Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species

A set of 398 simple sequence repeat markers (SSRs) have been developed and characterised for use with genetic studies of Brassica species. Small-insert (250–900 bp) genomic libraries from Brassica rapa, B. nigra, B. oleracea and B. napus, highly enriched for dinucleotide and trinucleotide SSR motifs, were constructed. Screening the clones with a mixture of oligonucleotide repeat probes revealed positive hybridisation to between 75% and 90% of the clones. Of these, 1,230 were sequenced. Primer pairs were designed for 398 SSR clones, and of these, 270 (67.8%) amplified a PCR product of the expected size in their focal and/or closely related species. A further screen of 138 primers pairs that produced a PCR product in B. napus germplasm found that 86 (62.3%) revealed length polymorphisms within at least one line of a test array representing the four Brassica species. The results of this screen were used to identify 56 SSRs and were combined with 41 SSRs that had previously shown polymorphism between the parents of a B. napus mapping population. These 97 SSR markers were mapped relative to a framework of RFLP markers and detected 136 loci over all 19 linkage groups of the oilseed rape genome.

[1]  S. Knapp,et al.  Simple sequence repeat map of the sunflower genome , 2002, Theoretical and Applied Genetics.

[2]  David B. Goldstein,et al.  Microsatellites: Evolution and Applications , 1999 .

[3]  C. Dean,et al.  Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. , 1998, Genome.

[4]  U. Lagercrantz,et al.  Mapping the Brassica Genome , 1993 .

[5]  A. Sharpe,et al.  Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). , 1995, Genome.

[6]  K. Edwards,et al.  Microsatellite libraries enriched for several microsatellite sequences in plants. , 1996, BioTechniques.

[7]  S. Kresovich,et al.  Simple sequence repeat (SSR)-based marker variation in Brassica nigra genebank accessions and weed populations , 1999, Euphytica.

[8]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .

[9]  U. Lagercrantz,et al.  Comparative genome mapping in Brassica. , 1996, Genetics.

[10]  S. Warwick,et al.  Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae) — chloroplast DNA variation in the genus Diplotaxis , 1992, Theoretical and Applied Genetics.

[11]  D. Struss,et al.  Microsatellite markers for genome analysis in Brassica. II. Assignment of rapeseed microsatellites to the A and C genomes and genetic mapping in Brassica oleracea L. , 2001, Theoretical and Applied Genetics.

[12]  D. Lydiate,et al.  Alignment of the conserved C genomes of Brassica oleracea and Brassica napus , 1996, Theoretical and Applied Genetics.

[13]  S. Henikoff,et al.  Perspectives Anecdotal, Historical and Critical Commentaries on Genetics a Reconsideration of the Mechanism of Position Effect , 2022 .

[14]  L. Zane,et al.  Strategies for microsatellite isolation: a review , 2002, Molecular ecology.

[15]  S. Kresovich,et al.  Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species , 1996, Theoretical and Applied Genetics.

[16]  K. Edwards,et al.  Transferability and genome specificity of a new set of microsatellite primers among Brassica species of the U triangle , 2002 .

[17]  U. Lagercrantz,et al.  RFLP mapping in Brassica nigra indicates differing recombination rates in male and female meioses. , 1995, Genome.

[18]  S. Kresovich,et al.  The potential for cross-taxa simple-sequence repeat (SSR) amplification between Arabidopsis thaliana L. and crop brassicas , 1998, Theoretical and Applied Genetics.

[19]  A. Sharpe,et al.  Frequent nonreciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus). , 1995, Genome.

[20]  V. Lombard,et al.  A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations , 2001, Theoretical and Applied Genetics.

[21]  K. Suwabe,et al.  Isolation and characterization of microsatellites in Brassica rapa L. , 2002, Theoretical and Applied Genetics.

[22]  R. Delourme,et al.  Development of an AFLP-based linkage map and localization of QTLs for seed fatty acid content in condiment mustard (Brassica juncea). , 2002, Genome.

[23]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[24]  A. Börner,et al.  Genetic mapping and tagging of wheat genes using RAPD, STS and SSR markers. , 2002, Cellular & molecular biology letters.

[25]  Nu.  Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. , 1935 .

[26]  D. Struss,et al.  Microsatellite markers for genome analysis in Brassica. I. development in Brassica napus and abundance in Brassicaceae species , 2001, Theoretical and Applied Genetics.

[27]  A. Paterson,et al.  Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. , 1994, Genetics.

[28]  D. Soltis,et al.  The dynamic nature of polyploid genomes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Steven G. Schroeder,et al.  Development and mapping of SSR markers for maize , 2002, Plant Molecular Biology.

[30]  G. King,et al.  An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations , 2000, Theoretical and Applied Genetics.

[31]  P. Lu,et al.  Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[32]  U. Lagercrantz,et al.  Amphidiploid Brassica juncea contains conserved progenitor genomes. , 2000, Genome.

[33]  K. Edwards,et al.  Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.) , 2000, Theoretical and Applied Genetics.

[34]  G. King,et al.  Integration of the cytogenetic and genetic linkage maps of Brassica oleracea. , 2002, Genetics.

[35]  W. Powell,et al.  How much effort is required to isolate nuclear microsatellites from plants? , 2003, Molecular ecology.