Search

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns) - genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted. [ABSTRACT FROM AUTHOR]

Rapeseed is one of the most important oilseeds crops worldwide. Although stem development greatly affects crop yield, its molecular mechanisms remain elusive in rapeseed. This study found a stem bending 1 (stb1) mutant in rapeseed with abnormal stem development and performed phenotype characterization, genetic analysis, quantitative trait locus mapping, and transcriptome analysis. The key stage of stem bending in stb1 mutant occurred at Biologische Bundesanstalt, Bundessortenamt and CHemical industry (BBCH) stages 59–61, from the end of stem elongation to early flowering. The number of vessels and the degree of development of stem xylem, sclerenchyma, and parenchyma cells were extremely lower in stb1 mutant than in elite cultivar ZS11. Genetic analysis revealed that stb1 is controlled by a single recessive locus located between markers Bn-A01-p2421445 and Bn-A01-p4230829 on chromosome A01. Using RNA-seq, identified 1631 genes that differentially expressed between mutant and normal F 2 plants in the shoot apical meristem and stem. The down-regulated genes were mainly overrepresented in auxin transport and coenzyme metabolism processes. Combining data on the auxin concentrations in stem and expression of candidate genes within the mapping interval in the mutant, it was speculated that the phenotype of the stb1 mutant may be caused by defects in polar auxin transport, as two auxin transport-related genes were obviously down-regulated in the mutant. Among them, BnSOS3-INTERACTING PROTEIN3 , which encodes a CBL-interacting protein kinase, was considered the most promising candidate gene for further investigation. These results lay a foundation for better understanding the molecular mechanisms of stem development in rapeseed. • Abnormal stem development of a stem bending 1 (stb1) mutant was found in rapeseed at the BBCH stages 59 to 61. • The stb1 is controlled by a single recessive locus located between markers Bn-A01-p2421445 and Bn-A01-p4230829. • The phenotype of stb1 may be caused by mutation of BnSOS3-INTERACTING PROTEIN3 that controls polar auxin transport. [ABSTRACT FROM AUTHOR]

Background: Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions. Results: High-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions. Conclusions: The combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus. [ABSTRACT FROM AUTHOR]