Meiotic recombination break points resolve at high rates at the 5' end of a maize coding sequence

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

Transposable elements (TEs) are genomic parasites that selfishly replicate at the expense of host fitness. Fifty years of evolutionary studies of TEs have concentrated on the deleterious genetic effects of TEs, such as their effects on disrupting genes and regulatory sequences. However, a flurry of recent work suggests that there is another important source of TEs' harmful effects-epigenetic silencing. Host genomes typically silence TEs by the deposition of repressive epigenetic marks. While this silencing reduces the selfish replication of TEs and should benefit hosts, a picture is emerging that the epigenetic silencing of TEs triggers inadvertent spreading of repressive marks to otherwise expressed neighboring genes, ultimately jeopardizing host fitness. In this Review, we provide a long-overdue overview of the recent genome-wide evidence for the presence and prevalence of TEs' epigenetic effects, highlighting both the similarities and differences across mammals, insects, and plants. We lay out the current understanding of the functional and fitness consequences of TEs' epigenetic effects, and propose possible influences of such effects on the evolution of both hosts and TEs themselves. These unique evolutionary consequences indicate that TEs' epigenetic effect is not only a crucial component of TE biology but could also be a significant contributor to genome function and evolution.

DAWN: a resource for yielding insights into the diversity among wheat genomes

BACKGROUND

Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets.

RESULTS

DAWN (Diversity Among Wheat geNomes) integrates data from the T. aestivum Chinese Spring (CS) IWGSC RefSeq v1.0 genome with public WGS and exome data from 17 and 62 accessions respectively, enabling researchers and breeders alike to investigate genotypic differences between wheat accessions at the level of whole chromosomes down to individual genes.

CONCLUSIONS

Using DAWN we show that it is possible to visualise small and large chromosomal deletions, identify haplotypes at a glance and spot the consequences of selective breeding. DAWN allows us to detect the break points of alien introgression segments brought into an accession when transferring desired genes. Furthermore, we can find possible explanations for reduced recombination in parts of a chromosome, we can predict regions with linkage drag, and also look at diversity in centromeric regions.

A genetic system on chromosome arm 1BL of wild emmer causes distorted segregation in common wheat

Nonrandom segregation ratios of alleles 'segregation distortion' can have a striking impact on transmission genetics, and with widespread availability of genetic markers has been shown to be a frequent phenomenon. To investigate the possible effect of genetic interaction on segregation distortion and genetic map construction, the segregation and mapping of genetic markers locatedon wheat chromosomes 1A and 1B were followed in four recombinant substitution line (RSL) populations, produced using four chromosome-arm substitution lines (CASLs 1AS, 1AL, 1BS and 1BL) of wild emmer (Triticum turgidum var. dicoccoides, accession TTD140) in the background of the common wheat (T. aestivum) cultivar Bethlehem (BLH), each crossed to BLH itself. Using these four RSL populations, four genetic maps of chromosome 1 arms were constructed. A total of 22 genetic markers representing 19 loci were assigned to chromosome 1A, and 32 markers representing 30 loci were assigned to 1B. For chromosome 1B, two linkage maps were also constructed using RFLP data of an F₂ population derived from the same cross combination as the RSLs. The RSL and F₂ maps varied in genetic distances, but showed the same linear order of DNA markers. Segregation analysis revealed strong selection against BLH alleles on chromosome 1B, skewing the allelic frequency distribution in favour of TTD in both F₂ and RSL populations at all marker loci. On the contrary, strong selection against TTD alleles on chromosome 1A was detected for some loci in the BLH × CASL1AL RSLs, and their distribution was significantly skewed to BLH. F₂ populations always showed more segregation distortion than the corresponding RSLs. More markers near the region of chromosome 1B shared by both CASL1BS and 1BL (∼55 cM on chromosome 1B across the centromere) showed significantly distorted segregation in the BLH × CASL1BL population than in thecorresponding BLH × CASL1BS populations. Six markers located on chromosome 1A region shared by CASL1AS and 1AL showed significantly distorted segregation in 1AL-RSL, while no marker showed distorted segregation in 1AS-RSL. These results indicated that genetic factor(s) in the centromere region cause the distorted segregation of genetic markers on wheat chromosome 1B.

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10⁻⁵). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny.

A Critical Assessment of 60 Years of Maize Intragenic Recombination

Until the mid-1950s, it was believed that genetic crossovers did not occur within genes. Crossovers occurred between genes, the "beads on a string" model. Then in 1956, Seymour Benzer published his classic paper describing crossing over within a gene, intragenic recombination. This result from a bacteriophage gene prompted Oliver Nelson to study intragenic recombination in the maize Waxy locus. His studies along with subsequent work by others working with maize and other organisms described the outcomes of intragenic recombination and provided some of the earliest evidence that genes, not intergenic regions, were recombination hotspots. High-throughput genotyping approaches have since replaced single gene intragenic studies for characterizing the outcomes of recombination. These large-scale studies confirm that genes, or more generally genic regions, are the most active recombinogenic regions, and suggested a pattern of crossovers similar to the budding yeast Saccharomyces cerevisiae. In S. cerevisiae recombination is initiated by double-strand breaks (DSBs) near transcription start sites (TSSs) of genes producing a polarity gradient where crossovers preferentially resolve at the 5' end of genes. Intragenic studies in maize yielded less evidence for either polarity or for DSBs near TSSs initiating recombination and in certain respects resembled Schizosaccharomyces pombe or mouse. These different perspectives highlight the need to draw upon the strengths of different approaches and caution against relying on a single model system or approach for understanding recombination.

Complexity of genetic mechanisms conferring nonuniformity of recombination in maize

Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F₂ populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.

Understanding and Manipulating Meiotic Recombination in Plants

Meiosis is a specialized cell division, essential in most reproducing organisms to halve the number of chromosomes, thereby enabling the restoration of ploidy levels during fertilization. A key step of meiosis is homologous recombination, which promotes homologous pairing and generates crossovers (COs) to connect homologous chromosomes until their separation at anaphase I. These CO sites, seen cytologically as chiasmata, represent a reciprocal exchange of genetic information between two homologous nonsister chromatids. This gene reshuffling during meiosis has a significant influence on evolution and also plays an essential role in plant breeding, because a successful breeding program depends on the ability to bring the desired combinations of alleles on chromosomes. However, the number and distribution of COs during meiosis is highly constrained. There is at least one CO per chromosome pair to ensure accurate segregation of homologs, but in most organisms, the CO number rarely exceeds three regardless of chromosome size. Moreover, their positions are not random on chromosomes but exhibit regional preference. Thus, genes in recombination-poor regions tend to be inherited together, hindering the generation of novel allelic combinations that could be exploited by breeding programs. Recently, much progress has been made in understanding meiotic recombination. In particular, many genes involved in the process in Arabidopsis (Arabidopsis thaliana) have been identified and analyzed. With the coming challenges of food security and climate change, and our enhanced knowledge of how COs are formed, the interest and needs in manipulating CO formation are greater than ever before. In this review, we focus on advances in understanding meiotic recombination and then summarize the attempts to manipulate CO formation. Last, we pay special attention to the meiotic recombination in polyploidy, which is a common genomic feature for many crop plants.

Genome-wide recombination dynamics are associated with phenotypic variation in maize

Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement.

The sh2-R allele of the maize shrunken-2 locus was caused by a complex chromosomal rearrangement

The mutant that originally defined the shrunken - 2 locus of maize is shown here to be the product of a complex chromosomal rearrangement. The maize shrunken-2 gene (sh2) encodes the large subunit of the heterotetrameric enzyme, adenosine diphosphate glucose pyrophosphorylases and a rate-limiting enzyme in starch biosynthesis. The sh2 gene was defined approximately 72 years ago by the isolation of a loss-of-function allele conditioning a shrunken, but viable seed. In subsequent years, the realization that this allele, termed zsh2-R or sh2-Reference, causes an extremely high level of sucrose to accumulate in the developing seed led to a revolution in the sweet corn industry. Now, the vast majority of sweet corns grown throughout the world contain this mutant allele. Through initial Southern analysis followed by genomic sequencing, the work reported here shows that this allele arose through a complex set of events involving at least three breaks of chromosome 3 as well as an intra-chromosomal inversion. These findings provide an explanation for some previously reported, unexpected observations concerning rates of recombination within and between genes in this region.

The molecular biology of meiosis in plants

Meiosis is the cell division that reshuffles genetic information between generations. Recently, much progress has been made in understanding this process; in particular, the identification and functional analysis of more than 80 plant genes involved in meiosis have dramatically deepened our knowledge of this peculiar cell division. In this review, we provide an overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy.

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.

A crossover hotspot near his-3 in Neurospora crassa is a preferential recombination termination site

During analysis of 148 unselected Neurospora crassa octads, an above average rate of crossing over was detected within a 360-base region near the 3' end of his-3, suggesting a hotspot for crossing over about 1.8 kb away from the recombination initiation site within cog. Homozygous deletion of the 360-base region increases exchanges in his-3 and on the far side of his-3 from cog, with the heterozygote showing an intermediate increase. We conclude that recombination events initiated at cog terminate within the 360-base sequence more often than in other sections of the cog-his-3 interval and, since some of these terminations will be resolved as crossovers, a cluster of crossovers at this location is the outcome. Removal of this termination site increases the chance that an event will reach his-3, resulting in recombination within the gene, or extend past it to yield a crossover on the other side of his-3. The deleted sequence has substantial predicted secondary structure, including a complex predicted stem-loop, suggesting that DNA secondary structure may be responsible for the termination.

Plant DNA recombinases: a long way to go

DNA homologous recombination is fundamental process by which two homologous DNA molecules exchange the genetic information for the generation of genetic diversity and maintain the genomic integrity. DNA recombinases, a special group of proteins bind to single stranded DNA (ssDNA) nonspecifically and search the double stranded DNA (dsDNA) molecule for a stretch of DNA that is homologous with the bound ssDNA. Recombinase A (RecA) has been well characterized at genetic, biochemical, as well as structural level from prokaryotes. Two homologues of RecA called Rad51 and Dmc1 have been detected in yeast and higher eukaryotes and are known to mediate the homologous recombination in eukaryotes. The biochemistry and mechanism of action of recombinase is important in understanding the process of homologous recombination. Even though considerable progress has been made in yeast and human recombinases, understanding of the plant recombination and recombinases is at nascent stage. Since crop plants are subjected to different breeding techniques, it is important to know the homologous recombination process. This paper focuses on the properties of eukaryotes recombinases and recent developments in the field of plant recombinases Dmc1 and Rad51.

Role of RAD51 in the repair of MuDR-induced double-strand breaks in maize (Zea mays L.)

Rates of Mu transposon insertions and excisions are both high in late somatic cells of maize. In contrast, although high rates of insertions are observed in germinal cells, germinal excisions are recovered only rarely. Plants doubly homozygous for deletion alleles of rad51A1 and rad51A2 do not encode functional RAD51 protein (RAD51-). Approximately 1% of the gametes from RAD51+ plants that carry the MuDR-insertion allele a1-m5216 include at least partial deletions of MuDR and the a1 gene. The structures of these deletions suggest they arise via the repair of MuDR-induced double-strand breaks via nonhomologous end joining. In RAD51- plants these germinal deletions are recovered at rates that are at least 40-fold higher. These rates are not substantially affected by the presence or absence of an a1-containing homolog. Together, these findings indicate that in RAD51+ germinal cells MuDR-induced double-strand breaks (DSBs) are efficiently repaired via RAD51-directed homologous recombination with the sister chromatid. This suggests that RAD51- plants may offer an efficient means to generate deletion alleles for functional genomic studies. Additionally, the high proportion of Mu-active, RAD51- plants that exhibit severe developmental defects suggest that RAD51 plays a critical role in the repair of MuDR-induced DSBs early in vegetative development.

The genomic dynamics and evolutionary mechanism of the Pi2/9 locus in rice

The Pi2/9 locus contains at least four resistance specificities to Magnaporthe grisea and belongs to a gene complex comprised of multiple genes that encode highly homologous nucleotide binding site (NBS) and leucine rich repeat (LRR) proteins. To investigate the genetic events involved in the evolution of the Pi2/9 locus, we analyzed the Pi2/9 locus at the inter- and intralocus levels in five rice cultivars. The NBS-LRR genes in the five cultivars belong to the same phylogenetic clade among rice NBS-LRR genes, and all have a phase-2 intron at the N-terminus. However, the paralogs within each haplotype show a significant sequence divergence and their N-terminal intron and 5' regulatory regions are very different. On the contrary, the orthologs from different haplotypes are highly similar, indicating an obvious orthologous relationship has been maintained during the evolution of the Pi2/9 locus. These results suggest that sequence diversification in the 5' regulatory regions and N-terminal introns of the paralogs may have led to suppression of meiotic recombination between the paralogs within each haplotype, facilitating the maintenance of the orthologous relationship among rice cultivars. Our observations provide valuable insight into the genomic dynamics and evolutionary mechanism of an NBS-LRR resistance-gene complex in rice.

Effects of trans-acting genetic modifiers on meiotic recombination across the a1-sh2 interval of maize

Meiotic recombination rates are potentially affected by cis- and trans-acting factors, i.e., genotype-specific modifiers that do or do not reside in the recombining interval, respectively. Effects of trans modifiers on recombination across the approximately 140-kb maize a1-sh2 interval of chromosome 3L were studied in the absence of polymorphic cis factors in three genetically diverse backgrounds into which a sequence-identical a1-sh2 interval had been introgressed. Genetic distances across a1-sh2 varied twofold among genetic backgrounds. Although the existence of regions exhibiting high and low rates of recombination (hot and cold spots, respectively) was conserved across backgrounds, the absolute rates of recombination in these sequence-identical regions differed significantly among backgrounds. In addition, an intergenic hot spot had a higher rate of recombination as compared to the genome average rate of recombination in one background and not in another. Recombination rates across two genetic intervals on chromosome 1 did not exhibit the same relationships among backgrounds as was observed in a1-sh2. This suggests that at least some detected trans-acting factors do not equally affect recombination across the genome. This study establishes that trans modifier(s) polymorphic among genetic backgrounds can increase and decrease recombination in both genic and intergenic regions over relatively small genetic and physical intervals.

Unequal sister chromatid and homolog recombination at a tandem duplication of the A1 locus in maize

Tandemly arrayed duplicate genes are prevalent. The maize A1-b haplotype is a tandem duplication that consists of the components, alpha and beta. The rate of meiotic unequal recombination at A1-b is ninefold higher when a homolog is present than when it is absent (i.e., hemizygote). When a sequence heterologous homolog is available, 94% of recombinants (264/281) are generated via recombination with the homolog rather than with the sister chromatid. In addition, 83% (220/264) of homolog recombination events involved alpha rather than beta. These results indicate that: (1) the homolog is the preferred template for unequal recombination and (2) pairing of the duplicated segments with the homolog does not occur randomly but instead favors a particular configuration. The choice of recombination template (i.e., homolog vs. sister chromatid) affects the distribution of recombination breakpoints within a1. Rates of unequal recombination at A1-b are similar to the rate of recombination between nonduplicated a1 alleles. Unequal recombination is therefore common and is likely to be responsible for the generation of genetic variability, even within inbred lines.

Localized breakdown in linkage disequilibrium does not always predict sperm crossover hot spots in the human MHC class II region

To investigate the relationship between meiotic crossover hot spots and block-like linkage disequilibrium (LD), we have extended our high-resolution studies of the human MHC class II region to a 90-kb segment upstream of the HLA-DOA gene. LD blocks in this region are not as well defined as in the neighboring 210-kb DNA segment but do show two regions of LD breakdown in which coalescent analysis indicates substantial historical recombination. Sperm crossover analysis of one region revealed a novel localized hot spot similar in intensity and morphology to most other MHC hot spots. Crossovers at this hot spot are not obviously affected by a large insertion/deletion polymorphism near the hot spot. The second region of LD breakdown, within the DPB1 gene, shows an extremely low level of sperm crossover activity and does not contain a sperm crossover hot spot. These results highlight the complexity of LD patterns and the importance of experimentally verifying crossover hot spots.

The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase)

Low copy number nuclear genes have been found to be useful for phylogenetic reconstruction at different taxonomic levels. This study investigated the utility of a single copy gene, cinnamoyl CoA reductase (CCR), for resolving phylogenetic relationships at the sectional level within Eucalyptus. The monophyly of sections Exsertaria and Latoangulatae was explored, using section Maidenaria as an outgroup, and the impact of intragenic recombination on phylogenetic reconstruction examined. Phylogenetic analysis did not resolve monophyletic groups. Latoangulatae and Maidenaria were polyphyletic or paraphyletic. Exsertaria species formed a clade but included a single Latoangulatae species (E. major). Recombination analysis identified two intragenic recombination events that involved species from different sections, which have probably been facilitated by inter-sectional hybridisation. One of the events most likely occurred prior to speciation, with several Latoangulatae species having the recombinant allele. The other event may have occurred after speciation, since only one of two E. globulus samples possessed the recombinant allele. This is the first detailed report of intragenic recombination in both CCR and Eucalyptus, and between species of different sections of a plant genus. The occurrence of intragenic recombination may explain the anomalous positions of some species within the phylogenetic tree, and indicates that phylogenetic analysis of Eucalyptus using nuclear genes will be problematic unless recombination is taken into account.

Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common Zea genetic background

Genetic distances across the a1-sh2 interval varied threefold in three near-isogenic stocks that carry structurally distinct teosinte A1 Sh2 haplotypes (from Z. mays spp. mexicana Chalco, Z. mays spp. parviglumis, and Z. luxurians) and a common maize a1::rdt sh2 haplotype. In each haplotype >85% of recombination events resolved in the proximal 10% of the approximately 130-kb a1-sh2 interval. Even so, significant differences in the distributions of recombination breakpoints were observed across subintervals among haplotypes. Each of the three previously detected recombination hot spots was detected in at least one of the three teosinte haplotypes and two of these hot spots were not detected in at least one teosinte haplotype. Moreover, novel hot spots were detected in two teosinte haplotypes. Due to the near-isogenic nature of the three stocks, the observed variation in the distribution of recombination events is the consequence of cis-modifications. Although generally negatively correlated with rates of recombination per megabase, levels of sequence polymorphisms do not fully account for the nonrandom distribution of recombination breakpoints. This study also suggests that estimates of linkage disequilibrium must be interpreted with caution when considering whether a gene has been under selection.

Meiosis: inducing variation by reduction

A brief introduction is presented with some thought on the origin of meiosis. Subsequently, a sequential overview of the diverse processes that take place during meiosis is provided, with an eye to similarities and differences between the different eukaryotic systems. In the final part, we try to summarize the available core meiotic mutants and make a comprehensive comparison for orthologous genes between fungal, plant, and animal systems.

MuDR transposase increases the frequency of meiotic crossovers in the vicinity of a Mu insertion in the maize a1 gene

Although DNA breaks stimulate mitotic recombination in plants, their effects on meiotic recombination are not known. Recombination across a maize a1 allele containing a nonautonomous Mu transposon was studied in the presence and absence of the MuDR-encoded transposase. Recombinant A1' alleles isolated from a1-mum2/a1::rdt heterozygotes arose via either crossovers (32 CO events) or noncrossovers (8 NCO events). In the presence of MuDR, the rate of COs increased fourfold. This increase is most likely a consequence of the repair of MuDR-induced DNA breaks at the Mu1 insertion in a1-mum2. Hence, this study provides the first in vivo evidence that DNA breaks stimulate meiotic crossovers in plants. The distribution of recombination breakpoints is not affected by the presence of MuDR in that 19 of 24 breakpoints isolated from plants that carried MuDR mapped to a previously defined 377-bp recombination hotspot. This result is consistent with the hypothesis that the DNA breaks that initiate recombination at a1 cluster at its 5' end. Conversion tracts associated with eight NCO events ranged in size from <700 bp to >1600 bp. This study also establishes that MuDR functions during meiosis and that ratios of CO/NCO vary among genes and can be influenced by genetic background.

Unintended effects and their detection in genetically modified crops

The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.

Pseudogenes: are they "junk" or functional DNA?

Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.

Pattern of diversity in the genomic region near the maize domestication gene tb1

Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species. The tb1 gene largely controls the increase in apical dominance in maize relative to teosinte, and a region of the tb1 locus 5' to the transcript sequence was a target of selection during maize domestication. To better characterize the impact of selection at a major "domestication" locus, we have sequenced the upstream tb1 genomic region and systematically sampled nucleotide diversity for sites located as far as 163 kb upstream to tb1. Our analyses define a selective sweep of approximately 60-90 kb 5' to the tb1 transcribed sequence. The selected region harbors a mixture of unique sequences and large repetitive elements, but it contains no predicted genes. Diversity at the nearest 5' gene to tb1 is typical of that for neutral maize loci, indicating that selection at tb1 has had a minimal impact on the surrounding chromosomal region. Our data also show low intergenic linkage disequilibrium in the region and suggest that selection has had a minor role in shaping the pattern of linkage disequilibrium that is observed. Finally, our data raise the possibility that maize-like tb1 haplotypes are present in extant teosinte populations, and our findings also suggest a model of tb1 gene regulation that differs from traditional views of how plant gene expression is controlled.

Rate and pattern of mutation at microsatellite loci in maize

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.

Extensive interallelic polymorphisms drive meiotic recombination into a crossover pathway

Recombinants isolated from most meiotic intragenic recombination experiments in maize, but not in yeast, are borne principally on crossover chromosomes. This excess of crossovers is not explained readily by the canonical double-strand break repair model of recombination, proposed to account for a large body of yeast data, which predicts that crossovers (COs) and noncrossovers (NCOs) should be recovered equally. An attempt has been made here to identify general rules governing the recovery of the CO and NCO classes of intragenic recombinants in maize. Recombination was analyzed in bz heterozygotes between a variety of mutations derived from the same or different progenitor alleles. The mutations include point mutations, transposon insertions, and transposon excision footprints. Consequently, the differences between the bz heteroalleles ranged from just two nucleotides to many nucleotides, indels, and insertions. In this article, allelic pairs differing at only two positions are referred to as dimorphic to distinguish them from polymorphic pairs, which differ at multiple positions. The present study has revealed the following effects at these bz heteroalleles: (1) recombination between polymorphic heteroalleles produces mostly CO chromosomes; (2) recombination between dimorphic heteroalleles produces both CO and NCO chromosomes, in ratios apparently dependent on the nature of the heteroalleles; and (3) in dimorphic heterozygotes, the two NCO classes are recovered in approximately equal numbers when the two mutations are point mutations but not when one or both mutations are insertions. These observations are discussed in light of a recent version of the double-strand break repair model of recombination that postulates separate pathways for the formation of CO and NCO products.

Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize

The 140-kb a1-sh2 interval of the maize genome contains at least four genes (a1, yz1, x1, and sh2). Partial sequence analysis of two haplotypes has revealed many single nucleotide polymorphisms and InDel polymorphisms, including several large structural polymorphisms. The physical positions of 101 meiotic recombination breakpoints are not distributed uniformly across the interval and are instead concentrated within three recombination hot spots. Two of these recombination hot spots are genic (a1 and yz1) and one is apparently nongenic. The x1 gene is not a recombination hot spot. Thus, these results suggest that not all hot spots are genes and indicate that not all genes are hot spots. Two of the 101 recombination events arose by means of either noncrossover events involving conversion tract lengths of at least 17 kb or double-crossover events. Only one recombination breakpoint mapped to the approximately 80-kb distal portion of the a1-sh2 interval that contains large amounts of repetitive DNA including retrotransposons; in this region the ratio of genetic to physical distance is less than 0.5% of the genome's average. These results establish that the retrotransposon faction of the maize genome is relatively inert recombinationally.

Numerous small rearrangements of gene content, order and orientation differentiate grass genomes

Comparative genetic mapping has indicated that the grass family (Poaceae) exhibits extensive chromosomal collinearity. In order to investigate microcollinearity in these genomes, several laboratories have begun to undertake comparative DNA sequence analyses of orthologous chromosome segments from various grass species. Five different regions have now been investigated in detail, with four regions sequenced for maize, rice and sorghum, plus two for wheat and one for barley. In all five of these segments, gene rearrangements were observed in at least one of the comparisons. Most of the detected rearrangements are small, involving the inversion, duplication, translocation or deletion of DNA segments that contain only 1-3 genes. Even closely related species, like barley and wheat or maize and sorghum, exhibit approximately 20% alterations in gene content or orientation. These results indicate that thousands of small genetic rearrangements have occurred in several grass lineages since their divergence from common ancestors. These rearrangements have largely been missed by genetic mapping and will both complicate and enrich the use of comparative genetics in the grasses.

Gene conversion within regulatory sequences generates maize r alleles with altered gene expression

The maize r locus encodes a transcription factor that regulates the developmental expression of the plant pigment anthocyanin. In an unusual example of gene regulatory diversity, the R-sc (Sc, strong seed color) and the R-p (P, plant color) alleles of r have nonoverlapping tissue specificity and nonhomologous 5' flanking sequences. Heterozygotes between wild-type P and Sc mutants with Ds6 transposable element inserts (r-sc:m::Ds6 or sc:m) produce colored seed derivatives (Sc+) during meiotic recombination. The sc:m alleles with Ds6 insertion in 3' regions of r produce crossover Sc+ derivatives. sc:m alleles with Ds6 elements inserted in 5' regions produce rare Sc+ derivatives borne on nonrecombinant chromosomes. Among 52 such noncrossover Sc+ derivatives, 18 are indistinguishable from the Sc progenitor in phenotype and DNA sequence [Scp(+) alleles]. The remaining 34 derivatives have strong Sc+ expression, including darkly pigmented aleurone, scutellum, coleoptile, and scutellar node [Scp(e) alleles]. The coleoptile and scutellar node phenotypes are unique from either progenitor but are similar to those of some naturally occurring r alleles. Both classes of Sc+ derivatives are explained by gene conversion between the promoter region of Sc:124 and a homologous region located proximal to P. The recombinational intermediate formed between sc:m alleles and P results in deletion of the Ds6 element alone or both Ds6 and a nearby unrelated transposable element-like sequence.

Structure of linkage disequilibrium and phenotypic associations in the maize genome

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.

Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.)

For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum, the genome is hexaploid, has a size of 1.6 x 10(10) bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed chromosome walking and positional cloning. Here, we demonstrate that chromosome walking using bacterial artificial chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (A(m) genome). BAC end sequences were mostly repetitive and could not be used for the first walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two walking steps resulted in a physical contig of 450 kb on chromosome 1A(m)S. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome chromosome walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.

Transposable element contributions to plant gene and genome evolution

Transposable elements were first discovered in plants because they can have tremendous effects on genome structure and gene function. Although only a few or no elements may be active within a genome at any time in any individual, the genomic alterations they cause can have major outcomes for a species. All major element types appear to be present in all plant species, but their quantitative and qualitative contributions are enormously variable even between closely related lineages. In some large-genome plants, mobile DNAs make up the majority of the nuclear genome. They can rearrange genomes and alter individual gene structure and regulation through any of the activities they promote: transposition, insertion, excision, chromosome breakage, and ectopic recombination. Many genes may have been assembled or amplified through the action of transposable elements, and it is likely that most plant genes contain legacies of multiple transposable element insertions into promoters. Because chromosomal rearrangements can lead to speciating infertility in heterozygous progeny, transposable elements may be responsible for the rate at which such incompatibility is generated in separated populations. For these reasons, understanding plant gene and genome evolution is only possible if we comprehend the contributions of transposable elements.

Genetic recombination in plants

Meiotic recombination generates novel allelic arrays on chromosomes. Recent experiments have revealed an extraordinarily nonrandom distribution of recombination breakpoints along the lengths of plant chromosomes; for example, recombination breakpoints often resolve within genic sequences, and thereby generate novel alleles. The mechanism by which recombination breakpoints are determined is an area of active investigation. In addition, recent developments are providing recombination-based technologies for creating targeted alterations in the architecture of plant genomes.

Functional genomics: probing plant gene function and expression with transposons

Transposable elements provide a convenient and flexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research.

Grass genomes

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.

Matrix attachment regions and structural colinearity in the genomes of two grass species

In order to gain insights into the relationship between spatial organization of the genome and genome function we have initiated studies of the co-linear Sh2/A1- homologous regions of rice (30 kb) and sorghum (50 kb). We have identified the locations of matrix attachment regions (MARs) in these homologous chromosome segments, which could serve as anchors for individual structural units or loops. Despite the fact that the nucleotide sequences serving as MARs were not detectably conserved, the general organizational patterns of MARs relative to the neighboring genes were preserved. All identified genes were placed in individual loops that were of comparable size for homologous genes. Hence, gene composition, gene orientation, gene order and the placement of genes into structural units has been evolutionarily conserved in this region. Our analysis demonstrated that the occurrence of various 'MAR motifs' is not indicative of MAR location. However, most of the MARs discovered in the two genomic regions were found to co-localize with miniature inverted repeat transposable elements (MITEs), suggesting that MITEs preferentially insert near MARs and/or that they can serve as MARs.

Arabidopsis thaliana mutants altered in homologous recombination

Homologous recombination contributes both to the generation of allelic diversity and to the preservation of genetic information. In plants, a lack of suitable experimental material has prevented studies of the regulatory and enzymatic aspects of recombination in somatic and meiotic cells. We have isolated nine Arabidopsis thaliana mutants hypersensitive to x-ray irradiation (xrs) and examined their recombination properties. For the three xrs loci described here, single recessive mutations were found to confer simultaneous hypersensitivities to the DNA-damaging chemicals mitomycin C (MMCs) and/or methyl methanesulfonate (MMSs) and alterations in homologous recombination. Mutant xrs9 (Xrays, MMSs) is reduced in both somatic and meiotic recombination and resembles yeast mutants of the rad52 epistatic group. xrs11 (Xrays, MMCs) is deficient in the x-ray-mediated stimulation of homologous recombination in somatic cells in a manner suggesting a specific signaling defect. xrs4 (Xrays, MMSs, MMCs) has a significant deficiency in somatic recombination, but this is accompanied by meiotic hyper-recombination. A corresponding phenotype has not been reported in other systems and thus this indicates a novel, plant-specific regulatory circuit linking mitotic and meiotic recombination.

Analysis of recombination sites within the maize waxy locus

Genetic fine structure analysis of the maize wx locus has determined that the ratio of genetic to physical distance within wx was one to two orders of magnitude higher than the average for the maize genome. Similar results have been found at other maize loci. In this study, we examined several mechanisms that could account for this pattern. First, crossovers in two other maize genes resolve preferentially at specific sites. By mapping exchanges between wx-B1 and wx-I relative to a polymorphic SstI site, we found no evidence for such a hotspot at wx. Second, deletion of promoter sequences from wx alleles had little effect on recombination frequencies, in contrast to results in yeast where promoter sequences are important for initiating recombination in some genes. Third, high levels of insertion polymorphism may suppress intergenic recombination. However, the presence of a 2-kb Ds element 470 bp upstream of the wx transcription start site did not further suppress recombination between Ds insertions in nearby wx sequences. Thus, none of these mechanisms is sufficient to explain the difference between intergenic and intragenic recombination rates at wx.

Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome

The bronze (bz) gene is a recombinational hotspot in the maize genome: its level of meiotic recombination per unit of physical length is > 100-fold higher than the genome's average and is the highest of any plant gene analyzed to date. Here, we examine whether recombination is also unevenly distributed within the bz gene. In yeast genes, recombination (conversion) is polarized, being higher at the end of the gene where recombination is presumably initiated. We have analyzed products of meiotic recombination between heteroallelic pairs of bz mutations in both the presence and absence of heterologies and have sequenced the recombination junction in 130 such Bz intragenic recombinants. We have found that in the absence of heterologies, recombination is proportional to physical distance across the bz gene. The simplest interpretation for this lack of polarity is that recombination is initiated randomly within the gene. Insertion mutations affect the frequency and distribution of intragenic recombination events at bz, creating hotspots and coldspots. Single base pair heterologies also affect recombination, with fewer recombination events than expected by chance occurring in regions of the bz gene with a high density of heterologies. We also provide evidence that meiotic recombination in maize is conservative, that is, it does not introduce changes, and that meiotic conversion tracts are continuous and similar in size to those in yeast.

Region-specific cis- and trans-acting factors contribute to genetic variability in meiotic recombination in maize

Understanding the genetic basis for variability in recombination rates is important for general genetic studies and plant-breeding efforts. Earlier studies had suggested increased recombination frequencies in particular F2 populations derived from the maize inbred A188. A detailed phenotypic and molecular analysis was undertaken to extend these observations and dissect the responsible factors. A heritable increase in recombination in the sh1-bz1 interval was observed in these populations. A factor causing an approximate twofold increase mapped to the A188 sh1-Bz1 region, behaved as a dominant, cis-acting factor, affected recombination equally in male and female sporogenesis and did not reduce the well-studied complete interference in the adjacent bz1-wx interval. This factor also did not increase recombination frequencies in the c1-sh1 and bz1-wx intervals, demonstrating independent control of recombination in adjacent intervals. Additional phenotypic analysis of recombination in the c1-sh1 and bz1-wx intervals and RFLP analysis of recombination along chromosomes 7 and 5 suggested that heritable factors controlling recombination in these intervals act largely independently and in trans. Our results show that recombination in these populations, and possibly maize in general, is controlled by both cis- and trans-acting factors that affect specific chromosomal regions.

Soybean pedigree analysis using map-based molecular markers: recombination during cultivar development

An analysis of the genome structure of soybean cultivars was conducted to determine if cultivars are composed of large regions of chromosomes inherited intact from one parent (indicative of minimal recombination) or if the chromosomes are a mixture of one parent's DNA interspersed with the DNA from the other parent (indicative of maximal recombination). Twenty-one single-cross-derived and 5 single-backcross-derived soybean cultivars and their immediate parents (47 genotypes) were analyzed at 89 RFLP loci to determine the minimal number and distribution of recombination events detected. Cultivars derived from single-cross and single-backcross breeding programs showed an average of 5.2 and 8.0 recombination events per cultivar, respectively. A homogeneity Chi-square test based upon a Poisson distribution of recombination events across 13 linkage groups indicated that the number of recombinations observed among linkage groups was random for the single-cross cultivars, but not for the single-backcross-derived cultivars. A twotailed t-test demonstrated that for some linkage groups, the number of recombinations per map unit exceeded the confidence interval developed from a t-distribution of recombinations standardized for map unit distance. Paired t-tests of the number of recombinations observed between linkage-group ends and the mid-portion of the linkage groups indicated that during the development of the cultivars analyzed in this study more recombinations were associated with the ends of linkage groups than with the middle region. Detailed analysis of each linkage group revealed that large portions of linkage groups D, F, and G were inherited intact from one parent in several cultivars. A portion of linkage group G, in contrast, showed more recombination events than expected, based on genetic distance. These analyses suggest that breeders may have selected against recombination events where agronomically favorable combinations of alleles are present in one parent, and for recombination in areas where agronomically favorable combinations of alleles are not present in either parent.

Correlation of genetic and physical maps at the A mating-type locus of Coprinus cinereus

The A mating type locus of Coprinus cinereus is remarkable for its extreme diversity, with over 100 different alleles in natural populations. Classical genetic studies have demonstrated that this hypervariability arises in part from recombination between two subloci of A, alpha and beta, although more recent population genetic data have indicated a third segregating sublocus. In this study, we characterized the molecular basis by which recombination generates nonparental A mating types. We mapped the frequency and location of all recombination events in two crosses and correlated the genetic and physical maps of A. We found that all recombination events were located in 6 kb of noncoding DNA between the alpha and beta subloci and that the rate of recombination in this noncoding region matched that generally observed for this genome. No recombination within gene clusters or within coding regions was observed, and the two alpha and beta subloci described in genetic analyses correlated with the previously characterized alpha and beta gene clusters. We propose that pairs of genes constitute both the sex determining and the hereditary unit of A.

Variation in the ratio of physical to genetic distance in intervals adjacent to the Mla locus on barley chromosome 1H

Variants of the pulsed-field gel electrophoresis technique were used in conjunction with two-dimensional DNA gel electrophoresis (2-DDGE) to determine the ratio of physical to genetic distance in two genetically defined intervals on barley chromosome 1H.2-DDGE analysis demonstrated that two loci that define a 0.3 cM interval, as determined by hybridization with BCD249, reside on a single 450-kb MluI fragment. This result indicates a maximum ratio of physical to genetic distance in this interval of 1500 kb/cM as compared to 3.7-4.2 Mb/cM for the barley genome as a whole. High molecular weight (HMW) DNA restricted with NotI and probed sequentially with MWG068 and BCD249 yield diffuse bands at approximately 2.8 Mb and 3.0 Mb in the C.I. 16151 and C.I. 16155 parental lines, respectively. These results suggest the maximum ratio of physical to genetic distance in the interval defined by these probes is 7.8 Mb/cM. Unique HMW DNA restriction fragment length polymorphisms (RFLP) were attributed to the presence of recombination breakpoints. Data from the recombination breakpoint analysis were used to estimate a ratio of physical to genetic distance of 2.5 Mb/cM in the Xbcd249.2-Xmwg068 interval and 0.465 Mb/cM in the Xbcd249.1-Xbcd249.2 interval. Both physical linkage and recombination breakpoint analysis indicate the Xbcd249.1-Xbcd249.2 interval is approximately five-fold smaller, physically, than the Xbcd249.2-Xmwg068 interval.