TABLE 1.

Oligonucleotides used for PCR-based recombinant mapping

			a1 haplotype
Primer name	Sequencea	Polymorphism	α-Yz1Ab	β-Sh2c	a1∷rdt sh2
αSNP4R	GTGTGGGGTCTAGAGAAGGG	SNP	+d	−e	−
αSNP5R	GCTTGAGGATCGAGTAGTGC	SNP	+	−	−
αIDP1R	TGAGAAACTTCTTTCGGCTCTG	IDP	+	−	−
αSNP6R	CAACACCAAACCCTTCAACCA	SNP	+	−	−
αSNP3R	CCAGCCTTTTTATCCCGCTC	SNP	+	−	−
αSNP3F	GCAAGAACACATTAGACACGTTA	SNP	+	−	−
β3694R	GTCTTCCCCACATAATATGCG	SNP	−	+	−
β3040R	CGAGGAGCAGACGTAGCGG	SNP	−	+	−
β2149R	CAACGTTCGCTGCAGGAC	SNP	−	+	−
yz4725	AAATGGTCAGGATAGCTTAGTT	IDP	+	+
yz5U-AbR	GGCTCCATATATCAAGCACA	IDP	+	+	−
Sh5379R	ACCAATGATACAGAGAGGCG	SNP	NAf	+	−
rdt444	AGCAAATAGCAATAATCAAGGCA	IDPg	−	−	+
rdtILR1	AGACAAATGTTCTGTAGGAAAC	SNP	−	−	+
yzrdtIDP1	GTTCACACAAAGTATTTTTTTCG	IDP	−	−	+
yz1410R	GGCTCCATATATCAAGCAGT	IDP	−	−	+
Shrdt1R	GACCAATGATACAGAGAGGCA	SNP	−	−	+
QZ1504	CCAGGGGATAAAACAATTCGT	U	+	+	+
A2775F	CACCATCATCCCGACGCTC	U	+	+	+
A2357	AGCCGACGGTGGAAGGGATG	U	+	+	+
XX390h	TCGGCTTGATTACCTCATTCT	U	+	+	+
A6458f	GGGAAGACGAAGCCATTGA	U	+	+	+
QZ1265h	TACTCCTCTCCAACTCCA	U	+	+	+
A1522	GGGAGTTTGGAGTTGGAGAGG	U	+	+	+
ajl002	TCAAGCTAAAAGAAAGAAACATT	U	+	+	+
a178R	TGCCAAATAACCATACCACA	U	+	+	+
QZ1742	TAGTTGGTAGCACGGTTGA	U	+	+	+
yz3UTRF	CGGGGGTTGCAGTCATTGAC	U	+	+	+
ZH1748	CACATCCCCGTCTCCT	U	+	+	+
yz792F	GCGGTTGCGGCTTGTAC	U	+	+	+
MY339	GCCTTTCCCCCATTACTATC	U	+	+	+

IDP, insertion/deletion polymorphism; SNP, single-nucleotide polymorphism; U, universal primer.

^aSequences are listed 5′–3′.

^bSequences specific to the interval in A1-b Sh2 extending from α to Yz1A.

^cSequences specific to the interval in A1-b Sh2 extending from β to Sh2.

^d+ indicates a primer that can amplify the corresponding interval.

^e− indicates a primer that cannot amplify the corresponding interval.

^fSh2 is not within the α-Yz1A interval. NA, not applicable.

^gPrimer specific to the rdt transposon insertion.

^hBoth primers (XX390 and QZ1265) amplify in each of the three haplotypes. In combination, however, these primers amplify a product only in the α-Yz1 interval.