High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets
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A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae.
A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.
KeywordsCarotenoid Amplify Fragment Length Polymorphism Lutein Total Carotenoid Single Nucleotide Polymorphism Marker
Conflict of interest
The authors declare that they have no conflict of interest.
The experiment conducted complies with the laws of the United States and Canada.
- Brown AF, Yousef GG, Jeffery EH, Klein PB, Wallig MA, Kushad MM, Juvik JA (2002) Glucosinolate profiles in broccoli: variation in levels and implications in breeding for cancer chemoprotection. J Am Soc Hortic Sci 127:807Google Scholar
- Brown AF, Jeffery EH, Juvik JA (2007) A polymerase chain reaction-based linkage map of broccoli and identification of quantitative trait loci associated with harvest date and head weight. J Am Soc Hortic Sci 132:507–513Google Scholar
- Farnham MW, Kopsell DA (2009) Importance of genotype on carotenoid and chlorophyll levels in broccoli heads. HortScience 44:1248–1253Google Scholar
- Kidwell KK, Osborn TC (1992) Simple plant DNA isolation procedures. In: Beckman JS, Osborn TC (eds) Plant genomes: methods for genetic and physical mapping, pp 1–13 Kluwer Academic, NetherlandsGoogle Scholar
- Nagaoka T, Doullah MAU, Matsumoto S, Kawasaki S, Ishikawa T, Hori H, Okazaki K (2010) Identification of QTLs that control clubroot resistance in Brassica oleracea and comparative analysis of clubroot resistance genes between B. rapa and B. oleracea. Theor Appl Genet 120:1335–1346PubMedCrossRefGoogle Scholar
- Ooijin VJW (2009) MapQTL® 6. Kyazma, NetherlandsGoogle Scholar
- Ruiz-Sola MÁ, Rodríguez-Concepción M (2012) Carotenoid biosynthesis in arabidopsis: a colorful pathway. The Arabidopsis Book 10:e0158Google Scholar
- Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348–1359PubMedCentralPubMedCrossRefGoogle Scholar