Oilseed crops are used to produce vegetable oil. Sesame (Sesamum indicum), an oilseed crop grown worldwide, has high oil content and a small diploid genome, but the genetic basis of oil production and quality is unclear. Here we sequence 705 diverse sesame varieties to construct a haplotype map of the sesame genome and de novo assemble two representative varieties to identify sequence variations. We investigate 56 agronomic traits in four environments and identify 549 associated loci. Examination of the major loci identifies 46 candidate causative genes, including genes related to oil content, fatty acid biosynthesis and yield. Several of the candidate genes for oil content encode enzymes involved in oil metabolism. Two major genes associated with lignification and black pigmentation in the seed coat are also associated with large variation in oil content. These findings may inform breeding and improvement strategies for a broad range of oilseed crops.

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.

Background: Intercropping, an essential cultivation pattern in modern agricultural systems, increases crop yields and soil quality. Cassava and peanut intercropping systems exhibit advantages in solar utilization and cadmium absorption, etc. However, the inner mechanisms need to be elucidated. In this study, Illumina MiSeq platform was used to reveal the rhizospheric microbes and soil quality in cassava/peanut intercropping systems, and the results provided a reference for the application of this method in studying other intercropping systems. Results: Both intercropping cassava/peanut (IP) and intercropping peanut/cassava (IC) systems significantly increased available N, available K, pH value, and urease activity, comparing with that in monocropping cassava (MC) and monocropping peanut (MP) system. However, there were few effects on the total N, total P, total K, available P, organic matter, protease activity, catalase activity, sucrase activity, and acid phosphatase activity. Both IP and MP soils contained more bacteria and fungi than those in the IC and MC soils, which were mainly made of Proteobacteria and Actinobacteria. Intercropping remarkably increased the number of Nitrospirae in IP and IC soils comparing those in MC and MP soils. Redundancy analysis (RDA) revealed that the abundances of DA101, Pilimelia, and Ramlibacter were positively correlated to the soil quality. These results suggest that intercropping enhances the available nitrogen content of soil through increasing the quantity of rhizospheric microbes, especially that of DA101 and Pilimelia. Conclusions: The cassava/peanut intercropping system improves soil quality through increasing the available nitrogen content and abundance of DA101, Pilimelia, and Ramlibacter in the soil.

No abstract

Background The sugarcane/peanut intercropping system is a specific and efficient cropping pattern in South China. Intercropping systems change the bacterial diversity of soils and decrease disease rates. It can not only utilized light, heat, water and land resources efficiently, but also increased yield and economic benefits of farmers. Methods We determined soil nutrients, enzymes and microbes in sugarcane/peanut intercropping system, and analyzed relevance of the soil physicochemical properties and the genes involved in N and P cycling and organic matter turnover by metagenome sequencing. Results The results showed that sugarcane/peanut intercropping significantly boosted the content of total nitrogen, available phosphorus, total potassium, organic matter, pH value and bacteria and enhanced the activity of acid phosphatase compared to monocropping. Especially the content of available nitrogen, available phosphorus and organic matter increased significantly by 20.1%, 65.3% and 56.0% in root zone soil of IP2 treatment than monocropping treatment. The content of available potassium and microbial biomass carbon, as well as the activity of catalase, sucrase and protease, significantly decreased in intercropping root zone soil. Intercropping resulted in a significant increase by 7.8%, 16.2% and 23.0% in IS, IP1 and IP2, respectively, of the acid phosphatase content relative to MS. Metagenomic analysis showed that the pathways involved in carbohydrate and amino acid metabolism were dominant and more abundant in intercropping than in monocropping. Moreover, the relative abundances of genes related to N cycling (glnA, GLUD1_2, nirK), P cycling (phoR, phoB) and organic matter turnover (PRDX2_4) were higher in the intercropping soil than in the monocropping soil. The relative abundance of GLUD1_2 and phoR were 25.5% and 13.8% higher in the IP2 treatment respectively,and bgIX was higher in IS treatment compared to the monocropping treatment. Genes that were significantly related to phosphorus metabolism and nitrogen metabolism (TREH, katE, gudB) were more abundant in intercropping than in monocropping. Conclusion The results of this study indicate that the intercropping system changed the numbers of microbes as well as enzymes activities, and subsequently regulate genes involved in N cycling, P cycling and organic matter turnover. Finally, it leads to the increase of nutrients in root zone soil and improved the soil environment.

Sugarcane/peanut intercropping is a highly efficient planting pattern in South China. However, the effects of sugarcane/peanut intercropping on soil quality need to be clarified. This study characterized the soil microbial community and the soil quality in sugarcane/peanut intercropping systems by the Illumina MiSeq platform. The results showed that the intercropping sugarcane (IS) system significantly increased the total N (TN), available N (AN), available P (AP), pH value, and acid phosphatase activity (ACP), but it had little effect on the total P (TP), total K (TK), available K (AK), organic matter (OM), urease activity, protease activity, catalase activity, and sucrase activity, compared with those in monocropping sugarcane (MS) and monocropping peanut (MP) systems. Both intercropping peanut (IP) and IS soils contained more bacteria and fungi than soils in the MP and MS fields, and the microbes identified were mainly Chloroflexi and Acidobacteria, respectively. Intercropping significantly increased the number of unique microbes in IS soils (68 genera), compared with the numbers in the IP (14), MS (17), and MP (16) systems. The redundancy analysis revealed that the abundances of culturable Acidobacteriaceae subgroup 1, nonculturable DA111, and culturable Acidobacteria were positively correlated with the measured soil quality in the intercropping system. Furthermore, the sugarcane/peanut intercropping significantly increased the economic benefit by 87.84% and 36.38%, as compared with that of the MP and MS, respectively. These results suggest that peanut and sugarcane intercropping increases the available N and P content by increasing the abundance of rhizospheric microbes, especially Acidobacteriaceae subgroup 1, DA111, and Acidobacteria.

Intercropping systems have been studied as a sustainable agricultural planting pattern to increase soil quality and crop yields. However, the relationships between metabolites and soil physicochemical properties remain poorly understood under sugarcane/peanut intercropping system. Thus, we determined the rhizosphere soil physicochemical properties, and analyzed rhizosphere soil metabolites and root metabolites by metabolomics method under monoculture and intercropping patterns of sugarcane and peanut. The results showed that pH, the contents of total phosphorus (P), total potassium (K), available nitrogen (N), available phosphorus (P), and available potassium (K) were higher in rhizosphere soil of intercropping peanut than monoculture peanut, and the content of total P was higher in rhizosphere soil of intercropping sugarcane than monoculture sugarcane. Sugarcane/peanut intercropping also significantly increased the activities of acid phosphatase and urease in rhizosphere soil. The metabolomics results showed that 32 metabolites, mainly organic acids and their derivatives (25.00%), nucleotides and their metabolites (18.75%), were detected in root and rhizosphere soil samples. In the MP-S (rhizosphere soil of monoculture peanut) vs. IP-S (rhizosphere soil of intercropping peanut) comparison, 47 differential metabolites (42 upregulated) were screened, including glycerolipids (19.15%), organic acids and their derivatives (17.89%), and amino acids and their metabolites (12.77%). In the MS-S (rhizosphere soil of monoculture sugarcane) vs. IS-S (rhizosphere soil of intercropping sugarcane) comparison, 51 differential metabolites (26 upregulated) were screened, including heterocyclic compounds (15.69%), glycerolipids (11.76%), and organic acids and their derivatives (9.80%). The metabolite species from MP-S, MS-S, IP-S, and IS-S were similar, but some metabolite contents were significantly different, such as adenine, adenosine, maltotriose, thermozeaxanthin-13 and PE-NMe (20:0/24:0). Adenine and adenosine were detected in root and rhizosphere soils, and their levels were increased in the intercropping treatment, which were mainly related to enhanced purine metabolism in root and rhizosphere soils under the sugarcane/peanut intercropping system. Importantly, adenine and adenosine were significantly positively correlated with total P and total K contents, acid phosphatase and urease activities, and pH. This study clarified that the sugarcane/peanut intercropping system could improve soil nutrients and enzymes and was related to purine metabolism.

Allopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species. To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA-start codon-targeted (SCoT) polymorphism and cDNA-high-frequency oligonucleotide-targeting active gene (cDNA-HFO-TAG) techniques, from the hybrids (F 1) and newly synthesized allopolyploid generations (S 0 to S 3) between tetraploid cultivated peanut Zhongkaihua No.4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the F 1 hybrid or immediately after chromosome doubling. Three types of gene expression changes were observed, including complete silence (gene from progenitors was not expressed in all progenies), incomplete silence (gene expressed only in some progenies) and new genes activation. Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions. The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG. These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments (TDFs) probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to the genetic diploidization of newly formed allopolyploids. Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.