Identification of Gene-Allele System Conferring Alkali-Tolerance at Seedling Stage in Northeast China Soybean Germplasm.

Salinization of cultivated soils may result in either high salt levels or alkaline conditions, both of which stress crops and reduce performance. We sampled genotypes included in the Northeast China soybean germplasm population (NECSGP) to identify possible genes that affect tolerance to alkaline soil conditions. In this study, 361 soybean accessions collected in Northeast China were tested under 220 mM NaHCO3:Na2CO3 = 9:1 (pH = 9.8) to evaluate the alkali-tolerance (ATI) at the seedling stage in Mudanjiang, Heilongjiang, China. The restricted two-stage multi-locus model genome-wide association study (RTM-GWAS) with gene-allele sequences as markers (6503 GASMs) based on simplified genome resequencing (RAD-sequencing) was accomplished. From this analysis, 132 main effect candidate genes with 359 alleles and 35 Gene × Environment genes with 103 alleles were identified, explaining 90.93% and 2.80% of the seedling alkali-tolerance phenotypic variation, respectively. Genetic variability of ATI in NECSGP was observed primarily within subpopulations, especially in ecoregion B, from which 80% of ATI-tolerant accessions were screened out. The biological functions of 132 candidate genes were classified into eight functional categories (defense response, substance transport, regulation, metabolism-related, substance synthesis, biological process, plant development, and unknown function). From the ATI gene-allele system, six key genes-alleles were identified as starting points for further study on understanding the ATI gene network.

Kinetically Controlled Nucleation Enabled by Tunable Microfluidic Mixing for the Synthesis of Dendritic Au@Pt Core/Shell Nanomaterials.

The nucleation stage plays a decisive role in determining nanocrystal morphology and properties; hence, the ability to regulate nucleation is critical for achieving high-level control. Herein, glass microfluidic chips with S-shaped mixing units are designed for the synthesis of Au@Pt core/shell materials. The use of hydrodynamics to tune the nucleation kinetics is explored by varying the number of mixing units. Dendritic Au@Pt core/shell nanomaterials are controllably synthesized and a formation mechanism is proposed. As-synthesized Au@Pt exhibited excellent ethanol oxidation activity under alkaline conditions (8.4 times that of commercial Pt/C). This approach is also successfully applied to the synthesize of Au@Pd core/shell nanomaterials, thus demonstrating its generality.

An Improved Genome-Wide Association Procedure Explores Gene-Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population.

In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene-allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADLDSF and AATDSF, 130-141 genes with 384-406 alleles were explored, and for DFM and its related ADLDFM and AATDFM, 124-135 genes with 362-384 alleles were explored, in a total of six gene-allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene-allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks.

Gene-allele system of shade tolerance in southern China soybean germplasm revealed by genome-wide association study using gene-allele sequence as markers.

KEY MESSAGE: Fifty-three shade tolerance genes with 281 alleles in the SCSGP were identified directly using gene-allele sequence as markers in RTM GWAS, from which optimized crosses, evolutionary motivators, and gene-allele networks were explored. Shade tolerance is a key for optimal cultivation of soybean inter/relay-cropped with corn. To explore the shade tolerance gene-allele system in the southern China soybean germplasm, we proposed using gene-allele sequence markers (GASMs) in a restricted two-stage multi-locus model genome-wide association study (GASM-RTM-GWAS). A representative sample with 394 accessions was tested for their shade tolerance index (STI), in Nanning, China. Through whole-genome re-sequencing, 47,586 GASMs were assembled. From GASM-RTM-GWAS, 53 main-effect STI genes with 281 alleles (2-13 alleles/gene) (totally 63 genes with 308 alleles, including 38 G × E genes with 191 alleles) were identified and then organized into a gene-allele matrix composed of eight submatrices corresponding to geo-seasonal subpopulations. The population featured mild STI changes (1.69 → 1.56-1.82) and mild gene-allele changes (92.5% alleles inherited, 0% alleles excluded, 7.5% alleles emerged) from the primitive (SAIII) to the derived seven subpopulations, but large transgressive recombination potentials and optimal crosses were predicted. The 63 STI genes were annotated into six biological categories (metabolic process, catalytic activity, response to stresses, transcription and translation, signal transduction and transport and unknown functions), interacted as gene networks. From the STI gene-allele system, 38 important alleles of 22 genes were nominated for further in-depth study. GASM-RTM-GWAS performed powerful and efficient in germplasm population genetic study comparing to other procedures through facilitating direct and thorough identification of its gene-allele system, from which genome-wide breeding by design could be achieved, and evolutionary motivators and gene-allele networks could be explored.

Dealloying of Pt1Bi2 intermetallic toward optimization of electrocatalysis on a Bi-continuous nanoporous core-shell structure.

Noble metal nanoporous materials hold great potential in the field of catalysis, owing to their high open structures and numerous low coordination surface sites. However, the formation of porous nanoparticles is restricted by particle size. Herein, we utilized a Pt1Bi2 intermetallic nanocatalyst to develop a dealloying approach for preparing nanoparticles with a bi-continuous porous and core-shell structure and proposed a mechanism for the formation of pores. The particle size used to form the porous structure can be <10 nm, which enhances the nanocatalyst's performance for the oxygen reduction reaction (ORR). This study provides a new understanding of the formation of porous materials via a dealloying approach.

Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication.

Although seed weight has increased following domestication from wild soybean (Glycine soja) to cultivated soybean (Glycine max), the genetic basis underlying this change is unclear. Using mapping populations derived from chromosome segment substitution lines of wild soybean, we identified SW16.1 as the causative gene underlying a major quantitative trait locus controlling seed weight. SW16.1 encodes a nucleus-localized LIM domain-containing protein. Importantly, the GsSW16.1 allele from wild soybean accession N24852 had a negative effect on seed weight, whereas the GmSW16.1 allele from cultivar NN1138-2 had a positive effect. Gene expression network analysis, reverse-transcription quantitative polymerase chain reaction, and promoter-luciferase reporter transient expression assays suggested that SW16.1 regulates the transcription of MT4, a positive regulator of seed weight. The natural variations in SW16.1 and other known seed weight genes were analyzed in soybean germplasm. The SW16.1 polymorphism was associated with seed weight in 247 soybean accessions, showing much higher frequency of positive-effect alleles in cultivated soybean than in wild soybean. Interestingly, gene allele matrix analysis of the known seed weight genes revealed that G. max has lost 38.5% of the G. soja alleles and that most of the lost alleles had negative effects on seed weight. Our results suggest that eliminating negative alleles from G. soja led to a higher frequency of positive alleles and changed genetic backgrounds in G. max, which contributed to larger seeds in cultivated soybean after domestication from wild soybean. Our findings provide new insights regarding soybean domestication and should assist current soybean breeding programs.

Transgressive Potential Prediction and Optimal Cross Design of Seed Protein Content in the Northeast China Soybean Population Based on Full Exploration of the QTL-Allele System.

Northeast China is a major soybean production region in China. A representative sample of the Northeast China soybean germplasm population (NECSGP) composed of 361 accessions was evaluated for their seed protein content (SPC) in Tieling, Northeast China. This SPC varied greatly, with a mean SPC of 40.77%, ranging from 36.60 to 46.07%, but it was lower than that of the Chinese soybean landrace population (43.10%, ranging from 37.51 to 50.46%). The SPC increased slightly from 40.32-40.97% in the old maturity groups (MG, MGIII + II + I) to 40.93-41.58% in the new MGs (MG0 + 00 + 000). The restricted two-stage multi-locus genome-wide association study (RTM-GWAS) with 15,501 SNP linkage-disequilibrium block (SNPLDB) markers identified 73 SPC quantitative trait loci (QTLs) with 273 alleles, explaining 71.70% of the phenotypic variation, wherein 28 QTLs were new ones. The evolutionary changes of QTL-allele structures from old MGs to new MGs were analyzed, and 97.79% of the alleles in new MGs were inherited from the old MGs and 2.21% were new. The small amount of new positive allele emergence and possible recombination between alleles might explain the slight SPC increase in the new MGs. The prediction of recombination potentials in the SPC of all the possible crosses indicated that the mean of SPC overall crosses was 43.29% (+2.52%) and the maximum was 50.00% (+9.23%) in the SPC, and the maximum transgressive potential was 3.93%, suggesting that SPC breeding potentials do exist in the NECSGP. A total of 120 candidate genes were annotated and functionally classified into 13 categories, indicating that SPC is a complex trait conferred by a gene network.

Germplasm Sources, Genetic Richness, and Population Differentiation of Modern Chinese Soybean Cultivars Based on Pedigree Integrated With Genomic-Marker Analysis.

Soybean is a native crop in China for ≈ 5,000 years. The 560 cultivars released in 2006-2015, commercialized with seeds available publicly, were collected (designated modern Chinese soybean cultivars, MCSCs), as a part of 2,371 ones released during ~100 years' breeding history. The MCSCs with their parental pedigrees were gathered, including 279, 155, and 126 cultivars from Northeast and Northwest China (NNC), Huang-Huai-Hai Valleys (HHH), and Southern China (SC), respectively. The MCSCs were tested in the field, genotyped with sequencing, and analyzed for their germplasm sources, genetic richness, and population differentiation based on pedigree integrated with genomic-marker analysis. The main results were as follows: (i) The MCSCs covering 12 of the global 13 MGs (maturity groups) showing different ecoregions with different cropping systems caused their different MG constitutions. (ii) Parental pedigree analysis showed 718 immediate parents and 604 terminal ancestors involved in MCSCs, from which 41 core-terminal ancestors were identified. (iii) NNC was richer in allele number and specific present/deficient alleles, and genetically distant from HHH and SC. (iv) The geographic grouping of MCSCs was partially consistent with marker-based clustering, indicating multiple genetic backgrounds in three eco-subpopulations. (v) Eleven major core-terminal ancestor-derived families were identified, including four derived from ancestors in NNC, four from HHH, and three from SC, containing 463 (82.68%) MCSCs with some cross-distribution among ecoregions. (vi) CGS (coefficient of genetic similarity) calculated from genomic markers showed more precision than COP (coefficient of parentage) using pedigree information in evaluating genetic relationship/differentiation. Overall, through pedigree and genomic-marker analyses, the germplasm constitutions of the three eco-subpopulations were relatively self-sufficient, and germplasm exchange is seriously required for further improvement.

Analysis of Behaviors of the Railway Subgrade with a New Waterproof Seal Layer.

This study proposes a new waterproof sealing layer to reduce the impact of water on subgrade beds. The proposed waterproof sealing layer is composed of a polyurethane adhesive (PA) mixture, which aims to control interlaminar deformation and prevent seepage. A variety of laboratory tests were first performed to analyze the attenuation characteristics and mechanical properties of various polyurethane polymer (PP)-improved gravel mixtures under thermohydraulic coupling effects. In addition, a waterproof performance model test of the PP-improved gravel layer was conducted to investigate its waterproof and drainage performance and hydraulic damage mechanism. Finally, the feasibility and effectiveness of the surface structure of the waterproof drainage subgrade bed containing the PA mixture was tested in combination with the treatment project of the Ciyaowan station of the Baoshen heavy-haul railway. According to the experimental and model results, (1) the waterproof layer containing the polyurethane mixture exhibited satisfactory stiffness, elasticity and flexibility. The waterproof layer containing the polyurethane mixture also controlled the deformation between layers, and its mechanical properties remained stable. (2) The waterproof layer with the dense polyurethane mixture performed well in terms of the waterproof aspect, and no infiltration occurred under cyclic load (3). Long-term field monitoring revealed that the effect of the implementation of a PP-improved gravel layer to treat mud pumping was remarkable. The settlement of the PP-improved gravel layer only reached 13.21 mm, and the settlement remained stable in the later stage.

Simultaneous Partial Nitrification and Denitrification Maintained in Membrane Bioreactor for Nitrogen Removal and Hydrogen Autotrophic Denitrification for Further Treatment.

Low C/N wastewater results from a wide range of factors that significantly harm the environment. They include insufficient carbon sources, low denitrification efficiency, and NH4+-N concentrations in low C/N wastewater that are too high to be treated. In this research, the membrane biofilm reactor and hydrogen-based membrane biofilm reactor (MBR-MBfR) were optimized and regulated under different operating parameters: the simulated domestic sewage with low C/N was domesticated and the domestic sewage was then denitrified. The results of the MBR-MBfR experiments indicated that a C/N ratio of two was suitable for NH4+-N, NO2--N, NO3--N, and chemical oxygen demand (COD) removal in partial nitrification-denitrification (PN-D) and hydrogen autotrophic denitrification for further treatment. The steady state for domestic wastewater was reached when the MBR-MBfR in the experimental conditions of HRT = 15 h, SRT = 20 d, 0.04 Mpa for H2 pressure in MBfR, 0.4-0.8 mg/L DO in MBR, MLSS = 2500 mg/L(MBR) and 2800 mg/L(MBfR), and effluent concentrations of NH4+-N, NO3--N, and NO2--N were 4.3 ± 0.5, 1.95 ± 0.04, and 2.05 ± 0.15 mg/L, respectively. High-throughput sequencing results revealed the following: (1) The genus Nitrosomonas as the ammonia oxidizing bacteria (AOB) and Denitratisoma as potential denitrifiers were simultaneously enriched in the MBR; (2) at the genus level, Meiothermus,Lentimicrobium, Thauera,Hydrogenophaga, and Desulfotomaculum played a dominant role in leading to NO3--N and NO2--N removal in the MBfR.

Growth period QTL-allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension.

Soybean (Glycine max (L.) Merr.) has been disseminated globally as a photoperiod/temperature-sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL-allele constitution using restricted two-stage multi-locus genome-wide association study (RTM-GWAS). Genotypes with 20 701 genome-wide SNPLDBs (single-nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL-allele matrix characterized with all QTL-allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10-12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12-21 days) or slower maturation (14-56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi-functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL-alleles relatively thoroughly using RTM-GWAS for direct matrix comparisons and subsequent analysis.

Transcriptomic and photosynthetic responses to grafting of the Nod1 gene in nodulated and non-nodulated soybeans.

Legume plants form symbiotic relationships with rhizobia to convert N2 into ammonia, and the nodulation status can affect plant development including photosynthesis. However, the relationship between nitrogen fixation and photosynthesis during carbon and nitrogen metabolism remains unclear. This study was undertaken to unravel regulation of nodulation and photosynthesis using a spontaneous nonnodulated soybean mutant by grafting. The results of inheritance and gene mapping showed that the nonnodulated mutant was controlled by a recessive gene overlapped with the reported rj1 locus, and might be a new rj1 allele with 1 bp deletion in the fourth exon in comparison to the sequence of normal nodulation plants. According to grafting results, soybean nodulation is obviously determined by the roots, not the seedlings. Moreover, nitrogen content along with related metabolic enzyme activity, and photosynthetic capacity were enhanced by nonnodulated scions grafted with nodulated roots. Contrary results were obtained for nodulated scions grafted with nonnodulated roots. A total of 853 differentially expressed genes (DEGs) in the leaves and 1874 in the roots were identified by transcriptome analyses of the grafting treatments. We identified 285 differential gene ontology (GO) terms and 57 differential pathway terms identified in the leaves, while 856 differential GO terms and 207 differential pathway terms in the roots. Twenty DEGs interacting at translation level were selected, and the results of transcriptome analyses were verified by q-PCR. These findings indicated that the nodulation-related Nod allelic gene increases the nitrogen content of nonnodulated plants, which affects the enzymes involved in nitrogen metabolism, leading to changes in hormone levels and further regulation of photosynthesis and carbon metabolism.

Integrated Systems Pharmacology and Surface Plasmon Resonance Approaches to Reveal the Synergistic Effect of Multiple Components of Gu-Ben-Ke-Chuan Decoction on Chronic Bronchitis.

INTRODUCTION: Gu-Ben-Ke-Chuan (GBKC) decoction, a well-known prescription composed of seven herbs, has been widely used for treating chronic bronchitis (CB). However, the pharmacological constituents of GBKC and the underlying mechanisms by which these components act on CB remain unclear. METHODS: Ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap) was first employed to rapidly identify compounds from GBKC. Thereafter, network pharmacology and molecular docking analyses were performed to identify the potential active constituents, candidate targets, and major pathways. Finally, the affinities between the key compounds and targets were verified via surface plasmon resonance (SPR) analysis. In addition, the anti-inflammatory effect of GBKC was verified using an LPS-induced inflammatory cell model based on the predicted results. RESULTS: A total of 53 major compounds were identified in the GBKC decoction. After network pharmacology-based virtual screening, 141 major targets and 39 main compounds were identified to be effective in the treatment of CB. The major targets were highly enriched in the tumor necrosis factor (TNF) signaling pathway, suggesting that GBKC could attenuate the inflammatory response in patients with CB. Furthermore, molecular docking results indicated that 20 pairs of components and target proteins relevant to the TNF pathway exhibited notable interactions. Among them, eight compound-target pairs exhibited good affinity as per SPR analysis. In addition, the production of interleukin 6 and TNF-α in LPS-induced MH-S cells was suppressed after GBKC treatment. CONCLUSION: This study successfully clarified the mechanism of action of GBKC against CB, which demonstrated that the integrated strategy described above is reliable for identifying the active compounds and mechanisms responsible for the pharmacological activities of GBKC decoction.

Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population.

The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05-0.18 and 1.20-4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2-4 and 2-6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.

Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean.

Annual wild soybean (G. soja) is the ancestor of the cultivated soybean (G. max). To reveal the genetic changes from soja to max, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on SojaCSSLP1 generated from NN1138-2(max)×N24852(soja). The SojaCSSLP5 was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (G, E2 and GmPRR3B) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in SojaCSSLP5. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.

Identification of Additive-Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines.

Seed weight and shape are important agronomic traits that affect soybean quality and yield. In the present study, we used image analysis software to evaluate 100-seed weight and seed shape traits (length, width, perimeter, projection area, length/width, and weight/projection area) of 155 novel recombinant inbred soybean lines (NJRISX) generated by crossing "Su88-M21" and "XYXHD". We examined quantitative trait loci (QTLs) associated with the six traits (except seed weight per projection area), and identified 42 additive QTLs (5-8 QTLs per trait) accounting for 24.9-37.5% of the phenotypic variation (PV). Meanwhile, 2-4 epistatic QTL pairs per trait out of a total of 18 accounted for 2.5-7.2% of the PV; and unmapped minor QTLs accounted for the remaining 35.0-56.7% of the PV. A total of 28 additive and 11 epistatic QTL pairs were concentrated in nine joint QTL segments (JQSs), indicating that QTLs associated with seed weight and shape are closely related and interacted. An interaction was also detected between additive and epistatic QTL pairs and environment, which made significant contributions of 1.4-9.5% and 0.4-0.8% to the PV, respectively. We annotated 18 candidate genes in the nine JQSs, which were important for interpreting the close relationships among the six traits. These findings indicate that examining the interactions between closely related traits rather than only analyzing individual trait provides more useful insight into the genetic system of the interrelated traits for which there has been limited QTL information.

Comprehensive Identification of Drought Tolerance QTL-Allele and Candidate Gene Systems in Chinese Cultivated Soybean Population.

Drought is one of the most important factors affecting plant growth and productivity. The previous results on drought tolerance (DT) genetic system in soybean indicated a complex of genes not only few ones were involved in the trait. This study is featured with a relatively thorough identification of QTL-allele/candidate-gene system using an efficient restricted two-stage multi-locus multi-allele genome-wide association study, on two comprehensive DT indicators, membership index values of relative plant weight (MPW) and height (MPH), instead of a single biological characteristic, in a large sample (564 accessions) of the Chinese cultivated soybean population (CCSP). Based on 24,694 multi-allele markers, 75 and 64 QTL with 261 and 207 alleles (2-12/locus) were detected for MPW and MPH, explaining 54.7% and 47.1% of phenotypic variance, respectively. The detected QTL-alleles were organized into a QTL-allele matrix for each indicator, indicating DT is a super-trait conferred by two (even more) QTL-allele systems of sub-traits. Each CCSP matrix was separated into landrace (LR) and released cultivar (RC) sub-matrices, which showed significant differentiation in QTL-allele constitutions, with 58 LR alleles excluded and 16 new ones emerged in RC. Using the matrices, optimal crosses with great DT transgressive recombinants were predicted. From the detected QTL, 177 candidate genes were annotated and validated with quantitative Real-time PCR, and grouped into nine categories, with ABA and stress responders as the major parts. The key point of the above results is the establishment of relatively full QTL-allele matrices composed of numerous gene functions jointly conferring DT, therefore, demonstrates the complexity of DT genetic system and potential of CCSP in DT breeding.

Bi-Phenotypic Trait May Be Conferred by Multiple Alleles in a Germplasm Population.

The Chinese soybean germplasm pool (CSGP) comprises annual wild (WA), farmers' landrace (LR) and released cultivar (RC) populations, and ecoregion subpopulations in WA/LR/RC (ecoregion IV/III/II/I). A representative sample consisted of 1,024 accessions was studied for pubescence color (PC) and flower color (FC). In the evolution from WA (brown PC and mainly purple FC) to LR then to RC, with above wild characteristic changed, while gray PC, and white FC emerged and their frequency increased. Using 36,952 genomic SNPLDB markers with 100,092 haplotypes, the association between markers and bi-phenotypic traits was detected using χ2 association analysis under single locus model and RTM-GWAS procedure under multi-locus model, respectively. Multiple markers co-associated with individual bi-phenotypic trait with the most significant markers containing multiple rather than two haplotypes even for a bi-phenotypic trait. On a marker/locus, each haplotype corresponds to two colors, except one (FC-1-5) out of 11 haplotypes for single color. The major candidate gene was annotated with its alleles identified from the population sequencing data. Similarly, multiple alleles identified and each corresponds to two colors except three (a8/a9/b3) out of 12 alleles for single color. The major haplotypes/alleles in LR and RC were traced to WA ecoregion subpopulations, the WA IV and WA III genotypes showed genetically more close to the cultivated subpopulations, therefore, WA from Ecoregion IV and III were inferred as the common ancestor for cultivated soybeans. The marker-haplotypes/gene-alleles not exactly coincided with the bi-phenotypic trait has challenged to the traditional Mendelian genetics, which was discussed and to be further studied.

Rubus chingii Hu: A Review of the Phytochemistry and Pharmacology.

Rubus chingii Hu (R. chingii), referred to as "Fu-Pen-Zi" in Chinese, has great medicinal and dietary values since ancient times. The dried fruits of R. chingii have been widely used in traditional Chinese medicine (TCM) for the treatment of kidney enuresis and urinary frequency for centuries. According to current findings, R. chingii has been reported to contain a variety of chemical constituents, mostly triterpenoids, diterpenoids, flavonoids, and organic acids. These compounds have been demonstrated to be the major bioactive components responsible for pharmacological effects such as anticomplementary, anticancer, antioxidant, antimicrobial, and anti-inflammatory functions. Therefore, this review focused on the up-to-date published data of the literature about R. chingii and comprehensively summarized its phytochemistry, pharmacology, quality control, and toxicity to provide a beneficial support to its further investigations and applications in medicines and foods.

Identifying a wild allele conferring small seed size, high protein content and low oil content using chromosome segment substitution lines in soybean.

KEY MESSAGE: A wild soybean allele conferring 100-seed weight, protein content and oil content simultaneously was fine-mapped to a 329-kb region on Chromosome 15, in which Glyma.15g049200 was predicted a candidate gene. Annual wild soybean characterized with small 100-seed weight (100SW), high protein content (PRC), low oil content (OIC) may contain favourable alleles for broadening the genetic base of cultivated soybeans. To evaluate these alleles, a population composed of 195 chromosome segment substitution lines (SojaCSSLP4), with wild N24852 as donor and cultivated NN1138-2 as recurrent parent, was tested. In SojaCSSLP4, 10, 9 and 8 wild segments/QTL were detected for 100SW, PRC and OIC, respectively. Using a backcross-derived secondary population, one segment for the three traits (q100SW15, qPro15 and qOil15) and one for 100SW (q100SW18.2) were fine-mapped into a 329-kb region on chromosome 15 and a 286-kb region on chromosome 18, respectively. Integrated with the transcription data in SoyBase, 42 genes were predicted in the 329-kb region where Glyma.15g049200 showed significant expression differences at all seed development stages. Furthermore, the Glyma.15g049200 segments of the two parents were sequenced and compared, which showed two base insertions in CDS (coding sequence) in the wild N24852 comparing to the NN1138-2. Since only Glyma.15g049200 performed differential CDS between the two parents but related to the three traits, Glyma.15g049200 was predicted a pleiotropic candidate gene for 100SW, PRC and OIC. The functional annotation of Glyma.15g049200 indicated a bidirectional sucrose transporter belonging to MtN3/saliva family which might be the reason that this gene provides a same biochemical basis for 100SW, PRC and OIC, therefore, is responsible for the three traits. This result may facilitate isolation of the specific gene and provide prerequisite for understanding the other two pleiotropic QTL.