Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2,E4, andDt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

Soybean is a major source of protein for human consumption and animal feed. Releasing new cultivars with high nutritional value is one of the major goals in soybean breeding. To achieve this goal, genome-wide association studies of seed amino acid contents were conducted based on 249 soybean accessions from China, US, Japan, and South Korea. The accessions were evaluated for 15 amino acids and genotyped by sequencing. Significant genetic variation was observed for amino acids among the accessions. Among the 231 single nucleotide polymorphisms (SNPs) significantly associated with variations in amino acid contents, fifteen SNPs localized near 14 candidate genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven amino acids in the other. Correlation coefficients among the amino acids within each group were high and positive, but the correlation coefficients of amino acids between the two groups were negative. Twenty-five SNP markers associated with multiple amino acids can be used to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration showed that selection efficiency of amino acids based on the markers significantly associated with all 15 amino acids was higher than that based on random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved seed quality.

Background: Derived from Hobbit as the female parent and Zao5241 as the male parent, the elite soybean cultivar Jidou17 is significantly higher yielding and shows enhanced qualities and stronger resistance to non-biological stress than its parents. The purpose of this study is to understand the difference in protein expression patterns between Jidou17 and its parental strains and to evaluate the parental contributions to its elite traits. Results: Leaves (14 days old) from Jidou17 and its parental cultivars were analysed for differential expressed proteins using an iTRAQ-based (isobaric tags for relative and absolute quantitation) method. A total of 1269 proteins was detected, with 141 and 181 proteins in Jidou17 differing from its female and male parent, respectively. Functional classification and an enrichment analysis based on biological functions, biological processes, and cellular components revealed that all the differential proteins fell into many functional categories but that the number of proteins varied greatly for the different categories, with enrichment in specific categories. A pathway analysis indicated that the differentiated proteins were mainly classified into the ribosome assembly pathway. Protein expression clustering results showed that the expression profiles between Jidou17 and its female parent Hobbit were more similar than those between Jidou17 and its male parent Zao5241 and between the two parental strains. Therefore, the female parent Hobbit contributed more to the Jidou17 genotype. Conclusions: This study applied a proven technique to study proteomics in 14-day-old soybean leaves and explored the depth and breadth of soybean protein research. The results provide new data for further understanding the mechanisms of elite cultivar development.

Identification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process. In this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar ‘Jidou 12’ and the salt-sensitive elite cultivar ‘Ji NF 58’ were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators. A major salt-tolerant QTL, which was flanked by SSR markers GMABAB and Barcsoyssr_03_1421 on chromosome 3, was identified based on single-marker regression, single trait composite interval mapping, and multiple interval mapping analysis. For STR, the LOD ranged from 19.8 to 20.1; R2 ranged from 44.3 to 44.7%; and the additive effect ranged from 0.876 to 0.885 among the three mapping methods. For SPAD, the LOD ranged from 10.6 to 11.0; R2 ranged from 27.0 to 27.6%; and the additive effect ranged from 1.634 to 1.679 among the three mapping methods. In this study, a major QTL conditioning salt tolerance on chromosome 3 was identified. The DNA markers closely associated with the QTLs might be useful in marker-assisted selection for soybean salt tolerance improvement in Huanghuaihai, China.