Genome-wide characterization of ovate family protein gene family associated with number of seeds per silique in Brassica napus

Genome-wide association study reveals genetic loci for seed density per silique in rapeseed (Brassica napus L.)

KEY MESSAGE

Two stable QTLs controlling seed density per silique were detected on chromosomes A09 and C05 in rapeseed via GWAS, and ARF18 was the only causal gene of QTL qSDPS-A09. Seed density per silique (SDPS) is a key agronomic trait that directly or indirectly affects seed yield in rapeseed (Brassica napus L.). Exploring the genetic control of SDPS is beneficial for increasing rapeseed production. In this study, we evaluated the SDPS phenotypes of 413 rapeseed cultivars (lines) across five natural environments and genotyped them by resequencing. A GWAS analysis was performed using 5,277,554 high-quality variants with the MLM_PCA + K and FarmCPU models. A total of 51 loci were identified to be significantly (p < - log10(1.88 × 10-6)) associated with SDPS, of which 5 were detected in all environments (except for SNP-2095656) by both GWAS models. Among the five loci, three were located on chromosome A09, whereas the other two loci were located on chromosome C05. The three loci on chromosome A09 and the two loci on chromosome C05 were physically close to each other. Therefore, only the two common candidate QTLs were integrated and named QTL qSDPS-A09 (320 kb) and qSDPS-C05 (331.48 kb), respectively. Sixty-seven and forty-eight candidate genes were initially identified on A09 and C05 and then narrowed down to 17 and 13 candidate genes, respectively, via LD block analyses. Gene-based association studies, haplotype analyses and expression analyses confirmed that three homologs of Arabidopsis auxin-response factor 18 (BnaA09G0559300ZS) was the most likely candidate genes underlying the QTL qSDPS-A09. ARF18Hap4 was identified as a favorable haplotype for high SDPS. These findings will aid in elucidating the genetic and molecular mechanisms of SDPS and promoting genetic modifications in rapeseed breeding.

Phylogenomic curation of Ovate Family Proteins (OFPs) in the U's Triangle of Brassica L. indicates stress-induced growth modulation

The Ovate Family Proteins (OFPs) gene family houses a class of proteins that are involved in regulating plant growth and development. To date, there is no report of the simultaneous functional characterization of this gene family in all members of U's Triangle of Brassica. Here, we retrieved a combined total of 256 OFP protein sequences and analyzed their chromosomal localization, gene structure, conserved protein motif domains, and the pattern of cis-acting regulatory elements. The abundance of light-responsive elements like G-box, MRE, and GT1 motif suggests that OFPs are sensitive to the stimuli of light. The protein-protein interaction network analysis revealed that OFP05 and its orthologous genes were involved in regulating the process of transcriptional repression through their interaction with homeodomain transcription factors like KNAT and BLH. The presence of domains like DNA binding 2 and its superfamily speculated the involvement of OFPs in regulating gene expression. The biotic and abiotic stress, and the tissue-specific expression analysis of the RNA-seq datasets revealed that some of the genes such as BjuOFP30, and BnaOFP27, BolOFP11, and BolOFP10 were highly upregulated in seed coat at the mature stage and roots under various chemical stress conditions respectively which suggests their crucial role in plant growth and development processes. Experimental validation of prominent BnaOFPs such as BnaOFP27 confirmed their involvement in regulating gene expression under salinity, heavy metal, drought, heat, and cold stress. The GO and KEGG pathway enrichment analysis also sheds light on the involvement of OFPs in regulating plant growth and development. These findings have the potential to serve as a forerunner for future studies in terms of functionally diverse analysis of the OFP gene family in Brassica and other plant species.