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A Dense Genetic Map of the Silkworm, Bombyx mori, Covering All Chromosomes Based on 1018 Molecular Markers
Yuji Yasukochiaa National Institute of Sericultural and Entomological Science (NISES), Tsukuba, Ibaraki 305-8634, Japan
Corresponding author: Yuji Yasukochi, National Institute of Sericultural and Entomological Science (NISES), Owashi 1-2, Tsukuba, Ibaraki 305-8634, Japan., yaskoch{at}nises.affrc.go.jp (E-mail).
Communicating editor: G. A. CHURCHILL
| ABSTRACT |
|---|
A dense linkage map was constructed for the silkworm, Bombyx mori, containing 1018 genetic markers on all 27 autosomes and the Z chromosome. Most of the markers, covering ~2000 cM, were randomly amplified polymorphic DNAs amplified with primer-pairs in combinations of 140 commercially available decanucleotides. In addition, eight known genes and five visible mutations were mapped. Bombyx homologues of engrailed and invected genes were found to be closely linked, as in Drosophila melanogaster. The average interval between markers was ~2 cM, equal to ~500 kb. The correspondence of seven linkage groups to counterparts of the conventional linkage map was determined. This map is the first linkage map in insects having a large number of chromosomes (n = 28) that covers all chromosomes without any gaps.
GENOME research is being conducted on an increasing number of organisms, but insufficient attention has been paid to insects, which account for the majority of animal species. Only the fruit fly, Drosophila melanogaster, has been exhaustively studied genetically and is a subject of a genome research project as a model organism (![]()
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Bombyx mori, the domesticated silkworm, is one of the most genetically studied insects, apart from D. melanogaster. More than 200 mutations have been placed on linkage maps covering 900.2 cM and maintained as genetic resources (![]()
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Recent progress in polymerase chain reaction (PCR)-based markers such as randomly amplified polymorphic DNA (RAPD; ![]()
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In this article, I present a dense linkage map of the silkworm mainly based on RAPDs using double primer pairs (![]()
| MATERIALS AND METHODS |
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Silkworm strains and isolation of DNA:
Silkworm strains C108 and p50 were identical to those used in the previous work (![]()
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Additional matings were carried out to identify correspondence between molecular and established linkage groups (ELGs). Two recessive mutant strains, NISES 912 (pe-re, ch) and 920 (lem, oc), were used for this purpose (![]()
RAPD analysis:
Oligonucleotide primers were purchased from Operon Technologies (Alameda, CA; kits A, D, H, I, T, R, and Y). The reaction was performed in a total reaction mixture of 15 µl consisting of 25 ng template DNA, 0.5 µM primers, 1 unit of Taq polymerase (Takara, Kyoto, Japan), 0.1 mM for each of the dNTPs (Pharmacia, Piscataway, NJ), 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, and 2.5 mM MgCl2. The amplification was carried out with a 3-min denaturation at 94°, followed by 45 cycles with a 1-min denaturation at 94°, a 2-min hybridization at 36°, and a 3-min elongation at 72°, ending with a 5-min final extension at 72°. The completed reaction (8 µl) was loaded on a binary gel [a mixture of 0.7% agarose (Takara) and 0.7% Synergel (Diversified Biotech, Boston) in 0.5x TBE buffer] and separated by electrophoresis. Gels were stained with ethidium bromide and photographed under UV light with Polaroid 667 film or a CCD-imaging processor (ATTO, Tokyo).
Establishment of expressed sequence tags (ESTs):
Sequences of cloned silkworm genes were obtained from the GSDB, DDBJ, EMBL, and NCBI nucleotide sequence databases. Primers listed in Table 1 were designed with a program Oligo ver. 4.0 (National Biosciences, Plymouth, MN). PCR reactions were performed in the same buffer as described above except that the MgCl2 concentration was 1.5 mM. The amplification was performed with a 3-min denaturation at 94°, followed by 45 cycles with a 1-min denaturation at 94°, a 2-min hybridization at 55°, and a 3-min elongation at 72°, followed by a 5-min final extension at 72°. Products were digested with eight restriction enzymes, AfaI, AluI, DraI, HaeIII, HhaI, HinfI, HpaI, and MboI, to screen restriction fragment length polymorphisms (RFLPs) and to confirm whether expected fragments were amplified (Table 1).
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Linkage analysis:
The presence or absence of each polymorphic marker was scored for all 166 F2 individuals. These data were processed to sort markers into linkage groups with the program MAPMAKER/Exp ver. 3.0 (![]()
Heteroduplex formation:
Equal amounts of PCR products from both parental strains and loading buffer (0.25% bromophenol blue, 0.25% xylene cyanol, 30% glycerol in H2O) were mixed and denatured at 95° for 5 min. Then a 15-min hybridization was performed at 55° and cooled to 4° and the reaction was loaded onto an agarose gel [3% Metaphor XR (FMC, Rockland, ME) in 0.5x TBE, 1 M urea] in an ice-cold chamber.
| RESULTS |
|---|
Detection of RAPDs with double primer pairs:
To obtain markers for linkage analysis, RAPD polymorphisms between two parental strains (C108 and p50) were screened using 140 10-mer commercially available primers. A total of 7757 primer combinations were tested and 1001 of them were selected for further analysis (Figure 1A). Small-scale linkage analysis was performed with 22 F2 progeny, and I found 757 primer combinations generating segregating banding patterns (Figure 1B). More detailed mapping was carried out with an additional 144 F2 progeny from the same single pair mating, and 1388 polymorphic bands generated from 719 primer pairs were finally used for map construction after eliminating unclear markers (data not shown; the list of RAPD markers used in this experiment will be available on http://ss.nises.affrc.go.jp/).
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Mapping of known genes:
I also tried to map cloned silkworm genes. ESTs were designed for more than 30 known sequences, and four of them showed clear polymorphisms between C108 and p50 (Table 1). Monomorphic PCR products were probed for RFLPs by digestion with a variety of restriction enzymes. As a result, I found RFLPs for three ESTs (Table 1). In addition, I used a previously reported intron length polymorphism of the prothoracicotropic hormone (PTTH) gene (![]()
Identification of linkage groups:
A total of 1388 RAPDs and eight ESTs were then grouped into linkage groups using MAPMAKER/Exp ver. 3.0. Sorting of markers revealed that there were 28 linkage groups that coincided with the haploid chromosome number of B. mori. However, there still remained the possibility that large gaps between markers might falsely assign markers on the same chromosomes to different linkage groups.
Achiasmatic oogenesis makes it possible to test whether linkage groups are really independent or not. As shown in Figure 2A, any F2 individual cannot be homozygous for both maternal and paternal dominant markers on the same autosome (![]()
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Typing was determined when more than two null scores of C108- or p50-dominant markers were confirmed for each putative linkage group. If paternal and maternal markers of the same linkage group were found to coexist in the same F2 individual, another PCR amplification was repeated until clear results were obtained. Even when linked markers on the same chromosome are separated by long gaps they cannot show inconsistent chromosome prints, and all 28 putative linkage groups were revealed to be independent from each other. Therefore, I concluded that the 28 linkage groups assembled by MAPMAKER covered all 27 autosomes and the Z chromosome.
Mapping of ESTs and visible markers:
Segregation patterns of visible markers, sex, and the p locus, revealed that 2 of the 28 linkage groups corresponded to ELG 1 and 2. Early chorion gene A4, previously identified on ELG 2 (![]()
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Intriguingly, Bombyx homologues of engrailed(en) and invected(inv) genes (![]()
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Map construction:
Achiasmatic oogenesis also facilitated evaluation of the reliability of the RAPD markers. False-negative signals could be detected, for example, when a maternal marker was absent in the progeny whose nonrecombinant chromosome was maternal. Exclusion of unreliable markers revealed by frequently generating false-negative signals greatly improved the accuracy of the linkage analysis. Out of 1388 RAPDs, 1010 were finally utilized for map construction.
C108-dominant and p50-dominant markers were separately ordered within each linkage group (![]()
An individual having a C108-derived nonrecombinant chromosome is not informative for calculating recombination values between C108-dominant markers because it must show positive signals regardless of the crossing over in the other chromosome (Figure 2A). Therefore, I used only individuals confirmed as having a p50-derived nonrecombinant chromosome to calculate genetic distances between C108-dominant markers, and vice versa. The presence or absence of markers in such individuals could be interpreted as BC1 data (Figure 2A; for examples, see behavior of markers A, D, and E in type B progeny and markers F, G, and J in type A progeny). On average, 61.7 individuals were informative for C108-dominant markers and 62.0 individuals were informative for p50-dominant markers.
Connecting the C108- and p50-dominant linkage groups:
Map construction as described above inevitably generated two linkage groups for each chromosome (Figure 4). Integration of the two groups required connecting markers between them. One candidate was codominant markers. The ESTs listed in Table 1 were useful for this purpose. In addition, I found a number of RAPDs that behaved like codominant markers. C108- and p50-dominant bands of such markers not only were of similar size but also generated putative heteroduplex products in heterozygotes (Figure 1B) as reported in previous work in the honeybee (![]()
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Other candidates for map integration were markers showing a segregation ratio of 1:1. Many of them were on the Z chromosome of the maternal strain (Figure 2B). In this case, segregation behavior of paternal dominant markers in F2 females could easily be integrated into those of maternal markers (Figure 2B).
On the other hand, heterozygosity in parental strains also leads to similar results. If a heterozygous dominant marker succeeds to an F1 female, the segregation behavior in F2 individuals would reveal the marker composition of the nonrecombinant chromosome, which would be reflected in chromosome print (Figure 2A; markers B and H). Only one marker, R121124, was classified in this category since its behavior completely agreed with chromosome print of Linkage Group O (Figure 3).
If an F1 male inherits a locus that was heterozygous in the parental strains, its segregation pattern is informative for linkage analysis in both types of F2 individuals, and is useful for connecting the two linkage groups (Figure 2A; markers C and I). I found several markers of this type (Table 2). Interestingly, some of these markers seemed to be clustered, suggesting that these chromosome regions of the parental strains remained heterozygous (Table 2). It may be a clue to the presence of recessive lethals.
The correspondence of molecular linkage groups to the conventional linkage groups:
For utilization of the genetic resources of the silkworm mutants for molecular analysis, it is desirable to map conventional mutations on the molecular linkage maps newly developed in this analysis. As a first step, I tried to find the correspondence of some of these molecular linkage groups with the conventional counterparts.
As described above, I could already find such relationships for ELG 1, 2, 19, and 22 (Figure 4). In addition, matings of C108 with two recessive mutant strains, NISES 912 (pe-re, ch) and 920 (lem, oc), were performed. pe(pink eye)-re(red eye) and oc (C translucent) loci belong to ELG 5, lem (lemon) to ELG 3, and ch (chocolate) to ELG 13, respectively (![]()
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| DISCUSSION |
|---|
RAPD analysis is superior to other methods for linkage analysis in many respects. It requires a small amount of DNA and no special apparatus, expensive reagents, or complicated procedures. Therefore, it is suitable for large-scale analysis at low cost. Because it does not depend on knowing any specific sequences, such as SSR, restriction sites, repetitive elements, or expressed sequences, there are no major limitations for improving map resolution.
In spite of these advantages, RAPD analysis has been treated as an uncertain method for mapping because of its so-called lower reproducibility. I improved reproducibility by screening a great number of primer pairs rather than single primers. It seems unusual that single primers are specifically utilized in RAPD analysis whereas double primers are commonly used in PCR for almost all other purposes. Using double primers has a great advantage, especially for constructing a dense map, due to the exponential increase of combinations of primer pairs using a limited number of primers (e.g., ![]()
The two main problems for utilization of double primers will be whether new information is obtained, and whether the banding patterns generated by this method are reproducible. As shown in Figure 1, the banding patterns generated with double primers were often quite different from those of each single primer, and many of them were amplified more consistently compared to using a single primer. For the 719 primer pairs that I used a result of prescreening nearly 8000 pairs, there was no evidence that the use of double primers reduced reproducibility. I concluded that double primer RAPD analysis was a cost-effective tool for large-scale linkage analysis of small organisms. Anyone can easily utilize my map just by purchasing seven kits of commercially available primers.
Estimation of the fraction of the genome covered by the mapped region is difficult because autosomes have two parallel series of linkage groups in these experiments (Figure 4), and the extent of overlap should be confirmed by linking markers. Linkage groups of C108-dominant markers covered 2300.8 cM, whereas those of p50-dominant markers covered 2359.9 cM. However, my mapping strategy overestimated genetic distances when precise behavior of the nonrecombinant chromosome was not identified and untyped F2 progeny (indicated as a dash in Figure 3) were excluded for calculation. Except for Linkage Group O, all autosomes retained this ambiguity (Figure 3). The sizes of Linkage Group O were 73.4 cM for C108-dominant markers and 116.4 cM for p50-dominant markers. If the calculation is performed just as for other groups, namely ignoring information obtained from R121124A, these sizes are 93.4 cM and 133.9 cM, respectively. In this case, the extent of overestimate varied from 15.0 to 27.2%. Using this value, the actual sizes of linkage groups were estimated as 1841.22020.5 cM for C108-dominant markers and 1894.22075.8 cM for p50-dominant markers. The mean intervals between markers were 3.543.89 cM for C108-dominant and 3.674.02 cM for p50-dominant markers. This resolution is sufficient for fine dissection of quantitative trait loci (QTL) or complex traits governed by multiple genes.
Considering potentially overlapping regions of the two series of linkage groups, the complete recombination length of B. mori was estimated to be ~2000 cM. Linkage maps previously reported cover 413 cM based on RFLPs (![]()
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Integration of linkage groups of C108- and p50-dominant markers is one of the remaining problems. It is critical to establish cost- and labor-saving methods to map codominant markers that connect both groups. PCR-based methods, such as SSCP (![]()
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The map reported here is the first molecular linkage map of insects having a large number of chromosomes (n = 28) with a one-to-one correspondence between linkage groups and chromosomes. The mapping strategy used in this experiment can be easily applied to other organisms having achiasmatic meioses found in heterozygous wild populations. The overall average distance of my map approaches nearly 2 cM/marker to date, and there are no fundamental limitations to improving it. We are now constructing a bacterial artificial chromosome (BAC; ![]()
| ACKNOWLEDGMENTS |
|---|
I particularly thank Dr. M. R. Goldsmith for critical discussion of the manuscript. I am also grateful to Dr. T. Shimada for kindly providing silkworm strains, Dr. T. Tamura, Dr. T. Kanda, Ms. Y. Takasu, and Mr. N. Komoto for useful suggestions and support, and Mr. N. Yonemura for setting up MAPMAKER. This work was partly supported by Enhancement of Center of Excellence, Special Coordination Funds for Promoting Science and Technology, The Science and Technology Agency, Japan.
Manuscript received May 4, 1998; Accepted for publication August 27, 1998.
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