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Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.

Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA - BMC Genomics (2008)

Bottom Line: Previous studies on the organization of the K allele concluded the integration of endogenous retrovirus 21 (ev21) into one of two large homologous segments located on the Z chromosome of late feathering chickens.The tandem duplication of this region results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2.The duplication resulted in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University and Research Centre, PO Box 338, 6700 AH Wageningen, The Netherlands. martin.elferink@wur.nl

ABSTRACT

Background: One of the loci responsible for feather development in chickens is K. The K allele is partially dominant to the k+ allele and causes a retard in the emergence of flight feathers at hatch. The K locus is sex linked and located on the Z chromosome. Therefore, the locus can be utilized to produce phenotypes that identify the sexes of chicks at hatch. Previous studies on the organization of the K allele concluded the integration of endogenous retrovirus 21 (ev21) into one of two large homologous segments located on the Z chromosome of late feathering chickens. In this study, a detailed molecular analysis of the K locus and a DNA test to distinguish between homozygous and heterozygous late feathering males are presented.

Results: The K locus was investigated with quantitative PCR by examining copy number variations in a total of fourteen markers surrounding the ev21 integration site. The results showed a duplication at the K allele and sequence analysis of the breakpoint junction indicated a tandem duplication of 176,324 basepairs. The tandem duplication of this region results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Sequence analysis revealed that the duplication is similar in Broiler and White Leghorn. In addition, twelve late feathering animals, including Broiler, White Leghorn, and Brown Layer lines, contained a 78 bp breakpoint junction fragment, indicating that the duplication is similar in all breeds. The breakpoint junction was used to develop a TaqMan-based quantitative PCR test to allow distinction between homozygous and heterozygous late feathering males. In total, 85.3% of the animals tested were correctly assigned, 14.7% were unassigned and no animals were incorrectly assigned.

Conclusion: The detailed molecular analysis presented in this study revealed the presence of a tandem duplication in the K allele. The duplication resulted in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Furthermore, a DNA test was developed to distinguish between homozygous and heterozygous late feathering males.

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The organization of the k+ and K alleles. The k+ allele contains two genes; PRLR (purple exons) and SPEF2 (black exons). The K allele contains the original genes and the two partial duplicate genes, dPRLR and SPEF2. The green box indicates the unoccupied ev21 integration site. One of the red boxes indicates an unoccupied and the other an occupied ev21 integration site. The large yellow and blue boxes indicate the 176.3 kb duplicated block. The grey arrows indicate transcriptional start and stop. The question mark indicates a transcript of unknown length.
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Figure 1: The organization of the k+ and K alleles. The k+ allele contains two genes; PRLR (purple exons) and SPEF2 (black exons). The K allele contains the original genes and the two partial duplicate genes, dPRLR and SPEF2. The green box indicates the unoccupied ev21 integration site. One of the red boxes indicates an unoccupied and the other an occupied ev21 integration site. The large yellow and blue boxes indicate the 176.3 kb duplicated block. The grey arrows indicate transcriptional start and stop. The question mark indicates a transcript of unknown length.

Mentions: To determine the size and orientation of the duplicated block, forward and reverse primers were designed for both ends (between marker STS_6 and STS_7, and between markers STS_13 and STS_14). A 1238 bp product was obtained spanning the breakpoint junction (marker STS_junction) in two late feathering males. With this marker, no PCR product was obtained from the DNA of the two EF birds. Sequence analysis of the PCR product obtained from the two LF males provided the exact breaking point. Based on the WASHUC2 assembly, the total length of the tandem duplication is 176,324 bp (GGAZ 9,966,364–10,142,688 bp). The tandem duplication of this region results in the partial duplication of two genes: the prolactin receptor (PRLR) and the gene encoding sperm flagellar protein 2 (SPEF2, also known as KPL2). The duplicated block included exons 1 to 11 and 558 bp of exon 12 of PRLR, and exons 1 to 5 of SPEF2 (Figure 1). No differences in the nucleotide sequences of the breakpoint junction fragments were observed between the Broiler and White Leghorn animals.


Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.

Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA - BMC Genomics (2008)

The organization of the k+ and K alleles. The k+ allele contains two genes; PRLR (purple exons) and SPEF2 (black exons). The K allele contains the original genes and the two partial duplicate genes, dPRLR and SPEF2. The green box indicates the unoccupied ev21 integration site. One of the red boxes indicates an unoccupied and the other an occupied ev21 integration site. The large yellow and blue boxes indicate the 176.3 kb duplicated block. The grey arrows indicate transcriptional start and stop. The question mark indicates a transcript of unknown length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2542384&req=5

Figure 1: The organization of the k+ and K alleles. The k+ allele contains two genes; PRLR (purple exons) and SPEF2 (black exons). The K allele contains the original genes and the two partial duplicate genes, dPRLR and SPEF2. The green box indicates the unoccupied ev21 integration site. One of the red boxes indicates an unoccupied and the other an occupied ev21 integration site. The large yellow and blue boxes indicate the 176.3 kb duplicated block. The grey arrows indicate transcriptional start and stop. The question mark indicates a transcript of unknown length.
Mentions: To determine the size and orientation of the duplicated block, forward and reverse primers were designed for both ends (between marker STS_6 and STS_7, and between markers STS_13 and STS_14). A 1238 bp product was obtained spanning the breakpoint junction (marker STS_junction) in two late feathering males. With this marker, no PCR product was obtained from the DNA of the two EF birds. Sequence analysis of the PCR product obtained from the two LF males provided the exact breaking point. Based on the WASHUC2 assembly, the total length of the tandem duplication is 176,324 bp (GGAZ 9,966,364–10,142,688 bp). The tandem duplication of this region results in the partial duplication of two genes: the prolactin receptor (PRLR) and the gene encoding sperm flagellar protein 2 (SPEF2, also known as KPL2). The duplicated block included exons 1 to 11 and 558 bp of exon 12 of PRLR, and exons 1 to 5 of SPEF2 (Figure 1). No differences in the nucleotide sequences of the breakpoint junction fragments were observed between the Broiler and White Leghorn animals.

Bottom Line: Previous studies on the organization of the K allele concluded the integration of endogenous retrovirus 21 (ev21) into one of two large homologous segments located on the Z chromosome of late feathering chickens.The tandem duplication of this region results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2.The duplication resulted in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University and Research Centre, PO Box 338, 6700 AH Wageningen, The Netherlands. martin.elferink@wur.nl

ABSTRACT

Background: One of the loci responsible for feather development in chickens is K. The K allele is partially dominant to the k+ allele and causes a retard in the emergence of flight feathers at hatch. The K locus is sex linked and located on the Z chromosome. Therefore, the locus can be utilized to produce phenotypes that identify the sexes of chicks at hatch. Previous studies on the organization of the K allele concluded the integration of endogenous retrovirus 21 (ev21) into one of two large homologous segments located on the Z chromosome of late feathering chickens. In this study, a detailed molecular analysis of the K locus and a DNA test to distinguish between homozygous and heterozygous late feathering males are presented.

Results: The K locus was investigated with quantitative PCR by examining copy number variations in a total of fourteen markers surrounding the ev21 integration site. The results showed a duplication at the K allele and sequence analysis of the breakpoint junction indicated a tandem duplication of 176,324 basepairs. The tandem duplication of this region results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Sequence analysis revealed that the duplication is similar in Broiler and White Leghorn. In addition, twelve late feathering animals, including Broiler, White Leghorn, and Brown Layer lines, contained a 78 bp breakpoint junction fragment, indicating that the duplication is similar in all breeds. The breakpoint junction was used to develop a TaqMan-based quantitative PCR test to allow distinction between homozygous and heterozygous late feathering males. In total, 85.3% of the animals tested were correctly assigned, 14.7% were unassigned and no animals were incorrectly assigned.

Conclusion: The detailed molecular analysis presented in this study revealed the presence of a tandem duplication in the K allele. The duplication resulted in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Furthermore, a DNA test was developed to distinguish between homozygous and heterozygous late feathering males.

Show MeSH