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Section 1 Taxonomy

1.1 Brassicaceae family

The Brassicaceae family consists of approximately 372 genera and over 4000 species worldwide (The Plant List 2013). Some members of the Brassicaceae family are agriculturally important crops. In addition to the commercially valuable species, many wild species of Brassicaceae grow as weeds, particularly in regions of North America, South America and Australia (Couvreur et al. 2010). The model plant Arabidopsis thaliana is also a member of this family, its genome the first plant genome sequenced. For these reasons, the biology, genetics and phylogeny of the Brassicaceae have been widely studied.

Approximately 58 genera and 200 species of native/introduced Brassicaceae are present in Australia (Australian National Botanic Gardens 2013). Species used as food crops are introduced and belong to the genus Brassica. Other introduced Brassicaceae include plants that are classified as weeds, the most important being:

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  Lepidium draba (hoary cress or white weed)
  
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  Diplotaxis tenuifolia (sand rocket, sand mustard or Lincoln weed)
  
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  Hirschfeldia incana (Buchan weed)
  
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  Myagrum perfoliatum (musk weed)
  
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  Raphanus raphanistrum (wild radish)
  
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  Rapistrum rugosum (turnip weed) (Parsons & Cuthbertson 2001)
  

Other introduced species of Brassicaceae are used as ornamental plants in Australia, such as Arabis albida (rock cress), Cheiranthus cheiri (wallflower) or Iberis amara (candytuft) (Parsons & Cuthbertson 2001). Native Australian Brassicaceae are in a number of genera, including Arabidella, Blennodia, Cardamine, Lepidium and Stenopetalum (Australian National Botanic Gardens 2013).

1.2 Brassica genus

The Brassica genus consists of approximately 100 species worldwide (Gomez-Campo & Prakash 1999; Purty et al. 2008). Many Brassica plants are common crops, from oilseeds to vegetables and condiments. Such crops include canola, mustard, cabbage, cauliflower, broccoli, Brussels sprouts and turnip. The most important Brassica oilseed crops worldwide are B. napus, B. rapa and B. juncea. The cultivation of B. napus and B. rapa is of major importance in North America and Europe. B. juncea is the predominant oilseed crop in India, Nepal and Bangladesh (Purty et al. 2008). B. napus is the main Brassica crop grown in Australia, with B. juncea representing only a minor part of oilseed production.

The genetic relationship between the Brassica oilseed species was largely established as a result of cytogenetic and breeding studies carried out in the 1930s (Figure 1) (Morinaga 1934; U.N. 1935). It was proposed that B. juncea (2n=36), B. napus (2n=38) and B. carinata (2n=34) were natural amphidiploid^a hybrids derived from combinations of the diploid species B. nigra (2n=16), B. oleracea (2n=18) and B. rapa (syn. campestris) (2n=20). B. napus is polyphyletic, deriving from multiple hybridisation events, with B. oleracea one of several maternal ancestors (Allender & King 2010; Chalhoub et al. 2014).

Figure 1. Genomic relationships between the main cultivated Brassica species, also known as U’s triangle. (n refers to the haploid number of chromosomes). According to Morinaga (1934) and U (1935). Adapted from Purty et al. (2008).

The genomic constitution of the species is described with the letters ‘A’, ‘B’, and ‘C’, each letter representing a haploid genome. Interspecific hybridization for Brassica spp. has been described as being unidirectional when happening naturally (Purty et al. 2008).

Cytogenetic relationships between the Brassica species have since been supported by studies of nuclear DNA contents, the artificial synthesis of amphidiploids, and the use of genome-specific chromosome markers. Flow cytometry experiments demonstrated that the B and C genomes contain 27% and 44% more DNA, respectively, than the A genome (Sabharwal & Dolezel 1993). As the nuclear genome content of a cell is proportional to the number of haploid chromosomes, this method has been used to identify ploidy level and genomic constitution of hybrid Brassica plants. Studies by Bennett & Leitch (2011) and Johnston et al. (2005) have determined the haploid DNA contents of the main oilseed species as:

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  527 Mbp for B. rapa
  
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  1,129-1,443 Mbp for B. napus
  
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  1,068 Mbp for B. juncea
  

For comparison, the haploid genome sizes of Arabidopsis thaliana, ecotype Columbia (family Brassicaceae) and Oryza sativa subsp. japonica are estimated to be 157 Mbp and 577 Mbp, respectively (Bennett & Leitch 2011).

Linkage group identification studies have shown that Brassica spp. have a hexaploid ancestor, derived from a whole genome triplication. Phylogenetic studies have shown that genome triplication happened after the split between the two genera Arabidopsis and Brassica (Lysak et al. 2005; Wang & Fristensky 2001). This triplication event has been supported by identification of syntenic genes^b between B. rapa and other Brassica species (Cheng et al. 2012).

Genome triplication was followed by a series of chromosome fusions, as shown by the presence of telomere-related sequences within B. nigra linkage groups (Johnston et al. 2005; Lagercrantz 1998). Phylogenetic trees based on Restriction Fragment Length Polymorphisms (RFLPs) (Song et al. 1990) or on chloroplast sequence analysis (Lysak et al. 2005) revealed two separate Nigra and Rapa/Oleracea lineages. These two lineages are estimated to have diverged quite recently, about 7.9 Mya.

Genome rearrangements (chromosome fusion, inversions, non-reciprocal translocations) have been widely described in artificial (re-synthetised) amphidiploid Brassica (Allender & King 2010; Parkin et al. 1995; Song et al. 1990). Interestingly, Panajbi et al. (2008) have shown that natural allopolyploid Brassica spp. have gone through few large scale genomic rearrangements.