A Detailed Linkage Map of Medaka, Oryzias latipes: Comparative Genomics and Genome Evolution

Corresponding author: Kiyoshi Naruse, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku 7-3-1, Tokyo 113-0033, Japan., naruse{at}biol.s.u-tokyo.ac.jp (E-mail)

Communicating editor: N. TAKAHATA

	ABSTRACT

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

We mapped 633 markers (488 AFLPs, 28 RAPDs, 34 IRSs, 75 ESTs, 4 STSs, and 4 phenotypic markers) for the Medaka Oryzias latipes, a teleost fish of the order Beloniformes. Linkage was determined using a reference typing DNA panel from 39 cell lines derived from backcross progeny. This panel provided unlimited DNA for the accumulation of mapping data. The total map length of Medaka was 1354.5 cM and 24 linkage groups were detected, corresponding to the haploid chromosome number of the organism. Thirteen to 49 markers for each linkage group were obtained. Conserved synteny between Medaka and zebrafish was observed for 2 independent linkage groups. Unlike zebrafish, however, the Medaka linkage map showed obvious restriction of recombination on the linkage group containing the male-determining region (Y) locus compared to the autosomal chromosomes.

GENETIC linkage maps using markers, such as phenotypic traits and expressed sequence tagged sites (ESTs), and anonymous DNA markers, such as random amplification of polymorphic DNA markers (RAPDs), amplified fragment length polymorphic markers (AFLPs), and microsatellites, are very effective tools for analyzing complex biological phenomena. Genetic maps with hundreds and thousands of mapped loci have been reported for various organisms (POSTLETHWAIT et al. 1994 , POSTLETHWAIT et al. 1998 ; WADA et al. 1995 ; DIB et al. 1997 ; DIETRICH et al. 1997 ; KNAPIK et al. 1998 ; YOUNG et al. 1998 ). These maps have been used for various kinds of biological analyses, such as position-based cloning (DIETRICH et al. 1997 ), quantitative trait locus analysis (LANDER and BOTSTEIN 1989 ), comparative vertebrate genomics (AMORES et al. 1998 ; POSTLETHWAIT et al. 1998 ), and detection of radiation-induced DNA mutations (SHIMADA and SHIMA 1997 ).

Medaka is a small freshwater fish native to Japan, Korea, and China (YAMAMOTO 1975 ; NARUSE et al. 1994 ). This fish has been used widely as an experimental animal because of its relatively short life cycle, high fecundity, transparent egg chorion, small size, and availability of several inbred lines (NARUSE et al. 1994 ). Medaka, zebrafish, Xiphophorus fish, and rainbow trout are members of the orders Beloniformes, Cypriniformes, Cyprinodontiformes, and Salmoniformes, respectively, distributed in relatively different taxonomic positions in teleost phylogeny (NELSON 1994 ; NARUSE 1996 ). Comparative genomics of these fish together with progression in the mammalian genome project should facilitate studies of the evolution of genome structure and function in vertebrates.

A Medaka linkage map was first described by AIDA 1921 . He demonstrated that the male-determining factor (Y) was linked with the gene that controls carotinoid deposition in xanthophores (R). Since Aida's study, over 60 visible mutants have been isolated and analyzed for linkage (TOMITA 1975 , TOMITA 1982 ), and a multipoint linkage map including 170 loci and 28 linkage groups has been established using RAPD fingerprints and allozyme analysis (WADA et al. 1995 ). As the Medaka haploid chromosome number is 24, this map has 4 excess linkage groups, indicating that at least four gaps remain to be filled in the map. The purpose of this study is to fill these gaps and to map expressed genes to compare the arrangement of orthologous genes among different species.

	MATERIALS AND METHODS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Strains and genetic crosses:
The AA2 (SHIMADA and SHIMA 1997 ) and HNI (HYODO-TAGUCHI and SAKAIZUMI 1993 ) strains are inbred strains established from Southern and Northern Medaka populations, respectively (SAKAIZUMI 1986 ). In the phenotypic trait loci, the genotypes of AA2 strain are b/b, lf/lf, and gu/gu and those of HNI strain are wild types. These two populations are genetically divergent and polymorphisms between them are identified easily (NARUSE et al. 1994 ; MATSUDA et al. 1997A , MATSUDA et al. 1997B ). The sequence average divergence between AA2 and HNI strains was ~0.8% in the coding regions and 2.6% in the intron regions. The insertions or deletions of nucleotides were also observed in the intron regions. By crossing AA2 female and (AA2 female x HNI male) F₁ male, 39 backcross progeny were obtained for genotyping.

Establishment of cell lines for a reference mapping panel:
A caudal fin was taken from each of the backcross progeny to establish the cell lines. The fins were sterilized with Dakin's solution, washed twice with PBS, and put into L-15 medium supplemented with 20% FBS at 33° (KOMURA et al. 1988 ). The remainder of each body was fixed in 100% ethanol.

Genomic DNA extraction:
Genomic DNA was extracted from the cultured backcross cell lines and the ethanol fixed bodies by proteinase K digestion followed by phenol-chloroform extraction and isopropanol precipitation.

Markers:
A total of 634 markers, including AFLPs, RAPDs, ESTs, internal repeat sequences (IRSs), sequence tagged sites (STSs), and 4 phenotypic markers, were used to establish the genetic linkage map.

Phenotypic markers:
Four phenotypic markers, Y (male-determining gene), b (colorless melanophore), lf (leucophore free), and gu (guanineless), were used. Recessive mutant phenotypes for the b, gu, or lf loci have been described by TOMITA 1982 and WADA et al. 1998 . At 2–3 months of age, the adult fish were sexed based on gonadal morphology and sexual dimorphism of the dorsal and anal fin sharp.

AFLP marker:
AFLP marker analysis (VOS et al. 1995 ) was performed using the AFLP analysis kit (GIBCO-BRL, Gaithersburg, MD) following the manufacturer's instructions. The AFLP markers were named using the enzymes and selective primer sets used and the product size. For example, EM8-1 was the largest AFLP band obtained using EcoRI and MseI and E-ACC and M-CTT selective primers. The AFLP markers identified after the initial survey of AFLPs were given an additional alphabetical identifier, such as EM8-d. The nomenclature for each locus using the combination of selective primers is shown in Table 1.

EST and STS markers:
To assign the loci encoding expressed genes to each linkage group, we used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Primers were designed on the basis of cDNA sequences previously described by others or sequences determined by us. PCR amplification of the genomic counterpart of the cDNA was carried out using LA-Taq DNA polymerase (Takara, Kyoto, Japan), using genomic DNA from the AA2, HNI, and F₁ strains as template. Amplifications were carried out in a PCR thermal cycler MP (Takara model TP-3000) as follows: denaturation at 95° for 5 min, followed by 30 amplification cycles of 98° for 20 sec, 55° for 40 sec, and 72° for 2 min, and a final extension of 72° for 5 min. When multiple bands were observed after amplification, the annealing temperature was increased to 60° or 65°. The amplified fragments were sequenced and analyzed for restriction sites, insertions/deletions, and allele-specific polymorphism. The fragments amplified from the genomic DNA of each backcross progeny were digested with the appropriate restriction enzymes, separated on a 12% slab polyacrylamide gel (DAVIS 1964 ) or 3% agarose gel, and stained with ethidium bromide. Table 2 lists the genes mapped in the present study. Most EST and STS markers except the Hox genes were genotyped on a 12% slab polyacrylamide gel. All Hox genes except Hoxa9a were genotyped on a 3% agarose gel. The mappings of the Hoxa4a and Hoxa5a genes and the Hoxc4a and Hoxc5a genes were done using the polymorphism on the intergenic regions between two genes. Thus, the same primer sequences were listed in Table 2. The UAA and UBA genes and Ki-ras gene and NK-1 marker could be amplified with the same primers. Therefore, the same sequences were listed in Table 2. For the amplification of the Bf/C2 gene, the nested PCR using two sets of primers was used. The same PCR conditions were used for the genotyping of the STS markers.

RAPD and IRS markers:
PCR amplification of RAPD markers was essentially the same as previously described (KUBOTA et al. 1995 ; WADA et al. 1995 ). Primers to amplify the intersequence between two short interspersed repetitive elements (NARUSE et al. 1992 ; SHIMODA et al. 1996 ; UCHIYAMA et al. 1996 ) were used for IRS fingerprinting (MCCARTHY et al. 1995 ). Primer sequences for RAPD and IRS fingerprinting are shown in Table 3. The locus designated IRS-AB is a marker obtained by PCR using the IRS-A and B primers. PCR amplification incorporating [³²P]dCTP for IRS fingerprinting was carried out using LA-Taq DNA polymerase (Takara, Kyoto, Japan) and the same conditions were used for EST and STS amplification. The PCR products were electrophoresed in a 5% urea long-range sequencing gel (FMC Bioproducts, Rockland, ME) and were visualized by autoradiography.

Linkage analysis:
Segregation of the markers was analyzed using a reference mapping panel and MAPMAKER Macintosh version 2 (LANDER et al. 1987 ; formatted for Macintosh by Dr. Tingy, Dupont Corp., Wilmington, DE). A minimum LOD score of 3.5 and maximum of 0.35 were used for grouping the markers. Marker orders were modified after visual analysis of the distribution of marker genotypes in the reference mapping panel.

	RESULTS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Medaka linkage map:
Linkage analysis of 634 markers, including 488 AFLPs, 76 ESTs, 28 RAPDs, 34 IRSs, 4 STSs, and 4 phenotypic markers, was used to construct a genetic map with 24 linkage groups corresponding to the haploid number of Medaka chromosomes (Fig 1). One EST marker (mfOR2) was not linked with any other markers under the linkage criteria used in the present study. The cumulative map length was 1354.5 cM. Table 4 shows the cumulative map length and number of loci in each linkage group. The previous map (WADA et al. 1995 ) consists of 170 markers in which 96 loci showed recombination in 20–100 meioses. The present map consists of 633 markers in which 258 loci showed recombination in 39 meioses. In comparison between the present and previous maps, the density of informative loci in the present map is 2.6 times higher than that in the previous map.

View larger version (143K): In this window In a new window Download PPT slide   Figure 1. A genetic linkage map of Medaka Oryzias latipes. Map distance from the top locus is described in terms of centimorgans (Kosambi mapping function) in parentheses. The EST and phenotypic markers are described with boldface characters. Markers in the box showed no recombination in 39 meioses.

Of 76 EST loci, 9 were unidentified expressed genes cloned by differential display to detect mRNA sequence differences between the HNI and AA2 strains. We have described these unidentified expressed genes as dd001 to dd0048. The genes Yc-1 and Yc-2 were identified initially as sex-linked markers (H. WADA, H. MITANI and A. SHIMA, unpublished results).

We renamed each linkage group according to the number of the AFLP, RAPD, and IRS markers for the following reasons. First, because the anonymous DNA markers were expected to be randomly distributed throughout the genome and because the number of markers on each linkage group may reflect the physical size of each chromosome, the order of the linkage groups may reflect the order of chromosome size. Second, 11 linkage groups (II, VIII, X, XIV, XIX, XXIII, XXIV, XXV, XXVI, XXVII, and XXVIII) previously published contained fewer than three loci and the correspondence of LGVII, IX, X, XIII, XXII, XXIV, XXVI, XXVII, and XXVIII to the linkage groups in the current map could not be determined. To reduce the possible confusion of the linkage group names we used arabic numerals instead of the roman numerals for the name of each linkage group. The names of the current linkage groups (LG) refer to the previous linkage groups (WADA et al. 1995 ) as follows: LG1, I; LG2, III; LG3, XII; LG4, V; LG5, VI; LG6, XI; LG8, XVII; LG12, II; LG13, XVIII; LG14, XX; LG15, XXI; LG16, IV; LG18, XIV; LG19, XVI; LG20, VIII; LG21, XV; LG22, XXIII; LG23, XXV; and LG24, XIX. Linkage groups LG7, LG9, LG10, LG11, and LG17 were newly identified linkage groups in the present study.

Linkage relationships:
Ten kinds of gene families were mapped in the present study: actin, caspase, fibroblast growth factor receptor, opsin (visual pigment), guanylyl cyclase, msx/msh type homeobox, hox, complement C3 and C4, olfactory receptor, and immunoglobulin super gene families. The members of the actin, caspase, fibroblast growth factor receptor, and guanylyl cyclase gene families were not linked. The red, green, and blue visual pigment genes were mapped to LG5. The violet and rhodopsin genes were located on LG23 and LG7, respectively. The Bf/C2, Msx/msh related gene (Msx4), hsc70, mfOR3, mfOR4, and Fgfr4 loci mapped to LG14. Linkage was detected between the major histocompatibility (MHC) class I A genes (UAA and UBA), LMP2, LMP7, Tap2, HoxA cluster, and the Ef-1A genes (LG11). The third MHC class I A gene, UCA, mapped to LG22. Twenty-two Hox genes mapped to seven different linkage groups (LG7, LG8, LG111, LG15, LG16, LG19, and LG21).

Linkage group 1 had a total map length of 44.2 cM, and 49 mapped loci. The male-determining factor, Y, was mapped to LG1, and, as previously reported, a phenotypic trait marker, lf locus (WADA et al. 1995 , WADA et al. 1998 ), was mapped to LG1 in the present study. The R locus has been reported to be linked with the Y locus (AIDA 1921 ). In addition to these loci, we have placed six EST markers, the caspase 3B gene, two C3 genes (KURODA et al. 2000 ), and three unidentified expressed genes (Yc-1, Yc-2, and dd048) on LG1. These loci were located on the X and Y chromosomes and genetic recombination was observed among the markers on LG1.

	DISCUSSION

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Establishment of cell lines for a reference mapping panel:
The accumulation of mapping data using the same mapping panel is very important for eliminating linkage relationship ambiguities among markers. Because the body of Medaka is small, the amount of DNA from each individual could be a limiting factor for data accumulation. To overcome this, we established 39 permanently growing cell lines from backcross progeny obtained by crossing AA2 female with (AA2 x HNI) F₁ male. Thus, DNA from these cell lines could be used, even for techniques such as RFLP analysis by Southern blotting, without exhausting the reserve of genomic DNA. Possible genetic alternations during cell subculture could be checked using DNA extracted from the remaining bodies or another typing panel. In our case, the data obtained from the cell lines were consistent with the typing data from another panel (KURODA et al. 1996 ; NAMIKAWA-YAMADA et al. 1997 ; data not shown).

Medaka linkage map:
The total map length in the present study was 1354.5 cM, while the previous map had a total length of 2480 cM (WADA et al. 1995 ). This difference may be due to an overestimation of interlocus map distance in the previous map resulting from distance calculation errors caused by the use of two typing panels. For example, four gaps of >20 cM and one linkage group consisting of only three loci and spanning 24 cM were present in the previous map (WADA et al. 1995 ). In the present study, we used only one mapping panel to minimize data calculation errors.

In this study, only 1 (mfOR2; SUN et al. 1999 ) of the 80 EST and STS markers was not linked to any other marker, indicating the present linkage map provides reasonably good coverage of the Medaka genome. The number of linkage groups was 24, the same number as Medaka's haploid chromosome number. Correspondence between the linkage group and the chromosome can be clarified by the identification of a marker near the centromere, because each chromosome has only one centromere. We are now trying to identify centromeric markers using gene-centromere mapping by diploid gynogenesis (NARUSE et al. 1988 ; NARUSE and SHIMA 1989 ; JOHNSON et al. 1996 ). To date we have found centromeric markers for LG1, LG8, LG12, LG14, and LG23 (data not shown). These 5 linkage groups correspond to five different chromosomes.

MHC gene organization:
Two MHC class I A genes (UAA and UBA) were linked to each other and were assigned to the same linkage group (LG11) as the LMP2, LMP7 (NAMIKAWA-YAMADA et al. 1997 ), and Tap2 genes. The MHC class II B (DAB) locus was mapped to LG18 and the B2m gene was mapped to LG23. No linkage was observed among the MHC class I A, MHC class II B, complement Bf/C2, C3, and C4 genes. These results indicate that the Medaka counterparts of the mammalian MHC genes are dispersed throughout the Medaka genome, except for the cluster of the MHC class I A gene and the genes involved in class I antigen presentation. A similar result has been reported in zebrafish (BINGULAC-POPOVIC et al. 1997 ) and rainbow trout (HANSEN et al. 1999 ), suggesting that a common euteleostei ancestor may have had a dispersed MHC organization. Whether the dispersed MHC is ancestral to, or derived from, the mammalian-type centralized MHC has yet to be determined; however, the genes involved in class I antigen presentation appear to constitute the core of the MHC.

Hox gene organization:
Mammals have ~40 Hox genes organized into four clusters on different chromosomes (SCOTT 1992 ). Although the pufferfish has four Hox clusters (APARICIO et al. 1997 ), recent studies of the Hox cluster organization of zebrafish, Danio rerio, show that the zebrafish has at least seven Hox clusters, suggesting a Hox cluster duplication in an ancestor of the zebrafish lineage (AMORES et al. 1998 ). In the present study, 22 Hox genes were mapped to seven different linkage groups in Medaka. This indicates that Medaka has at least seven Hox clusters and suggests that this fish may also have additional duplications of the Hox clusters. Medaka, pufferfish, and zebrafish are members of Beloniformes in Acanthopterigii, Tetranodon in Acanthopterigii, and Cypriniformes in Ostariophysi, respectively (NELSON 1994 ). Medaka and zebrafish are distributed in largely different taxonomic positions in teleost phylogeny (NELSON 1994 ; NARUSE 1996 ). The additional duplications of Hox clusters seem to have happened at least before the divergence of Medaka and zebrafish, suggesting the ancestor of these species is probably a common ancestor of all teleosts. If this is the case, almost all teleosts should have the extra "fish" Hox clusters, and the lineage-specific loss of Hox genes or clusters, as observed in pufferfish, might explain the remarkable variation in teleost morphology.

Conservation of synteny:
The Bf/C2, Msx4, and Fgfr4 genes were linked in both Medaka and zebrafish, although the gene order was different: Fgfr4-Bf/C2-Msx4 in Medaka and Bf/C2-Fgfr4-Msxd in zebrafish (POSTLETHWAIT et al. 1998 ). These results suggest a rearrangement in gene order between the two fish. The synteny among MHC class I A genes, LMP2, LMP7, Tap2, and the HoxA cluster loci was conserved between Medaka (LG11) and zebrafish (LG19; BINGULAC-POPOVIC et al. 1997 ; POSTLETHWAIT et al. 1998 ). The Ef-1a locus was located on LG11 in Medaka. In mammals, the MHC class I A genes, LMP2, LMP7, HoxA cluster, and Ef-1a loci, were mapped to the same chromosome (http://www4.ncbi.nlm.nih.gov/Omim/). Thus, conserved synteny was found between the mammals, zebrafish (AMORES et al. 1998 ; POSTLETHWAIT et al. 1998 ), and Medaka. Further accumulation of mapping information for orthologous genes of Medaka and other fish would promote an understanding of genome evolution in vertebrates.

Sex chromosomes and sex-linked genes:
Although the Medaka sex chromosome was cytologically identified as one of the largest chromosomes by fluorescent in situ hybridization (FISH) analysis, no difference in morphology between the X and Y chromosomes was observed (MATSUDA et al. 1998 ). If the size of the chromosome and recombination frequency represent the physical size of the DNA in the chromosome, the largest number of markers should be detected on LG1. Although LG1 has the largest number of markers (49), map length was 44.2 cM, which corresponds to only ~20 markers (633 x 44.2/1354.5; see Table 4). On LG1, two large clusterings of markers were observed, one with 19 markers and another with 13 markers. Map distance between these two regions was 2.6 cM, which corresponds to only a single crossover event in the 39 fish. Such large clusters of loci were not observed in zebrafish chromosomes, strongly suggesting a restriction of recombination on Medaka's sex chromosomes compared to its autosomes, although no morphological differences between X and Y chromosomes were observed.

The map presented in this study is the most detailed linkage map of Medaka currently available and has the marker density equivalent of a skeletal level map. Using the reference typing panel established in the present study, we can easily map newly identified genes and DNA markers linked with phenotypic traits of interest, without misassignment of genes or ambiguities in gene order.

	ACKNOWLEDGMENTS

We thank Drs. H. Hori and Y. Bessho at Nagoya University for sequence information of MHC class II B and tyrosinase genes. This work was supported by the Research for the Future Program (JSPS-RFTF96L00401) from the Japanese Society for the Promotion of Science to A.S. and grants from the Ministry of Education, Science, Sports and Culture, Japan to K.N. and H.M.

Manuscript received August 14, 1999; Accepted for publication November 29, 1999.

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