A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp. pekinensis) Selection

Abstract

Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.

Natural variation in a calreticulin gene causes reduced resistance to Ca2+ deficiency‐induced tipburn in Chinese cabbage (Brassica rapa ssp. pekinensis)

“…The evenly distributed SNPs along the 10 chromosomes (Figure S1A) and the marker density (4.1 SNPs/kb) were sufficient to meet the requirements of GWA mapping. The population structure of the 194 lines has been previously well evaluated by Su et al (). To understand the population stratification of the mapping panel, principle component (PC) analysis was conducted for the association panel based on the SNP markers.…”

“…The population structure of the 194 lines has been previously well evaluated by Su et al (2018). To understand the population stratification of the mapping panel, principle component (PC) analysis was conducted for the association panel based on the SNP markers.…”

Gene Expression Analysis in Response to Vernalization in Chinese Cabbage (<i>Brassica rapa</i> L.)

“…Vernalization refers to prolonged exposure to cold temperature, and is usually required to facilitate flowering in Brassicaceae. Because Chinese cabbage can sense low temperatures during seed germination (seed-vernalization-responsive type), it sometimes un-dergoes early flowering/bolting due to low temperatures that occur during production in the fall (Shea et al, 2018;Su et al, 2018). Premature bolting leads to a decline in commercial quality and a loss of market value.…”

“…In Chinese cabbage, the reduced transcription of FLC could be an important factor in premature bolting (Itabashi et al, 2018;Shea et al, 2018;Su et al, 2018;Takada et al, 2019). There are four FLC paralogs in B. rapa and at least three of them act as floral repressors (Kawanabe et al, 2016;Kim et al, 2007;Schranz et al, 2002;Takada et al, 2019).…”

Illuminating Crop Adaptation Using Population Genomics

“…Indeed, the expression patterns of B. napus FT and FLC homoeologs vary in expression between different ecotypes (Figure 1), indicating that promoter variation in floral regulatory genes is an essential factor in the creation of adaptive variation and needs to be considered in knowledge-based breeding approaches. The phenomenon of promoter-driven adaptation may also hold true for other closely related crops: For example, selection against premature bolting in spring-type Brassica rapa ecotypes was shown to be highly associated with promoter variation in a copy of VERNALIZATION INSENSITIVE 3 (VIN3) (Su et al, 2018). Interestingly, similar effects are observed in cereals, where mutations in promoter sequences of the cereal gene VERNALIZATION 1 (VRN1) also associate with eco-geographic adaptation (Deng et al, 2015).…”