Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (<i>Meleagris gallopavo</i>)

Chaves, Lee; Knutson, Todd P.; Krueth, Stacy B.; Reed, Kent M.

doi:10.1111/j.1365-2052.2005.01396.x

Cited by 19 publications

(11 citation statements)

References 15 publications

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“…Although separated by approximately 40 million years of evolution (Romanov and Dodgson, 2006), numerous studies have described the highly homologous and syntenic relationship between the turkey and chicken genomes (Reed et al, 2003(Reed et al, , 2005Axelsson et al, 2005;Chaves et al, 2006). Chicken DNA sequences were successfully utilized in the design of primers for amplification of turkey MHC regions indicating further homology between the species, even in the most polymorphic and positively selected region of the genome.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the turkey MHC chromosome through genetic and physical mapping

Chaves

Krueth

Reed

2007

Cytogenet Genome Res

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Previous studies in the chicken have identified a single microchromosome (GGA16) containing the ribosomal DNA (rDNA) and two genetically unlinked MHC regions, MHC-B and MHC-Y. Chicken DNA sequence from these loci was used to develop PCR primers for amplification of homologous fragments from the turkey (Meleagris gallopavo). PCR products were sequenced and overgo probes were designed to screen the CHORI 260 turkey BAC library. BAC clones corresponding to the turkey rDNA, MHC-B and MHC-Y were identified. BAC end and subclone sequencing confirmed identity and homology of the turkey BAC clones to the respective chicken loci. Based on subclone sequences, single-nucleotide polymorphisms (SNPs) segregating within the UMN/NTBF mapping population were identified and genotyped. Analysis of SNP genotypes found the B and Y to be genetically unlinked in the turkey. Silver staining of metaphase chromosomes identified a single pair of microchromosomes with nucleolar organizer regions (NORs). Physical locations of the rDNA and MHC loci were determined by fluorescence in situ hybridization (FISH) of the BAC clones to metaphase chromosomes. FISH clearly positioned the rDNA distal to the Y locus on the q-arm of the MHC chromosome and the MHC-B on the p-arm. An internal telomere array on the MHC chromosome separates the B and Y loci.

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Section: Discussionmentioning

confidence: 99%

Characterization of the turkey MHC chromosome through genetic and physical mapping

Chaves

Krueth

Reed

2007

Cytogenet Genome Res

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“…Microsatellite markers included those developed at the University of Minnesota (MNT; Reed et al, 2005 and references therein; Chaves et al, 2006), Roslin Institute (RHT; Burt et al, 2003), Tuskegee University (TUM; Huang et al, 1999) and Purdue University (WT; Latch et al, 2002). In addition, 70 markers developed for chicken (ADL, LEI, ROS and UMA) and quail (GUJ) and 42 unpublished turkey markers (MTW; Wageningen University, courtesy of Richard Crooijmans), MGP (Agricultural Biotechnology Hungary, courtesy of Laslo Varga) and MNT (University of Minnesota, KM Reed) were also included.…”

Section: Genetic Markersmentioning

confidence: 99%

An integrated and comparative genetic map of the turkey genome

Reed¹,

Chaves²,

Mendoza³

2007

Cytogenet Genome Res

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An integrated genetic linkage map was developed for the turkey (Meleagris gallopavo) that combines the genetic markers from the three previous mapping efforts. The UMN integrated map includes 613 loci arranged into 41 linkage groups. An additional 105 markers are tentatively placed within linkage groups based on two-point LOD scores and 19 markers remain unlinked. A total of 210 previously unmapped markers has been added to the UMN turkey genetic map. Markers from each of the 20 linkage groups identified in the Roslin map and the 22 linkage groups of the Nte map are incorporated into the new integrated map. Overall map distance contained within the 41 linkage groups is 3,365 cM (sex-averaged) with the largest linkage group (94 loci) measuring 533.1 cM. Average marker interval for the map was 7.86 cM. Sequences of markers included in the new map were compared to the chicken genome sequence by ‘BLASTN’. Significant similarity scores were obtained for 95.6% of the turkey sequences encompassing an estimated 91% of the chicken genome. A physical map of the chicken genome based on positions of the turkey sequences was built and 36 of the 41 turkey linkage groups were aligned with the physical map, five linkage groups remain unassigned. Given the close similarities between the turkey and chicken genomes, the chicken genome sequence could serve as a scaffold for a genome sequencing effort in the turkey.

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“…We assembled the reads into genomic contigs to extract SSR sequences. The utilization of NGS technology delivers more coverage than the conventional whole-genome sequencing approach (24). This coverage includes more SSR markers, as recorded in this study.…”

Section: Discussionmentioning

confidence: 95%

“…Putative camel homologs were found on each chromosome of bovine genome, except for BTA 25, 28, and Y. One camel SSR locus was placed on BTA 6,7,8,12,16,19,24, and 26, while BTA 11 and 14 reached 5 SSRs each with an average of 2 loci per chromosome. Conversely, 3 markers showed matches to unassigned contigs (UN).…”

Section: Resultsmentioning

confidence: 99%

Identification of simple sequence repeat markers in the dromedary(Camelus dromedarius) genome by next-generation sequencing

Sadder¹,

Migdadi²,

Alhaidary³

et al. 2015

Turk J Vet Anim Sci

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The availability of molecular markers in camels is limited. The aim of this study was to develop new simple sequence repeat (SSR) markers. Four breeds of pooled dromedary genome were sequenced at low coverage utilizing Roche and Illumina platforms. A total of 65,746 contigs, covering approximately 52 Mb (2316 contigs > 2 kb), were assembled. The partial genome revealed 613 SSR loci with a minimum number of 5 repeat units. Comparative chromosomal location for 60 camel loci was predicted against bovine genome assembly Baylor Btau_4.6.1/bosTau7. Ten markers (16.7%) returned matches with a >100 score and >80% identity. SSR abundance was 1 in every 84.3 kb of contigs. The SSR loci mainly comprised di-(80.8%), tri-(10.8%), tetra-(7.6%), and pentamer (0.8%) motifs. (TA)n and (AC)n were the most abundant (58.6%) dimers. Thirty SSR loci were experimentally characterized for both dromedary (16 animals) and Bactrian camels. The number of alleles ranged from 1 to 3, and the average number of fragments scored per animal ranged from 0.81 to 2. Polymorphic information content ranged from 0 to 0.66 with a mean value of 0.38. These SSR markers will be a valuable resource for further genetic studies of camels and related species.

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Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo)

Cited by 19 publications

References 15 publications

Characterization of the turkey MHC chromosome through genetic and physical mapping

Characterization of the turkey MHC chromosome through genetic and physical mapping

An integrated and comparative genetic map of the turkey genome

Identification of simple sequence repeat markers in the dromedary(Camelus dromedarius) genome by next-generation sequencing

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