Quantitative trait loci analysis of individual and total isoflavone contents in soybean seeds

Soybean isoflavones play diverse roles in human health, including cancers, osteoporosis, heart disease, menopausal symptoms and pabulums. The objective of this study was to identify the quantitative trait loci (QTL) associated with the isoflavones daidzein (DC), genistein (GeC), glycitein (GlC) and total isoflavone contents (TIC) in soybean seeds. A population of 184 F_21:0 recombinant inbred lines derived from a ‘Xiaoheidou’ בGR8836’ cross was planted in pot and field conditions to evaluate soybean isoflavones. Twenty-one QTL were detected by composite interval mapping. Several QTL were associated with the traits for DC, GeC, GlC and TIC only. QDGeGlTIC4_1 and QDGlTIC12_1 are reported first in this study and were associated with the DC, GeC, GlC and TIC traits simultaneously. The QTL identified have potential value for marker-assisted selection to develop soybean varieties with desirable isoflavone content.     

Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds

Despite their medicinal, pharmaceutical, and nutritional importance of isoflavones, the genetic basis controlling the amounts of isoflavones in soybean seeds is still not well understood. The main obstacle is the great variability in the content of isoflavone in seeds harvested from different environments. In this study, quantitative trait loci (QTL) for the content of different isoflavones including daidzein, genistein, and glycitein were investigated in a population of recombinant inbred lines derived from the cross of “Hwangkeum” (Glycine max) by “IT182932” (Glycine soja). Seeds analyzed were harvested in three different experimental environments. QTL analyses for isoflavone content were conducted by composite interval mapping across a genomewide genetic map. Two major QTL were mapped to soybean chromosomes 5 and 8, which were designated QDZGT1 and QDZGT2, respectively. Both loci have not been previously reported in other isoflavone sources. The results from this study will be useful in cloning genes that can control the contents of isoflavones in soybean and for the development of soybean lines containing a high or low isoflavone content.     

Biotic elicitors as a means of increasing isoflavone concentration of soybean seeds

Soybean (Glycine max) seeds contain isoflavones that have positive impacts on human health. Four greenhouse experiments were conducted to determine if isoflavone concentration of mature soybean seeds could be increased using elicitor compounds. The effects on soybean seed isoflavone concentrations following foliar applications of two lipo‐chitooligosaccharides (LCO) [Bj V (C_18:1 MeFuc) and Bj V (Ac, C¹⁶, MeFuc)], chitosan, actinomycetes spores (Streptomyces melanosporofaciens strain EF‐76) and yeast extract at different concentrations and growth stages were evaluated. Combined chitosan seed treatment and foliar applications were also evaluated. Concentrations of daidzein, genistein, glycitein, and total isoflavones were determined by HPLC. Foliar applications of LCOs, chitosan, and actinomycetes caused a marked increase in individual and total isoflavone concentration (ranging between 21% and 84%) of mature seeds when compared to untreated control plants. There were limited differences between the different concentrations and stages of application tested for chitosan and actinomycetes; however, response to LCOs was greatest at higher concentrations (i.e. 10^‐6 M) when applied at the early podding stage. Compared to untreated plants, combined seed treatment and foliar applications of chitosan increased individual and total isoflavone concentration of mature soybean seeds by 16% to 93%. Trends were similar for different cultivars, however, the magnitude of the response varied. Finally, response to foliar applications of yeast extract was highly concentration dependent with increases of up to 56% in total isoflavone observed with 2 mg mL^‐1. Results indicate that elicitors hold promise as a way of increasing isoflavone concentration of mature soybean seeds.     

The additive genetic variance after bottlenecks is affected by the number of loci involved in epistatic interactions

Abstract We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of "pure" epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distributions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks.     

Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds

Background  

Soybean (Glycine max [L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their contribution to human health and plant defense systems. However, attempts to modify seed isoflavone contents have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved.     

Identification of QTL underlying isoflavone contents in soybean seeds among multiple environments

Soybean isoflavones are valued in certain medicines, cosmetics, foods and feeds. Selection for high-isoflavone content in seeds along with agronomic traits is a goal of many soybean breeders. The aim of the study was to identify the quantitative trait loci (QTL) underlying seed isoflavone content in soybean among seven environments in China. A cross was made between ‘Zhongdou 27’, a soybean cultivar with higher mean isoflavone content in the seven environments (daidzein, DZ, 1,865 μg g⁻¹; genistein, GT, 1,614 μg g⁻¹; glycitein, GC, 311 μg g⁻¹ and total isoflavone, TI, 3,791 μg g⁻¹) and ‘Jiunong 20’, a soybean cultivar with lower isoflavone content (DZ, 844 μg g⁻¹; GT, 1,046 μg g⁻¹; GC, 193 μg g⁻¹ and TI, 2,061 μg g⁻¹). Through single-seed-descent, 130 F₅-derived F₆ recombinant inbred lines were advanced. A total of 99 simple-sequence repeat markers were used to construct a genetic linkage map. Seed isoflavone contents were analyzed using high-performance liquid chromatography for multiple years and locations (Harbin in 2005, 2006 and 2007, Hulan in 2006 and 2007, and Suihua in 2006 and 2007). Three QTL were associated with DZ content, four with GT content, three with GC content, and five with TI content. For all QTL detected the beneficial allele was from Zhongdou 27. QTL were located on three (DZ), three (GC), four (GT) and five (TI) molecular linkage groups (LG). A novel QTL was detected with marker Satt144 on LG F that was associated with DZ (0.0014 > P > 0.0001, 5% < R ² < 11%; 254 < DZ < 552 μg g⁻¹), GT (0.0027 > P > 0.0001; 4% < R ² < 9%; 262 < GT < 391 μg g⁻¹), and TI (0.0011 > P > 0.0001; 4% < R ² < 15%; 195 < TI < 871 μg g⁻¹) across the various environments. A previously reported QTL on LG M detected by Satt540 was associated with TI across four environments and TI mean (0.0022 > P > 0.0001; 3% < R ² < 8%; 182 < TI < 334 μg g⁻¹) in China. Because both beneficial alleles were from Zhongdou 27, it was concluded that these two QTL would have the greatest potential value for marker-assisted selection for high-isoflavone content in soybean seed in China. G. Zeng, D. Li and Y. Han have equal contributions to the paper.     

Inhibitors of lipase activities in soybean and other oil seeds

In the cotyledon extracts of seedlings of many oil seeds, including soybean, sunflower, cucumber, and peanut, the in vitro lipase activity was too low to account for the observed in vivo lipolysis. The low in vitro lipase activity was due to the presence of lipase inhibitors in the extracts. The inhibitors from soybean were characterized based on their effects on the hydrolysis of trilinolein by corn, pancreatic, and Rhizopus lipases. The inhibitors were not dialyzable and unaltered by RNase and β-galactosidase treatment. However, they were sensitive to heating and protease digestion. The inhibitory effect of the inhibitors was expressed irrespective of the sequence of the addition of lipase, substrate, and inhibitors to the assay medium. The inhibitory effect was equally expressed when the inhibitors were added either before or after the lipase reaction had been in progress. The inhibitory effect of the inhibitors was independent of the amount of lipase present in the assay, but was dependent on the amount of substrate added. High substrate concentration eliminated totally the inhibitory effect of the inhibitors. Most of the inhibitors were recovered in the soluble fraction in subcellular fractionation. They were present in the 2-4S and not in the 7S, and 11S (storage proteins) protein fraction. There was a gradual decrease of the inhibitors in the cotyledons in the postgerminative growth. We suggest that the inhibitors are proteins which bind to the surface of the substrate micelles. The binding prevents the normal functioning of lipase which acts on the interfacial area between the aqueous medium and the micelle surface.     

Estimation of loci involved in non-shattering of seeds in early rice domestication

Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1. We produced backcross recombinant inbred lines having chromosomal segments from IR36 in the genetic background of wild rice, O. rufipogon W630. Histological and quantitative trait loci analyses of abscission layer formation were conducted. In the analysis of quantitative trait loci, a strong peak was observed close to sh4. We, nevertheless, found that some lines showed complete abscission layer formation despite carrying the IR36 allele at sh4, implying that non-shattering of seeds of IR36 could be regulated by the combination of mutations at sh4 and other seed-shattering loci. We also genotyped qSH3, a recently identified seed-shattering locus. Lines that have the IR36 alleles at sh4 and qSH3 showed inhibition of abscission layer formation but the degree of seed shattering was different from that of IR36. On the basis of these results, we estimated that non-shattering of seeds in early rice domestication involved mutations in at least three loci, and these genetic materials produced in this study may help to identify novel seed-shattering loci.     

Identification and validation of quantitative trait loci controlling seed isoflavone content across multiple environments and backgrounds in soybean

Soybean is important throughout the world not only due to the high seed protein and oil but also owing to the seed isoflavone. To improve the isoflavone concentration in seeds, detecting and mining the stable and reliable quantitative trait loci (QTLs) and related genes in multiple environments and genetic backgrounds become more and more important. In view of this, a F_6:7 recombinant inbred line (RIL) population of 345 lines derived from a cross between Zheng 92116 and Liaodou14 (ZL) was genotyped using 1739 polymorphic SNP and 127 SSR markers in this study and was phenotyped for individual and total seed isoflavone in four environments over 2 years. In total, 48 additive QTLs, which explained 3.00–29.83% of seed isoflavone variation, were identified. Of them, eight QTLs (qDA1_1, qGA1_1, qTIA1_1, qDA1_2, qGA1_2, qTIA1_2, qDA1_3, qTIA1_3) with phenotypic variation explained (PVE) ranging from 14.09 to 28.59% for daidzin, genistin, and total isoflavone were located on the same region of linkage group (LG) A1. These QTLs were further verified in another RIL population derived from Zheng 92116 × Qihuang 30 (ZQ). Meanwhile, the other four overlapping QTLs on linkage group B1, which were associated with glycitin content (qGLB1_1, qGLB1_2, qGLB1_3, qGLB1_4) and explained 16.52 to 29.83% of phenotypic variation, were also verified using the ZQ population. Moreover, the individuals with different genotypes at the common flanking SNP markers for these QTLs on LGs A1 and B1 in the two mapping populations showed significant different isoflavone content, which further validate the QTL mapping results. And also, some candidate genes might participate in the isoflavone biosynthesis processes were found in these stable QTL regions. Thus, the novel and stable QTLs identified and verified in this study could be applied in marker-assisted selection breeding or map-based candidate genes cloning in soybean seed isoflavone genetic improvement in future.     

Mapping of epistatic quantitative trait loci in four-way crosses

Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.     

UDP-glucuronic acid:soyasapogenol glucuronosyltransferase involved in saponin biosynthesis in germinating soybean seeds

We detected UDP-glucuronic acid:soyasapogenol glucuronosyltransferase (UGASGT) activity in the microsomal fraction from germinating soybean (Glycine max [L.] Merr.) seed. A microsomal fraction was isolated from germinating soybean seed and treated with various detergents to solubilize the enzyme. UGASGT activity was monitored throughout purification using UDP-[U-(14)C]glucuronic acid and soyasapogenol B as substrates. Purification of UGASGT was achieved by HiTrap Q, Superdex 200, and HiTrap Blue chromatography procedures. This resulted in >205-fold enrichment relative to the starting homogenate. UGASGT was found to require divalent cations for activity. Studies on the substrate specificity of UGASGT demonstrated that the specificity for the sugar residue transferred was very high, as activity was scarcely found when UDP-glucuronic acid was replaced by other UDP sugars: UDP-glucose and UDP-galactose. Soyasapogenols, which are the aglycons of soybean saponin, are usable acceptors, but glycyrrhetinic acid, sophoradiol, beta-amyrin, and flavonoids are not. These findings suggest that this UGASGT was a specific enzyme for UDP-glucuronic acid as a donor and soyasapogenols as acceptors, and that it was related to the biosynthesis of the sugar chain in soybean saponin. This study provides a basis for the molecular characterization of a key enzyme in saponin biosynthesis in soybean. The isolation of the gene may enable its use in the elucidation of the biosynthesis and physiological role of saponins in soybean.     

Metabolic engineering of isoflavone genistein in Brassica napus with soybean isoflavone synthase

Genistein, 4′,5,7-trihydroxyisoflavone, is an isoflavonoid compound predominantly restricted to legumes and known to possess phyto-oestrogenic and antioxidative activities. The key enzyme that redirects phenylpropanoid pathway intermediates from flavonoids to isoflavonoids is the isoflavone synthase (IFS). Brassica napus is a non-legume oilseed crop with vegetative tissues producing phenylpropanoids and flavonoids, but does not naturally accumulate isoflavones due to the absence of IFS. To demonstrate whether exogenous IFS is able to use endogenous substrate to produce isoflavone genistein in oilseed crop, the soybean IFS gene (GmIFS2) was incorporated into B. napus plants. The presence of GmIFS2 in B. napus was shown to direct the synthesis and accumulation of genistein derivatives in leaves up to 0.72 mg g⁻¹ DW. In addition, expression levels for most B. napus genes in the phenylpropanoid pathway were altered. These results suggest that the heterologous GmIFS2 enzyme is functionally active at using the B. napus naringenin as a substrate to produce genistein in oilseed rape.     

Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments

Soybean seed and pod traits are important yield components. Selection for high yield style in seed and pod along with agronomic traits is a goal of many soybean breeders. The intention of this study was to identify quantitative trait loci (QTL) underlying seed and pod traits in soybean among eleven environments in China. 147 recombinant inbred lines were advanced through single-seed-descent method. The population was derived from a cross between Charleston (an American high yield soybean cultivar) and DongNong594 (a Chinese high yield soybean cultivar). A total of 157 polymorphic simple sequence repeat markers were used to construct a genetic linkage map. The phenotypic data of seed and pod traits [number of one-seed pod, number of two-seed pod, number of three-seed pod, number of four-seed pod, number of (two plus three)-seed pod, number of (three plus four)-seed pod, seed weight per plant, number of pod per plant] were recorded in eleven environments. In the analysis of single environment, fourteen main effect QTLs were identified. In the conjoint analysis of multiple environments, twenty-four additive QTLs were identified, and additive QTLs by environments interactions (AE) were evaluated and analyzed at the same time among eleven environments; twenty-three pairs of epistatic QTLs were identified, and epistasis (additive by additive) by environments interactions (AAE) were also analyzed and evaluated among eleven environments. Comparing the results of identification between single environment mapping and multiple environments conjoint mapping, three main effect QTLs with positive additive values and another three main effect QTLs with negative additive values, had no interactions with all environments, supported that these QTLs could be used in molecular assistant breeding in the future. These different effect QTLs could supply a good foundation to the gene clone and molecular asisstant breeding of soybean seed and pod traits.     

Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F₆-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 × TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (P<0.01) in Met and Cys concentrations, with a range of 5.1–7.3 (g kg⁻¹ seed dry weight) for Cys and 4.4–8.8 (g kg⁻¹ seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.     

QTL, additive and epistatic effects for SCN resistance in PI 437654

PI 437654 is a unique accession because of its resistance to nearly all HG types (races) of soybean cyst nematode (Heterodera glycines Ichinohe; SCN). Objectives of this study were to confirm and refine the locations and gene action associated with SCN resistance previously discovered in PI 437654, and to identify new QTLs that may have been missed because of low coverage with genetic markers used in previous studies. Using 205 F_7:9 RILs and 276 SSR and AFLP molecular markers covering 2,406.5 cM of 20 linkage groups (LGs), we confirmed and refined the locations of major SCN resistance QTLs on LG-A2, -B1, and -G previously identified in PI 437654 or other resistant sources. We found that these major QTLs have epistatic effects among them or with other loci for SCN resistance. We also detected some new QTLs with additive or epistatic effects for SCN resistance to different HG types (races) on all LGs except LGs-B2 and -D1b. The QTL on LG-G was associated with resistance to HG types 2.5.7, 1.2.5.7, 0, and 2.7 (races 1, 2, 3, and 5), and it contributed a large proportion of the additive effects. The QTL on LG-A2 was associated with resistance to HG types 2.5.7 and 0 (races 1 and 3). The QTL on LG-B1, associated with resistance to HG types 2.5.7, 0, 2.7 (races 1, 3, and 5), was the similar QTL found in PI 90763 and PI 404198B. In addition to QTL on LGs-A2, -B1 and -G, a novel additive QTL associated with SCN resistance to HG types 0, 2.7, and 1.3.5.6.7 (race 3, 5, and 14) was identified on LG-I flanked by Sat_299 and Sat_189. Several minor QTLs on LGs-C1, D1a, H, and K were also found to be associated with SCN resistance. Confirmation of the new resistance QTL is underway by evaluating another RIL population with a different genetic background.     

大豆乳清中蛋白质和异黄酮的超滤分离技术

研究了用超滤技术分离大豆乳清中的蛋白质和异黄酮的工艺条件. 结果表明,大豆乳清在超滤之前要进行预处理以减轻膜污染;通过2因素3水平正交试验,确定了最佳的预处理工艺：按大豆乳清中固形物含量的5%,向其中加入CaCl₂,并在85 ℃下加热15 min,在此条件下,蛋白质的沉淀率为49.8%,异黄酮的保留率为90.4%;通过单因素试验,确定了比较合适的超滤条件：选择切割分子量（MWCO）为10000的聚醚砜膜,超滤压力选择51～68 kPa,超滤温度选择30 ℃～40 ℃.在此条件下,大豆乳清中蛋白质的截留率为83.9%,而异黄酮的截留率为7.6%.     

Estimation of additive, dominance and epistatic variance components using finite locus models implemented with a single-site Gibbs and a descent graph sampler

In a previous contribution, we implemented a finite locus model (FLM) for estimating additive and dominance genetic variances via a Bayesian method and a single-site Gibbs sampler. We observed a dependency of dominance variance estimates on locus number in the analysis FLM. Here, we extended the FLM to include two-locus epistasis, and implemented the analysis with two genotype samplers (Gibbs and descent graph) and three different priors for genetic effects (uniform and variable across loci, uniform and constant across loci, and normal). Phenotypic data were simulated for two pedigrees with 6300 and 12,300 individuals in closed populations, using several different, non-additive genetic models. Replications of these data were analysed with FLMs differing in the number of loci. Simulation results indicate that the dependency of non-additive genetic variance estimates on locus number persisted in all implementation strategies we investigated. However, this dependency was considerably diminished with normal priors for genetic effects as compared with uniform priors (constant or variable across loci). Descent graph sampling of genotypes modestly improved variance components estimation compared with Gibbs sampling. Moreover, a larger pedigree produced considerably better variance components estimation, suggesting this dependency might originate from data insufficiency. As the FLM represents an appealing alternative to the infinitesimal model for genetic parameter estimation and for inclusion of polygenic background variation in QTL mapping analyses, further improvements are warranted and might be achieved via improvement of the sampler or treatment of the number of loci as an unknown.     

Estimation of maternal,sex-linked and additive x additive epistatic gene effects for body size of Tribolium

Summary The genetic structure of two quantitative traits, 13-day larval weight and pupal weight, in two unselected populations of Tribolium castaneum was investigated by the genetic model of Carbonell et al. (1983). The variability among two and three-way crosses was analyzed into components due to: general and specific combining abilities, maternal, sex-linkage, specific reciprocal and additive-by-additive epistasis. Also, indirect evidence of higher order epistasis was studied. It is concluded that the heterotic trait larval weight is highly affected by sex-linked genes and by non-additive gene action with additive-by-additive as well as higher order epistasis playing major roles. Pupal weight, on the other hand, is determined mostly by additive gene action although epistasis is also a significant source for genetic variability. Both traits are significantly influenced by maternal effects.Journal Paper No. 9033 from Purdue University Agricultural Experiment Station. Based in part on PhD Theses submitted by the first two authors at Purdue University