Maize genome structure variation: interplay between retrotransposon polymorphisms and genic recombination

Abstract

Although maize (Zea mays) retrotransposons are recombinationally inert, the highly polymorphic structure of maize haplotypes raises questions regarding the local effect of intergenic retrotransposons on recombination. To examine this effect, we compared recombination in the same genetic interval with and without a large retrotransposon cluster. We used three different bz1 locus haplotypes, McC, B73, and W22, in the same genetic background. We analyzed recombination between the bz1 and stc1 markers in heterozygotes that differ by the presence and absence of a 26-kb intergenic retrotransposon cluster. To facilitate the genetic screen, we used Ds and Ac markers that allowed us to identify recombinants by their seed pigmentation. We sequenced 239 recombination junctions and assigned them to a single nucleotide polymorphism-delimited interval in the region. The genetic distance between the markers was twofold smaller in the presence of the retrotransposon cluster. The reduction was seen in bz1 and stc1, but no recombination occurred in the highly polymorphic intergenic region of either heterozygote. Recombination within genes shuffled flanking retrotransposon clusters, creating new chimeric haplotypes and either contracting or expanding the physical distance between markers. Our findings imply that haplotype structure will profoundly affect the correlation between genetic and physical distance for the same interval in maize.

Figure 1.

Organization of McC, B73, and W22 bz1 Haplotypes. Each haplotype is identified by the name of the line from which it was extracted, followed by the size of the cloned NotI (N) fragment in parentheses. The eight genes (bz1, stc1, rpl35A, tac6058, hypro1, znf, tac7077, and uce2) are shown as pentagons pointing in the direction of transcription, with exons in peach and introns in yellow. The same symbols are used for gene fragments carried by helitrons HelA and HelB, which are represented as bidirectional arrows below the line in McC and W22. The vacant site for HelA in B73 is marked with a short vertical stroke. Dashed lines represent deletions. Retrotransposons are indicated by closed triangles of different colors. DNA transposons are indicated by open triangles of red and orange. Small insertions are indicated in light blue and numbered as by Wang and Dooner (2006). Only the genes have been drawn to scale.

Figure 2.

Genetic Scheme for Identifying Recombinants in McC/B73 (Top) and McC/W22 (Bottom) Heterozygous Haplotypes. The cartoon depicts the spotted (bz-m) and solid purple (Bz) parental phenotypes at left and the solid bronze (bz) recombinant phenotype at right. The sh1 flanking alleles condition either shrunken or plump seeds; the wx1 flanking alleles condition either waxy or nonwaxy seeds (shown here as staining light or dark with iodine for diagrammatic purposes only). Recombination anywhere between the Ds2(D1) element in bz1 and the Ac6087 element in stc1 gives rise to Sh bz recombinants, most of which will also carry wx. Recombination between Ac6087 and sh1 gives rise to Sh bz-m recombinants. The reciprocal recombinants of both classes are sh Bz. The stc1 and bz transcripts are indicated by the wavy arrows. A 26-kb retrotransposon cluster containing Tekay, a Zeon solo LTR, and a Mu1-Xilon nest separates stc1 from bz in the Bz-B73, but not the Bz-W22, haplotype. The small triangles represent indel polymorphisms (Ins3, Ins5, and Ins6 [Wang and Dooner, 2006]) used to assign Sh bz recombinants to one of four intervals within the larger Ds2(D1)-Ac6087 interval.

Figure 3.

Distribution of Recombination Junctions within the Ds2(D1)-Ac6087 Genetic Interval among Sh bz Recombinants from McC/B73 (Top) and McC/W22 (Bottom) Heterozygotes. As in Figure 1, exons are in peach and introns are in yellow; the stop codon for each gene is indicated by a red octagon. The retrotransposon cluster in B73 is in maroon and drawn in a smaller scale than the rest of the interval. Polymorphisms are represented as vertical lines (SNPs) or blue triangles (indels), numbered as indicated by Wang and Dooner (2006). The number of recombination junctions in each subinterval defined by these polymorphisms is shown beneath the common McC haplotype in each heterozygote, single-digit numbers in black and double-digit numbers in red. The Ds2(D1)-Ac6087 genetic interval was subdivided into five segments for analysis: bz1, intergenic region, and three roughly equally sized stc1 segments. Significantly different estimates of genetic distances for a segment in the two heterozygotes are indicated in red. See text for additional details.

Figure 4.

Generation of New Chimeric Haplotypes in McC/B73 Heterozygotes by Recombination within the stc1 Gene. (A) Diagram illustrating how an exchange event in stc1 recombines the flanking retrotransposon clusters, producing a novel haplotype that lacks both clusters. (B) CHEF gel DNA gel blot analysis of parental and recombinant haplotypes (NotI digest, stc1 probe). M, size markers in kilobases; McC, bz-m2(D1) stc1-M1(Ac6087); B73 (left), B73 Bz1-B73 stc1-B73 introgressed into W22; B73 (right), B73 Bz1-B73 stc1-B73 from the original B73 inbred; CO (left) and CO (right), Sh bz wx crossovers resulting from exchanges in stc1 gene intervals 3 and 4 (see Figure 3), respectively.

Figure 5.

Frequencies of Recombinants (Solid Lines) and Polymorphisms (Dashed Lines) in the 6.7-kb Interval between Ds2(D1) and Ac6087. bz1 is to the left and stc1 is to the right. The 6.7-kb interval has been divided into 67 100-bp segments. Segments that make up fractions of an interval have been assigned a number of crossovers in proportion to the fraction of the interval constituted by that segment. The intergenic region lies between intervals 9 and 24.