an increase during the R2-R3 stages. Most of the accessions in the study achieved maximum rate of CC between R2-R3 stages. We measured Light interception (LI), defined here as the ratio of Photosynthetically Active Radiation (PAR) transmitted through the canopy to the incoming PAR or the radiation above the canopy. LI was found to be significantly correlated with CC parameters, highlighting the relationship between canopy structure and light interception. The study also explored the impact of plant shape on LI and CO2 assimilation. Plant shape was characterized into distinct quantifiable parameters and by modeling the impact of plant shape on LI and CO2 assimilation, we found that plants with broad and flat shapes at the top maybe more photosynthetically efficient at low light levels, while conical shapes were likely more advantageous when light was abundant. Shoot architecture of plants in this study was described in terms of whole plant, branching and leaf-related traits. There was significant variation for the shoot architecture traits between different accessions, displaying high reliability. We found that that several shoot architecture traits such as plant height, and leaf and internode-related traits strongly influenced CC and LI. CONCLUSION: In conclusion, this study provides insight into the relationship between soybean shoot architecture, canopy coverage, and light interception. It demonstrates that novel shoot architecture traits we have defined here are genetically variable, impact CC and LI and contribute to our understanding of soybean morphology. Correlations between different architecture traits, CC and LI suggest that it is possible to optimize soybean growth without compromising on light transmission within the soybean canopy. In addition, the study underscores the utility of integrating low-cost 2D phenotyping as a practical and cost-effective alternative to more time-intensive 3D or high-tech low-throughput methods. This approach offers a feasible means of studying basic shoot architecture traits at the field level, facilitating a broader and efficient assessment of plant morphology.

Branch angle and leaflet shape are associated with canopy coverage in soybean.

Early canopy coverage is a desirable trait that is a major determinant of yield in soybean (Glycine max). Variation in traits comprising shoot architecture can influence canopy coverage, canopy light interception, canopy-level photosynthesis, and source-sink partitioning efficiency. However, little is known about the extent of phenotypic diversity of shoot architecture traits and their genetic control in soybean. Thus, we sought to understand the contribution of shoot architecture traits to canopy coverage and to determine the genetic control of these traits. We examined the natural variation for shoot architecture traits in a set of 399 diverse maturity group I soybean (SoyMGI) accessions to identify relationships between traits, and to identify loci that are associated with canopy coverage and shoot architecture traits. Canopy coverage was correlated with branch angle, number of branches, plant height, and leaf shape. Using previously collected 50K single nucleotide polymorphism data, we identified quantitative trait locus (QTL) associated with branch angle, number of branches, branch density, leaflet shape, days to flowering, maturity, plant height, number of nodes, and stem termination. In many cases, QTL intervals overlapped with previously described genes or QTL. We also found QTL associated with branch angle and leaflet shape located on chromosomes 19 and 4, respectively, and these QTL overlapped with QTL associated with canopy coverage, suggesting the importance of branch angle and leaflet shape in determining canopy coverage. Our results highlight the role individual architecture traits play in canopy coverage and contribute information on their genetic control that could help facilitate future efforts in their genetic manipulation.

Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system.

BACKGROUND: Iron deficiency chlorosis (IDC) is an abiotic stress in soybean [Glycine max (L.) Merr.] that causes significant yield reductions. Symptoms of IDC include interveinal chlorosis and stunting of the plant. While there are management practices that can overcome these drastic yield losses, the preferred way to manage IDC is growing tolerant soybean varieties. To develop varieties tolerant to IDC, breeders may easily phenotype up to thousands of candidate soybean lines every year for severity of symptoms related to IDC, a task traditionally done with a 1-5 visual rating scale. The visual rating scale is subjective and, because it is time consuming and laborious, can typically only be accomplished once or twice during a growing season. RESULTS: The goal of this study was to use an unmanned aircraft system (UAS) to improve field screening for tolerance to soybean IDC. During the summer of 2017, 3386 plots were visually scored for IDC stress on two different dates. In addition, images were captured with a DJI Inspire 1 platform equipped with a modified dual camera system which simultaneously captures digital red, green, blue images as well as red, green, near infrared (NIR) images. A pipeline was created for image capture, orthomosaic generation, processing, and analysis. Plant and soil classification was achieved using unsupervised classification resulting in 95% overall classification accuracy. Within the plant classified canopy, the green, yellow, and brown plant pixels were classified and used as features for random forest and neural network models. Overall, the random forest and neural network models achieved similar misclassification rates and classification accuracy, which ranged from 68 to 77% across rating dates. All 36 trials in the field were analyzed using a linear model for both visual score and UAS predicted values on both dates. In 32 of the 36 tests on date 1 and 33 of 36 trials on date 2, the LSD associated with UAS image-based IDC scores was lower than the LSD associated with visual scores, indicating the image-based scores provided more precise measurements of IDC severity. CONCLUSIONS: Overall, the UAS was able to capture differences in IDC stress and may be used for evaluations of candidate breeding lines in a soybean breeding program. This system was both more efficient and precise than traditional scoring methods.

Correction to: Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system.

[This corrects the article DOI: 10.1186/s13007-019-0478-9.].

An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype.

Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a ß-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.

Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean.

Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.