BackgroundRecent innovation in the field of genome engineering encompasses numerous levels of plant genome engineering which attract the substantial excitement of plant biologist worldwide. RNA-guided CRISPR Cas9 system has appeared a promising tool in site-directed mutagenesis due to its innovative utilization in different branches of biology. CRISPR-Cas9 nuclease system have supersedes all previously existed strategies and their associated pitfalls encountered with site-specific mutagenesis.Results Here we demonstrated an efficient sequence specific integration/mutation of FAD2–2 gene in soybean using CRISPR-Cas9 nuclease system. A single guided RNA sequence was designed with the help of a number of bioinformatics tools aimed to target distinct sites of FAD2–2 loci in soybean. The binary vector (pCas9-AtU6-sgRNA) has been successfully transformed into soybean cotyledon using Agrobacterium tumafacien. Taken together our findings complies soybean transgenic mutants subjected to targeted mutation were surprisingly detected in our target gene. Furthermore, the detection of Cas9 gene, BAR gene, and NOS terminator were carried out respectively. Southern blot analysis confirmed the stable transformation of Cas9 gene into soybean. Real time expression with qRT-PCR and Sanger sequencing analysis confirmed the efficient CRISPR-Cas9/sgRNA induced mutation within the target sequence of FAD2–2 loci. The integration of FAD2–2 target region in the form of substitution, deletions and insertions were achieved with notably high frequency and rare off-target mutagenesis.ConclusionHigh frequent mutation efficiency was recorded as 21% out of all transgenic soybean plants subjected to targeted mutagenesis. Furthermore, Near-infrared spectroscopy (NIR) indicates the entire fatty acid profiling obtained from the mutants seeds of soybean. A considerable modulation in oleic acid content up to (65.58%) whereas the least level of linoleic acid is (16.08%) were recorded. Based on these finding CRISPR-Cas9 system can possibly sum up recent development and future challenges in producing agronomically important crops.Electronic supplementary materialThe online version of this article (10.1186/s12896-019-0501-2) contains supplementary material, which is available to authorized users.

Root systems can display variable genetic architectures leading to nutrient foraging or improving abiotic stress tolerance. Breeding for new soybean varieties with efficient root systems has tremendous potential in enhancing resource use efficiency and plant adaptation for challenging climates. In this study, root related traits were analyzed in a panel of 260 spring soybean with genome-wide association study (GWAS). Genotyping was done with specific locus amplified fragment sequencing (SLAF-seq), and five GWAS models (GLM, MLM, CMLM, FaST-LMM, and EMMAX) were used for analysis. A total of 179,960 highly consistent SNP markers distributed over the entire genome with an inter-marker distance of 2.36 kb was used for GWAS analysis. Overall, 27 significant SNPs with a phenotypic contribution ranging from 20 to 72% and distributed on chromosomes 2, 6, 8, 9, 13, 16 and 18 were identified and two of them were found to be associated with multiple root-related traits. Based on the linkage disequilibrium (LD) distance of 9.5 kb for the different chromosomes, 11 root and shoot regulating genes were detected based on LD region of a maximum 55-bp and phenotypic contribution greater than 22%. Expression analysis revealed an association between expression levels of those genes and the degree of root branching number. The current study provides new insights into the genetic architecture of soybean roots, and the underlying SNPs/genes could be critical for future breeding of high-efficient root system in soybean.

Influences of planting density and nitrogen rate have been investigated frequently in targeted wheat (Triticum aestivum L.) research. Few studies have investigated interactions between these inputs. The objective was to determine the combine effect of N and seeding rates on culm morph‐physiological traits for lodging tolerance and grain yield. The experiment used a split‐split randomized block design using two wheat varieties ‘AnNong0711’ and ‘YanNong19’, split by four seeding (180, 240, 300, and 375 × 104 ha−1) and four N rates (0, 180, 240, and 300 kg ha−1). Lodging traits of plant height, culm height center of gravity, and internode length, increased (p < .05) however, stem diameter, wall thickness, and stem breaking strength decreased with increasing N and seeding rate. Stem breaking strength was negatively correlated with culm height center of gravity (r = −.869, p = .01), internode length (r = −.872, p < .01), and lignin (r = −.746, p < .01) but positively correlated with internode diameter (r = .715, p < .05) and wall thickness (r = .696, p < .05). Culm lodging index and cellulose showed positive correlation (r = .807 and .913 respectively) with lignin. Compared to YanNong19, AnNong0711 showed higher grain yield and culm lodging index of 9 and 20.49%, respectively. For improved grain yield, 180 plants m−2 was optimal in surface combinations with 210 kg N ha−1 for AnNong0711 and 200 kg N ha−1 for YanNong19. These combinations of seeding and N rates could successfully mitigate lodging and improve grain yield.

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