The time to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI) in soybean (Glycine max [L.] Merr) are important characteristics of growth stage traits (GSTs) in Chinese summer-sowing soybean, and are influenced by genetic as well as environmental factors. To better understand the molecular mechanism underlying the initiation times of GSTs, we investigated four GSTs of 309 diverse soybean accessions in six different environments and Best Linear Unbiased Prediction values. Furthermore, the genome-wide association study was conducted by a Fixed and random model Circulating Probability Unification method using over 60,000 single nucleotide polymorphism (SNP) markers to identify the significant quantitative trait nucleotide (QTN) regions with phenotypic data. As a result, 212 SNPs within 102 QTN regions were associated with four GSTs. Of which, eight stable regions were repeatedly detected in least three datasets for one GST. Interestingly, half of the QTN regions overlapped with previously reported quantitative trait loci or well-known soybean growth period genes. The hotspots associated with all GSTs were concentrated on chromosome 10. E2 (Glyma10g36600), a gene with a known function in regulating flowering and maturity in soybean, is also found on this chromosome. Thus, this genomic region may account for the strong correlation among the four GSTs. All the significant SNPs in the remaining 7 QTN regions could cause the significant phenotypic variation with both the major and minor alleles. Two hundred and seventy-five genes in soybean and their homologs in Arabidopsis were screened within ± 500 kb of 7 peak SNPs in the corresponding QTN regions. Most of the genes are involved in flowering, response to auxin stimulus, or regulation of seed germination, among others. The findings reported here provide an insight for genetic improvement which will aid in breeding of soybean cultivars that can be adapted to the various summer sowing areas in China and beyond.

Counting the soybean pods automatically has been one of the key ways to realize intelligent soybean breeding in modern smart agriculture. However, the pod counting accuracy for whole soybean plants is still limited due to the crowding and uneven distribution of pods. In this paper, based on the VFNet detector, we propose a deformable attention recursive feature pyramid network for soybean pod counting (DARFP-SD), which aims to identify the number of soybean pods accurately. Specifically, to improve the feature quality, DARFP-SD first introduces the deformable convolutional networks (DCN) and attention recursive feature pyramid (ARFP) to reduce noise interference during feature learning. DARFP-SD further combines the Repulsion Loss to correct the error of predicted bboxse coming from the mutual interference between dense pods. DARFP-SD also designs a density prediction branch in the post-processing stage, which learns an adaptive soft distance IoU to assign suitable NMS threshold for different counting scenes with uneven soybean pod distributions. The model is trained on a dense soybean dataset with more than 5300 pods from three different shapes and two classes, which consists of a training set of 138 images, a validation set of 46 images and a test set of 46 images. Extensive experiments have verified the performance of proposed DARFP-SD. The final training loss is 1.281, and an average accuracy of 90.35%, an average recall of 85.59% and a F1 score of 87.90% can be achieved, outperforming the baseline method VFNet by 8.36%, 4.55% and 7.81%, respectively. We also validate the application effect for different numbers of soybean pods and differnt shapes of soybean. All the results show the effectiveness of the DARFP-SD, which can provide a new insight into the soybean pod counting task.