Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.

BackgroundSoybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq).ResultsSLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, ‘Huapidou’, and a cultivated soybean, ‘Qihuang26’, which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively.ConclusionsWith SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5035-9) contains supplementary material, which is available to authorized users.

The first soybean [Glycine max (L.) Merr.] breeding program in China was established in the northeast in 1913. A trend analysis of widely grown cultivars across Chinese soybean breeding history may provide a better perspective on the genetic progress in soybean. The objective of the current study was to assess the genetic change of 15 phenological, yield, and agronomic traits on widely grown cultivars in northeast China. Sixty-four soybean cultivars representing a span of 84 yr of release were included. The field experiments were conducted at three sites in each region during 2009, 2010, and 2011, and the annual genetic changes were obtained by regression analysis. The results showed that the yield gain in widely grown cultivars of different regions ranged from 6 to 16 kg ha −1 yr −1 due to improvements in different yield components in the last nine decades. In addition, modern cultivars demonstrated more upright plant architecture, fewer branches, shorter height, higher lodging resistance, and earlier flowering than obsolete cultivars. However, changes were insignificant in the height of the bottom pod and the node number. The changing rates of yield and phenological traits across these decades were constant, while that of agronomic traits were discontinuous. Days to flowering, branch number, and lodging score were more responsive to environments in new cultivars than in old cultivars. In conclusion, these findings indicate a substantial improvement in the yield, agronomic, and phenological traits resulted from long-term genetic breeding. This study also provides insight into developing new strategies for soybean genetic improvement in China and worldwide. Corresponding authors (hantianfu@ caas.cn; wucunxiang@caas.cn). Abbreviations: 100-SW, 100-seed weight; BLUE, best linear unbiased estimator; BLUP, best linear unbiased predictor; BN, branch number; C, cultivar; CV, coefficient of variability; DTF, days to first flower; DTM, days to maturity; E, environment; HBP, height of the bottom pod; JL, Jilin-Liaoning region; LS, lodging score; MG, maturity group; MSH, midsouth Heilongjiang region; NH, north Heilongjiang region; NN, node number; PH, plant height; PPP, number of pods per plant; R/V, ratio of the reproductive period to the vegetative period; RP, reproductive period; SPP, seeds per plant; SPPOD, seeds per pod; YPP, yield per plant.

Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT-1, GT-2, GTγ, SIP1, SH4 and GTδ. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Thirteen segmental duplicated gene pairs were identified and all of them experienced a strong purifying selective pressure during evolution. Various stress-responsive cis-elements presented in the promoters of soybean trihelix genes, suggesting that the trihelix genes might respond to the environmental stresses in soybean. The expression analysis suggests that trihelix genes are involved in diverse functions during soybean development, flood or salinity tolerance, and plant immunity. Our results provide genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.