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. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure. The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly. This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Leaf Area Index (LAI) is an important parameter which can be used for crop growth monitoring and yield estimation. Many studies have been carried out to estimate LAI with remote sensing data obtained by sensors mounted on Unmanned Aerial Vehicles (UAVs) in major crops; however, most of the studies used only a single type of sensor, and the comparative study of different sensors and sensor combinations in the model construction of LAI was rarely reported, especially in soybean. In this study, three types of sensors, i.e., hyperspectral, multispectral, and LiDAR, were used to collect remote sensing data at three growth stages in soybean. Six typical machine learning algorithms, including Unary Linear Regression (ULR), Multiple Linear Regression (MLR), Random Forest (RF), eXtreme Gradient Boosting (XGBoost), Support Vector Machine (SVM) and Back Propagation (BP), were used to construct prediction models of LAI. The results indicated that the hyperspectral and LiDAR data did not significantly improve the prediction accuracy of LAI. Comparison of different sensors and sensor combinations showed that the fusion of the hyperspectral and multispectral data could significantly improve the predictive ability of the models, and among all the prediction models constructed by different algorithms, the prediction model built by XGBoost based on multimodal data showed the best performance. Comparison of the models for different growth stages showed that the XGBoost-LAI model for the flowering stage and the universal models of the XGBoost-LAI and RF-LAI for three growth stages showed the best performances. The results of this study might provide some ideas for the accurate estimation of LAI, and also provide novel insights toward high-throughput phenotyping of soybean with multi-modal remote sensing data.

Soybean [Glycine max (L.) Merr.] is one of the most important crops in the world. It is a major source of vegetable oil for consumption and protein meal for animal feeds and has also been widely used in human food industries because of its nutritive and health benefits. To provide useful information for soybean quality improvement, seed individual sugars, total sugar, protein, oil, and dietary fiber were genetically analyzed in replicated trials with 323 germplasm lines grown in South Dakota and 137 cultivars and breeding lines grown in Virginia. The results indicated significant differences among the genotypes for all traits investigated. Environment effect and genotype × environment interaction were also significant in most cases. Heritability estimates were high (94.45–97.79%) for all traits in the germplasm population, and higher in the population of breeding lines for most traits. High genotypic correlation existed between sucrose and total sugar, which helps improvement of digestible sugars and sweetness in soybean food. However, attention should be paid to the lines with higher sucrose but lower oligosaccharides, since stachyose was positively associated with total sugar. Genotypic correlations between seed sugars and protein were insignificant or very low in most cases, implying that alteration of seed sugars might not necessarily affect protein. In some cases, however, there might be negative correlations between seed sugars and oil or dietary fiber in soybean. This study also identified some unique germplasm lines with a desired level of a specific seed composition: one with high sucrose, five with low raffinose, 15 with high total sugar, seven with high protein, and four high in both sucrose and total sugar.