The reference genetic linkage map for the multinational Brassica rapa genome sequencing project

Abstract

We describe the construction of a reference genetic linkage map for the Brassica A genome, which will form the backbone for anchoring sequence contigs for the Multinational Brassica rapa Genome Sequencing Project. Seventy-eight doubled haploid lines derived from anther culture of the F(1) of a cross between two diverse Chinese cabbage (B. rapa ssp. pekinensis) inbred lines, 'Chiifu-401-42' (C) and 'Kenshin-402-43' (K) were used to construct the map. The map comprises a total of 556 markers, including 278 AFLP, 235 SSR, 25 RAPD and 18 ESTP, STS and CAPS markers. Ten linkage groups were identified and designated as R1-R10 through alignment and orientation using SSR markers in common with existing B. napus reference linkage maps. The total length of the linkage map was 1,182 cM with an average interval of 2.83 cM between adjacent loci. The length of linkage groups ranged from 81 to 161 cM for R04 and R06, respectively. The use of 235 SSR markers allowed us to align the A-genome chromosomes of B. napus with those of B. rapa ssp. pekinensis. The development of this map is vital to the integration of genome sequence and genetic information and will enable the international research community to share resources and data for the improvement of B. rapa and other cultivated Brassica species.

Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L.

“…Many comparative genetic mapping studies between Brassica species and A. thaliana have highlighted the complexity of the Brassica genome with its extensive replicated nature, as well as frequent appearance of chromosomal rearrangements (Kim et al 2009, Parkin et al 2005, Suwabe et al 2006. In the present study, comparison of B. rapa map with A. thaliana using 147 UGMS and SSR markers loci revealed majority large syntenic regions showing consistency with previously reported syntenic regions (Choi et al 2007, Iniguez-Luy et al 2009, Kim et al 2009, Li et al 2009, Suwabe et al 2006. However, we could not detect all the previously reported conserved chromosomal segments in B. rapa genome due to the lack of molecular markers.…”

“…Furthermore, 651 previously developed SSR primer pairs were used as potential anchor markers to facilitate crossreferencing with other mapping studies. Primer pairs with the prefix "MB" were developed by Lagercrantz et al (1993), "MR" by Uzunova and Ecke (1999), "BRAS" and "CB" by Piquemal et al (2005), "Ra", "Ol", Na" and "Ni" by Lagercrantz et al (1993) and Lowe et al (2002Lowe et al ( , 2004, "BRMS" by Suwabe et al (2002Suwabe et al ( , 2006, "BrFLC" by Kim et al (2006), "ENA", "nia" and "cnu" by Choi et al (2007) and by Kim et al (2009), "BnGMS" by Cheng et al (2009) and FITO markers were obtained by Iniguez-Luy et al (2008).…”

“…LGs were designated as A1-A10 according to international unified Brassica LG nomenclature based on multiple anchor markers mapped on each LG (referred to as R by Choi et al 2007, Suwabe et al 2006 or A by Kim et al 2009). The marker order in the current map was in general agreement with previously published linkage maps (Kim et al 2009, Lowe et al 2004, Piquemal et al 2005, Suwabe et al 2006.…”

“…pekinensis) was chosen by the Multinational Brassica rapa Genome Sequencing Project as a model for Brassica A genome sequencing in 2003 (Yang et al 2005). The high economic importance of B. rapa as a vegetable and source of oilseeds and fodder crop led to the development of several molecular markers and construction of several genetic linkage maps in this species during the last two decades (Choi et al 2007, Kim et al 2006, Kim et al 2009, Suwabe et al 2002. With the exception of Kim et al (2006) who used sequence tagged sites (STS) and Li et al (2009) who used single nucleotide polymorphisms (SNP) markers from expressed genes in their studies, the majority of the above-mentioned studies used anonymous markers and the genetic linkage exhibited with QTL often may be only due to a physical linkage and statistical relationship.…”

Mapping QTLs for mineral accumulation and shoot dry biomass under different Zn nutritional conditions in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

“…Subsequently several additional maps were constructed based on different molecular markers and F 2 , recombinant inbred lines (RILs) or DH populations (Chyi et al 1992;Teutonico and Osborn 1994;Kole et al 1997;Suwabe et al 2006;Kim et al 2006;Choi et al 2007). The recent development of Brassica simple sequence repeat (SSR) markers facilitates the anchoring of linkage groups to one common reference map and allows the comparison of map positions in studies involving different populations (Suwabe et al 2006;Choi et al 2007). Furthermore the syntenic relationship with the related genus Arabidopsis is now well established (reviewed by Schranz et al 2006) and allows the comparison of map positions between Brassica and Arabidopsis.…”