Table 1.

Site-specific PCR analysis of Au SINE insertional polymorphism within genes in Triticum and Aegilops species

No.	Gene accession numbera	Gene productb	Primer R sequencec	Primer L sequencec	Location within gened	Existence of Au SINE in the genomee
						AA	BB*	BB#	DD	AABB	AABBDD
1	TRIAE_CS42_1DL_TGACv1_061151_AA0187150	DnaJ homolog subfamily C member 13	GAATTTAGTTTGCGGTTCCAAG	TGTGGTACATATCCATGCGTTT	Intron	√	√	√	√	√	√
2	TRIAE_CS42_2BL_TGACv1_129350_AA0379730	CLPTM1-like membrane protein cnrB	ACGAAGAACTAAAAGCCGTGAA	CTGCTATACCATGCGATCGTT	Intron	√	√	√	√	√	√
3	TRIAE_CS42_7BL_TGACv1_577050_AA1863990	Predicted protein	CGTATTCAAAGATGTTCCACGA	GGCTGGGTTAAGATTGTTTTTG	Exon	√	√	√	√	√	√
4	TRIAE_CS42_7BS_TGACv1_591977_AA1927210	Predicted protein	ATGAAGACAACAAGTGCCACAC	GAATAAACATGCCATTCTGCAA	100 bp downstream	√	√	√	√	√	√
5	TRIAE_CS42_4DS_TGACv1_363130_AA1183390	Rht-D1b	TTGCATCAACTCACCATGAAAT	ATGTGTGAACCGACAACTGAAG	Intron	√	√	√	√	√	√
6	TRIAE_CS42_4DL_TGACv1_342699_AA1119920	Superoxide dismutase [Cu–Zn] 3	GCGACACACCAAAAATTTCATA	GCACCACCTGCTGATACACTTA	Intron	√	√	√	√	√	√
7	TRIAE_CS42_U_TGACv1_640941_AA2079970	Disease resistance protein RPP13-like	TTACTGGGACCTTCCACACC	GCCATCCATTTCCATTTCAG	Exon	×	×	×	×	×	√
8	TRIAE_CS42_1BS_TGACv1_050314_AA0170550	Putative Serine/threonine-protein kinase CBK1	ACATGGATGAGCAGGACTAGGT	TCAGAGGGGTCAGGAATAGAAA	Intron	×	×	×	×	×	√
9	TRIAE_CS42_7BL_TGACv1_577920_AA1886220	Zinc transporter ten-like	CCCAAAGATCGCTAGATCAGA	TGTTCAAACACGGGGATGTA	Intron	×	×	×	×	√	√
10	TRIAE_CS42_1BL_TGACv1_032021_AA0124300	Putative E3 ubiquitin-protein ligase HERC1	TCCTTCTCAGGGCGTAGAAA	TTGGTTTACATTCACAGGATCAA	Intron	×	×	×	×	√	√
11	TRIAE_CS42_1BS_TGACv1_049809_AA0161910	Predicted protein	TGTCTGGTGCTTGTGAAGAAAC	ATCGAATCACATCCCTTTCAGT	Intron	×	×	×	×	√	√
12	TRIAE_CS42_6BL_TGACv1_499645_AA1588080	Rho guanine nucleotide exchange factor 8	TCCTTTCCTACCCACAGATCAT	CGCAGACTGATTCCCTGTCTAT	Intron	×	×	×	×	√	√
13	TRIAE_CS42_5AL_TGACv1_377324_AA1245930	Putative ATP-dependent RNA helicase DHX36	AGCATTGGGGAGTTTCTATCAG	TAAGAGCCCAACAAATGTCAAA	Intron	×	×	×	×	√	√
14	TRIAE_CS42_5BL_TGACv1_406235_AA1342580	Predicted protein	TGAGTGGCAAAACTCTCAGATG	GCCTACATCGACCAAATTCTTC	Intron	×	×	×	×	√	√
15	TRIAE_CS42_2AL_TGACv1_093126_AA0272720	Cell division protein FtsZ homolog 1, chloroplastic	AGTGCCTGACGTGGTAAGAAAT	GAATTTCTGTTTGCAGTGCTTG	Intron	×	×	×	×	√	√
16	TRIAE_CS42_2BL_TGACv1_130367_AA0409600	Exocyst complex component 2	GTGAGAACTGAGCATGAACTGG	ATCCATTAGGCCTTGGGTAACT	Intron	×	×	×	×	√	√
17	TRIAE_CS42_3B_TGACv1_220590_AA0709880	Josephin family protein	CAGCTGTACACTTCAAACCAATG	TATGATTTGATCCGAAATGCAA	Intron	×	×	×	×	√	√
18	TRIAE_CS42_1BS_TGACv1_049553_AA0156720	Predicted protein	GCTATCGCCTGGTTATGAGTTC	AAGAGGATCATTTGCTTTTCCA	Exon/Intron	×	×	×	×	√	√
19	TRIAE_CS42_2BS_TGACv1_146572_AA0468420	2-dehydro-3-deoxyphosphooctonate aldolase	GCAGACATTTTTGCTCAACCTT	CATGATGATTCCCTTGATGTTG	Intron	×	×	×	×	√	√
20	TRIAE_CS42_2AL_TGACv1_096183_AA0317680	ATP-dependent RNA helicase SUPV3L1, mitochondrial	ATCTACGCCTTATTTGCTCTGG	GGTAAAGTGTGCCTTTTTGAGG	Intron	×	×	×	×	√	√
21	TRIAE_CS42_2BL_TGACv1_129880_AA0398630	Oligoribonuclease	TGCTAGTGGACTCAACCAAATC	TGGCCTCAGAGCCTAGTAACA	Intron	×	×	×	×	√	√
22	TRIAE_CS42_1AL_TGACv1_000103_AA0003430	Predicted protein	CAGACCACAATGGGTATGGTTA	CCATAGAACTCCATCAACATCG	intron	×	×	×	×	√	√
23	TRIAE_CS42_5BL_TGACv1_405351_AA1325650	MADS-box transcription factor 14	CTAGGTCCATCTGGTCCCTAAAG	CTTTGACTACCCCACATTAGCTG	Intron	×	×	×	×	√	√
24	TRIAE_CS42_5BL_TGACv1_404700_AA1308770	E3 ubiquitin-protein ligase AIP2	AGATTTGTGATAGCAGCACCAG	TTGTGAGTTACCTTGAGCCTAGC	Intron	×	×	×	×	√	NA
25	TRIAE_CS42_2DL_TGACv1_158055_AA0507480	Chloride channel protein CLC-c	CAGCTGTGCTGATTTGCCTA	GAAAGGATGATGCAGAGTTTCA	Intron	×	×	×	√	×	√
26	TRIAE_CS42_2DS_TGACv1_177403_AA0575920	5′–3′ exoribonuclease 3	CATGGCATAACATCGAACAAAA	AGCCGCCTTTTTGAATTTTACT	Intron	×	×	×	√	×	√
27	TRIAE_CS42_4DS_TGACv1_361106_AA1161070	Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1	TCTCCCTCACAGATCACTTCAA	TTAGCCACAAGTTTGGATAGGC	Intron	×	×	×	√	×	√
28	TRIAE_CS42_4DL_TGACv1_343519_AA1135850	Conserved oligomeric Golgi complex subunit 6-like	GTGCCAAGTGAATGAAGTCAAG	CTGACACCATGGTACCCTAACA	Intron	×	×	×	√	×	√
29	TRIAE_CS42_6DL_TGACv1_526989_AA1696800	Serine/threonine-protein kinase	TAGTCTCTAATTTGCGGGTCCA	CACGCATGTCACCAAACATTA	Intron	×	×	×	√	×	√
30	TRIAE_CS42_4AL_TGACv1_290382_AA0984800	ERBB-3 BINDING PROTEIN 1	TACCGTCAGCAGAACACCAC	TGAGATGTGTGAGAAGGGTGA	Intron	√	×	×	×	√	√
31	TRIAE_CS42_5AL_TGACv1_378959_AA1255190	Leucine zipper protein	AGATTGCTGGAAAATAAGGACAA	TTTTGGATCGTGCCTAGGAG	Intron	√	×	×	×	√	√
32	TRIAE_CS42_2AL_TGACv1_093836_AA0287830	Putative pectinesterase/ pectinesterase inhibitor 51	TCTCCCTTTGTCACTTTTGCTT	GAAGCATCTTTCTGCCATCTTT	Intron	√	×	×	×	√	√
33	TRIAE_CS42_3AS_TGACv1_211370_AA0689310	C3H2C3 RING-finger protein	CCTCAGGAGGTGAATTGCTC	TTAACCCGCCTCACTTTGTC	Exon/Intron	√	×	×	×	√	NA
34	TRIAE_CS42_7AL_TGACv1_558277_AA1791890	ELAV-like protein 1	ATAGCCAGTGGTAGGCCACA	ACACTGACCGGATTTGAACC	Intron	×	√	√	×	√	√
35	TRIAE_CS42_2BS_TGACv1_145935_AA0449980	Mediator of RNA polymerase II transcription subunit 14-like	CCCAAAAGATGAAATAGCAACC	GAAGAGGAAGGGCCAGTATGTT	Intron	×	×	√	×	√	√
36	TRIAE_CS42_5BL_TGACv1_407697_AA1358910	Calcineurin-like metallo-phosphoesterase superfamily protein	GTACATCAGTAGCGCAATGGAA	GAACTCCCAAGAAGAGGACCTT	intron	×	×	√	×	√	√
37	TRIAE_CS42_4AL_TGACv1_288293_AA0943850	Rho GTPase-activating protein 7	CCCTCAAATGCAAAGCGTAT	CTCCTCATGCTACGACGACA	Intron	√	√	×	√	√	√
38	TRIAE_CS42_7DS_TGACv1_624740_AA2063030	Kanadaptin	CATGTGTGCTTCCAAGATCG	ACCATGACTGGAATCGAAGG	Intron	√	×	√	√	√	√
39	TRIAE_CS42_4DL_TGACv1_342534_AA1116030	Serine-aspartate repeat-containing protein I-like	TGGAACCTGTCGGCTCTATTAT	AAGAATGATGGTCATGGATGTG	Intron	×	√	√	√	√	√
40	TRIAE_CS42_1BS_TGACv1_049347_AA0149810	SIN3 transcription regulator family member B	ACACGGCATATGGGTAATTGA	ATTCTGGCCACGTGATCTCTAT	Intron	√	×	√	√	√	√

^aGene accessions from EnsemblPlants (http://plants.ensembl.org/Triticum_aestivum)

^bBased on gene annotation from EnsemblPlants with e value < 10⁻¹⁰.

^cPrimers were designed from Au SINE-flanking sequences.

“NA (Not available)” represents monomorphic cases in which the original genome that displays Au SINE insertion in the gene cannot be determined

^dLocation of Au SINE within or adjacent the gene: exon, intron, exon/intron junction or downstream of the gene

^eAA = T. urartu, BB^* = Ae. searsii, BB^# = Ae. speltoides, DD = Ae. tauschii, AABB = T. turgidum, AABBDD = T. aestivum, “√"-full site in at least one accession of the same species; “×" empty site in all accessions of the same species, NA data not available