Table IX. PCR testing of IGG markers for three-way genome analysis.

A set of 32 IGG markers were selected for PCR testing. DNA from S. lycopersicum (L), S. pennellii (P), S. tuberosum (T), and S. sitiens (S) was amplified and polymorphism was scored. PCR gel results are shown in Figure 7, B to D. N/A, Comparison could not be made because one or more genotypes did not amplify under the conditions tested; No, base pair difference was not easily identified; Yes, base pair difference (on 2% agarose gels) between genotypes was easily identified. *, Did not amplify in S. sitiens.

Markera	IGG IDb	Polymorphism Type								Amplicon Sizee			Primer Forward (5′–3′)	Primer Reverse (5′–3′)
		Two-Wayc						Three-Wayd
		L versus P	L versus T	P versus T	L versus S	P versus S	T = S	LPT	LPS	L	P	T
M-1	IGG_HPT14B_754	Yes	Yes	Yes	Yes	No	No	Yes	No	991	737	584	AGAGAACTTAGTGCAGGCAG	TGCTCTGGGTCTCCTAGTTC
M-2*	IGG_HPT14B_926	Yes	Yes	Yes	N/A	N/A	N/A	Yes	N/A	1,247	1,519	765	TCACAATCATCACGGAGCAAC	ACCACAGCTTCTACGCCTTA
M-3	IGG_HPT14B_1105	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	1,103	809	682	TGAAACACGAAAGGAGCTTGT	AGCCGTTCATCAGCAATCAA
M-4	IGG_HPT14B_1608	Yes	Yes	Yes	Yes	No	No	Yes	No	1,093	1,508	725	TACTCGCTCTTCATGACGCT	CTAATTCGCAGCAAATCGAAAC
M-5	IGG_HPT14B_4592	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	943	1,121	751	ATTGCATACCCACTGCGAGG	CAGGCGGATGTGTGAGTTAT
M-6	IGG_HPT14B_4936	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	1,327	582	671	AAGAGAGGCATTCGAGGGAG	CATGCGCCACGTGTACTC
M-7	IGG_HPT14B_5427	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	792	932	527	TGTTGAGGGCTGGTGGATAC	CTGTAGCAGGCTCATCTTAAAAC
M-8	IGG_HPT14B_6347	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	969	1,196	1,449	CTCATGGCCACGAATGTCTG	GGTGGTGGCAGTAACGTTTC
M-9	IGG_HPT14B_8121	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	824	1,150	1,366	AGAGCCGCCTTTCCTCCTA	TTTCAAGCTGGCATTCGAGC
M-10*	IGG_HPT14B_8235	Yes	Yes	Yes	N/A	N/A	N/A	Yes	N/A	1,056	649	885	TTACCACGTTCTCCAGCAGG	CTCATGAAAACCTCCGACCTG
M-11	IGG_HPT14B_8264	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	898	1,097	1,358	GCCGCTACTTCTCGATCAAA	TTGTTCAGGTGCCTCGTG
M-12	IGG_HPT14B_8563	Yes	N/A	N/A	Yes	Yes	N/A	N/A	Yes	651	430	913	AAAAGGAAGCGCGAGATGAG	CCAGTGGAGCAGGTTACTC
M-13*	IGG_HPT14B_8811	Yes	Yes	Yes	N/A	N/A	N/A	Yes	N/A	579	1,012	815	CAAGGATCTGGCTGGGTAGT	GGTACCCTTGCTCGATTAGATAG
M-14	IGG_HPT14B_8853	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	841	1,247	1,051	TCCAACTCCGGACAAAGGT	TCTCACGGTATAAGCAGAGCA
M-15	IGG_HPT14B_9447	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	875	1,111	1,368	AGGGCACGTACCAGCATAAA	ATGATGGGATGCTGTCGACA
M-16	IGG_HPT14B_10635	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	963	786	615	TAAGCTGTAACGCAATCCCG	CCCTGTGGAGCCAACAAT
M-17*	IGG_HPT14B_11038	Yes	Yes	Yes	N/A	N/A	N/A	Yes	N/A	1,371	1,120	907	TGACAGTTCAAGCCCACAG	GTGAACACTCCCTGACTTTGT
M-18	IGG_HPT14B_15532	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	1,425	1,148	611	TTATCTTGCTGTGCTTGCCC	CAAGTTTATGGGGTGGCACA
M-19	IGG_HPT14B_15683	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	464	528	846	CGTTTGATGGTTGGTGCGTA	TAGTCTACGCGGCGCATC
M-20	IGG_HPT14B_15777	Yes	Yes	Yes	Yes	No	No	Yes	No	877	718	1,225	GGCACTTGTGAGCAGTATCC	TGCAAGTCGACAGTATCTAACA
M-21	IGG_HPT14B_21272	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	469	554	899	GGGATCTTCGCACCTAAATCC	ATTCCGACTGCCTGGTGTTT
M-22	IGG_HPT14B_21501	Yes	Yes	Yes	Yes	No	Yes	Yes	No	1,290	983	765	CTTCCCTCATCTCGTCGGG	AATGCGTGCAGAAGAAGACG
M-23	IGG_HPT14B_23704	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	1,034	783	1,406	GCGGCGGATTGGGAAATC	CGGCGAGTAGGAGAACTGAG
M-24	IGG_HPT14B_24108	Yes	Yes	Yes	Yes	No	No	Yes	No	779	933	1,504	GCTTATGCGGGTTTGTTAGAAA	CGGTATAACTTCACGGCATTAAG
M-25	IGG_HPT14B_25784	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	463	590	902	GCATCTTCTCAACGTACCTCTC	CCAGTTTTACCACCTAAACCGG
M-26	IGG_HPT14B_26897	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	1,393	1,104	897	TGTCACCAGCATACTTTGTCA	ACTGATAACTGGGTGAAAGGTG
M-27	IGG_HPT14B_26991	Yes	Yes	Yes	No	Yes	No	Yes	No	1,051	866	1,333	CTGGAAGCAGCAGGTATTCT	GCTCGGATTGCATTCACTTG
M-28	IGG_HPT14B_27175	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	863	1,050	728	AGGAGAAGACTGGCGGAAAG	TGGAAAGCACAGAAACAGATGA
M-29	IGG_HPT14B_27897	Yes	N/A	N/A	Yes	Yes	N/A	N/A	Yes	972	480	1,339	AAGTGCTGGCGTAAATTCAC	AGTGTGTTTGTGAGTGAAGCA
M-30	IGG_HPT14B_28355	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	1,469	1,148	964	TGGACCCCTATTGACTTAGTTGT	GTAGGGAGGGGCACATAACC
M-31	IGG_HPT14B_28659	Yes	Yes	Yes	No	Yes	No	Yes	No	1,234	1,026	758	TGGTTGCCTTGGCTTAGAAG	TGAACCACTCAACGCGGG
M-32	IGG_HPT14B_29367	Yes	Yes	Yes	Yes	No	No	Yes	No	830	1,207	1,011	CCTGAATCCCTGAGAATCCCA	AACACTGTTTAGAAGCCGGT

^aMarker number used in PCR experiments.

^bIGGPIPE spreadsheet identifier number for the IGG marker.

^cTwo-way markers have two distinct amplicon sizes in two species.

^dThree-way markers have three distinct sizes in three species.

^ePredicted amplicon sizes. S. sitiens has no predicted size due to the absence of a reference genome.