Functional Divergence of G and Its Homologous Genes for Green Pigmentation in Soybean Seeds

The degradation of chlorophyll in mature soybean seeds is closely related to the development of their yellow color. In this study, we examined G, its homologue G-like (GL), and their mutant alleles and investigated the relationship between these genes and chlorophyll accumulation in the seed coats of mature seeds. Transient expression of G and GL proteins fused with green fluorescent protein revealed that both were localized in plastids. Overexpression of G resulted in the accumulation of chlorophyll in the seed coats and cotyledons of mature seeds, indicating that high expression levels of G result in chlorophyll accumulation that exceeds its metabolism in the seeds of yellow soybean. Analysis of near isogenic lines at the G locus demonstrated a significant difference in the chlorophyll content of the seed coats and cotyledons of mature seeds when G and mutant g alleles were expressed in the d1d2 stay-green genetic background, indicating that the G protein might repress the SGR-independent degradation of chlorophyll. We examined the distribution of mutant alleles at the G and GL loci among cultivated and wild soybean germplasm. The g allele was widely distributed in cultivated soybean germplasm, except for green seed coat soybean lines, all of which contained the G allele. The gl alleles were much fewer in number than the g alleles and were mainly distributed in the genetic resources of cultivated soybean from Japan. None of the landraces and breeding lines investigated in this study were observed to contain both the g and gl alleles. Therefore, in conclusion, the mutation of the G locus alone is essential for establishing yellow soybeans, which are major current soybean breeding lines.

Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

The models of soybean varieties adapted to dry conditions

The article presents the analysis of early-ripening and mid-ripening promising and cultivated soybean varieties that received a comprehensive evaluation under irrigation conditions over the past period (2016-2018) of breeding with the increase in atmospheric drought and dry hot wind days to 77 with a long-term average annual indicator of 47 days with a relative humidity of less than 30%. We developed the scientifically based model of highly productive soybean varieties (2021-2023) with a yield of 2.8-3.8 t/ha and the growth season of 105-122 days. The model is based on the established correlations of the main morphological and biological characteristics with the grain productivity of irrigated sowing. The model of soybean varieties reflects characteristics that ensure the responsiveness of plants to watering and resistance to prolonged manifestations of atmospheric drought: a long growth season, low linear plant growth, significant leaf surface area, photosynthetic potential, dry biomass yield, number of plants before harvesting, thousand-seed weight, long-term duration of the “flowering-beans filling” period. The model is complemented by the indicators of high protein and fat content in seeds, as well as their yield from a unit of harvesting area.

Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean

Background Soybean is an economically important crop which flowers predominantly in response to photoperiod. Several major loci controlling the quantitative trait for reproductive timing have been identified, of which allelic combinations at three of these loci, E1, E2, and E3, are the dominant factors driving time to flower and reproductive period. However, functional genomics studies have identified additional loci which affect reproductive timing, many of which are less understood. A better characterization of these genes will enable fine-tuning of adaptation to various production environments. Two such genes, E1La and E1Lb, have been implicated in flowering by previous studies, but their effects have yet to be assessed under natural photoperiod regimes. Results Natural and induced variants of E1La and E1Lb were identified and introgressed into lines harboring either E1 or its early flowering variant, e1-as. Lines were evaluated for days to flower and maturity in a Maturity Group (MG) III production environment. These results revealed that variation in E1La and E1Lb promoted earlier flowering and maturity, with stronger effects in e1-as background than in an E1 background. The geographic distribution of E1La alleles among wild and cultivated soybean revealed that natural variation in E1La likely contributed to northern expansion of wild soybean, while breeding programs in North America exploited e1-as to develop cultivars adapted to northern latitudes. Conclusion This research identified novel alleles of the E1 paralogues, E1La and E1Lb, which promote flowering and maturity under natural photoperiods. These loci represent sources of genetic variation which have been under-utilized in North American breeding programs to control reproductive timing, and which can be valuable additions to a breeder’s molecular toolbox.

A Large Root Phenome Dataset Wide-Opened the Potential for Underground Breeding in Soybean

The root is the most critical plant organ for water and nutrient acquisition. Although the root is vital for water and nutrient uptake, the diverse root characters of soybean still need to be identified owing to the difficulty of root sampling. In this study, we used 150 wild and 50 cultivated soybean varieties to collect root image samples. We analyzed root morphological traits using acquired-image. Except for the main total length (MTL), the root morphological traits for most cultivated and wild plants were significantly different. According to correlation analysis, the wild and cultivated plants showed a significant correlation among total root length (TRL), projected area (PA), forks, total lateral length (TLL), link average diameter, and MTL. In particular, TRL was highly correlated with PA in both cultivated (0.92) and wild (0.82) plants compared with between MTL (0.43 for cultivated and 0.27 for wild) and TLL (0.82 for cultivated and 0.52 for wild). According to principal component analysis results, both plants could be separated; however, there was some overlap of the traits among the wild and cultivated individuals from some regions. Nevertheless, variation among the cultivated plants was higher than that found in the wild plants. Furthermore, three groups, including MTL, TLL, and the remaining traits, could explain all the variances.

Screening of Vietnamese soybean genotypes for Agrobacterium-mediated transgenic transformation

Soybean [Glycine max (L) Merr.] is one of the most important crops used for human food and animal feed globally. Transgenic soybean covers more than 74% of the global soybean production area, which is an achievement of genetically modified programs. The Agrobacterium-mediated method is commonly used for soybean transformation, but the efficiency of this method is affected by various factors including genotypes. Screening of the soybean genotypes suitable for Agrobacterium-infection and plant regeneration is the most important step to establish an efficient genetic transformation system. In this study, we screened thirty Vietnamese soybean genotypes including seventeen cultivated soybean genotypes (CSG) and thirteen local soybean genotypes (LCG) for shoot regeneration ability and transient infection via Agrobacterium tumefaciens method. Two CSG cultivars, DT22 and VX93, had significantly high efficiencies for shoot regeneration and transient infection compared with the control genotypes Jack and William 82. The shoot regeneration of DT22 and VX93 was 92.32% with 5.75 shoots/explant and 93.35% with 5.92 shoots/explant, respectively, whereas the control genotypes Jack and William 82 had 91.35% with 4.6 shoots/explant and 82.64% with 5.7 shoots/explant. Similarly, the transient infection of DT22 and VX93 was 84% and 86%, respectively, which was comparable with that of Jack (86%) William (82%). The success of transgenic development was confirmed by the β-Glucuronidase staining, PCR, and Basta leaf painting. The results indicated that cultivars DT22 and VX93 could be used for stable Agrobacterium-media transformation. Keywords: Soybean, Agrobacterium, transformation, transient infection, transgenic.

Comparison of Phenolic and Flavonoid Compound Profiles and Antioxidant and α-Glucosidase Inhibition Properties of Cultivated Soybean (Glycine max) and Wild Soybean (Glycine soja)

Wild soybean (Glycine soja Sieb.et Zucc; WS) has been used as a traditional food in China for many years and contains significantly higher levels of isoflavones than cultivated soybean (Glycine max; CS), but the secondary metabolites, including flavonoids and the phenolic composition differences between them, remain unclear. The results showed that WS possessed significantly higher total phenolic and flavonoid content and exhibited better antioxidant and α-glucosidase inhibition activities as well as excellent protective effects against H2O2-induced oxidative injury in a human endothelial cell line. Through metabolomic analysis, 642 metabolites were identified, and 238 showed differential expression, with 151 upregulated and 87 downregulated. A total of 79 flavonoid compounds were identified, 42 of which were upregulated in WS. 2′-Hydroxygenistein, garbanzol, protocatechuic aldehyde, ligustilide, and resveratrol were the most discriminated compounds in WS. The metabolic pathway analysis of differential metabolites related to the biosynthesis of flavonoids and phenolic acids were the biosynthesis of phenylpropanoids, flavonoids, isoflavonoids, flavones, and flavonols. This study substantially elucidated differences in the content of flavonoids and biological activities between WS and CS, which is useful information for the effective utilization of these two black soybean species in food processing.