Bulk Segregant Analysis Sequencing and RNA-Seq Analyses Reveal Candidate Genes Associated with Sepal Color Phenotype of Eggplant (<i>Solanum melongena</i> L.)

Eggplant is a highly significant vegetable crop and extensively cultivated worldwide. Sepal color is considered one of the major commercial traits of eggplant. Eggplant sepals develop from petals, and sepals have the ability to change color by accumulating anthocyanins, but whether the eggplants in sepal and their biosynthetic pathways are the same as those in petals is not known. To date, little is known about the underlying mechanisms of sepal color formation. In this study, we performed bulked segregant analysis and transcriptome sequencing using eggplant sepals and obtained 1,452,898 SNPs and 182,543 InDel markers, respectively, as well as 123.65 Gb of clean data using transcriptome sequencing. Through marker screening, the genes regulating eggplant sepals were localized to an interval of 2.6 cM on chromosome 10 by bulked segregant analysis sequencing and transcriptome sequencing and co-analysis, combined with screening of molecular markers by capillary electrophoresis. Eight possible candidate genes were then screened to further interpret the regulatory incentives for the eggplant sepal color

Neutron radiation effects on linear CCDs at different clock pulse frequency

The experiments of reactor neutron radiation effects on linear CCDs are presented. The output voltage in dark field after neutron radiation are presented and compared at different clock pulse frequency. The degradation phenomena are analyzed in depth. The mean dark signal (KD) and dark signal non-uniformity (DSNU) versus neutron fluence is investigated at different clock pulse frequency. The degradation mechanisms of the dark signal and DSNU in linear CCDs are analyzed. The flux of the reactor neutron beams was about 1.33 × 108 n/cm2/s. The samples were exposed to 1MeV neutron-equivalent fluences of 1 × 1011, 5 × 1011, and 1 × 1012 n/cm2, respectively

Risk factor analysis of progressive spinal deformity after resection of intramedullary spinal cord tumors in patients who underwent laminoplasty: A report of 105 consecutive cases

OBJECTIVE Laminoplasty has been used in recent years as an alternative approach to laminectomy for preventing spinal deformity after resection of intramedullary spinal cord tumors (IMSCTs). However, controversies exist with regard to its real role in maintaining postoperative spinal alignment. The purpose of this study was to examine the incidence of progressive spinal deformity in patients who underwent laminoplasty for resection of IMSCT and identify risk factors for progressive spinal deformity. METHODS Data from IMSCT patients who had undergone laminoplasty at Beijing Tsinghua Changgung Hospital between January 2014 and December 2016 were retrospectively reviewed. Univariate tests and multivariate logistic regression analysis were used to assess the statistical relationship between postoperative spinal deformity and radiographic, clinical, and surgical variables. RESULTS One hundred five patients (mean age 37.0 ± 14.5 years) met the criteria for inclusion in the study. Gross-total resection (\u3e 95%) was obtained in 79 cases (75.2%). Twenty-seven (25.7%) of the 105 patients were found to have spinal deformity preoperatively, and 10 (9.5%) new cases of postoperative progressive deformity were detected. The mean duration of follow-up was 27.6 months (SD 14.5 months, median 26.3 months, range 6.2–40.7 months). At last follow-up, the median functional scores of the patients who did develop progressive spinal deformity were worse than those of the patients who did not (modified McCormick Scale: 3 vs 2, and p = 0.04). In the univariate analysis, age (p = 0.01), preoperative spinal deformity (p \u3c 0.01), extent of tumor involvement (p \u3c 0.01), extent of abnormal tumor signal (p = 0.02), and extent of laminoplasty (p \u3c 0.01) were identified as factors associated with postoperative progressive spinal deformity. However, in subsequent multivariate logistic regression analysis, only age ≤ 25 years and preoperative spinal deformity emerged as independent risk factors (p \u3c 0.05), increasing the odds of postoperative progressive deformity by 4.1- and 12.4-fold, respectively (p \u3c 0.05). CONCLUSIONS Progressive spinal deformity was identified in 25.7% patients who had undergone laminoplasty for IMSCT resection and was related to decreased functional status. Younger age (≤ 25 years) and preoperative spinal deformity increased the risk of postoperative progressive spinal deformity. The risk of postoperative deformity warrants serious reconsideration of providing concurrent fusion during IMSCT resection or close follow-up after laminoplasty

Induction of Male Sterility by Targeted Mutation of a Restorer-of-Fertility Gene with CRISPR/Cas9-Mediated Genome Editing in <i>Brassica napus</i> L.

Brassica napus L. (canola, oil seed rape) is one of the world’s most important oil seed crops. In the last four decades, the discovery of cytoplasmic male-sterility (CMS) systems and the restoration of fertility (Rf) genes in B. napus has improved the crop traits by heterosis. The homologs of Rf genes, known as the restoration of fertility-like (RFL) genes, have also gained importance because of their similarities with Rf genes. Such as a high non-synonymous/synonymous codon replacement ratio (dN/dS), autonomous gene duplications, and a possible engrossment in fertility restoration. B. napus contains 53 RFL genes on chromosomes A9 and C8. Our research aims to study the function of BnaRFL11 in fertility restoration using the CRISPR/Cas9 genome editing technique. A total of 88/108 (81.48%) T0 lines, and for T1, 110/145 (75%) lines carried T-DNA insertions. Stable mutations were detected in the T0 and T1 generations, with an average allelic mutation transmission rate of 81%. We used CRISPR-P software to detect off-target 50 plants sequenced from the T0 generation that showed no off-target mutation, signifying that if the designed sgRNA is specific for the target, the off-target effects are negligible. We also concluded that the mutagenic competence of the designed sgRNAs mediated by U6-26 and U6-29 ranged widely from 31% to 96%. The phenotypic analysis of bnarfl11 revealed defects in the floral structure, leaf size, branch number, and seed production. We discovered a significant difference between the sterile line and fertile line flower development after using a stereomicroscope and scanning electron microscope. The pollen visibility test showed that the pollen grain had utterly degenerated. The cytological observations of homozygous mutant plants showed an anther abortion stage similar to nap-CMS, with a Orf222, Orf139, Ap3, and nad5c gene upregulation. The bnarfl11 shows vegetative defects, including fewer branches and a reduced leaf size, suggesting that PPR-encoding genes are essential for the plants’ vegetative and reproductive growth. Our results demonstrated that BnaRFL11 has a possible role in fertility restoration. The current study’s findings suggest that CRISPR/Cas9 mutations may divulge the functions of genes in polyploid species and provide agronomically desirable traits through a targeted mutation

Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.)

Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding

DataSheet_1_The chromosome-scale reference genome and transcriptome analysis of Solanum torvum provides insights into resistance to root-knot nematodes.pdf

Solanum torvum (Swartz) (2n = 24) is a wild Solanaceae plant with high economic value that is used as a rootstock in grafting for Solanaceae plants to improve the resistance to a soil-borne disease caused by root-knot nematodes (RKNs). However, the lack of a high-quality reference genome of S. torvum hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for S. torvum combining PacBio long reads (HiFi reads), Illumina short reads and Hi-C scaffolding technology. The assembled genome size is ~1.25 Gb with a contig N50 and scaffold N50 of 38.65 Mb and 103.02 Mb, respectively as well as a BUSCO estimate of 98%. GO enrichment and KEGG pathway analysis of the unique S. torvum genes, including NLR and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 NLR genes were highly expressed in roots and fibrous roots and that three homologous NLR genes (Sto0288260.1, Sto0201960.1 and Sto0265490.1) in S. torvum were significantly upregulated after RKN infection. Two ABC transporters, ABCB9 and ABCB11 were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the S. torvum will provide insights into RKN resistance.</p