Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Species.

We have estimated the average genetic diversity of two annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 accessions. Among the perennials, showed the highest nucleotide diversity.

Genome-wide Scan for Seed Composition Provides Insights into Soybean Quality Improvement and the Impacts of Domestication and Breeding.

The complex genetic architecture of quality traits has hindered efforts to modify seed nutrients in soybean. Genome-wide association studies were conducted for seed composition, including protein, oil, fatty acids, and amino acids, using 313 diverse soybean germplasm accessions genotyped with a high-density SNP array. A total of 87 chromosomal regions were identified to be associated with seed composition, explaining 8%-89% of genetic variances.

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population.

Genetic improvement toward optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors.

Genetic Characterization of the Soybean Nested Association Mapping Population.

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [ (L.) Merr.] genotypes to the common cultivar.

Mapping novel aphid resistance QTL from wild soybean, Glycine soja 85-32.

Two novel QTLs conferring aphid resistance were mapped and validated on soybean chromosomes 8 and 16, respectively. Closely linked markers were developed to assist breeding for aphid resistance. Soybean aphid, Aphis glycines Matsumura, is a highly destructive pest for soybean production.

Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses.

Background: Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association study (GWAS) are two complementary and powerful tools to connect phenotypic differences to the underlying contributing loci. Linkage analysis is based on progeny derived from two parents, given sufficient sample size and biological replication, it usually has high statistical power to map alleles with relatively small effect on phenotype, however, linkage analysis of the bi-parental population can't detect quantitative trait loci (QTL) that are fixed in the two parents.

High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases.

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean. Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively.

Molecular Characterization of Resistance to Soybean Rust (Phakopsora pachyrhizi Syd. & Syd.) in Soybean Cultivar DT 2000 (PI 635999).

Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & Syd., has been identified in many soybean germplasm accessions and is conferred by either dominant or recessive genes that have been mapped to six independent loci (Rpp1 -Rpp6), but No U.

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean.

Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood.

Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea.

Background: Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P.

Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.

Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.].

Draft genome sequence of Diaporthe aspalathi isolate MS-SSC91, a fungus causing stem canker in soybean.

Diaporthe aspalathi (Syn. Diaporthe phaseolorum var. meridionalis) is the causal agent of the southern stem canker (SSC) disease in soybean.

Phenotypic variation and identification of quantitative trait loci for ozone tolerance in a Fiskeby III × Mandarin (Ottawa) soybean population.

Soybean quantitative trait loci for ozone response. Ground-level ozone reduces yield in crops such as soybean (Glycine max (L.) Merr.

Characterization of Soybean Storage and Allergen Proteins Affected by Environmental and Genetic Factors.

There is limited information on the influence of genetic and environmental variability on soybean protein composition. This study aimed to determine the role of genotype (G), environments (E), and the interrelationship of genotype and environment (G×E) on soybean seed protein. Three sets of nine soybean genotypes were grown in replicated trials at Maryland, South Carolina, and South Dakota.

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01.

Background: A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.

A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection.

Population structure analyses and genome-wide association studies (GWAS) conducted on crop germplasm collections provide valuable information on the frequency and distribution of alleles governing economically important traits. The value of these analyses is substantially enhanced when the accession numbers can be increased from ∼1,000 to ∼10,000 or more. In this research, we conducted the first comprehensive analysis of population structure on the collection of 14,000 soybean accessions [Glycine max (L.

Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max).

Twenty-two loci for soybean SW and candidate genes conditioning seed development were identified; and prediction accuracies of GS and MAS were estimated through cross-validation and validation with unrelated populations. Soybean (Glycine max) is a major crop for plant protein and oil production, and seed weight (SW) is important for yield and quality in food/vegetable uses of soybean. However, our knowledge of genes controlling SW remains limited.

Genome-Wide Association Study of Ureide Concentration in Diverse Maturity Group IV Soybean [Glycine max (L.) Merr.] Accessions.

Ureides are the N-rich products of N-fixation that are transported from soybean nodules to the shoot. Ureides are known to accumulate in leaves in response to water-deficit stress, and this has been used to identify genotypes with reduced N-fixation sensitivity to drought. Our objectives in this research were to determine shoot ureide concentrations in 374 Maturity Group IV soybean accessions and to identify genomic regions associated with shoot ureide concentration.

Genomic consequences of selection and genome-wide association mapping in soybean.

Background: Crop improvement always involves selection of specific alleles at genes controlling traits of agronomic importance, likely resulting in detectable signatures of selection within the genome of modern soybean (Glycine max L. Merr.).

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb.

Fingerprinting Soybean Germplasm and Its Utility in Genomic Research.

The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement.

Confirmation of delayed canopy wilting QTLs from multiple soybean mapping populations.

QTLs for delayed canopy wilting from five soybean populations were projected onto the consensus map to identify eight QTL clusters that had QTLs from at least two independent populations. Quantitative trait loci (QTLs) for canopy wilting were identified in five recombinant inbred line (RIL) populations, 93705 KS4895 × Jackson, 08705 KS4895 × Jackson, KS4895 × PI 424140, A5959 × PI 416937, and Benning × PI 416937 in a total of 15 site-years. For most environments, heritability of canopy wilting ranged from 0.

Fine Mapping and Characterization of Candidate Genes that Control Resistance to Cercospora sojina K. Hara in Two Soybean Germplasm Accessions.

Frogeye leaf spot (FLS), caused by the fungus Cercospora sojina K. Hara, may cause a significant yield loss to soybean growers in regions with a warm and humid climate. Two soybean accessions, PI 594891 and PI 594774, were identified to carry a high level of resistance similar to that conditioned by the Rcs3 gene in 'Davis'.

Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm.

Background: Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments.