Soybean genomics research community strategic plan: A vision for 2024-2028.

This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028).

High-throughput phenotyping of soybean () transpiration response curves to rising atmospheric drying in a mapping population.

In soybean (Glycine max ), limiting whole-plant transpiration rate (TR) response to increasing vapor pressure deficit (VPD) has been associated with the 'slow-wilting' phenotype and with water-conservation enabling higher yields under terminal drought. Despite the promise of this trait, it is still unknown whether it has a genetic basis in soybean, a challenge limiting the prospects of breeding climate-resilient varieties. Here, we present the results of a first attempt at a high-throughput phenotyping of TR and stomatal conductance response curves to increasing VPD conducted on a soybean mapping population consisting of 140 recombinant inbred lines (RIL).

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean.

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477).

Genomic predictions of genetic variances and correlations among traits for breeding crosses in soybean.

Parental selection is perhaps the most critical decision a breeder makes, establishing the foundation of the entire program for years to come. Cross selection based on predicted mean and genetic variance can be further expanded to multiple-trait improvement by predicting the genetic correlation ( ) between pairs of traits. Our objective was to empirically assess the ability to predict the family mean, genetic variance, superior progeny mean and genetic correlation through genomic prediction in a soybean population.

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.

Cataloging SCN resistance loci in North American public soybean breeding programs.

Soybean cyst nematode (SCN) is a destructive pathogen of soybeans responsible for annual yield loss exceeding $1.5 billion in the United States. Here, we conducted a series of genome-wide association studies (GWASs) to understand the genetic landscape of SCN resistance in the University of Missouri soybean breeding programs (Missouri panel), as well as germplasm and cultivars within the United States Department of Agriculture (USDA) Uniform Soybean Tests-Northern Region (NUST).

A genomic analysis of the University of Nebraska Replicated Recurrent Selection program.

The inbred-hybrid system of maize breeding closely resembles a reciprocal full-sib (RFS) selection program. Studying changes in genetic variation as a result of RFS selection can help illuminate long-standing questions regarding the relative roles of selection and genetic drift and help understand the nature of adaptation occurring in selection programs. The University of Nebraska-Lincoln Replicated Recurrent Selection (UNL-RpRS) program underwent eight cycles of replicated RFS and S1-progeny selection, making it a powerful system to study genomic changes accompanying selection for inter-population performance.

A genome-wide analysis of the USDA Soybean Isoline Collection.

The USDA Soybean Isoline Collection has been an invaluable resource for the soybean genetics and breeding community. This collection, established in 1972, consists of 611 near-isogenic lines (NILs) carrying one or multiple genes conferring traits that had been determined to exhibit Mendelian inheritance. It has been used in multiple studies on the genetic basis, physiology, and agronomy of these qualitative traits.

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.

Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean.

Increasing the rate of genetic gain for seed yield remains the primary breeding objective in both public and private soybean [Glycine max (L.) Merr.] breeding programs.

Plant Breeding for Intercropping in Temperate Field Crop Systems: A Review.

Monoculture cropping systems currently dominate temperate agroecosystems. However, intercropping can provide valuable benefits, including greater yield stability, increased total productivity, and resilience in the face of pest and disease outbreaks. Plant breeding efforts in temperate field crops are largely focused on monoculture production, but as intercropping becomes more widespread, there is a need for cultivars adapted to these cropping systems.

Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean.

The soybean ( L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States.

The utility of genomic prediction models in evolutionary genetics.

Variation in complex traits is the result of contributions from many loci of small effect. Based on this principle, genomic prediction methods are used to make predictions of breeding value for an individual using genome-wide molecular markers. In breeding, genomic prediction models have been used in plant and animal breeding for almost two decades to increase rates of genetic improvement and reduce the length of artificial selection experiments.

Optimization of training sets for genomic prediction of early-stage single crosses in maize.

Training population optimization algorithms are useful for efficiently training genomic prediction models for single-cross performance, especially if the population is extended beyond only realized crosses to all possible single crosses. Genomic prediction of single-cross performance could allow effective evaluation of all possible single crosses between all inbreds developed in a hybrid breeding program. The objectives of the present study were to investigate the effect of different levels of relatedness on genomic predictive ability of single crosses, evaluate the usefulness of deterministic formula to forecast prediction accuracy in advance, and determine the potential for TRS optimization based on prediction error variance (PEVmean) and coefficient of determination (CDmean) criteria.

Identification and Fine-Mapping of a Soybean Quantitative Trait Locus on Chromosome 5 Conferring Tolerance to Iron Deficiency Chlorosis.

CORE IDEAS: 'Fiskeby III' harbors a combination of abiotic stress traits, including iron deficiency chlorosis (IDC) tolerance. An IDC quantitative trait locus on chromosome Gm05 was identified in genome-wide association studies and biparental populations. Fine-mapping resolved a 137-kb interval containing strong candidate genes.

Characterizing introgression-by-environment interactions using maize near isogenic lines.

Significant introgression-by-environment interactions are observed for traits throughout development from small introgressed segments of the genome. Relatively small genomic introgressions containing quantitative trait loci can have significant impacts on the phenotype of an individual plant. However, the magnitude of phenotypic effects for the same introgression can vary quite substantially in different environments due to introgression-by-environment interactions.

Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize.

Single-cross hybrids have been critical to the improvement of maize ( 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.

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.].

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.

Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss's Wilt of Maize.

Goss's bacterial wilt and leaf blight is a disease of maize caused by the gram positive bacterium subsp. (). First discovered in Nebraska, Goss's wilt has now spread to major maize growing states in the United States and three provinces in Canada.

Multi-trait Improvement by Predicting Genetic Correlations in Breeding Crosses.

The many quantitative traits of interest to plant breeders are often genetically correlated, which can complicate progress from selection. Improving multiple traits may be enhanced by identifying parent combinations - an important breeding step - that will deliver more favorable genetic correlations ( ). Modeling the segregation of genomewide markers with estimated effects may be one method of predicting in a cross, but this approach remains untested.

Genome-Wide Association Mapping of Host-Plant Resistance to Soybean Aphid.

Soybean aphid [ Matsumura (Hemiptera: Aphididae)] is the most damaging insect pest of soybean [ (L.) Merr.] in the Upper Midwest of the United States and is primarily controlled by insecticides.

Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program.

Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced.

Dissecting the Genetic Basis of Local Adaptation in Soybean.

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation.