Segregation and Linkage Analysis of 75 Novel Microsatellite DNA Markers in Pair Crosses of Japanese Abalone (Haliotis discus hannai) Using the 5′-Tailed Primer Method

Sekino, Masashi; Kobayashi, Toshimasa; Hara, Motoaki

doi:10.1007/s10126-005-6179-6

Cited by 25 publications

(17 citation statements)

References 45 publications

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“…Genotype configurations of markers were categorized into three expected segregation types when nullallele segregation was allowed: 1:1:1:1-ratio type ($ 3 #: AB 3 CD or AB 3 AC), 1:1 $ type (AB 3 AA or CC), and 1:1 # type (AA or CC 3 AB). All statistical analyses described below were completed using JoinMap 4.0 (Kyazma B.V., Wageningen, The Netherlands) with the cross-pollinating coding scheme, which handles the data containing various genotype configurations with unknown linkage phases (Sekino et al 2006). Segregation data from expected 1:1:1:1-type markers into 1:1 $-and 1:1 #-type markers were partitioned by creating maternal and paternal data sets using JoinMap 4.0 to perform linkage analysis for each sex ( Jacobs et al 1995;Viruel et al 1995).…”

Section: Methodsmentioning

confidence: 99%

“…INKAGE maps are powerful research tools for mapping quantitative trait loci (QTL) to complement marker-assisted selection in many species, including aquaculture species (Lander and Botstein 1989;Sakamoto et al 2000;Fishman et al 2001;Nichols et al 2003;Hubert and Hedgecock 2004;Moen et al 2004Moen et al , 2008Chistiakov et al 2005;Lee et al 2005;Gharbi et al 2006;Liu et al 2006;Sekino et al 2006;Phillips et al 2007;Sekino and Hara 2007; for a recent review, see Danzmann and Gharbi 2007). However, marker density for all aquacultured species is still low.…”

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confidence: 99%

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Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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“…Microsatellite analysis: The source of microsatellite markers used in this study was as follows: two markers suffixed with Hdd in Sekino and Hara (2001), six markers with Hd in Hara and Sekino (2005), 111 markers with Afa and Awb in Sekino et al (2005Sekino et al ( , 2006, and 15 markers with Ahdh in Sekino and Hara (2007). These markers turned out to be informative in at least one of the three mapping families on the basis of our preliminary marker screening.…”

Section: Methodsmentioning

confidence: 99%

“…In both cases, Cy5-fluorescent dye was conjugated to the 59 end of the primers (Sigma Genosys, Hokkaido, Japan) so that amplified alleles could be detected on an ALFexpress/ALFexpress II DNA sequencer (GE Healthcare Bio-Sciences, Piscataway, NJ). PCR assays were performed as described in Sekino et al (2005) for the dye-primer method and in Sekino et al (2006) for the 59-tailed primer method.…”

Section: Methodsmentioning

confidence: 99%

Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers

Sekino

Hara

2007

Genetics

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This study presents linkage maps for the Pacific abalone (Haliotis discus hannai) based on 180 microsatellite DNA markers. Linkage mapping was performed using three F 1 outbred families, and a composite linkage map for each sex was generated by incorporating map information from the multiple families. A total of 160 markers are placed on the consolidated female map and 167 markers on the male map. The numbers of linkage groups in the composite female and male maps are 19 and 18, respectively; however, by aligning the two maps, 18 linkage groups are formed, which are consistent with the haploid chromosome number of H. discus hannai. The female map spans 888.1 cM (Kosambi) with an average spacing of 6.3 cM; the male map spans 702.4 cM with an average spacing of 4.7 cM. However, we encountered several linkage groups that show a high level of heterogeneity in recombination rate between families even within the same sex, which reduces the precision of the consolidated maps. Nevertheless, we suggest that the composite maps are of significant potential use as a scaffold to further extend the coverage of the H. discus hannai genome with additional markers.

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“…The existence of null alleles is considered the most likely cause of heterozygote deficiencies (Callen et al, 1993). Null alleles, a locus-dependent effect, have been reported in many other mollusks, including Pacific oyster (Hedgecock et al, 2004), Japanese abalone (Sekino et al, 2006), small abalone (Zhan et al, 2009), and bay scallop (Zhan et al, 2007).…”

Section: Discussionmentioning

confidence: 97%

New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations

Kim¹,

An²,

Kang³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Manila clam (Ruditapes philippinarum) is a valuableand intensively exploited shellfish species in Korea. Despite its importance, information on its genetic background is scarce. For the genetic characterization of R. philippinarum, expressed sequence tagderived microsatellite markers were developed using next-generation sequencing. A total of 5879 tandem repeats containing di-to hexanucleotide repeat motifs were obtained from 236,746 reads (mean = 413 bp). Of the 62 loci screened, 24 (38.7%) were successfully amplified, and 10 were polymorphic in 144 individuals from 2 manila clam populations (Incheon and Geoje, Korea). The number of alleles ranged from 2 to 17 in the Incheon population and from 3 to 13 in the Geoje population (overall A R = 7.21). The mean observed and expected heterozygosities were estimated to be 0.402 and 0.555, respectively. Hence, there is less genetic variability in the Geoje population than in the Incheon population, although no significant reductions of genetic diversity were found between the populations (P > 0.05). However, significant genetic differentiation was detected between the populations (F ST = 0.064, P < 0.001). Significant deviations from Hardy-Weinberg equilibrium and high inbreeding coefficients (mean F IS = 0.22-0.26) were detected in both populations. The 10 novel polymorphic microsatellite loci used in this study will be useful for future genetic mapping studies and for characterizing population structures, monitoring genetic diversity for successful aquaculture management, and developing conservation strategies for manila clam populations in Korea.

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Segregation and Linkage Analysis of 75 Novel Microsatellite DNA Markers in Pair Crosses of Japanese Abalone (Haliotis discus hannai) Using the 5′-Tailed Primer Method

Cited by 25 publications

References 45 publications

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers

New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations

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