A Genetic and Cytogenetic Map for the Duck (Anas platyrhynchos)

doi:10.1534/genetics.105.053256

Journal List > Genetics > v.173(1); May 2006

Genetics. 2006 May; 173(1): 287–296.

doi: 10.1534/genetics.105.053256.

PMCID: PMC1461431

A Genetic and Cytogenetic Map for the Duck (Anas platyrhynchos)

Yinhua Huang,^* Yonghui Zhao,^* Chris S. Haley,^† Shengqiang Hu,^‡ Jinping Hao,^‡ Changxin Wu,^§ and Ning Li^*¹

^*State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, People's Republic of China, ^†Roslin Institute, Roslin, Midlotthian EH25 9PS, United Kingdom, ^‡Gold Star Duck Production, Beijing 100076, People's Republic of China and ^§College of Animal Science and Technology, China Agricultural University, Beijing 100094, People's Republic of China

¹Corresponding author: State Key Laboratory for Agrobiotechnology, China Agricultural University, Yuanmingyuan, West Rd. 2, Haidian District, Beijing 100094, People's Republic of China. E-mail: ninglbau/at/public3.bta.net.cn

Communicating editor: G. Gibson

Received November 8, 2005; Accepted February 24, 2006.

Abstract

A genetic linkage map for the duck (Anas platyrhynchos) was developed within a cross between two extreme Peking duck lines by linkage analysis of 155 polymorphic microsatellite markers, including 84 novel markers reported in this study. A total of 115 microsatellite markers were placed into 19 linkage groups. The sex-averaged map spans 1353.3 cM, with an average interval distance of 15.04 cM. The male map covers 1415 cM, whereas the female map covers only 1387.6 cM. All of the flanking sequences of the 155 polymorphic loci—44 monomorphic loci and a further 41 reported microsatellite loci for duck—were blasted against the chicken genomic sequence, and corresponding orthologs were found for 49. To integrate the genetic and cytogenetic map of the duck genome, 28 BAC clones were screened from a chicken BAC library using the specific PCR primers and localized to duck chromosomes by FISH, respectively. Of 28 BAC clones, 24 were detected definitely on duck chromosomes. Thus, 11 of 19 linkage groups were localized to 10 duck chromosomes. This genetic and cytogenetic map will be helpful for the mapping QTL in duck for breeding applications and for conducting genomic comparisons between chicken and duck.

MOLECULAR genetic maps will provide insight into the genome organization and chromosomal localization of cloned genes and also a framework for the identification and localization of major genes associated with economically important traits (Crittenden et al. 1993). The rapid progress being made in the development of genetic maps for humans and mice has led to a recent boom in the construction of genome maps for many farm animals. High-density linkage maps are now available for many species, such as pigs, cattle, sheep, and goats. In contrast, mapping studies in avian species are much less advanced except in the chicken. To construct saturated genetic maps for more bird species, the isolation of many polymorphic genetic markers, particularly microsatellite markers, is a prerequisite. Although many chicken markers were available, it was difficult to screen the microsatellite marker for the duck by cross-species amplification from this species because of the poor conservation of the microsatellite sequences between the species (Huang et al. 2005).

Microsatellites or simple sequence repeats are tandem repeated motifs of 1–6 bases found in all prokaryotic and eukaryotic genomes and present in both coding and noncoding regions. Despite the fact that the mechanism of evolution is still unclear, microsatellites are being widely employed in forensics, genetic mapping, population genetics, evolutionary studies, and investigation of social systems (Chakraborty et al. 1997; Buchholz et al. 1998; Chowdhury and Bansal 2001; Jernej and Branka 2001; Burt et al. 2003; Harry et al. 2003; Huang et al. 2004; Knutson et al. 2004).

The Peking duck, the most common type of duck breed for meat, was exported to the United States and Britain from China in the early part of the last century. Many ducks raised for their meat have originated from this breed. Ducks, belonging to the order Anseriformes, diverged from the chicken (Galliformes) ~110 million years ago (Tuinen and Hadly 2004). According to paleontological data, the main radiation of the modern duck took place during the Miocene, 5–23 million years ago (Olson 1985). Ducks, together with the ostrich, emu, peacock, turkey, quail, and other birds, play a major role in studies of bird evolution. Up to now, most available molecular data concerning ducks have come from evolutionary studies based on the analysis of mitochondrial DNA sequence (Cooper et al. 1996; Liu et al. 1996; Sraml et al. 1996; Johnson and Sorenson 1998, 1999; Donne-Gousse et al. 2002). However, information about genetic markers in the duck is limited (Buchholz et al. 1998; Maak et al. 2000, 2003; Paulus and Tiedemann 2003; Stai and Hughes 2003; Huang et al. 2005). In addition, comparative mapping between the duck and chicken genome gains importance as the Chicken Genome Project moves toward functional genomics, i.e., the functional characterization of large regions of sequenced DNA. A good comparative genetic map based on the orthologous microsatellite markers will provide the substrates for major gene identification (Reed et al. 2005a,b). Up to now, most available comparative data between ducks and chickens have come from the analysis of chromosome painting (Guttenbach et al. 2003). Herein, the preliminary genetic map was developed in an inbred Peking duck resource population (line VI cross with line V) on the basis of linkage analysis of 103 novel genetic markers from the microsatellite-enriched library (Huang et al. 2005), together with 137 reported microsatellite loci (Cathey et al. 1996; Fields and Scribner 1997; Buchholz et al. 1998; Maak et al. 2000; Genet et al. 2003; Stai and Hughes 2003; Huang et al. 2005). In addition, the preliminary genetic map was integrated with the cytogenetic map based on fluorescence in situ hybridization (FISH) using 28 chicken heterologous BAC clones.

MATERIALS AND METHODS

Resource population:

In collaboration with Gold Star Duck Production (Beijing), an experimental population with a total of 224 G₂ individuals was created containing 12 full-sib families of a cross between two extreme Peking duck lines (line LVI and LV). Four male individuals of generation 1 were the offspring of LVI, and 12 female individuals of generation 1 were the offspring of LV. A routine phenol/chloroform extraction method was used to extract and purify the duck genomic DNA. The DNA was quantified using agarose gel electrophoresis. The DNA concentration was estimated by comparison with molecular standard markers.

Sequencing of clones and designing of primers:

A library enriched for (CA)_n, (CAG)_n, (GCC)_n, and (TTTC)_n was constructed from a female Peking duck (Huang et al. 2005). Plasmids, extracted from clones of the microsatellite-enriched library, were sequenced with the BigDye kit on PRISM 377 DNA sequencers (ABI, Columbia, MD). Oligo6.0 was used to design PCR products ranging from 100 to 400 bp. One primer in each pair was labeled with either 6-FAM or HEX fluorescent dye (AuGCT Biotechnology, Beijing, People's Republic of China).

Optimization of mutiplex PCR and muti-run:

The annealing temperature of the microsatellite primers was determined using an authorized Thermal Cycler (Eppendorf, Hamburg, Germany). DNA amplification was performed in a total volume of 10 μl, with 40 ng duck DNA, 50 mm KCl, 1.5 mm MgCl2, 10 mm Tris, HCl (pH 8.3), 1 mm tetramethylammonium chloride, 0.1% Triton X-100, 0.01% gelatin, 200 mm dNTP, 0.2–2 pmol of each primer, and 2.5 units Taq polymerase. The PCR reaction conditions were denaturing for 5 min at 94°, followed by 94° for 40 sec, 58° ± 10° for 30 sec or 1 min, and 72° for 30 sec or 1 min, with a final 30-min elongation step at 72°. PCR primer pairs with similar annealing temperatures and different amplification product sizes were combined in mutiplex PCR reactions. Primer pairs unsuitable for mutiplex PCR were used in independent reactions; however, the products could be run in the same lane (muti-run) of the gel if their sizes were sufficiently different (>60 bp).

Linkage analysis:

Mutiplex PCR products or independent PCR products were diluted by 10–70 times. A mixture of 1 μl diluted PCR product, 12 μl deoinized formadide (Amresco), and 0.2 μl Genescan-350 ROX or Genescan-500 ROX (ABI) internal standard was run on a 3100 pop-4 (ABI) using a 3100 genetic analyzer (ABI). The fragment sizes of PCR products were analyzed using the Genescan 3.7 and Genemapper 1.1 software (ABI). Although the genotypes were performed automatically by Genemapper 1.1 software after the panel and bin were defined, all individual genotypes were checked manually twice (each time before and after export to Excel). In addition, typing errors detected with the CRIMAP program (using the PREPARE option) were rechecked within Genescan 3.7 and corrected where necessary.

The genotyping data were extracted from Excel worksheets and reformatted into the Gen file for the CRIMAP Version 2.4 linkage analysis program (Green et al. 1990). Initially, a two-point linkage analysis in which polymorphic markers were analyzed against each other (LOD score ≥3.0) was performed. Then markers that distributed into the same linkage group were used to build the map using the CRIMAP-ALL option. Next the order of the framework loci was checked using the CRIMAP–FLIPS function. Finally, the marker distance on a linear map was determined by the CRIMAP–BUILD option.

The linkage maps were drawn using MapChart 2.1 software (Voorrips 2002).

Identifying the orthologous microsatellite DNA of duck in the chicken genome:

The flanking sequences of duck microsatellite DNA were analyzed in a megaBLAST search against the National Center for Biotechnology Information with the default parameters on http://www.ncbi.nlm.nih.gov/genome/seq/ggablast.html. The unique match sequences with an E-value smaller than e-25 from chicken were used as orthologs to the duck microsatellite DNA.

Screening and preparing probes:

The BAC clones used for FISH mapping were screened by 4D, two-step PCR from a HindIII, female white-silk chicken BAC library with inserts from vector pBeloBAC11 using specific PCR primers (http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixII) which were designed from the orthologous sequences of the duck microsatellite in chicken genome (Liu et al. 2003). Screened positive clones were confirmed further by sequencing analysis of PCR products. A routine phenol/chloroform extraction method was used to extract and purify the chicken BAC genomic DNA. The BIONICK labeling system was used to prepare DNA probes combined with biotin-14-dATP (Invitrogen, San Diego).

FISH:

Metaphase chromosomes were prepared from fetal fibroblast cultures of Peking duck by standard cytogenetic techniques. The method of FISH was modified from Coppieters et al. (1994). Briefly, chromosome slides were hardened at 65° for 2 hr, denatured at 70° for 2.5 min in 70% formamide, 2× SSC, and dehydrated in an ethanol series at −20°. Probe, which was labeled with biotin-14-dATP, was coprecipitated with a 50-fold excess of salmon sperm DNA and a 50-fold excess of sonicated chicken genome DNA. The denatured precipitation was dissolved in hybridization solution to a final concentration of 50 ng/μl and prehybridized for 40 min at 37°. Hybridization was performed for 48 hr at 37° in a humid chamber. Probes were detected with FITC-conjugated avidin (Vector, Burlingame, CA) and signals were amplified by biotinlated antiavidin (Vector). Chromosomes were counterstained with 0.5 μg/ml propidium iodide. Images were taken with an epifluorescence microscope equipped with a DP70 CCD camera (Olympus, Tokyo) and dealt with software Video TesT-FISH (Video TesT, St. Petersburg, Russia).

RESULTS

Isolation and characterization of microsatellite loci:

To isolate the specific microsatellite markers for duck, a total of 1025 plasmids, extracted from the microsatellite-enriched library (Huang et al. 2005), were sequenced according to the procedures described in materials and methods; 753 (73.46%) were found to contain (CA)_n, (CAG)_n, (GCC)_n, (TTTC)_n, (TC)_n, (TCC)_n, (TTCC)_n, (TTTTC)_n, (TTGCC)_n, (TTCCTC)_n, (AAC)_n, (AAAC)_n, (TA)_n, or (TTTA)_n microsatellites with five or more repeats, and 5 contained (TCTCTTTC)_n, (TTTCCCTCTTTC)_n, or (CTTCTTTC)_n with six or more repeats. Of the 758 sequences, 539 (71.11%) contained >12 bp of uninterrupted core repeats. Of the 539 clones, 93 were found to contain two microsatellites and 92 were duplicates; 223 (41.37%) did not provide sufficient sequence information in the region flanking the repeat for development of PCR primers, and 224 were used to design for primers. Of the 224 pairs of primers, 103 were suitable for genotyping with the expected size fragments after the modification of annealing temperature or extension time (see http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixI). Polymorphisms of the markers were detected in 31 unrelated G₀ individuals according to the optimized mutiplex PCR. Of the 103 primer pairs, 84 were polymorphic, and for the remaining 19 loci, only one allele was found in the population.

All the 103 novel duck microsatellite sequences were submitted to GenBank (AY493281–AY493347 and AY587022–AY587057). Information for 103 novel microsatellite markers, including GenBank accession number, microsatellite repeat sequence, sequence of the PCR primers, optimal annealing temperature for PCR, length of PCR products, number of alleles, observed heterozygosity, as well as the polymorphism information content, are shown in Appendix I (http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixI).

In addition, 137 duck-specific microsatellite markers, which were reported by Fields and Scribner (1997), Buchholz et al. (1998), Maak et al. (2000, 2003), Genet et al. (2003), Stai and Hughes (2003), Paulus and Tiedemann (2003), and Huang et al. (2005), were amplified from Peking duck genomic DNA and 96 of them yielded specific amplified products after the modification of annealing temperature or extension time (see http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixI). Of these 96 loci, 71 exhibited sequence length polymorphisms, while for the remainder only one allele was observed in the 31 unrelated G₀ individuals.

Thus, a total of 155 polymorphic loci were genotyped in the resource population with 12 full-sib families. A total of 650 alleles were observed for these polymorphic loci, and the number of alleles per locus ranged from 2 to 18 with an average of 4.19. Among the polymorphic markers, the highest heterozygosity (0.97) was observed at CAUD019 and the lowest herterozygosity (0.03) at CAUD064 (http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixI). A total of 63 (40.65%) loci had heterozygosities >0.50. The polymorphism information content (PIC) of 155 loci ranged from 0.03 to 0.90. The percentage of the loci with a PIC >0.50 was 35.48% (55), with a PIC between 0.25 and 0.5, 49.03% (76); and with a PIC <0.25, 15.48% (24). In addition, 149 of 155 polymorphic loci for which the number of informative meioses varied from 9 to 427, the average being 196.33, were useful to linkage analysis. The remaining 6 loci were polymorphic but had no informative meioses in our pedigree and so were not useful for linkage analysis.

Genetic linkage map:

A total of 115 markers were placed into 19 genetic groups, and 34 polymorphic markers were unlinked with any markers by two-point analysis with LOD scores >3.0 using CRIMAP Version 2.4 (Green et al. 1990) (see Figure 1 and Table 1). Thirteen linkage groups composed three or more loci, whereas the remaining 6 groups each contained 2 markers. The sex-averaged map spanned 1353.3 cM. The marker interval of each linkage group ranged from 0 to 62.2 cM. The markers were distributed among 90 distinct positions; thus the average marker interval was 15.04 cM. On this sex-averaged map, 17.78% (16) of the intervals between markers varied from 0 to 5 cM, 25.56% (23) ranged from 5 to 10 cM, 30% (27) varied from 10 to 20 cM, and 26.67% (24) were >20 cM.

Figure 1.

Sex-average map in Kosambi centimorgans for the duck consisting of 19 linkage groups. The markers in boldface type were physically assigned to duck chromosomes by FISH with chicken BAC probe. Two principles were used in naming the linkage groups of duck: (more ...)

TABLE 1

Parameters of the duck genetic and cytogenetic maps

Sex-specific maps have also been constructed. The length of the male map was 1415 cM, with an average intermarker distance of 16.26 cM, whereas the female map was 1387.6 cM, with the average intermarker spacing of 17.13 cM. The male map comprised linkage groups ranging in length from 0 to 347.2 cM, while the female map contained linkage groups with a length ranging 0 to 398.8 cM (see Table 1). The length of the male map is 1.02-fold that of the female map, and that of the sex-averaged map was shorter than both of the sex-specific maps and 0.98 times as long as the female map.

Orthologs of duck microsatellite sequence in the chicken genome:

To search for orthologs, 240 flanking sequences of duck microsatellite DNA were blasted against chicken genomic sequence as described in materials and methods. The corresponding orthologous sequences were found for 49 of the 240 examined (see Table 2). The position in the duck genetic map, the physical position in the chicken genome, the physical position in the duck genome, primer sequences for the screening of chicken BAC clones, as well as repeats of the orthologous sequences are listed in Table 2.

TABLE 2

The position in duck genetic map, physical position in chicken, and core repeat of the orthologous loci

Of the 49 duck microsatellite loci with orthologs in the chicken genome, 27 were placed into 15 genetic groups, 18 were unlinked with any markers, and the rest were not genotyped in the above resource population. Sequencing comparisons showed that the core repeats in the chicken for 25 of the orthologous loci were the same or similar to the corresponding one of the duck, but were different for 7 orthologous loci. Moreover, for the remaining 17 of these duck microsatellite loci the core repeats were absent from the orthologous loci in the chicken.

Integration of genetic and cytogenetic map:

To integrate the genetic and cytogenetic map in the duck genome, 28 BAC clones were screened by 4D, two-step PCR from a chicken BAC library using the specific PCR primers and were localized to duck chromosomes by FISH, respectively. Fluorescent signals were detected on duck chromosomes in 24 clones (see Figure 2; http://www.genetics.org/cgi/content/full/genetics.105.053256/AppendixII). Among them, 3 clones (CB0509A6, CB0041G5, and CB0234B11) were situated on duck chromosome 1, 3 clones (CB0742G10, CB0729A5, and CB0828G1) on chromosome 2, 2 clones (CB0593C11 and CB0385F11) on chromosome 3, 2 clones (CB1342G10 and CB0432E11) on chromosome 4, 2 clones (CB0839F6 and CB0480D5) on chromosome 5, 1 clone (CB0375F10) on chromosome 7, 1 clone (CB0857E5) on chromosome 8, 1 clone (CB0096E9) on chromosome 9, 5 clones (CB0320C6, CB0478A3, CB0664E4, CB0098H2, and CB0228F1) on chromosome 10, and 4 clones (CB0222B3, CB0082E7, CB0247E2, and CB0168F8) on the other small chromosomes. Thus, 9 of 19 linkage groups (CAU1, CAU2, CAU4, CAU5, CAU9, CAU10, CAU11, CAU16, and CAU18) were assigned to 9 pairs of duck chromosomes, respectively. Two unlinked groups (CAU3 and CAU17) were placed on the same duck chromosome 3. Moreover, 1 unlinked marker was mapped on chromosome 1, 1 on chromosome 4, 1 on chromosome 7, 1 on chromosome 8, 2 on chromosome 10, and 1 on one pair of the microchromosome.

Figure 2.

FISH mapping of six orthologous loci to duck chromosomes with chicken BAC probes: (a) CAUD023, (b) CAUD138, (c) CAUD091, (d) CAUD109, (e) AMU6, and (f) CAUD044.

Among the 24 orthologous loci, which were located on duck chromosomes using chicken BAC clones, 3 (2 from CAU1 and 1 unlinked marker) were located on chicken chromosome 1, 3 (all from CAU2) on chicken chromosome 2, 2 (1 from CAU3 and 1 from CAU17) on chicken 3, 2 (1 from CAU4 and 1 from CAU18) on chicken chromosome 4, 2 (all from CAU5) on chicken chromosome 5, 1 (1 unlinked marker) on chicken chromosome 7, 1 (1 unlinked marker) on chicken chromosome 8, 1 (1 from CAU9) on chicken chromosome 9, 5 (3 from CAU10 and 2 unlinked markers) on chicken chromosome 10, 1 (1 from CAU11) on chicken chromosome 11, 1 (1 unlinked marker) on chicken chromosome 12, 1 (1 from CAU16) on chicken chromosome 26, and the other (1 unlinked marker) was not assigned to a chicken chromosome.

DISCUSSION

Evaluation of the mix-enriched library:

The percentage of clones that contained microsatellite sequence (73.46%) in this enriched microsatellite library is similar to that in the ostrich-enriched microsatellite library (Tang et al. 2003) and higher than the percentage observed in the chicken-enriched microsatellite library (Cheng et al. 1995). Some highly enriched libraries (>90%) have been constructed in cichlid fish and plant (Jernej and Branka 2001; Carleton et al. 2002). Two reasons may account for the difference in enrichment level. One is that the procedure used to construct the library is different. The second is that the frequency of microsatellite DNA regions generally increases with increasing genome sizes (Gibbs et al. 1997; Garner 2002). In our enriched library, 41.37% of the clones, which contain microsatellite repeats, are not suitable to develop PCR primers because of the short flanking sequence. This percentage is higher than that observed in chicken and ostrich (Cheng et al. 1995; Tang et al. 2003). As in chicken and ostrich, small imperfect (TG)_n microsatellites scattered in a 100- to 200-bp region and duplicated sequences are also found (Cheng et al. 1995; Tang et al. 2003).

In our modified enrichment procedure, four different probes of the microsatellite motifs were employed for capturing DNA fragments. The majority (83.69%) of the microsatellite sequences isolated in this study contained one or more purposed repeat motifs. The results suggested that (CA)_n, (CAG)_n, (GCC)_n, or (TTTC)_n repeats are randomly distributed in the duck genome. (CA)_n, (CAG)_n, and (TTTC)_n repeats have been found in mammalian and avian species (Cheng et al. 1995; Band and Ron 1996; McConnell et al. 1999). The (GCC)_n repeat, however, which is abundant in the human genome (Kleiderlein et al. 1998; Chowdhury and Bansal 2001), is rare in other animal species. In addition to the above microsatellite motif repeats, other repeats were also found in this duck library. This result suggested that the mix-enriched library would be efficient to isolate microsatellite DNA from species for which the content of repeat cores was unknown.

Estimation of genetic map:

A comprehensive genetic linkage map would speed the process of molecular studies in ducks, ranging from the construction of a comparative genetic map to gene identification of quantitative difference in growth, meat quantity, and disease susceptibility. Here, a primary genetic map for duck composed of 19 linkage groups, including 115 microsatellite markers with the averaged coverage of 1353.3 cM, was developed in a population with 224 G₂ individuals. Although the average marker spacing of the map is only 15.04 cM, 26.67% of this map still has regions where the distance between two adjacent markers is considerably >20 cM. The objectives of future work on the duck genetic map will be to increase the genome coverage and add more markers in those regions.

With the differences in recombination frequencies being detected on the sex chromosomes or in typing errors, there can be large differences between the male and female maps (Rappold 1993; Kondo et al. 2001). We have observed differences in the recombination rates between the sexes (see Table 1), but the differences are smaller than those observed in other species such as humans, pigs, dogs, tiger pufferfish, and zebrafish (Archibald et al. 1995; Dib et al. 1996; Neff et al. 1999; Singer et al. 2002; Kai et al. 2005), and more similar to those observed in chicken and Pacific oyster (Groenen et al. 1998; Hubert and Hedgecock 2004). Although the overall difference in the length of the male map is larger than that of the female map, several of the female linkage groups were larger than their male counterparts.

Conservation of microsatellite DNA sequence between duck and chicken:

To construct comparative genetic maps for model species and less-studied species, the isolation of the orthologous markers, especially microsatellite marker, is a prerequisite. In recent years, several attempts have been made to amplify microsatellite loci specific for some model species, such as chicken, pig, and cattle, from genomic DNA of related species. The success rates of the heterologous amplification with microsatellite primers in closely related species ranged from 16.23 to 62.89% (Moore et al. 1991; Kemp et al. 1995; Fields and Scribner 1997; Baratti et al. 2001; Kayang et al. 2002; Reed et al. 2003; Kim et al. 2004). Studies show that it was difficult to screen microsatellite markers for duck by cross-species amplification from chicken loci (Huang et al. 2005). In this article, the conservation of microsatellite DNA between duck and chicken was estimated by sequence Blast comparisons at 240 loci. Results showed that only 20.42% microsallite loci were conserved in both species. Of the orthologs, 40.82% (20) with a core repeat >15 bp were suitable for designing primers in the above species. The variance in the flanking sequences of the orthologous loci ranged from 75 to 99%. Thus, <8.3% orthologous polymorphic microsatellite loci could be isolated by heterologous amplification between duck and chicken.

Integration of genetic and cytogenetic map by heterologous hybridization:

The full utilization of genetic maps requires knowledge of the correspondence between the genetic and cytogenetic maps. Several methods have been used to correlate genetic and cytogenetic maps (Stephens et al. 2004). FISH provides the most direct way of physically mapping DNA sequences on chromosomes. However, FISH mapping of eukaryotic genomes depends heavily on the development of recombinant DNA BAC libraries. Because of a lack of large insert libraries, FISH mapping in less-developed species has usually been performed using heterologous BAC clones (Bonnet et al. 2001). In this study, 10 duck loci were assigned to duck macrochromosomes, 10 loci to small macrochromosomes, and 4 loci to microchromosomes using chicken BAC clones. Much research has shown strong chromosome homology between macrochromosomes in different bird species (Masabanda et al. 2004). In our research, 19 orthologous loci (CAUD023, CAUD069, AMU182, APH12, CAUD049, CAUD138, CAUD091, CAUD128, CAUD109, AMU6, CAUD111, CAUD022, APH20, CAUD038, AMU52, AMU174, CAUD044, CAUD080, and CAUD123) were assigned to the same macrochromosome or small macrochromosome in duck and chicken, respectively, 1 orthologous locus (CAUD021) was located on duck chromosome 4, but uncertain in the chicken genome. Moreover, 1 orthologous locus (CAUD108) was located on the duck microchromosome, but on chicken chromosome 4. However, the physical mapping of the 3 orthologous loci, which were localized on the microchromosomes in chicken, was uncertain in the duck genome.

Microsatellites are excellent genetic markers because of their high polymorphism and abundant distribution throughout the genome. A microsatellite-based genetic map is an essential tool for linkage mapping of monogenic as well as polygenic traits of interest (Ihara et al. 2004). However, only 137 microsatellite markers specific for waterfowl were previously reported and a genetic map for duck has not been developed (Fields and Scribner 1997; Buchholz et al. 1998; Maak et al. 2000, 2003; Genet et al. 2003; Paulus and Tiedemann 2003; Stai and Hughes 2003; Huang et al. 2005). The goals of this study were construction of a genetic map and the integration of genetic and cytogenetic maps. The resulting genetic and cytogenetic maps will be helpful in mapping QTL in ducks and in conducting genomic comparisons between chicken and duck. In addition, this map and the novel microsatellite loci will be useful for population genetic studies and in pedigree control and breeding applications in managed or commercially bred populations.

Acknowledgments

The authors acknowledge Y. Q. Zhao (State Key Laboratory for Agrobiotechnology, China Agricultural University) for suggesting the sequence comparison. This research was funded by a grant from the State Major Basic Research Development Program of China and Natural Scientific Foundation of China. C.S.H. acknowledges Biotechnology and Biological Sciences Research Council funding.

Notes

Sequence data from this article have been deposited with the GenBank Data Library under accession nos. AY493281–AY493347 and AY587022–AY587057.

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