A preliminary linkage map of the chicken genome

Bumstead, Nat; Pałyga, Jan

doi:10.1016/0888-7543(92)90143-g

Cited by 155 publications

(80 citation statements)

References 18 publications

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“…Mapping studies were carried out using the Compton mapping reference population, which was derived from a cross between the inbred White Leghorn lines N and 15I (Bumstead & Palyga, 1992). Southern blots of HindIII-or EcoRI-digested DNA of the parent birds and 56 progeny of this population were probed with the H3-H4 PCR product.…”

Section: Chromosomal Mapping Of Eav-hpmentioning

confidence: 99%

Novel endogenous retroviral sequences in the chicken genome closely related to HPRS-103 (subgroup J) avian leukosis virus.

Smith

Toye

Howes

et al. 1999

Journal of General Virology

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HPRS-103, the prototype of avian leukosis virus (ALV) subgroup J, is a recently identified retrovirus associated with myeloid leukosis in meat-type chickens. Although this virus shows high sequence identity to other ALV subgroups within the gag and pol genes, its env gene is highly diverged (with only about 40 % sequence identity) from other ALV subgroups. On the other hand, the sequence of the env gene of HPRS-103 was 75 % identical to that of E51, a member of the EAV family of endogenous avian retroviruses. It is reported here that the chicken genome also contains another EAV-related element, EAV-HP, showing much greater sequence identity (over 97 %) to the HPRS-103 env gene. Southern blotting analysis showed that EAV-HP-related sequences were distinct from EAV-0 and were present in all lines of chicken examined and in grey jungle fowl, but were absent from several other avian species. The potential role of these endogenous sequences in the evolution of ALV subgroup J viruses is discussed.

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Section: Chromosomal Mapping Of Eav-hpmentioning

confidence: 99%

Novel endogenous retroviral sequences in the chicken genome closely related to HPRS-103 (subgroup J) avian leukosis virus.

Smith

Toye

Howes

et al. 1999

Journal of General Virology

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“…The first map, based on the Compton (C) population, employed about 100 markers in 18 linkage groups that contained 585 cM (Bumstead & Palyga, 1992). In the second map, based on the East Lansing (EL) population, 98 markers were described in 19 linkage groups that contained 590 cM (Levin et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

Genetic linkage map of chicken chromosome 1 from a Brazilian resource population

Nones

Ledur

Ruy

et al. 2005

Sci. agric. (Piracicaba, Braz.)

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A genetic map provides insight into genome organization and chromosomal location of markers and genes, and is important for quantitative trait loci (QTL) mapping. The objective of this study was to use a Brazilian resource population to construct a linkage map for chicken chromosome 1. Eighty microsatellite markers were tested and 26 informative markers were typed in an experimental F 2 population developed by two generations of crossbreeding between a broiler sire line and a layer line. A total of 649 F 2 individuals from seven full-sib families with about 95 F 2 offspring each were genotyped. Multi-locus linkage analysis resulted in a chromosome 1 map of 26 ordered markers. Locus order was in general agreement with other published linkage maps, except for two discrepancies: 1) order of loci MCW10 and MCW208 was reversed in this map relative to the Wageningen linkage map, 2) markers ADL234 and LEI68, that were mapped to the same position in Compton, East Lansing and Wageningen populations, were separated by a distance of 5.9 centimorgans in our population. The higher number of informative meioses from our population could explain these differences. This map is an important first step in our effort to map QTL in the Brazilian chicken resource population, and complements the international consensus map information. Key words: microsatellites, poultry, mapping MAPA GENÉTICO DE LIGAÇÃO DO CROMOSSOMO 1 DA GALINHA DE UMA POPULAÇÃO BRASILEIRA RESUMO: Um mapa genético proporciona o entendimento da organização do genoma e da localização cromossômica de marcadores e genes, e é importante para o mapeamento de locos controladores de características quantitativas (QTL). O objetivo deste estudo foi utilizar uma população brasileira para construir um mapa de ligação do cromossomo 1 da galinha. Oitenta marcadores microssatélites foram testados e 26 marcadores informativos foram genotipados em uma população F 2 experimental, desenvolvida em duas gerações de um cruzamento entre uma linha macho de corte e uma linhagem de postura. Foram genotipados um total de 649 indivíduos F 2 de sete famílias de irmãos completos com cerca de 95 F 2 cada uma. A análise de ligação Multi-locus gerou um mapa do cromossomo 1 com 26 marcadores ordenados. A ordem dos locos foi em geral semelhante àquela de outros mapas de ligação publicados, exceto por duas discrepâncias: 1) a ordem entre os marcadores MCW10 e MCW208 foi invertida no presente mapa quando comparado com o mapa de ligação de Wageningen, 2) Os marcadores ADL234 e LEI68 que foram mapeados na mesma posição nas populações de Compton, East Lansing e Wageningen foram separados por uma distância de 5,9 centimorgans na presente população. O maior número de meioses informativas desta população pode explicar esta diferença. Este mapa é o primeiro passo no esforço de mapear QTL na população brasileira o qual pode também ser usado para complementar a informação do mapa consenso internacional da galinha.

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“…To date, three linkage maps have been constructed using molecular markers (RFLP, RAPD, AFLP, and SSR) from three reference chicken populations: Compton (Bumstead and Palyga, 1992), East Lansing (Levin et al, 1994) and Wageningen (Groenen et al, 1998). Groenen et al (2000) integrated these three maps into a chicken consensus linkage map, covering 3800 cM, and Schmid et al (2005) updated this map, covering 4200 cM.…”

Section: Introductionmentioning

confidence: 99%

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Rosário¹,

Margarido²,

Boschiero³

et al. 2010

Genet. Mol. Res.

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ABSTRACT. Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F 2 reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F 2 population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information.

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A preliminary linkage map of the chicken genome

Cited by 155 publications

References 18 publications

Novel endogenous retroviral sequences in the chicken genome closely related to HPRS-103 (subgroup J) avian leukosis virus.

Novel endogenous retroviral sequences in the chicken genome closely related to HPRS-103 (subgroup J) avian leukosis virus.

Genetic linkage map of chicken chromosome 1 from a Brazilian resource population

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

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