Genetic Variation and Divergence of Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Brassica rapa

Abstract

Alterations in leaf adaxial-abaxial (ad-ab) polarity are one of the main factors that influence leaf curvature. In Chinese cabbage, leaf incurvature is an essential prerequisite to the formation of a leafy head. Identifying ad-ab patterning genes and investigating their genetic variation may facilitate elucidation of the mechanisms underlying leaf incurvature during head formation. Comparative genomic analysis of 45 leaf ad-ab patterning genes in Brassica rapa based on 26 homologs of Arabidopsis thaliana indicated that these genes underwent expansion and were retained after whole genome triplication (WGT). We also assessed the nucleotide diversity and selection footprints of these 45 genes in a collection of 94 Brassica rapa accessions that were composed of heading and non-heading morphotypes. Six of the 45 genes showed significant negative Tajima's D indices and nucleotide diversity reduction in heading accessions compared to those in non-heading accessions, indicating that they underwent purifying selection. Further testing of the BrARF3.1 gene, which was one of the selection signals from a larger collection, confirmed that purifying selection did occur. Our results provide genetic evidence that ad-ab patterning genes are involved in leaf incurvature, which is associated with formation of a leafy head, as well as promote an understanding of the genetic mechanism underlying leafy head formation in Chinese cabbage.

Keywords: Brassica rapa; Chinese cabbage; adaxial-abaxial polarity; genetic variation; leafy head; purifying selection.

Figure 1

Leaf morphology of heading and non-heading B. rapa in mature stage. (A) The leafy head of heading B. rapa (Chinese cabbage), and its incurved leaves from inside to outside. (B) The non-heading B. rapa (pak choi) with flat leaves from inside to outside. Scale bars: 10 cm.

Figure 2

Nucleotide diversity (π) (A) and Tajima's D (B) indices in 45 candidate genes of three groups: whole collection (All), and H-Br and NH-Br groups. The genes for which Tajima's D is significant in the 94 accessions collection are indicated (^*P < 0.05), as well as in All, H-Br, and NH-Br subgroups.

Figure 3

Nucleotide bias distribution in the BrARF3.1 gene between heading and non-heading B. rapa accessions. A non-synonymous mutation (G to C) in the BrARF3.1 gene was observed in a larger B. rapa germplasm collection consisting of 300 accessions; C, G, and H represent the genotype of C, G and hybrid, respectively.