DNA methylation plays an important role in plant growth and development, and in regulating the activity of transposable elements (TEs).  Research on DNA methylation-related (DMR) genes has been reported in Arabidopsis, but little research on DMR genes has been reported in Brassica rapa and Brassica oleracea, the genomes of which exhibit significant differences in TE content.  In this study, we identified 78 and 77 DMR genes in Brassica rapa and Brassica oleracea, respectively.  Detailed analysis revealed that the numbers of DMR genes in different DMR pathways varied in B. rapa and B. oleracea.  The evolutionary selection pressure of DMR genes in B. rapa and B. oleracea was compared, and the DMR genes showed differential evolution between these two species.  The nucleotide diversity (π) and selective sweep (Tajima’s D) revealed footprints of selection in the B. rapa and B. oleracea populations.  Transcriptome analysis showed that most DMR genes exhibited similar expression characteristics in B. rapa and B. oleracea.  This study dissects the evolutionary differences and genetic variations of the DMR genes in B. rapa and B. oleracea, and will provide valuable resources for future research on the divergent evolution of DNA methylation between B. rapa and B. oleracea.

Whole genome duplication (WGD) and tandem duplication (TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution.  We analyzed the genomes of three Solanaceae species (Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication (WGT) event.  The analysis was used to investigate the phenomenon of tandem gene evolution with (S. lycopersicum) or without WGT (V. vinifera).  Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene (TDG) clusters than the Solanaceae species that experienced the WGT event.  Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs (absolute dosage) accumulated during long-term evolution.  In addition, WGD and TD show a significant bias in the functional categories of the genes retained.  WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance.  WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission.  The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events.  These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.  

Grain zinc (Zn) and iron (Fe) concentrations and their responses to foliar application of micronutrients in 28 Chinese wheat landraces and 63 cultivars were investigated in a two-year field experiment.  The average grain Zn and Fe concentrations were 41.8 mg kg^–1 (29.0−63.3 mg kg^–1) and 39.7 mg kg^–1 (27.9−67.0 mg kg^–1), respectively.  Compared with cultivars, landraces had greater grain Zn (11.0%) and Fe (4.8%) concentrations but lower harvest index (HI), grain weight per spike (GWS), grain number per spike (GNS) and thousand grain weight (TGW).  Both Zn and Fe concentrations were negatively and significantly correlated with HI, GWS, and GNS, while showed a poor association with TGW, suggesting that lower HI, GWS, and GNS, but not TGW, accounted for higher Zn and Fe concentrations for landraces than for cultivars.  Grain Zn concentrations of both cultivars and landraces significantly increased after foliar Zn spray and the increase was two-fold greater for landraces (12.6 mg kg^–1) than for cultivars (6.4 mg kg^–1).  Foliar Fe spray increased grain Fe concentrations of landraces (3.4 mg kg^–1) and cultivars (1.2 mg kg^–1), but these increases were not statistically significant.  This study showed that Chinese wheat landraces had higher grain Zn and Fe concentrations than cultivars, and greater increases occurred in grain Zn concentration than in grain Fe concentration in response to fertilization, suggesting that Chinese wheat landraces could serve as a potential genetic source for enhancing grain mineral levels in modern wheat cultivars.

Cold stress is a major problem in rice production.  To rapidly identify genes for cold tolerance in Dongxiang wild rice (DWR, Oryza rufipogon Griff.), sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant (R) and susceptible (S) bulks of a backcross inbred lines (BILs) population (derived from Oryza sativa×O. rufipogon) and their parents.  Single nucleotide polymorphisms (SNP)-index graphs and corresponding Δ(SNP-index) graphs (at 99 and 95% confidence levels) for R- and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes.  Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon.  Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion (InDel) markers (12-7 and 12-16) that were linked with candidate genes on chromosome 12 in DWR.  These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.

An experiment was conducted to investigate the effect of dietary supplementation with flavonoid from Scutellaria baicalensis Georgi (SBGFN) as SBGFN-zinc (SBGFN-Zn) on growth performance, meat quality, immune responses and antioxidation of broilers.  A total of 450 one-d-old Arbor Acres male broilers were randomly allocated to 5 treatments with 6 replicates of 15 birds per replicate for each treatment in a completely randomized design.  Birds were fed a SBGFN-unsupplemented corn-soybean meal basal diet (control) or the basal diet supplemented with 60, 120, 180 or 240 mg SBGFN kg^–1 from SBGFN-Zn for 42 d.  Dietary SBGFN supplementation affected (P<0.03) drip loss in thigh muscle, total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px) activity in liver of broilers at 42 d of age.  Chicks fed the diets supplemented with 120, 180 and 240 mg SBGFN kg^–1 had lower (P<0.03) drip loss of thigh muscle than those fed the control diet.  Chicks fed the diet supplemented with 180 mg SBGFN kg^–1 had higher (P<0.03) liver T-SOD and GSH-Px activity than those fed the diets supplemented with 0, 60 and 120 mg SBGFN kg^–1.  The results from the present study indicate that dietary supplementation with 180 mg SBGFN kg^–1 as SBGFN-Zn improved both meat quality and antioxidative ability of broilers.   

We investigated the soil microbiologic characteristics, and the yield and sustainable production of winter wheat, by conducting a long-term fertilization experiment.  A single application of N, P and K (NPK) fertilizer was taken as the control (CK) and three organic fertilization treatments were used: NPK fertilizer+pig manure (T1), NPK fertilizer+straw return (T2), NPK fertilizer+pig manure+straw return (T3).  The results showed that all three organic fertilization treatments (T1, T2 and T3) significantly increased both soil total N (STN) and soil organic carbon (SOC) from 2008 onwards.  In 2016, the SOC content and soil C/N ratios for T1, T2 and T3 were significantly higher than those for CK.  The three organic fertilization treatments increased soil microbial activity.  In 2016, the activity of urease (sucrase) and the soil respiration rate (SRS) for T1, T2 and T3 were significantly higher than those under CK.  The organic fertilization treatments also increased the content of soil microbial biomass carbon (SMBC) and microbial biomass nitrogen (SMBN), the SMBC/SMBN ratio and the microbial quotient (qMB).  The yield for T1, T2 and T3 was significantly higher than that of CK, respectively.  Over the nine years of the investigation, the average yield increased by 9.9, 13.2 and 17.4% for T1, T2 and T3, respectively, compared to the initial yield for each treatment, whereas the average yield of CK over the same period was reduced by 6.5%.  T1, T2, and T3 lowered the coefficient of variation (CV) of wheat yield and increased the sustainable yield index (SYI).  Wheat grain yield was significantly positively correlated with each of the soil microbial properties (P<0.01).  These results showed that the long-term application of combined organic and chemical fertilizers can stabilize crop yield and make it more sustainable by improving the properties of the soil.

    Tassel branch number (TBN) is the principal component of maize tassel inflorescence architecture and is a typical quantitative trait controlled by multiple genes. The main objective of this research was to detect quantitative trait loci (QTLs) for TBN. The maize inbred line SICAU1212 was used as the common parent to develop BC₁S₁ and recombinant inbred line (RIL) populations with inbred lines 3237 and B73, respectively. The two related populations consisted of 123 and 238 lines, respectively. Each population was grown and phenotyped for TBN in two environments. Eleven QTLs were detected in the BC₁S₁ population, located on chromosomes 2, 3, 5, and 7, accounted for 4.45–26.58% of the phenotypic variation. Two QTLs (qB11Jtbn2-1, qB12Ctbn2-1, qBJtbn2-1; q11JBtbn5-1, qB12Ctbn5-1, qBJtbn5-1) that accounted for more than 10% of the phenotypic variation were identified. Three QTLs located on chromosomes 2, 3 and 5, exhibited stable expression in the two environments. Ten QTLs were detected in the RIL population, located on chromosomes 2, 3, 5, 8, and 10, accounted for 2.69–13.58% of the TBN variation. One QTL (qR14Dtbn2-2) explained >10% of the phenotypic variation. One common QTL (qB12Ctbn2-2, qR14Dtbn2-2, qRJtbn2-2) was detected between the two related populations. Three pairs of epistatic effects were identified between two loci with or without additive effects and accounted for 1.19–4.26% of the phenotypic variance. These results demonstrated that TBN variation was mainly caused by major effects, minor effects and slightly modified by epistatic effects. Thus, identification of QTL for TBN may help elucidate the genetic basis of TBN and also facilitate map-based cloning and marker-assisted selection (MAS) in maize breeding programs.