Evidence for two domestication lineages supporting a middle-eastern origin forBrassica oleraceacrops from diversified kale populations

Abstract

Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.

Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata)

“…In this project, a collection of 308 cabbage accessions from diverse geographical origins and genetic backgrounds, obtained from germplasm banks and breeding companies (mostly F1 hybrids) was studied (Supplementary Table S1 and Cai et al 2022 ). This cabbage collection included white, red, savoy, and pointed accessions; early, middle, and late types; for industry, fresh, and storage usage.…”

“…In this study, we utilized the genotypic dataset produced by Cai et al 2022 . DNA isolation, sequence-based genotyping, and variant calling were as described by Cai et al 2022 .…”

“…In this study, we utilized the genotypic dataset produced by Cai et al 2022 . DNA isolation, sequence-based genotyping, and variant calling were as described by Cai et al 2022 . Cai and colleagues genotyped 912 globally distributed accessions representing ten B. oleracea morphotypes, wild B. oleracea , and wild C9 Brassica species.…”

“…Basically, this resequencing data (Illumina reads) were aligned to the JZS v1 cabbage reference genome (Liu et al 2014 ), which is composed of 385 Mb of sequences that were anchored to the nine physical chromosomes of cabbage and 131 Mb unanchored scaffolds that were grouped into a so-called chromosome zero (C00). In total, Cai et al 2022 detected 742,169 raw biallelic single nucleotide polymorphisms (SNPs) using SAMtools v1.9 (Li et al 2009 ) and BCFtools v1.10 (Li 2011 ). To obtain high-quality SNPs, Cai et al 2022 filtered these raw SNPs with strict criteria.…”

“…In 2014, the first reference genome "JZS v1" (Liu et al 2014) was published, followed by an improved version "JZS v2" (Cai et al 2020) with a 20% increase in the total length of the sequence assembly. In addition, Cai et al (2022) and Mabry et al (2021) studied the genetic variation in large B. oleracea collection with genomic data. Cai et al generated 330,383 high-quality single nucleotide polymorphism (SNP) markers.…”