Academic journal article Genetics

A Sequence-Tagged Linkage Map of Brassica Rapa

Academic journal article Genetics

A Sequence-Tagged Linkage Map of Brassica Rapa

Article excerpt

ABSTRACT

A detailed genetic linkage map of Brassica rapa has been constructed containing 545 sequence-tagged loci covering 1287 cM, with an average mapping interval of 2.4 cM. The loci were identified using a combination of 520 RFLP and 25 PCR-based markers. RFLP probes were derived from 359 B. rapa EST clones and amplification products of 11 B. rapa and 26 Arabidopsis. Including 21 SSR markers provided anchors to previously published linkage maps for B. rapa and B. napus and is followed as the referenced mapping of R1-R10. The sequence-tagged markers allowed interpretation of the pattern of chromosome duplications within the B. rapa genome and comparison with Arabidopsis. A total of 62 EST markers showing a single RFLP band were mapped through 10 linkage groups, indicating that these can be valuable anchoring markers for chromosome-based genome sequencing of B. rapa. Other RFLP probes gave rise to 2-5 loci, inferring that B. rapa genome duplication is a general phenomenon through 10 chromosomes. The map includes five loci of FLC paralogues, which represent the previously reported BrFLC-1, -2, -3, and -5 and additionally identified BrFLC3 paralogues derived from local segmental duplication on R3.

THE genus Brassica includes oilseed, vegetable, fodder, and condiment crops. Brassica rapa (syn. campestris; A genome), B. napus (AC genome), B. juncea (AB), and B. carinata (BC) contribute 12%of the global supply of edible vegetable oil (LABANA and GUPTA 1993). B. rapa and B. oleracea (C genome) provide many vegetables that contribute to a healthy human diet, being a valuable source of dietary fiber, vitamin C, and other health-enhancing factors such as anticancer compounds (FAHEY and TALALAY 1995). The Brassica A genome therefore has worldwide importance in agriculture, with the quality and economic value of derived products such as processed oils and kimchi being dependent upon appropriate combinations of alleles. B. rapa includes a variety of vegetables crops such as Chinese cabbage, Pakchoi, turnip, and broccoletto as well as oilseed crops such as turnip rape and sarson (GOMEZ-CAMPO 1999).

The high degree of neutral DNA polymorphisms of most Brassica species (FIGDORE et al. 1988) has facilitated the development of molecular linkage maps, with at least 15 described to date for B. oleracea (SLOCUM et al. 1990; KIANIAN and QUIROS 1992; LAN et al. 2000), B. rapa (SONG et al. 1991; CHYI et al. 1992; TEUTENICO and OSBORN 1994), B. nigra (LAGERCRANTZ and LYDIATE 1996), B. Juncea (CHEUNG et al. 1997; PRADHAN et al. 2003), and B. napus (LANDRY et al. 1991; UZUNOVA et al. 1995). Where common sets of DNA markers and/or parental genotypes have been used, it has been possible to designate linkage groups according to a common nomenclature (PARKIN et al. 1995, 2005; BUTRUILLE et al. 1999; SEBASTIAN et al. 2000). Thus for B. napus linkage groups N1-N10 representing the A genome correspond to B. rapa R1-R10, and linkage groups N11- N19 representing the C genome correspond to B. oleracea O1-O9. BOHUON et al. (1996) demonstrated that marker order and linkage group structure had been conserved between the diploid (B. oleracea) and amphidiploid (B. napus) C genomes. In this study, we generated a detailed linkage map using sequenced EST clones derived from tissue-specific libraries of B. rapa. To establish the identity of linkage groups corresponding to R1-R10, we used SSR markers from SUWABE et al. (2002) and LOWE et al. (2004).

The Brassica genomes are closely related to the model plant Arabidopsis thaliana, diverging 20 MYA (KOCH et al. 2001), and remain collinear. Comparative mapping of RFLP probes among the three diploid species B. rapa (n = 10), B. oleracea (n = 9), and B. nigra (n = 8) has suggested that genomes of the Brassica species are composed of three rearranged variants of an ancestral genome and descended from a common hexaploid ancestor (LAGERCRANTZ and LYDIATE 1996). All comparative studies of Arabidopsis and Brassica to date have revealed extensive duplications, with Arabidopsis segments being conserved an average of three times within the diploid Brassica genomes (TRUCO et al. …

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