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. Because of the small seed weight difference between the two parents in most families of previous studies, these populations are not suitable to detect QTL that have considerable effects on seed weight. GWAS is based on unrelated individuals to detect alleles associated with the trait under investigation. The ability of GWAS to capture major seed weight QTL depends on the frequency of the accessions with small and large seed weight in the population being investigated. Our objective was to identify QTL that had a pronounced effect on seed weight using a selective population of soybean germplasm accessions and the approach of GWAS and fixation index analysis. We selected 166 accessions from the USDA Soybean Germplasm Collection with either large or small seed weight and could typically grow in the same location. The accessions were evaluated for seed weight in the field for two years and genotyped with the SoySNP50K BeadChip containing >42,000 SNPs. Of the 17 SNPs on six chromosomes that were significantly associated with seed weight in two years based on a GWAS of the selective population, eight on chromosome 4 or chromosome 17 had significant Fst values between the large and small seed weight sub-populations. The seed weight difference of the two alleles of these eight significant SNPs varied from 8.1 g to 11.7 g/100 seeds in two years. We also identified haplotypes in three haplotype blocks with significant effects on seed weight. These findings were validated in a panel with 3753 accessions from the USDA Soybean Germplasm Collection. This study highlighted the usefulness of selective genotyping populations coupled with GWAS and fixation index analysis for the identification of QTL with substantial effects on seed weight in soybean. This approach may help geneticists and breeders to more efficiently identify major QTL controlling other traits. The major regions and haplotypes we have identified that control seed weight differences in soybean will facilitate the identification of genes regulating this important trait.

Phomopsis seed decay of soybean is a major cause of poor-quality soybean seed. The disease is caused primarily by the fungal pathogen Phomopsis longicolla. Aggressiveness of isolates of P. longicolla from soybean and other Phomopsis spp. from other hosts were compared by inoculating 2-week-old soybean plants of cv. Williams 82. There were significant (P ≤ 0.0001) differences among isolates based on stem length and stem lesion length. The P. longicolla soybean isolate PL16, from Mississippi, caused the shortest stem length while the non-soybean isolate P9, from Illinois, caused the greatest stem lesion length. The type isolate of P. longicolla, PL31 (Fau 600), was one of the 3 most aggressive isolates among all 48 isolates tested. The velvetleaf isolate P9 was the most aggressive among 13 isolates from non-soybean hosts. This study provided the first evaluation of aggressiveness of P. longicolla isolates from different geographic origins and the first demonstration that Phomopsis spp. isolated from cantaloupe, eggplant, and watermelon infected soybean. Knowledge about the variability of the pathogen is important for selecting isolates for breeding soybean lines with broad-based resistance to Phomopsis seed decay.

Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the mechanism of the disease development, the genome of an isolate, MSPL10–6, from Mississippi, USA was sequenced, de novo assembled, and analyzed. The genome of MSPL 10–6 was estimated to be approximately 62 Mb in size with an overall G + C content of 48.6%. Of 16,597 predicted genes, 9866 genes (59.45%) had significant matches to genes in the NCBI nr database, while 18.01% of them did not link to any gene ontology classification, and 9.64% of genes did not significantly match any known genes. Analysis of the 1221 putative genes that encoded carbohydrate-activated enzymes (CAZys) indicated that 715 genes belong to three classes of CAZy that have a direct role in degrading plant cell walls. A novel fungal ulvan lyase (PL24; EC 4.2.2.-) was identified. Approximately 12.7% of the P. longicolla genome consists of repetitive elements. A total of 510 potentially horizontally transferred genes were identified. They appeared to originate from 22 other fungi, 26 eubacteria and 5 archaebacteria. The genome of the P. longicolla isolate MSPL10–6 represented the first reported genome sequence in the fungal Diaporthe-Phomopsis complex causing soybean diseases. The genome contained a number of Pfams not described previously. Information obtained from this study enhances our knowledge about this seed-borne pathogen and will facilitate further research on the genomic basis and pathogenicity mechanism of P. longicolla and aids in development of improved strategies for efficient management of Phomopsis seed decay in soybean.

Field experiments were set up in 1991 to test if suppressive soil to soybean root diseases could be developed with continuous long-term soybean cropping in black soil of Northeast China. Based on the field observation in 2007, 2009, and 2011, soybean root growth was promoted, and the severities of root disease were reduced in a field with continuous long-term cropping with soybean. Population densities of the pathogens (Fusarium spp. and Heterodera glycines) in the soybean cropping field were significantly (P < 0.05) lower than rotation of soybean with wheat or corn. Higher levels of biological control agents (Trichoderma harzianum, Pochonia chlamydosporia, or Paecilomyces lilacinus) also were found in the long-term soybean cropping field. Therefore, continuous long-term cropping of soybean in black soil of Northeast China could develop suppressive soil to soybean root diseases.