Soybean Domestication Research Articles

Characterization of Cu/Zn-SOD enzyme activities and gene expression in soybean under low nitrogen stress.

Superoxide dismutase (SOD) plays an important role in antioxidant defense in nearly all cells, and is speculated to be closely related to plant resistance to biotic and abiotic stresses, such as drought, salt, heavy metal and pathogen attack. However, little is known about the effects of SOD activity and its isoenzymes on low nitrogen stress tolerance and its effects on adaptability of plants to nitrogen limitation. Ten SOD isoenzymes were identified in soybean root, stem, leaf and mature seed, and were classified into three families (α.1, β.1-4 and γ.1-5). SOD activity was significantly elevated in soybean leaf and root. Conversely, under low-nitrogen conditions, only β.2 isoenzyme activity, belonging to the Cu/Zn-SOD family, was induced obviously in the root of soybean cultivar cv. WS01-15. Moreover, the expression of three Cu/Zn-SOD genes was analyzed under low nitrogen stress. GmCZ-SOD1 gene was induced significantly in soybean root under low nitrogen stress. Interestingly, evolutionary analysis showed that this gene underwent a strong artificial selection during soybean domestication, suggesting that the Cu/Zn-SOD gene plays an essential role in the adaptive evolution of soybean nitrogen limitation resistance. GmCZ-SOD is important for adaptability of soybean to nitrogen limitation and these results provide useful information to unravel its biological role in low nitrogen resistance in plants. © 2015 Society of Chemical Industry.

Domestic soybean to compensate the European protein deficit: illusion or real market opportunity?

This article is an attempt to analyse the potential for EU-grown soybean to become a credible market alternative in order to reduce the European protein deficit. The analysis is conducted from the perspective of the European feed industry. The market analysis shows that the EU has very little control on its soybean supply. Moreover, the nature of the EU protein deficit calls for an increase of the availability of protein-rich ingredients. With a favourable outlook from the point of view of the demand, the most relevant growth model should be determined in order to improve the competiveness of soybean for EU arable crops farmers. The two main options are niche markets as a first step to reach mainstream supply or a more direct approach towards mainstream supply which would very probably require public support.

국내산 대두(Glycine max. Merr)자원의 플라보노이드 대사체 동정 및 열처리 효과

BACKGROUND: Soy isoflavones, structurally similar to endogenous estrogens, may affect human body through both hormonally mediated and non-hormonally related mechanisms. Heat processing could change chemical compositions. The effects of different thermal processes, and HTHP(high temperature and high pressure) on the composition of isoflavone compounds and total amount of domestic soybeans were investigated in this study. METHOD AND RESULTS: Three different kinds of soybean samples were collected from RDA-Genebank. The samples were extracted using methanol, distilled water, and formic acid based solvent. Also the same solvents were used for mobile phase in UPLC/ToF/MS. All of the isoflavone compounds were analyzed based on the aglycone type of external standard for quantification. The standard calibration curve presented linearity with the correlation coefficient R2 > 0.98, analysed from 1 to 50 ppm concentration. The total isoflavone contents does not change by treatment within the same breed. While boiling and HTHP processes tend to increase the contents of aglycone and -glucosides, fresh soybeans retained the high concentration of malonylglucosides. CONCLUSION: These results have to be considered while developing an effective functional food, from the health while point of view using soybeans.

GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean.

Loss of seed-coat impermeability was essential in the domestication of many leguminous crops to promote the production of their highly nutritious seeds. Here we show that seed-coat impermeability in wild soybean is controlled by a single gene, GmHs1-1, which encodes a calcineurin-like metallophosphoesterase transmembrane protein. GmHs1-1 is primarily expressed in the Malpighian layer of the seed coat and is associated with calcium content. The transition from impermeability to permeability in domesticated soybean was caused by artificial selection of a point mutation in GmHs1-1. Interestingly, a number of soybean landraces evaded selection for permeability because of an alternative selection for seed-coat cracking that also enables seed imbibition. Despite the single origin of the mutant allele Gmhs1-1, the distribution pattern of allelic variants in the context of soybean population structure and the detected signature of genomic introgression between wild and cultivated soybeans suggest that Gmhs1-1 may have experienced reselection for seed-coat permeability.

Functional marker development of miR1511-InDel and allelic diversity within the genus Glycine.

BackgroundSingle-stranded non-protein coding small RNAs, 18–25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have been reported for the detection of genetic diversity or sequence variation in soybean, one of the most important legume crops in worldwide for seed protein and oil content. Recently, with the available of public genomic databases, there has been a shift from the labor-intensive development of PCR-based markers to sequence-based genotyping and the development of functional markers within genes, often coupled with the use of RNA information. But thus far miRNA-based markers have been only developed in rice and tobacco. Here we report the first functional molecular miRNA marker, miR1511-InDel, in soybean for a specific single copy locus used to assess genetic variation in domesticated soybean (Glycine max [L.] Merr) and its wild progenitor (Glycine soja Sieb. & Zucc.).ResultsWe genotyped a total of 1,669 accessions of domesticated soybean (G. max) and its wild progenitor G. soja which are native throughout the China and parts of Korea, Japan and Russia. The results indicate that the miR1511 locus is distributed in cultivated soybean and has three alleles in annual wild soybean. Based on this result, we proposed that miR-InDel marker technology can be used to assess genetic variation. The inclusion of geo-reference data with miR1511-InDel marker data corroborated that accessions from the Yellow River basin (Huanghuai) exhibited high genetic diversity which provides more molecular evidence for gene diversity in annual wild soybean and domestication of soybean.ConclusionsThese results provide evidence for the use of RNA marker, miRNA1511-InDel, as a soybean-specific functional maker for the study of genetic diversity, genotyping of germplasm and evolution studies. This is also the first report of functional marker developed from soybean miRNA located within the functional region of pre-miRNA1511.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1665-3) contains supplementary material, which is available to authorized users.

Characteristics of soybean sprout locally cultivated in the Jeonju region, used for Bibimbap and Kongnamul-gukbap

BackgroundJeonju has been named by United Nations Educational, Scientific and Cultural Organization (UNESCO) as a Creative City of Gastronomy since 2012. The title was awarded based on foods and traditional culture. Jeonju's homemade food preparation style, which has been passed down for thousands of years, was highly praised. Jeonju bibimbap and kongnamul-gukbap are the representative foods of Jeonju city. Soybean sprout cultivated locally in the Jeonju region is famous for being one of the “Jeonju 10 delicacies”, and is one of the essential food ingredients in Jeonju bibimbap and kongnamul-gukbap. This study was conducted to provide basic data on why Jeonju soybean sprout has been famous nationwide for a long time. MethodsThe analyses of proximate components, minerals, vitamin C content, and sensory evaluation using quantitative descriptive analysis were conducted on raw soybeans and soybean sprouts cultivated using groundwater from Jeonju, along with raw domestic soybeans, and Chinese soybeans from other regions. ResultsSoybean sprouts cultivated with groundwater from the Jeonju region resulted in a sweeter taste and a more delicious and crunchier texture. It also resulted in a less undesirable ‘beany’ flavor. As a result, these soybean sprouts are superior overall compared with those grown in other regions regardless of the fact whether the origin of the raw material was domestic or from China (p < 0.001). Even though the soybean sprouts cultivated from Chinese soybeans were very good in the overall acceptability, they had a grassy and bean-like flavor because of a high linolenic acid content. ConclusionSoybean sprouts cultivated using Chinese soybeans in Jeonju were better in the overall acceptability than those grown in other regions because the Jeonju product contained two to three times less amino acids, such as leucine, tyrosine, and phenylalanine, than the other regional products, which tasted bitter. The cultivating water may affect the free amino-acid content of soybean sprouts and their taste.

ANALYSIS IMPORT POLICY OF SOYBEAN ON ECONOMICS PERFORMANCE OF INDONESIAN SOYBEAN

Trade liberalization is closely related to the opening of market access for Indonesian products to the world and vice versa. Since the soybean trade out of BULOG control began in 1998, soybean imports increased very rapidly (Sudaryanto and Swastika, 2007). This research aims to determine the general picture of soybean economy, factors analyses that influence the economic performance of Indonesian soybean and findings the alternative of policies that can reduce soybean imports in Indonesia. Methods of data analysis are descriptive analysis, 2SLS simultaneous equations, and simulation of policy alternatives. Results of the analysis of the factors that affect the economic performance of Indonesian soybean, consists of 1) The area of soybean harvest is influenced significantly by the price of domestic soybean and domestic prices of corn, 2) Productivity soybean influenced significantly by the domestic prices of soybean and fertilizer prices, 3) soybean demand influenced significantly by population, domestic prices of soybean, 4) domestic prices of soybean significantly affected by world prices of soybean, exchange rates, and soybean supply, 5) Imports of soybean influenced significantly by the domestic demand of soybean and soybean production. Therefore, policy scenarios should be made to reduce soybean imports, including by carrying out the expansion of soybean harvest policy, the policy of increasing the productivity of soybean, the policy of subsidizing the price of fertilizer.

The Impact of Market Support in Developed Countries on the Competitiveness of Indonesian Soybean

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Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.

Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.

Impacts of nucleotide fixation during soybean domestication and improvement

BackgroundPlant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time.ResultsAnalysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases.ConclusionsOur analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0463-z) contains supplementary material, which is available to authorized users.

Analysis of Factors on the US Soybean Pricing in China’s Import Market – Based on principal component analysis

Using quarterly data from 2002 to 2014, based on principal component analysis, this paper studies the factors affecting the US soybean pricing in China’s import market, and results show that China’s soybean import quantity from the US has positive impact on the US soybean pricing in China’s import market, but its impact is very weak. China’s gross domestic product, China’s domestic soybean production price index, the yuan-dollar exchange rate, the yuan-Argentine peso exchange rate and the yuan-Brazilian real exchange rate have negative impact on the US soybean pricing in China’s import market. According to this, there are some recommendations: maintain the growth of gross domestic product; improve soybean TFP to reduce soybean producer price index reasonably; take advantage of the exchange rate mechanism effectively to adjust the cost of soybean imports.

A comprehensive analysis of the Cupin gene family in soybean (Glycine max).

Cupin superfamily of proteins, including germin and germin-like proteins (GLPs) from higher plants, is known to play crucial roles in plant development and defense. To date, no systematic analysis has been conducted in soybean (Glycine max) incorporating genome organization, gene structure, expression compendium. In this study, 69 putative Cupin genes were identified from the whole-genome of soybean, which were non-randomly distributed on 17 of the 20 chromosomes. These Gmcupin proteins were phylogenetically clustered into ten distinct subgroups among which the gene structures were highly conserved. Eighteen pairs (52.2%) of duplicate paralogous genes were preferentially retained in duplicated regions of the soybean genome. The distributions of GmCupin genes implied that long segmental duplications contributed significantly to the expansion of the GmCupin gene family. According to the RNA-seq data analysis, most of the Gmcupins were differentially expressed in tissue-specific expression pattern and the expression of some duplicate genes were partially redundant while others showed functional diversity, suggesting the Gmcupins have been retained by substantial subfunctionalization during soybean evolutionary processes. Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen Gmcupins had selected site(s), with all SNPs in Gmcupin10.3 and Gmcupin07.2 genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication. Taken together, our results contribute to the functional characterization of Gmcupin genes in soybean.

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

ANALISIS SIMULASI KEBIJAKAN UNTUK MENINGKATKAN PRODUKSI KEDELAI NASIONAL

&lt;em&gt;Soybean is the main strategic food commodities after paddy and maize, as stated in the UU No. 7 Tahun 1996. Since 2009 until now, national soybean consumption has reach about 2 illion tones per year, but national soybean production just able to satisfy around 900 thousand tones per year, so it drawbacks met from imported soybeans. Contribution quantity of soybean imports reached more 70 persen of the domestic soybean demand per year, this is opposite to the Government aim has launched several years ago to become self-sufficient in soybeans at 2014. So that, we need a policy government to support soybeans self-sufficiency program. Soybeans self-sufficient will be achieved when the national soybeans production can meet the domestic soybeans demand, so that, the policy needs to be done is how to increase the quantity of the national soybeans production. In this study, a simulation analysis was conducted to provide the some alternative policy to improve soybeans production. The results of the analysis concluded that the national soybeans production will increase, at least 15 percent per year by increasing 25 percent the quantity of soybean seeds, 15 percent area harvested, 20 percent of imported soybean prices, 25 percent of national soybeans price, 30 percent soybean import tariffs, and the last is decreasing 150 percent of the quantity soybean imports. Simulation is determined based on the average growth rate of the historical data used.&lt;/em&gt;

Identification of active VQ motif-containing genes and the expression patterns under low nitrogen treatment in soybean.

Plant VQ motif-containing protein family plays crucial roles in plant growth, seed development, and defense responses in Arabidopsis. However, its function in soybean is still not well defined. We aim to identify the VQ gene family, and explore the genetic variation of active GmVQ genes in soybean and their expression patterns under low nitrogen stresses. A total of 74 VQ motif-containing genes were identified in soybean genome, and were clustered into five distinct subfamilies (GmVQI-V) with each gene having two or three copies except GmVQ55 (GmVQIV) with single copy. Fourteen genes with relatively high expression level, at least in one tissue, were defined as active GmVQ genes. Most of these active GmVQ genes specifically expressed in soybean pod shell (7/74), root (9/74) and/or nodule (10/74) respectively. Single nucleotide polymorphism (SNP) analysis in cultivated and wild soybeans revealed there were selected site(s) in GmVQ6, GmVQ7, GmVQ10, GmVQ26 and GmVQ61, which means that these genes have undergone artificial selection during soybean domestication. After low nitrogen treatment, enhanced expression of VQ genes was noticed in specific tissues, such as GmVQ53, GmVQ26, GmVQ58, GmVQ61, GmVQ70 and GmVQ6 in shoot, and GmVQ53, GmVQ58, GmVQ48 in root. On the contrary, suppressed expression of GmVQ57, GmVQ21 and GmVQ1 genes was noticed in root after the treatment. Duplicated copy of the active GmVQ genes showed similar expression pattern, suggesting that these genes might be complete copies. The results suggested that soybean VQ-motif containing genes may act as positive or negative regulators in soybean growth, development and nitrogen metabolism. Taken together, our results provided useful information for functional characterization of soybean GmVQ genes to unravel their biological roles.

A Slower Pace of Soybean Consumption Is Needed

For the 2013-14 marketing year, the USDA projects the domestic soybean crush at 1.7 billion bushels and projects exports at 1.495 billion bushels. With seed, feed, and residual use of 109 million bushels, consumption at the projected level would leave year ending stocks of 150 million bushels, or 4.5 percent of projected consumption. The projection of the domestic crush is 11 million bushels, or 0.7 percent, larger than the crush during the previous marketing year and 45 million bushels larger than projected in September 2013. Based on estimates from the National Oilseed Processors Association (NOPA), the crush during September 2013, the first month of the marketing year, was nine percent less than the crush during September 2012. The monthly crush, however, exceeded that of a year earlier in each month from October through December 2013, with the cumulative crush during those three months exceeding last year’s crush by 2.5 percent. While the total crush during the first four months of the marketing year is only marginally larger than that of a year ago, the recent pace has exceeded expectations and suggests that the marketing year total could exceed the current USDA projection.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

BackgroundArtificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.ResultsA total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.ConclusionsGiven the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.

Functional characterization of the orthologs of At NST 1/2 in Glycine soja (Fabaceae) and the evolutionary implications

The secondary cell wall in plant cells is a highly organized structure that provides mechanical support to the tissue and the entire plant body. Glycine soja, the presumed ancestor of domesticated soybean, differs from the domesticated soybean in an array of morphological characters. The remarkable difference is the stem phenotype, which is often attributed to the thickness of secondary cell walls. Hence, it is of great importance to understand the genetic basis underlying the regulation of secondary wall thickening in these two species. Here, we report that GlycineNST1A/B are functional orthologs of AtNST1/2, which have been shown to act as the master switches of secondary cell wall thickening. GlycineNST1A/B are preferentially expressed in organs undergoing secondary wall deposition, and GmNST1A/B are expressed at twofold the level of GsNST1A/B in mature stem. The overexpression of GsNST1A/B disrupts overall plant development by inducing ectopic deposition of massive secondary walls in normally parenchyma cells in Arabidopsis. Furthermore, expression analyses suggest that the ectopic secondary wall is achieved by upregulating the expression of a series of cell wall-associated transcription factors and secondary wall biosynthetic genes. Together, these results indicate that GsNST1A/B, as the key regulators, are capable of activating the entire secondary wall biosynthetic pathway in Arabidopsis, and also suggest that the genetic circuit of secondary wall development is conserved between Fabaceae and Brassiaceae.

PERTUMBUHAN DAN PRODUKSI BEBERAPA VARETAS KEDELAI TERHADAP INOKULASI BRADYRHIZOBIUM

Growth and Production of soybean varieties of Bradyrhizobium inoculation. Demand of soybean as a protein source continues to increase, but the increasing of domestic soybean production is still low so it must import from abroad. This is due to the decline in soil fertility and agricultural land conversion to residential. The solution, soybean planting can be done by optimizing the existing land commonly called agricultural intensification. In this research, agricultural intensification is done by adding Bradyrhizobium as biofertilizer. symbiosis between soybean plants with these bacteria can directly fix the nitrogen (N) from the air and can save in the N fertilizer of inorganic form. The objective of the research was to know the responses of the soybean varieties toward Bradyrhizobium inoculation. The split plot design with three replication was used, Bradyrhizobium as main plot and soybean varieties (Anjasmoro, Burangrang, Mitani, Grobogan, Tanggamus, Detam 1, and Detam 2) as sub plot. The result showed that the Bradyrhizobium were not significant affected on all of parameters. The varieties significantly affected on plant height at 5 weeks after planted, flower initiation, the time of harvest, the seed weights per plant, and 100 seeds weight. Interaction between Bradyrhizobium inoculation and soybean varieties were not significant on all of parameters . Keyword : growth, soybean, inoculation, bradyrhizobium, variety

Development of a chromosome segment substitution line population with wild soybean (Glycine soja Sieb. et Zucc.) as donor parent

Chromosome segment substitution line (CSSL) population is potential in precisely detecting and pyramiding genes/QTL/segments due to the genetic background noise removed. To exploit and utilize the favorable wild alleles, a CSSL population with 151 lines (SojaCSSLP1) was generated using a wild soybean (Glycine soja Sieb. et Zucc.) N24852 as donor parent and the elite cultivar NN1138-2 as its genetic background. An improved CSSL construction strategy was used, i.e. continuous backcross after initial crossing followed with alternation of backcross and selfing combined with marker-assisted selection based on pedigree DNA pools and phenotypic differences among pedigrees. The SojaCSSLP1 with an average recovery ratio of 95.7 % of the NN1138-2 genome could cover the entire genome of wild soybean. Four wild alleles/segments for each of the two wild characteristics, longer plant height (PH) and more number of nodes on main stem (NN), in a total of six segments, were detected with additive effects all positive. Among them, Satt243 on Chr.10 and Sat_286 on Chr.19 associated with both PH and NN while Satt338 and SOYGPATR on Chr.4 and Satt314 neighboring with Satt192 on Chr.12 had the former and latter on each chromosome associated with PH and NN, respectively. That could explain the high positive correlation between the two traits (r = 0.88). Compared with those in the literature, three QTL/segments for PH and one for NN were detected also among cultivated soybeans, indicating allele differentiation happened not only between wild and cultivated but also among cultivated soybeans. Therefore these QTL/segments might be the key ones to explain the domestication and evolution of soybean. In addition, SojaCSSLP1 should be also potential in studies for multiple wild traits due to its broad variation.