The maize Ab10 meiotic drive system maps to supernumerary sequences in a large complex haplotype

Abstract

The meiotic drive system on maize abnormal chromosome 10 (Ab10) is contained within a terminal domain of chromatin that extends the long arm of Ab10 to approximately 1.3 times the size of normal chromosome 10L. Ab10 type I (Ab10-I) does not recombine with normal chromosome 10 (N10) over an approximately 32-cM terminal region of the long arm. Comparative RFLP mapping demonstrates that multiple independent rearrangements are responsible for the current organization of Ab10-I, including a set of nested inversions and at least one long supernumerary segment at the end of the chromosome. Four major meiotic drive functions, i.e., the recombination effect, smd3, 180-bp neocentromere activity, and the distal tip function, all map to the distal supernumerary segment. TR-1-mediated neocentromere activity (the fifth known drive function) is nonessential in the type II variant of Ab10 and maps to a central region that may include a second supernumerary insertion. Both neocentromere activity and the recombination effect behave as dominant gain-of-function mutations, consistent with the view that meiotic drive involves new or alien gene products. These and other data suggest that the Ab10 meiotic drive system was initially acquired from a related species and that a complex haplotype evolved around it.

Figure 1.—

Graphical representations of the N10 and Ab10-I chromosomes. The illustration shows the breakpoints of the deficiency chromosomes used or described in this study as well as the mapped meiotic functions (see Hiatt and Dawe 2003b for a more complete description). The genetic lengths are indicated for comparison, but more detail on map distances is provided in Figures 2 and 8. The differential segment (with three chromomeres), central euchromatin, knob, and distal tip are indicated. Letters represent known genes. The segment including the W (W2), O (O7), and L (L13) genes is inverted on Ab10-I.

Figure 2.—

Three maps of the region distal to R on N10. Mroczek 10 is from data presented here, Genetic 2005 10 is a consensus map that combines several genetic and RFLP maps, and IBM2 neighbors 10 is the most recently computed genetic map from a population of inbred lines (http://www.maizegdb.org). Actual genetic distances between loci (in centimorgans) are indicated below the Mroczek and Genetic 2005 maps. The position where N10 and Ab10 diverge (Rhoades 1942) is marked 2 cM from R on the Genetic 2005 map; most, if not all, of the 32 cM distal to this position are present on Ab10 in rearranged form. The isu163 locus was added to the IBM2 map on the basis of its tight linkage to rz569a on the CU 99 10 map. The three loci used for sample sequencing are indicated beneath the IBM2 neighbors 10 map (and marked with tree-like symbols). The maps have been normalized to the same length and include only those markers used in the Ab10-I mapping effort.

Figure 3.—

RFLP mapping of Ab10-I. The first lane contains DNA from the (N10/N10) W23 inbred. The remaining lanes contain DNA from plants heterozygous for N10 (W23) and the chromosome indicated. DNA was digested with HindIII (uaz251, csu571b, csu48) or BglII (npi421b). RFLPs specific to Ab10-I and their approximate molecular weights are indicated with arrows. Only portions of the gels are shown. The uaz251, csu571, and npi421 probes hybridize to more than one gene; in these cases we do not know if the nonpolymorphic bands shown are from N10 or one of the homologs elsewhere. (A) The uaz251c probe shows a polymorphic band in Ab10-I and all of the deficiencies. The data indicate that uaz251c maps proximal to the Df(C) breakpoint. (B) An Ab10-I-specific csu571b fragment is absent in Df(C) but present in Df(I). The data show that csu571b maps between these two markers. (C) The csu48 marker maps between the Df(I) and Df(F) breakpoints. (D) The npi421b marker maps between Df(F) and Df(H) breakpoints.

Figure 4.—

The Ab10-I molecular map. The RFLPs are positioned with respect to the deficiencies used in the mapping effort. The comparison of Ab10-I to N10 reveals two nested inversions, the larger in blue and the smaller in red and blue (to indicate that region has been inverted twice). Only a very small segment of the region distal to Df(K) (containing the Sr2 locus) can be confirmed as having been derived from N10; the remaining DNA is supernumerary. Supernumerary DNA is indicated in green. Below the Ab10-I map are the N10 RFLP maps from Figure 2. The boundaries of the inversions are indicated with brackets of the appropriate color. As noted, the position of L13 appears to be incorrect on the Genetic 2005 map, since both L13 and csu571b lie in the Df(C)–Df(I) interval.

Figure 5.—

Three known variants of Ab10. Line drawings of each chromosome were adapted from previous images (Longley 1937; Rhoades and Dempsey 1985; Kato and Lopez 1990). Actual chromosome images of the haplotype domains are shown in larger view above Ab10-I and Ab10-II. Chromosome images were computationally extracted (and straightened; Dawe et al. 1994) from in situ-hybridized pachytene spreads of strains homozygous for the respective chromosomes. TR-1 repeats are in red and 180-bp repeats in green.

Figure 6.—

Neocentromere leaders in Ab10-I and Ab10-II lines. Each image represents a partial projection from a 3D data set. DNA is shown in blue, the 180-bp repeat in green, and the TR-1 repeat in red. Arrows point to leaders. (A) TR-1-mediated leader activity at anaphase II in a strain homozygous for Ab10-I. (B) 180-bp-mediated leader activity at anaphase II in a strain homozygous for Ab10-II. (C) 180-bp-mediated leaders at prometaphase II in a homozygous Ab10-II line. At this stage multiple leaders were observed emanating from single knobs. Two images from different data sets are shown (outlined with dotted lines).

Figure 7.—

Results of sequencing the 3′ UTR from csu48. (A) Alignment of the sequences obtained here, showing only the polymorphisms. The numbers above indicate the bases relative to the appropriate GenBank entries (BV682883–BV682889). (B) A neighbor-joining tree showing the phylogenetic relationships among the seven sequences.

Figure 8.—

The positions of six putative chromosome break points that separate Ab10 and N10. The addition of alien chromatin—and the major meiotic drive functions—to the end of chromosome 10L was a key event in Ab10-I evolution (labeled 1). There are at least two separate inversions in the central euchromatin, requiring four chromosomal breakage events (labeled 2–5). The length and polymorphism (with Ab10-II) of the differential segment suggests that it contains an insertion and perhaps other rearrangements (labeled 6). Estimated genetic distances are shown below the cartoon. The distance between R and Df(F) was estimated by Rhoades and Dempsey (1985) to be 32 cM; the Genetic 2005 10 map shows the distance between O7 and Sr2 to be 13 cM, and the supernumerary region cannot be measured, but by cytological comparison appears to be at least 10 cM.