Rapid and precise genotyping of porcine microsatellites

Yue, Gen Hua; Beeckmann, Petra; Bartenschlager, H.; Moser, G.; Geldermann, H.

doi:10.1002/(sici)1522-2683(19991101)20:17<3358::aid-elps3358>3.0.co;2-b

Cited by 26 publications

(23 citation statements)

References 17 publications

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“…Three of the six-plexes produced anomalous bands (bands that were not produced when the SSR markers were amplified by one-plex PCR). Multiplexed SSR primers occasionally amplify extra bands analogous to random amplified fragment length polymorphisms (RAPDs) (Williams et al 1992;Mitchell et al 1997;Ponce et al 1999;Yue et al 1999). The anomalous bands in the present study were produced by PCR-multiplex Set 4 (112 bp), 9 (134 bp) and 13 (103, 115 and 129 bp) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Gethi et al (2002) assembled a genome-wide collection of 44 SSR marker loci into 17 two-to five-plexes for multiplex PCR genotyping in maize. Numerous PCR-multiplexes have been described for genotyping SSR marker loci in humans and animals (Chamberlain et al 1988;Williams et al 1992;Mutirangura et al 1993;Shuber et al 1993;Henegariu et al 1994Henegariu et al , 1997Fritz et al 1996;Heyen et al 1997;ChavarriagaAguirre et al 1998;Luikart et al 1999;Neff et al 1999;Yue et al 1999;Ruitberg et al 2001;Krenke et al 2002;Master et al 2002;Wallin et al 2002; http:// www.cstl.nist.gov/biotech/strbase/multiplx.htm). The development of genome-wide PCR-multiplexes for crop plants other than maize (Gethi et al 2002) and sunflower (Table 2) are surely forthcoming and only limited by time and resources.…”

Section: Discussionmentioning

confidence: 99%

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PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower

2003

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Simple sequence repeat (SSR) and other DNA sequence-tagged site markers can be genotyped more rapidly and cost efficiently by simultaneously amplifying multiple loci (multiplex PCR). The development of PCR-multiplexes for a nearly genome-wide framework of 78 SSR marker loci in cultivated sunflower ( Helianthus annuus L.) is described herein. The most outstanding single-locus SSR markers in the public collection (300 out of 1,089) were identified and screened for polymorphisms among 24 elite inbred lines, preparatory to selecting SSR markers for testing in multiplex PCRs. The selected SSR markers produced robust PCR products, amplified a single locus each, were polymorphic among elite inbred lines (minimum, mean and maximum heterozygosities were 0.08, 0.53 and 0.85, respectively), and supply a dense genome-wide framework of predominantly or completely codominant, single-locus DNA markers for molecular breeding and genomics research in sunflower. Thirteen six-locus multiplex PCRs were developed for 78 SSR marker loci strategically positioned throughout the sunflower genome (three to five per linkage group) by identifying compatible SSR primer combinations and optimizing multiplex PCR protocols. The multiplexed SSR markers, when coupled with 17 complementary SSR marker loci, create a 'standard genotyping' set ideal for first-pass scans of the genome, as are often needed when screening bulked-segregant DNA samples or mapping phenotypic trait loci. The minimum, mean and maximum heterozygosities of the multiplexed SSR markers were 0.38, 0.62 and 0.83, respectively. The PCR-multiplexes increase genotyping throughput, reduce reagent costs, and are ideal for repetitive genotyping applications where common sets of SSR marker loci are required or advantageous.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower

2003

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“…These methods are actually not suitable for large‐scale parentage assignment for routine selection. Hence, more cost‐effective and time‐saving multiplex‐PCR genotyping systems (Yue, Beeckmann, Bartenschlager, Moser & Geldermann 1999) should be developed. Ideally, all (8–10) markers should be amplified in one PCR reaction and then genotyped.…”

Section: Discussionmentioning

confidence: 99%

Estimating reproductive success of brooders and heritability of growth traits in Asian sea bass (Lates calcarifer) using microsatellites

Wang

Zhu

et al. 2008

Aquaculture Research

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Asian sea bass (Lates calcarifer) is one of the most important marine food ¢sh species in Asia and Australia. To estimate the reproductive success of broodstock and heritabilities of growth-related traits, two independent full-factorial crosses (PI and PII) were created by crossing 10 males and 10 females. At 90 days post hatch (dph), the body weight (BW) and total length (TL) of 804 individuals from PI and 900 individuals from PII were measured and tissues samples of each ¢sh were collected. Parents and o¡spring were genotyped with nine polymorphic microsatellites. Out of 1704 o¡spring from the two crosses, 98.7% were assigned to their parents. In PI, 19 of 20 parents produced o¡spring, while in PII, only ¢ve parents contributed to o¡spring. Low contribution of parents to o¡spring could lead to reduced genetic variation in the next generation. Heritabilities for growth-related traits were estimated using the pedigrees reconstructed using microsatellite genotypes. The estimates of heritability were 0.22 AE 0.16 and 0.25 AE 0.18 for BW, 0.31 AE 0.14 and 0.24 AE 0.21 for TL and 0.22 AE 0.22 and 0.15 AE 0.09 for Fulton's condition factor in the two crosses respectively. Body weights at 90 dph and at harvest (289 dph) were sig-ni¢cantly correlated (r 5 0.601, Po0.01). Therefore, growth-related traits could be improved by exploiting additive genetic e¡ects through selective breeding, and broodstock candidates could be selected early in the production cycle. BW, body weight; TL, total length; K, Fulton's condition factor. ÃÃ Signi¢cance at P 5 0.01.Reproduction and heritability of growth traits in Lates calcarifer C M Wang et al.

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“…Genotyping of microsatellites was carried out using either an automated A.L.F. DNA sequencer (Pharmacia) or an ABI 377 DNA sequencer as described previously (Yue et al, 1999;Yue et al, 2000). Genotype data of the German Landrace were obtained from an earlier study (Laval et al, 2000) and used for comparison.…”

Section: Methodsmentioning

confidence: 99%

Molecular genetic analysis of the Chinese Erhualian pig breed

Yue¹,

Gl²

2004

SA J. An. Sci.

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The Chinese Erhualian is one of the most prolific pig breeds in the world, but it is in danger of being replaced by other exotic pig breeds because of its slow growth rate and high fat content in the body. To obtain some genetic information for conservation, we analysed the Erhualian pigs by using a PCR-RFLP for the calcium-release-channel (CRC) gene, nine polymorphic microsatellites and the complete mtDNA D-loop sequences, and compared these data with those from other pig breeds from Europe and Asian. The PCR-RFLP analysis of the CRC gene showed that the frequency of the C allele associated with stress resistance was 100% in the Erhualian pigs. Neighbour-Joining trees constructed on the basis of mtDNA D-loop sequences and the microsatellite analysis clearly showed that the Erhualian pigs were located in a separate branch. These data suggest that the Erhualian pigs are different from other breeds. Microsatellite analysis showed that the average allele number (5.3/locus) in the Erhualian pig was intermediate as compared with that (4.8-7.0/locus) in the three European pig breeds. The expected heterozygosity was higher in the Erhualian pig (0.78) than that in these European pig breeds (0.59-0.72), whereas the observed heterozygosity was higher in the European breeds (0.51-0.64) than in the Erhualian pig (0.46). In the Erhualian pig, the fixation index (F IS ) was as high as 0.41. These data suggest a high level of inbreeding and/or subpopulation in the Erhualian pigs. For conservation of the germplasm in the Erhualian pigs, it is necessary to take measures to reduce inbreeding and/or subpopulation.

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Rapid and precise genotyping of porcine microsatellites

Cited by 26 publications

References 17 publications

PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower

PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower

Estimating reproductive success of brooders and heritability of growth traits in Asian sea bass (Lates calcarifer) using microsatellites

Molecular genetic analysis of the Chinese Erhualian pig breed

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