Abstract
The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species.
Highlights
Brassica rapa L. is an agriculturally important food crop, consisting of morphotypes that produce leafy vegetables, swollen root vegetables, and vegetable oil (Cartea et al, 2011)
We constructed a large single nucleotide polymorphism (SNP) data set for 333 diverse, globally representative accessions of B. rapa assembled from the USDA National Plant Germplasm System (NPGS) in order to infer the population structure and phylogenetic relationship of the 10 sampled subspecies
We identified a number of accessions that were misclassified as B. rapa, as well as several individuals that appear to have incorrect subspecies identification
Summary
(genome AA, 2n = 2x = 20) is an agriculturally important food crop, consisting of morphotypes that produce leafy vegetables, swollen root vegetables, and vegetable oil (Cartea et al, 2011) These subspecies include the oilseed morphotypes ssp. Rapa (turnip); and Asian leafy vegetables ssp. These various subspecies have traditionally been classified by crop use and morphology (Bonnema et al, 2011; McGrath and Quiros, 1992). Duthie and Fuller (1882) considered yellow sarson a variety of B. rapa and brown sarson and toria a variety of Brassica napus L. Rapa), Singh (1958) argued yellow and brown sarson were varieties of B. campestris Trilocularis and brown sarson and toria to be ssp. Beyond the difficulties of taxonomically grouping numerous intraspecific varieties, the failure to recognize distinctions among parent lines can sometimes lead to seeds of different species being mixed together in germplasm collections, which further complicates taxonomic assignment of Brassica crops (Gupta and Pratap, 2007)
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