Conjunctive Analyses of BSA-Seq and BSR-Seq to Reveal the Molecular Pathway of Leafy Head Formation in Chinese Cabbage

Abstract

As the storage organ of Chinese cabbage, the leafy head was harvested as a commercial product due to its edible value. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-Seq (BSR) were performed with F 2 separation progeny to study the molecular mechanism of leafy head formation in Chinese cabbage. BSA-Seq analysis located four candidate regions containing 40 candidate genes, while BSR-Seq analysis revealed eight candidate regions containing 607 candidate genes. The conjunctive analyses of these two methods identified that Casein kinase gene BrCKL8 (Bra035974) is the common candidate gene related with leafy head formation in Chinese cabbage, and it showed high expression levels at the three segments of heading type plant leaves. The differentially expressed genes (DEGs) between two set pairs of cDNA sequencing bulks were divided into two categories: one category was related with five hormone pathways (Auxin, Ethylene, Abscisic acid, Jasmonic acid and Gibberellin), the other category was composed of genes that associate with the calcium signaling pathway. Moreover, a series of upregulated transcriptional factors (TFs) were also identified by the association analysis of BSR-Seq analysis. The leafy head development was regulated by various biological processes and effected by diverse external environment factors, so our research will contribute to the breeding of perfect leaf-heading types of Chinese cabbage.

Genetic analysis of the “head top shape” quality trait of Chinese cabbage and its association with rosette leaf variation

“…QTLs have been identified for Chinese cabbage heading traits, such as head diameter, head height, and HWe, which are all important components of head yield and quality 9 , 11 – 13 . Seq-BSA revealed genomic regions enriched with candidate genes related to plant hormones associated with Chinese cabbage heading type and leafy head formation 14 , 15 . In addition, several studies have described gene expression profiles during Chinese cabbage development and constructed rosette and inner leaf gene expression networks 16 – 19 .…”

Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis

“…Although there are many methods for analyzing trait-gene association analysis [ 20 , 21 , 22 ], BSA-Seq is still one of the most popular methods and used extensively for various taxa [ 18 , 23 , 24 , 25 , 26 ]. The greatest advantage of BSA-Seq is its simplicity in terms of both sample collection and data analysis.…”

“…The aim of the latter is to annotate the functions of the genes in the mapped regions by aligning the reference genome sequence of the species. With the development of DNA sequencing technology, NGS-based BSA has been used to map important genes in many plants, such as the yellow rind formation gene in watermelon [ 14 ], the branching habit trait in cultivated peanut [ 15 ], a candidate nicosulfuron sensitivity gene in maize [ 16 ], grain-shape-related loci in rice [ 17 ] and genes associated with the heading type of Chinese cabbage [ 18 ]. A large number of studies have proven that bulked segregant analysis is a reliable method for identifying loci associated with traits in plants.…”

Frequent Gain- and Loss-of-Function Mutations of the BjMYB113 Gene Accounted for Leaf Color Variation in Brassica Juncea

“…BSA in combination with RNA-seq is an e cient method to map and clone causal genes BSR-seq, an e cient and economic method, has been widely applied to identify genes that control important traits in many crops, including wheat (Li et al 2020), cabbage (Li et al 2019), watermelon (Sun et al 2020), rice (Gao et al 2019), cauli ower (Zhao et al 2020), Chinese kale (Tang et al 2017). In this study, the MPL gene was also cloned through the BSR-seq analysis of F 2 segregating populations.…”