Non-vernalization requirement in Chinese kale caused by loss of BoFLC and low expressions of its paralogs

Abstract

Key message We identified the loss ofBoFLC gene as the cause of non-vernalization requirement inB. oleracea. Our developed codominant marker ofBoFLCgene can be used for breeding program ofB. oleraceacrops. Abstract Many species of the Brassicaceae family, including some Brassica crops, require vernalization to avoid pre-winter flowering. Vernalization is an unfavorable trait for Chinese kale (Brassica oleracea var. chinensis Lei), a stem vegetable, and therefore it has been lost during its domestication/breeding process. To reveal the genetics of vernalization variation, we constructed an F2 population through crossing a Chinese kale (a non-vernalization crop) with a kale (a vernalization crop). Using bulked segregant analysis (BSA) and RNA-seq, we identified one major quantitative trait locus (QTL) controlling vernalization and fine-mapped it to a region spanning 80 kb. Synteny analysis and PCR-based sequencing results revealed that compared to that of the kale parent, the candidate region of the Chinese kale parent lost a 9,325-bp fragment containing FLC homolog (BoFLC). In addition to the BoFLC gene, there are four other FLC homologs in the genome of B. oleracea, including Bo3g005470, Bo3g024250, Bo9g173370, and Bo9g173400. The qPCR analysis showed that the BoFLC had the highest expression among the five members of the FLC family. Considering the low expression levels of the four paralogs of BoFLC, we speculate that its paralogs cannot compensate the function of the lost BoFLC, therefore the presence/absence (PA) polymorphism of BoFLC determines the vernalization variation. Based on the PA polymorphism of BoFLC, we designed a codominant marker for the vernalization trait, which can be used for breeding programs of B. oleracea crops.

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

“…oleracea consists of four paralogs: FLC1 , FLC2 , FLC3 , and FLC5 . Our pan-genomic analysis identified a large deletion (9428 bp) in the genome of Chinese kale that resulted in absence of the entire BoFLC2 gene ( Figure 6 A), consistent with previous findings ( Golicz et al., 2016 ; Tang et al., 2022 ). The genome region harboring this SV showed a strong selection signal between Chinese kale and other morphotypes ( Figure 6 B and Supplemental Figure 14A ).…”

“…Several genes involved in these biological processes have been identified. The BoFLC2 gene, for instance, has a notable effect on differences in flowering time and vernalization response among various B. oleracea cultivars ( Okazaki et al., 2007 ; Golicz et al., 2016 ; Tang et al., 2022 ). Evidence of parallel selection has been observed in four subgenome loci within B. rapa and a similar set within B. oleracea , including the gene BoKAN2.2 , which plays a role in leafy head formation ( Cheng et al., 2016 ).…”

Advancements in Molecular Mechanism Research on Bolting Traits in Vegetable Crops

“…Li et al [136] identified a 215 bp deletion in the BoFLC2 gene intron I, which slowed its silencing activity, leading to late flowering in cabbage. Tang et al [137] noted that the 9325 bp loss of the BoFLC gene caused a non-vernalization requirement, leading to the development of its codominant marker for breeding B. oleracea crops.…”