Comparative genetic mapping in Boechera 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) of Arabidopsis complicates comparisons. Arabidopsis shows extensive genome and chromosome reshuffling compared to its close relatives Arabidopsis lyrata and Capsella rubella, both with n = 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 = 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 = 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 = 8 to n = 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. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers DU 667459 to DU 708532.

Figure 1.

Relationships, number of species, and base-chromosome numbers for the eight tribes of lineage I of the Brassicaceae. A recent taxonomic classification for the Brassicaceae (Al-Shehbaz et al., 2006) proposed 24 tribes and recognized three monophyletic lineages (I–III). Within lineage I there is additional support for the monophyly of the three tribes Camelineae (including Arabidopsis, A. lyrata, and C. rubella), Boechereae (including B. stricta), and Halimolobodeae. Most species of the eight tribes within lineage I have a base-chromosome number of x = 8. Karyotype number reduction has occurred several times, including in the Boechereae (x = 7).

Figure 2.

Comparative genome organization of the inferred ancestral karyotype (n = 8) based on published genetic maps of A. lyrata and C. rubella (A), and B. stricta using our F₂ genetic mapping results (B). A, Genome blocks of the ancestral karyotype (AK) are labeled by the letters A to X. Each block is one of eight colors, corresponding to each chromosome. Centromeric positions are indicated by the colored circles. Since only the Arabidopsis genome is currently sequenced, the boundaries of the blocks are defined by their flanking Arabidopsis Genome Initiative At locus names. Each block is considered to be in the upright orientation in the ancestral karyotype. Blocks that are inverted relative to Arabidopsis are indicated by upside-down text of the At locus names. B, Genetic map and genomic blocks for B. stricta. The seven LGs are labeled as BstLG1 to BstLG7. Marker positions (in cM) are shown on the left hand and the corresponding marker name shown on the right hand of each LG. Genomic blocks, as defined above, are arranged onto the LGs based on sequence similarity of the markers to Arabidopsis. Three LGs are completely conserved (Bst4 = AK4, BstLG6 = AK6, and BstLG7 = AK7). Incongruity of color/letter order of the blocks indicates genomic rearrangements in Boechera relative to the ancestral karyotype. Two blocks (A and C) are subdivided in Boechera (A₁ and A₂; C₁ and C₂). Blocks that are inverted in Boechera (blocks C₁ and C₂) are represented by their names being inverted and by a downward pointing arrow.

Figure 3.

A parsimonious model of genomic changes describing the evolution of the B. stricta (n = 7) genome from the ancestral karyotype (n = 8). A, A reciprocal translocation occurring between the centromeric regions of AK3 and AK8 would result in the formation of BstLG3 (with blocks F and G now fused with W and X) and a second chromosome (made up of blocks V and H). A chromosomal fusion between the telomeric regions of block H and block K (of AK5) would result in the formation of BstLG5. It is equally possible that the chromosomal fusion between block H (of AK3) and block K (of AK5) occurred before the reciprocal translocation event. The combination of the reciprocal translocation and chromosomal fusion events would account for the karyotype reduction from n = 8 to n = 7. B, A pericentric inversion of AK1 with one breakpoint between blocks A₁ and A₂ and the other between blocks C₁ and C₂ would result in a rearranged chromosome. A reciprocal translocation between the centromeric regions of the rearranged AK1 and AK2 would result in BstLG1 (including blocks D, C₁, and A₁) and BstLG2 (including blocks C₂, A₂, B, and E). [See online article for color version of this figure.]

Figure 4.

The collection sites of the maternal and paternal parents of our mapping population of B. stricta differ substantially in abiotic environments. A, The maternal SAD12 locality in Colorado is a sagebrush grassland in a river valley occurring at an elevation of 2,530 m, at a latitude of 38.7° N, has an average monthly precipitation of 43.0 mm, an average monthly high temperature of 8.5°C, and an average monthly low temperature of −6.9°C. B, The paternal LTM locality in Idaho is a subalpine meadow occurring at an elevation of 2,390 m, at a latitude of 45.7° N, has an average monthly precipitation of 94.7 mm, an average monthly high temperature of 9.2°C, and an average monthly low temperature of −3.5°C. The two sites are approximately 1,000 km apart. [See online article for color version of this figure.]