S1. Loci derived from chicken Z chromosome-linked genes.

Gene / Cytogenetic position / Accession No. / Reference. / Locus / Primer locations / Primer sequences (5´-3´) / PCR conditions[a]
Aldolase B,
Fructose biphosphate (ALDOB) / p1.2 / M10946 / [1] / ALDOB-4 / Exon 4
Exon 5 / F:GGCAGGAACAAATGGAGAAACT
R:GCCAGAACCTGAAAACAGGAG / 58-35
ALDOB-6 / Exon 6
Exon 7 / F:AGACCATGATCTCCAGCGCT
R:CCTTCCAGGTAGACATGATG / 56-37
ALDOB-7 / Exon 7
Exon 8 / F:GTTCCTGGTGATTCCTGATTC
R:CAGATTCCTGCAAGAAAGAGG / 61-40
Brahma protein (BRM) / p.1.2 / X91638 / [2] / BRM-12 / Exon 12
Exon 13 / F:CCCTATCTCATCATTGTTCC
R:CACAGAAGGAGCCCATTTGT / 55-35
BRM-15 / Exon 15
Exon 16 / F:AGCACCTTTGAACAGTGGTT
R:TACTTTATGGAGACGACGGA / 60-35
Chromo-helicase-
DNA-binding on the Z chromosome
protein (CHDZ) / q1.6-2.1 / AF004397 / [3] / CHDZ-15 / Exon 15
Exon 16 / F:TAGAGAGATTGAGAACTACAGT
R:GACATCCTGGCAGAGTATCT / 50-35
CHDZ-18 / Exon 18
Exon 19 / F:TACATACAGGCTCTACTCCT
R:CCCCTTCAGGTTCTTTAAAA / 60-5+
55-27
CHDZ-20 / Exon 20
Exon 21 / F:GAAGAGAGCTGAAACTCGG
R:TCATCTTCATCCATATTGG / 58-5+
50-30
CHDZ-24 / Exon 24
Exon 25 / F:CATTCACCTGCACTCCTGAG
R:GGCCTTTAAAGGACARTTCA / 50-35
Growth hormone receptor (GHR) / p2.2 / D13154 / [4] / GHR-5.1 / Intron 5[b] / F:GCTTCCATTATGTATCTTACC
R:TTTGGCTTCTAGAGTTTTGCA / 58-35
GHR-5.2 / Intron 5 / F:ATGTTATTGCTTGTTCAGAGTG
R:GAGTATTTGGAATAAAACAGCC / 58-35
GHR-exon9
/ Exon 9 / F:TGTTGTACTTTCTCCAGGGC
R:TCTGCCTCACAGAAATAGGTG / 52-39
Protein kinase C inhibitor (PKCI) / q1.1 / AB026676 / [5] / PKCI-2 / Exon 1
Intron 2 / F:GATATCTCACCCCAAGCTCCAAC
R:CCCACTACTTCAGACAACATA / 47-35
Prolactin receptor (PRLR) / p2.2 / AJ011128 / [6] /

PRLR-UN

/ UN / F:GGAAAAGATAAGCGAGATGGAG
R:CTTCTCAGCTTGACTGTCCTG / 58-39
Patched (PTCH) / q1.2-1.6 / U40074 / [7] / PTCH-6 / Exon 6
Exon 7 / F:CCATTTTCTTCCAAGCAATA
R:TTTCTTGACAGTCCATAGCA / 53-40
Spindlin (SPINZ) / q1.1 / AB047853 / [8] / SPINZ-2 / Exon 2
Exon 3 / F:TATGGACTAGAACTGCACAAAG
R:AGACCATCCCCCTCCATTCATC / 51-40
Very low density lipoprotein/
Vitellogenin receptor (VLDLR) / p1.3 / X80207 / [9] / VLDLR-7 / Exon 7
Exon 8 / F:CAGAAGTGGAGAATGCATAG
R:ACAGTCACATTCATAGCCAA / 60-35
VLDLR-8 / Exon 8
Exon 9 / F:GTTATTGGCTATGAATGTGA
R:GTTGATACAGATTTGGCTAC / 57-35
VLDLR-9 / Exon 9
Exon 10 / F:AAGTGTGAATGTAGCCGTGG
R:TCGGTTGGTGAAAATCAGAC / 62-35
VLDLR-12
/ Exon 12
Exon 13 / F:GTTCCTTCCTCATCCTCTTG
R:ATAGACTGCCTCGTTCTCTC / 55-35

1.Burgess, D.G. and E.E. Penhoet, Characterization of the chicken aldolase B gene. Journal of Biological Chemistry, 1985. 260(8): p. 4604-14.

2.Goodwin, G.H., Isolation of cDNAs encoding chicken homologues of the yeast SNF2 and Drosophila Brahma proteins. Gene, 1997. 184(1): p. 27-32.

3.Griffiths, R. and R.M. Korn, A CHD1 gene is Z chromosome linked in the chicken Gallus domesticus. Gene, 1997. 197(1-2): p. 225-229.

4.Tanaka, M., et al., Double antenna structure of chicken prolactin receptor deduced from the Cdna sequence. Biochemical and Biophysical Research Communications, 1992. 188(2): p. 490-496.

5.Hori, T., et al., Wpkci, encoding an altered form of PKCI, is conserved widely on the avian W chromosome and expressed in early female embryos: Implication of its role in female sex determination. Molecular Biology of the Cell, 2000. 11(10): p. 3645-3660.

6.Dunn, I.C., et al., Genetic mapping of the chicken prolactin receptor gene: a candidate gene for the control of broodiness. British Poultry Science, 1998. 39: p. S23-S24.

7.Marigo, V., et al., Conservation in hedgehog signaling: Induction of a chicken patched homolog by Sonic hedgehog in the developing limb. Development, 1996. 122(4): p. 1225-1233.

8.Itoh, Y., et al., Chicken spindling genes on W and Z chromosomes: transcriptional expression of both genes and dynamic behavior of spindlin in interphase and mitotic cells. Chromosome Research, 2001. 9(4): p. 283-299.

9.Bujo, H., et al., Chicken oocyte growth is mediated by an 8 ligand-binding repeat member of the Ldl receptor family. Embo Journal, 1994. 13(21): p. 5165-5175.

[a]PCR conditions: Annealing temperature-number of cycles. All PCR reactions followed this three step format: (1:) 95 for 15 min/ 1 cycle; (2:) (94 for 30 sec, annealing temp for 30 sec, 72 for 1 min) number of cycles; (3:) 72 for 10 min/one cycle. For some loci step two were run two times with different annealing temperatures and number of cycles.

[b] Primers designed in introns are flycatcher specific.