The genetic control of leaf and petal allometric variations in Arabidopsis thaliana

An integrated QTL and RNA-seq analysis revealed new petal morphology loci in Brassica napus L

BACKGROUND

Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding.

RESULTS

In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals.

CONCLUSIONS

The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.

Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed

Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants.

Genome-Wide Investigation and Expression Analysis of K+-Transport-Related Gene Families in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Potassium (K⁺) transport and channel systems play vital roles in plant growth, development and responses to various stresses. In this study, 44 putative K⁺-transport-related genes (18K⁺ uptake permease (KUP)/high-affinity K⁺ (HAK)/K⁺ transporter (KT) family genes and 26 channel genes, including 18 Shaker family genes and 8K⁺ channel outward (KCO) family genes) were identified in the genome of Chinese cabbage (Brassica rapa ssp. pekinensis). To clarify the molecular evolution of each family in Chinese cabbage, phylogenetic analysis and assessments of the gene structures, conserved motifs, chromosomal locations, gene duplications, expression patterns and cis-acting elements of the 44 putative K⁺-transport-related genes were performed. The phylogenetic analysis showed that these genes could be classified into five clades [KUP/HAK/KTs, KCOs, K_out, K_in (KAT) and K_in (AKT)] and that the members of a given clade shared conserved exon-intron distributions and motif compositions. These K⁺-transport-related genes were unevenly distributed over all ten chromosomes, including four duplicated gene pairs that implied an expansion of K⁺-transport-related genes in Chinese cabbage. Analyses of Illumina RNA-seq data for these 44K⁺-transport-related genes indicated tissue-/organ-specific expression patterns. In addition, an overall evaluation showed that the expression levels of KUP/HAK/KT genes were significantly higher than those of potassium channel genes in six tissues. Promoter cis-acting element analysis revealed that these 44K⁺-transport-related genes may be associated with responses to 10 abiotic stresses, primarily light, methyl jasmonate (MeJA) and abscisic acid (ABA). Our results provide a systematic and comprehensive overview of K⁺-transport-related gene families in Chinese cabbage and establish a foundation for further research on K⁺ absorption and transport functions.