Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.

Silique length (SL) is an important yield trait and positively correlates with seeds per silique and seed weight. In the present study, two double haploid (DH) populations, established from crosses Zhongshuang11 × R11 (ZR) and R1 × R2 (RR), containing 280 and 95 DH lines, respectively, were used to map quantitative trait loci (QTL) for SL. A high-dense genetic map from ZR population was constructed comprising 14,658 bins on 19 linkage groups, with map length of 2,198.85 cM and an average marker distance of 0.15 cM. Genetic linkage map from RR population was constructed by using 2,046 mapped markers anchored to 19 chromosomes with 2,217-cM map length and an average marker distance of 1.08 cM. Major QTL qSL_ZR_A09 and qSL_RR_A09b on A09 were identified from ZR and RR populations, respectively. Both QTL could be stably detected in four environments. QTL qSL_RR_A09b and qSL_ZR_A09 were located on 68.5-70.8 cM and 91.33-91.94 cM interval with R2 values of 14.99-39.07% and 15.00-20.36% in RR and ZR populations, respectively. Based on the physical positions of single nucleotide polymorphism (SNP) markers flanking qSL_ZR_A09 and gene annotation in Arabidopsis, 26 genes were identified with SNP/Indel variation between parents and two genes (BnaA09g41180D and BnaA09g41380D) were selected as the candidate genes. Expression analysis further revealed BnaA09g41180D, encoding homologs of Arabidopsis fasciclin-like arabinogalactan proteins (FLA3), as the most promising candidate gene for qSL_ZR_A09. The QTL identification and candidate gene analysis will provide new insight into the genomic regions controlling SL in Brassica napus as well as candidate genes underlying the QTL.

Gray mold, caused by the fungus Botrytis cinerea, is the most significant postharvest disease of kiwifruit. In the present study, iTRAQ with LC-ESI-MS/MS was used to identify the kiwifruit proteins associated with the response to B. cinerea. A total of 2,487 proteins in kiwifruit were identified. Among them, 292 represented differentially accumulated proteins (DAPs), with 196 DAPs having increased, and 96 DAPs having decreased in accumulation in B. cinerea-inoculated vs. water-inoculated, control kiwifruits. DAPs were associated with penetration site reorganization, cell wall degradation, MAPK cascades, ROS signaling, and PR proteins. In order to examine the corresponding transcriptional levels of the DAPs, RT-qPCR was conducted on a subset of 9 DAPs. In addition, virus-induced gene silencing was used to examine the role of myosin 10 in kiwifruit, a gene modulating host penetration resistance to fungal infection, in response to B. cinerea infection. The present study provides new insight on the understanding of the interaction between kiwifruit and B. cinerea.

Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis "Hongyang" at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of "Hongyang." AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology.

Field plot experiments were conducted over 3 years (from April 2014 to November 2016) in a double-rice (Oryza sativa L.) cropping system in subtropical China to evaluate the effects of N fertilizer placement on grain yield and N recovery efficiency (NRE). Different N application methods included: no N application (CK); N broadcast application (NBP); N and NPK deep placement (NDP and NPKDP, respectively). Results showed that grain yield and apparent NRE significantly increased for NDP and NPKDP as compared to NBP. The main reason was that N deep placement (NDP) increased the number of productive panicle per m-2. To further evaluate the increase, a pot experiment was conducted to understand the N supply in different soil layers in NDP during the whole rice growing stage and a 15N tracing technique was used in a field experiment to investigate the fate of urea-15N in the rice-soil system during rice growth and at maturity. The pot experiment indicated that NDP could maintain a higher N supply in deep soil layers than N broadcast for 52 days during rice growth. The 15N tracing study showed that NDP could maintain much higher fertilizer N in the 5-20 cm soil layer during rice growth and could induce plant to absorb more N from fertilizer and soil than NBP, which led to higher NRE. One important finding was that NDP and NPKDP significantly increased fertilizer NRE but did not lead to N declined in soil compared to NBP. Compared to NPK, NPKDP induced rice plants to absorb more fertilizer N rather than soil N.

Melatonin (N-acetyl-5-methoxytryptamine), a naturally occurring small molecule, can protect plants against abiotic stress after exogenous treatmenting with it. It is not known if melatonin homologs, such as 5-methoxytryptamine and 5-methoxyindole, that are easy and more cost-effective to synthesize can stimulate the plant immune system in the same manner as melatonin. In the present study, we assessed the biological activity of the melatonin homologs, 5-methoxytryptamin and 5-methoxyindole. The results showed that melatonin and its homologs all induced disease resistance against Phytophthora nicotianae in Nicotiana benthamiana plants. The application of all three compounds also induced stomatal closure and the production of reactive oxygen species. Gene expression analysis indicated that the expression of genes involved in hydrogen peroxide (H2O2), nitric oxide (NO) production, and salicylic acid (SA) biosynthesis was significantly upregulated by all three compounds. Four homologs of the melatonin receptors were identified by blasting search with the phytomelatonin receptor in Arabidopsis. Molecular docking studies were also used to identify four putative melatonin receptors in N. benthamiana. Further experimentation revealed that silencing of the melatonin receptors trP47363 and trP13076 in N. benthamiana compromised the induction of stomatal closure, PR-1a gene expression and SA accumulation by all three compounds. Collectively, our data indicate that the induction of defense responses in N. benthamiana by melatonin, 5-methoxytryptamine, and 5-methoxyindole involves the melatonin receptors trP47363 and trP13076.

Heterodera avenae is an important soil-borne pathogen that affects field crops worldwide. Chemical nematicides can be used to control the nematode, but they bring toxicity to the environment and human. Trichoderma longibrachiatum has been shown to have the ability to control H. avenae cysts, but detailed microscopic observations and bioassays are lacking. In this study, we used microscopic observations and bioassays to study the effect of T. longibrachiatum T6 (TL6) on the eggs and second stage juveniles (J2s) of H. avenae, and investigate the role of TL6 in inducing the resistance to H. avenae in wheat seedling at physiological and biochemical levels. Microscopic observations recorded that TL6 parasitized on the H. avenae eggs, germinated, and produced a large number of hyphae on the eggs surface at the initial stage, thereafter, the eggs were completely surrounded by dense mycelia and the contents of eggs were lysed at the late stage. Meanwhile, the conidia suspension of TL6 parasitized on the surface of J2s, produced a large number of hyphae that penetrated the cuticle and caused deformation of the nematodes. TL6 at the concentration of 1.5 × 107 conidia ml-1 had the highest rates of parasitism on eggs and J2s, reflected by the highest hatching-inhibition of eggs and the mortality of J2s. In the greenhouse experiments, wheat seedlings treated with TL6 at 1.5 × 107 conidia ml-1 had reduced H. avenae infection, and increased plant growth significantly compared to the control. The cysts and juveniles in soil were reduced by 89.8 and 92.7%, the juveniles and females in roots were reduced by 88.3 and 91.3%, whereas the activity of chitinase and β-1, 3-glucanase, total flavonoids and lignin contents in wheat roots were increased significantly at different stage after inoculation with the eggs and TL6 conidia in comparison to the control. Maximum activity of chitinase and β-1, 3-glucanase were recorded at the 20th and 15th Days after inoculation with TL6 and thereafter it declined. The maximum contents of total flavonoids and lignin were recorded at the 35th and 40th Days after inoculation with TL6. After being stained with the rapid vital dyes of acridine orange (AO) and neutral red (NR), the frozen and infected eggs and J2s of H. avenae changed color to orange and red, respectively, while the color of eggs and J2s in control group did not change. Therefore, our results suggest that TL6 is potentially an effective bio-control agent for H. avenae. The possible mechanisms by which TL6 suppresses H. avenae infection are due to the direct parasitic and lethal effect of TL6 on the eggs and J2s activity, and the induced defense response in wheat plants together.

It is well established that a high external NH(+) 4 concentration depresses many processes in plant development, but the underlying mechanisms are still not well understood. To determine whether the negative effects of high levels of NH(+) 4 are related to competitive cation uptake, wheat was grown in a field with moderate (18 g N m(-2)) and high (30 g N m(-2)) supplies of NH(+) 4 in the presence or absence of additional K(+) (6 g K2O m(-2)) to examine culm mechanical strength, the main components of the vascular bundle, nitrogen (N) remobilization and the grain-filling rate. The results indicated that an excessive supply of NH(+) 4 significantly decreased culm mechanical strength, the cellulose and lignin contents of vascular bundles, the N remobilization efficiency (NRE) and the grain-filling rate compared with a moderate level of NH(+) 4. The additional provision of K(+) considerably alleviated these negative effects of high NH(+) 4, resulting in a 19.41-26.95% increase in culm mechanical strength during grain filling and a 34.59% increase in the NRE. An assay using the scanning ion-selective electrode technique (SIET) showed that the net rate of transmembrane K(+) influx decreased by 84.62%, and measurements using flame photometry demonstrated that the K(+) content decreased by 36.13% in wheat plants subjected to high NH(+) 4. This study indicates that the effects of high NH(+) 4 on culm mechanical strength, cellulose and lignin contents, the NRE and the grain-filling rate are probably associated with inhibition of K(+) uptake in wheat.

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.

The majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL) for resistance to pod shatter in an unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH) and inter-mated (IF2) crosses derived from R1 (resistant to pod shattering) and R2 (prone to pod shattering) accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02, and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09) and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06) could be repeatedly detected across environments in a diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those that appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.

Grain protein content (GPC) and yield are of two important traits in wheat, but their negative correlation has hampered their simultaneous improvement in conventional breeding. Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is an important genetic resource for wheat quality improvement. In this study, we report a genome-wide association study (GWAS) using 13116 DArT-seq markers to characterize GPC in 161 wheat lines derived from wild emmer. Using a general linear model, we identified 141 markers that were significantly associated with GPC, and grouped into 48 QTL regions. Using both general linear model and mixed linear model, we identified four significant markers that were grouped into two novel QTL regions on chromosomes 2BS (QGpc.cd1-2B.1) and 7BL (QGpc.cd1-7B.2). The two QTLs have no negative effects on thousand kernel weight (TKW) and should be useful for simultaneous improvement of GPC and TKW in wheat breeding. Searches of public databases revealed 61 putative candidate/flanking genes related to GPC. The putative proteins of interest were grouped in four main categories: enzymes, kinase proteins, metal transport-related proteins, and disease resistance proteins. The linked markers and associated candidate genes provide essential information for cloning genes related to high GPC and performing marker-assisted breeding in wheat.

In Cucurbitaceae crops, the first flower node (FFN) is an important agronomic trait which can impact the onset of maturity, the production of female flowers, and yield. However, the gene responsible for regulating FFN in bitter gourd is unknown. Here, we used a gynoecious line (S156G) with low FFN as the female parent and a monoecious line (K8-201) with high FFN as the male parent to obtain F1 and F2 generations. Genetic analysis indicated that the low FFN trait was incompletely dominant over the high FFN trait. A major quantitative trait locus (QTL)-Mcffn and four minor effect QTLs-Mcffn1.1, Mcffn1.2, Mcffn1.3, and Mcffn1.4 were detected by whole-genome re-sequencing-based QTL mapping in the S156G×K8-201 F2 population (n=234) cultivated in autumn 2019. The Mcffn locus was further supported by molecular marker-based QTL mapping in three S156G×K8-201 F2 populations planted in autumn 2019 (n=234), autumn 2020 (n=192), and spring 2022 (n=205). Then, the Mcffn locus was fine-mapped into a 77.98-kb physical region on pseudochromosome MC06 using a large S156G×K8-201 F2 population (n=2,402). MC06g1112, which is a homolog of FLOWERING LOCUS T (FT), was considered as the most likely Mcffn candidate gene according to both expression and sequence variation analyses between parental lines. A point mutation (C277T) in MC06g1112, which results in a P93S amino acid mutation between parental lines, may be responsible for decreasing FFN in bitter gourd. Our findings provide a helpful resource for the molecular marker-assisted selective breeding of bitter gourd.

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant development and stress response. In the present study, GmWRKY16 encoding a WRKY transcription factor in soybean was functionally characterized in Arabidopsis. GmWRKY16 is a nuclear protein that contains a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has the characteristics of transcriptional activation ability, presenting a constitutive expression pattern with relative expression levels of over fourfold in the old leaves, flowers, seeds and roots of soybean. The results of quantitative real time polymerase chain reaction (qRT-PCR) showed that GmWRKY16 could be induced by salt, alkali, ABA, drought and PEG-6000. As compared with the control, overexpression of GmWRKY16 in Arabidopsis increased the seed germination rate and root growth of seedlings in transgenic lines under higher concentrations of mannitol, NaCl and ABA. In the meantime, GmWRKY16 transgenic lines showed over 75% survival rate after rehydration and enhanced Arabidopsis tolerance to salt and drought with higher proline and lower MDA accumulation, less water loss of the detached leaves, and accumulated more endogenous ABA than the control under stress conditions. Further studies showed that AtWRKY8, KIN1, and RD29A were induced in GmWRKY16 transgenic plants under NaCl treatment. The expressions of the ABA biosynthesis gene (NCED3), signaling genes (ABI1, ABI2, ABI4, and ABI5), responsive genes (RD29A, COR15A, COR15B, and RD22) and stress-related marker genes (KIN1, LEA14, LEA76, and CER3) were regulated in transgenic lines under drought stress. In summary, these results suggest that GmWRKY16 as a WRKY TF may promote tolerance to drought and salt stresses through an ABA-mediated pathway.