Comparative Genetic Mapping inBoechera stricta, a Close Relative of Arabidopsis

Abstract

The angiosperm family Brassicaceae contains both the research model Arabidopsis (Arabidopsis thaliana) and the agricultural genus Brassica. Comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, the reduced genome size and chromosome number (n 5 5) of Arabidopsis complicates comparisons. Arabidopsis shows extensive genome and chromosome reshuffling compared to its close relatives Arabidopsis lyrata and Capsella rubella, both with n 5 8. To facilitate comparative genomics across the Brassicaceae we recently outlined a system of 24 conserved chromosomal blocks based on their positions in an ancestral karyotype of n 5 8, rather than by their position in Arabidopsis. In this report we use this system as a tool to understand genome structure and evolution in Boechera stricta (n 5 7). B. stricta is a diploid, sexual, and highly self-fertilizing species occurring in mostly montane regions of western North America. We have created an F 2 genetic map of B. stricta based on 192 individuals scored at 196 microsatellite and candidate gene loci. Single-nucleotide polymorphism genotyping of 94 of the loci was done simultaneously using an Illumina bead array. The total map length is 725.8 cM, with an average marker spacing of 3.9 cM. There are no gaps greater than 19.3 cM. The chromosomal reduction from n 5 8 to n 5 7 and other genomic changes in B. stricta likely involved a pericentric inversion, a chromosomal fusion, and two reciprocal translocations that are easily visualized using the genomic blocks. Our genetic map will facilitate the analysis of ecologically relevant quantitative variation in Boechera.Comparative genetic mapping between related organisms within a phylogenetic framework is a powerful method for understanding genome evolution. Comparative mapping in the grass family (Poaceae) has been successful in detecting collinear genomic regions between a number of domesticated cereal and forage crops, leading to the formulation of the crop circle with rice (Oryza sativa) at the center (Moore et al., 1995;Devos, 2005). Rice was selected as the reference point because of its small genome and vast genomic resources, and not because it was phylogenetically well positioned to facilitate comparisons within the family. An analogous situation occurs in the dicot family Brassicaceae, which contains both the model species Arabidopsis (Arabidopsis thaliana) as well as the domesticated Brassica species. To date, most comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, several of the factors that made Arabidopsis ideal for genome sequencing, particularly its reduced genome size and chromosome number (157 Mb, n 5 5; AGI, 2000;Johnston et al., 2005), complicate its use as a standard in comparative genomics. Recent phylogenetic results have demonstrated that genome and chromosome reduction in Arabidopsis are derived characteristics from its close relatives with...

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

“…Phylogenetic reconstructions showed that both ACK-like parental genomes (i.e., paralogous gene copies a1 and a2) of the Australian mesopolyploids are nested within the paraphyletic tribe Camelineae and the closely related Boechereae. It was shown that karyotypes of all so far analyzed taxa from three tribes of Lineage I (Camelineae, Boechereae, and Descurainieae) resemble or were derived from the ACK (Figure 4; Lysak et al, 2006 and references therein; Schranz et al, 2007;Roosens et al, 2008). Here, we showed that species of two other Camelineae genera (Crucihimalaya and Transberingia), considered as potential parental genomes of the Australian species, descended from the ACK.…”

“…However, the two parental genomes while having the ACK-like structure could already have deviated by chromosome number. Chromosome number reductions from n = 8 to n = 7 to 4 occurred repeatedly in Brassicaceae Schranz et al, 2007;Mandá ková and Lysak, 2008; this study).…”

“…"a1" and "a2" identify the two genome copies present in the genomes of Australian Brassicaceae species, whereas "b" indicates the most recent common ancestor for the two genome copies. Species within the crucifer Lineage I with karyotype resembling the ACK or karyotype derived from the ACK (in parenthesis with the extant chromosome number) are mapped onto the phylogenies Schranz et al, 2007;Roosens et al, 2008; incidence is appraised (e.g., Wood et al, 2009). Conversely, polyploid-like increases of chromosome number can be caused by serial centric fissions as reported for some orchids (Leitch et al, 2009) and cycads (Caputo et al, 1996).…”

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium inBoechera stricta, a Wild Relative of Arabidopsis

“…We chose 69 loci located on linkage groups 2-7 of the B. stricta genetic map (Schranz et al 2007b). Loci on linkage group 1 (LG1) were not selected because this chromosome showed low levels of recombination in the mapping population (Schranz et al 2007b).…”

“…We chose 69 loci located on linkage groups 2-7 of the B. stricta genetic map (Schranz et al 2007b). Loci on linkage group 1 (LG1) were not selected because this chromosome showed low levels of recombination in the mapping population (Schranz et al 2007b). Primers were designed using either PRIMER3 or PRIMACLADE software (Rozen and Skaletsky 2000;Gadberry et al 2005), and the length of the PCR products ranged from 600 to 800 bp.…”