Development and Validation of Gene-Based SSR Markers in the Genus Mesembryanthemum

Table 5

List and characteristics of Mesembryanthemum expressed sequence tag-simple sequence repeat (EST-SSR) markers.

Locus name	Primer sequence (5′ ⟶ 3′)	Tm (°C)	Expected size (bp)	GenBank no.	Putative function
PMA01	CCA​ACA​GAA​CCA​TCA​GCA​GC/GCT​TCA​CAA​AAC​CTT​ACA​CCC​T	59.48/59.04	176	CA834522.1	PREDICTED: transcription factor VIP1 (Beta vulgaris subsp. vulgaris)
PMA02	AGC​ATC​ACA​TTC​AAA​TCC​ACT​CT/AGA​GTC​AAG​AAG​AAA​AGG​AGG​GT	58.40/59.02	189	CA838453.1	No significant similarity found
PMA03	TAC​AAC​CAG​ACC​ACA​CAC​GG/AAT​CAT​CAT​CCA​ACA​AGA​AGT​GAA​T	59.89/57.29	194	AI366624.1	PREDICTED: gibberellin-regulated protein 1 isoform X2 (Beta vulgaris subsp. vulgaris)
PMA04	TCT​ATA​GAC​TAT​CGC​GGC​CG/AGA​GAC​GGT​GAG​CAC​TTT​CG	58.63/60.04	246	BE033938.1	No significant similarity found
PMA05^§	AAT​GTC​GAC​CAC​TCT​GCT​CC/ACT​CCA​GTA​GCT​ATT​GAG​TAC​CA	59.75/58.13	238	AI823067.1	No significant similarity found
PMA06^§	GCA​GAA​GTT​GAT​GAA​GAA​GCC​T/TTG​ATG​GGC​CGC​TAC​AAG​G	58.92/60.08	397	BE033380.1	Hypothetical protein TanjilG_11831 (Lupinus angustifolius)
PMA07	TGG​GAT​TGC​TTG​CTG​ATC​GT/AGA​AAG​GGC​AGC​AAC​TTG​GT	60.04/60.11	234	CA840307.1	Uncharacterized protein LOC110732016 isoform X2 (Chenopodium quinoa)
PMA08	TAC​AAC​CAG​ACC​ACA​CAC​GG/AAT​CAT​CAT​CCA​ACA​AGA​AGT​GAA​T	59.89/57.29	195	CA834353.1	PREDICTED: gibberellin-regulated protein 1 isoform X2 (Beta vulgaris subsp. vulgaris)
PMA09	TAC​AAC​CAG​ACC​ACA​CAC​GG/AAT​CAT​CAT​CCA​ACA​AGA​AGT​GAA​T	59.89/57.29	194	BM300798.1	PREDICTED: gibberellin-regulated protein 1 isoform X2 (Beta vulgaris subsp. vulgaris)
PMA10	TCC​TTG​ATC​CGA​TCT​GAC​TGA​C/GGA​GAG​GGG​TGT​TTT​GGT​CA	59.31/59.52	249	BM300496.1	No significant similarity found
PMA11^§	TAC​AAC​CAG​ACC​ACA​CAC​GG/AGA​ATC​CAA​TTT​TCC​AAC​CGA​CA	59.89/58.85	167	AW053699.1	PREDICTED: gibberellin-regulated protein 1 isoform X2 (Beta vulgaris subsp. vulgaris)
PMA12	TGG​TGA​AGC​TTT​GAT​CGA​ACG/TGT​TTT​GGT​TTC​ATG​GCC​CA	59.2/58.5	493	BE034914.1	RecName: full = antimicrobial peptide 1; flags: precursor
PMA13	TAC​AAC​CAG​ACC​ACA​CAC​GG/AAT​CAT​CAT​CCA​ACA​AGA​AGT​GAA​T	59.89/57.29	195	BE033529.1	gibberellin-regulated protein 1-like (Chenopodium quinoa)
PMA14^§	AGT​CCT​GAT​CCA​ATT​CGC​GG/GGA​CTA​CGA​GGA​GTG​TGT​GC	60.18/60.11	197	BE033452.1	PREDICTED: Uncharacterized protein At1g03900 (Beta vulgaris subsp. vulgaris)
PMA15	GCA​GCA​ACC​CCA​CCA​ACT​AA/ACT​CAC​ATA​CCC​AAG​AAT​TCC​A	60.83/57.07	203	BM300387.1	Similar to mipB gene product in Mesembryanthemum crystallinum, encoded by GenBank accession number L36097; MIP homolog; method: conceptual translation supplied by author, partial (Mesembryanthemum crystallinum)
PMA16	CCT​TCC​TTT​CTC​CAT​CAG​CCA/CTT​GGC​TAA​CAC​CGC​AAC​AC	59.72/60.04	240	BE034350.1	transmembrane 9 superfamily member 2-like (Chenopodium quinoa)
PMA17^§	ACT​GAT​GAT​CTG​TGG​TTG​TAT​ACA/TCT​CCA​ACA​CAA​AAG​AAG​ATT​ATG​GA	57.46/58.77	214	BE035316.1	No significant similarity found
PMA18	CGA​TGA​GCA​GAG​GAG​AGA​GA/GAG​GAG​GTT​TTG​TGG​TGG​GG	58.03/60.54	240	BE036430.1	PREDICTED: 40S ribosomal protein S27-2-like (Nelumbo nucifera)
PMA19	AGT​TTT​CTT​TTC​CCT​CCT​CCT​CA/GAA​ATA​GGA​GCG​GGC​GAA​GA	59.28/59.9	228	BE036273.1	Hypothetical protein M569_05046 (Genlisea aurea)
PMA20^§	TTT​CCA​ATG​TCG​GTG​CTC​CA/TGG​CGT​AAC​GGA​TCA​AAT​TTG	59.89/57.52	248	BM301706.1	No significant similarity found
PMA21^§	TCT​AGT​AGT​GCC​CTG​CCT​GT/TCC​CCA​ATA​CAA​CCT​TTC​CCC	59.96/59.64	222	BE036540.1	24-methylenesterol C-methyltransferase 3 (Spinacia oleracea)
PMA22	CGG​CTA​TGT​CCT​CAC​CTG​TG/AGA​CGC​CTC​ACA​GAA​CTA​GTC	60.18/59.19	244	CA834703.1	RecName: full = ferredoxin-1, chloroplastic; AltName: full = ferredoxin I; flags: precursor
PMA23^§	CCT​GCT​TTG​TTA​TTG​CTA​CAT​CGT/TAA​ACG​CCA​GCC​AAT​TGA​GG	59.91/58.83	244	BE036370.1	No significant similarity found
PMA24	CCA​CCT​CCA​AGT​TCT​CCC​CT/TCG​AGT​TCT​CAT​CCA​TGG​CG	60.84/59.9	195	CA840662.1	PREDICTED: E3 ubiquitin ligase BIG BROTHER-related isoform X2 (Theobroma cacao)
PMA25	CAC​GGG​AAA​TTG​GAG​GGT​CA/GTG​GAA​ATG​TAC​ACG​ATA​CGC​A	59.96/59.08	332	BE036805.1	Protein SRC2-like (Chenopodium quinoa)
PMA26	GGG​CAT​GTA​TAA​TTA​TTC​CCC​AAT​GG/GGT​CCC​CGT​TAA​AGC​CCC	60.13/60.04	557	BE035036.1	No significant similarity found
PMA27	TCC​TCC​CTC​ACT​CAC​TTT​CAC/CGG​GTG​GGT​GCG​AAA​GAA​TA	59.03/60.39	241	DY032226.1	No significant similarity found
PMA28	GAC​CCG​CCA​ATC​TTC​TTC​CT/TCT​GAT​GGT​GCC​TTC​CTC​AC	59.75/59.38	239	BM301459.1	CASP-like protein 4C1 (Chenopodium quinoa)
PMA29^§	TTT​TCC​ACT​AAA​TTT​GCA​CCC​TT/AGA​GCA​ATG​GAA​TGT​GGA​AGT​CT	57.38/59.99	250	DR995796.1	PREDICTED: ferredoxin-NADP reductase, leaf isozyme, chloroplastic (Malus domestica)
PMA30^§	TGT​GTG​GAG​CTT​GAT​CAG​GG/ATG​AGT​ACT​ACA​GAT​ACC​GTT​CTT​T	59.67/57.36	218	BE035606.1	Hypothetical protein, partial (Vitis vinifera)
PMA31	CAC​TGT​GGT​TTG​CTC​TGC​TT/GGG​GAA​AAG​GGT​GTA​ATA​GAA​AGG	58.97/59.05	236	BE034885.1	No significant similarity found
PMA32^§	CCC​GGG​CTG​CAG​GAA​TTC/ACC​CAA​TTT​AGC​GGC​CAC​AT	60.83/60.32	236	BE034671.1	No significant similarity found
PMA33	AGT​GGA​GGG​AGA​AAG​GGG​AA/TTT​CGT​GTT​TTA​CCA​TAA​TCC​GAA	59.8/57.2	190	CA837391.1	No significant similarity found
PMA34	ACT​ATT​TGA​TGA​AGC​ACC​TGA​ATG/TCC​CAG​GCT​CCC​AAT​ATA​CCA	57.55/60.06	208	BE577295.1	PREDICTED: zinc finger CCCH domain-containing protein 66 (Beta vulgaris subsp. vulgaris)
PMA35	TTC​CCG​TCA​TCT​CCC​TCT​CT/ACC​AAT​GGC​GGA​GAA​AGT​GT	59.37/59.89	239	AI822921.1	PREDICTED: V-type proton ATPase subunit c″2 (Pyrus x bretschneideri)
PMA36	AGA​CAT​GCA​AAT​TCA​ATC​AAC​CT/TTT​GTA​AAA​GAG​GGC​CCG​GG	57.27/60.25	258	BE033663.1	No significant similarity found
PMA37	CTC​ACC​TCT​TCG​TCT​CCA​GC/ATT​CCA​CCC​TCG​ACG​AAT​CC	59.83/59.54	215	BE035371.1	PREDICTED: mitochondrial uncoupling protein 5 (Beta vulgaris subsp. vulgaris)
PMA38^§	TGG​AAG​ACT​TGC​TCT​CTG​ACT/CCC​CTA​AAT​TTT​AAA​AGC​GGC​C	58.4/58.47	244	BE036658.1	PREDICTED: uncharacterized protein LOC104896568 (Beta vulgaris subsp. vulgaris)
PMA39	CAC​CCT​TCC​ATT​CAA​TGT​TCC​A/CCT​AGA​TTG​AAA​GCG​AAA​GGG​G	58.84/59.05	250	BM300354.1	No significant similarity found
PMA40^§	GCA​TTT​ATT​CCT​TTT​CTA​CAT​CTT​GC/AGA​TGT​GTT​TCC​GGG​TAT​TCC​T	57.65/59.16	227	CA835303.1	chloroplast envelope membrane protein (chloroplast) (Mesembryanthemum crystallinum)
PMA41	TCT​CTC​TCC​TCC​ATT​GTT​GAT​TGT/GTG​GCC​GGA​GAT​ATG​AGC​TG	59.47/60.32	194	BM300809.1	No significant similarity found
PMA42	CCA​CCA​GTC​ACA​ATA​TTA​CAC​GC/AGA​CGA​ATA​GGT​TAG​TGT​GTT​CAG​T	59.94/59.76	693	BE034183.1	No significant similarity found
PMA43	CTT​CCC​TCA​GGC​TGC​GAG/AGG​GTT​AGG​CAT​TGT​TGT​TGG​A	59.81/60.16	247	BE033637.1	PREDICTED: peptidyl-prolyl cis-trans isomerase 1 (Vigna angularis)
PMA44^§	TGC​AAT​ATC​TGG​AAA​CGC​GA/TGA​AAT​GAT​AGA​GAG​ATC​CAC​CAG​G	57.98/59.69	297	CA835421.1	chloroplast envelope membrane protein (chloroplast) (Mesembryanthemum crystallinum)
PMA45	TCC​TGT​GCT​CAT​TTT​CCT​CTG​T/TTC​CGC​CCC​TGT​CCT​AAA​TG	59.63/59.75	295	BE036291.1	No significant similarity found
PMA46	CTC​CGA​CAT​GCA​GAA​CTC​CC/GCT​AGC​TGG​TCT​GGG​TTG​AA	60.46/59.68	243	BG269304.1	No significant similarity found
PMA47	TCG​GGC​TGC​AGG​AAT​TCG/GGC​AAG​CAA​AAC​AAC​AAG​GA	60.13/57.69	250	BE034598.1	Hypothetical protein BVRB_5g115740 (Beta vulgaris subsp. vulgaris)
PMA48^§	CTG​AGT​CCC​GTT​GCT​AGA​CC/GTG​TAT​GAC​GTT​GCG​CTC​G	59.83/59.66	242	BE033493.1	No significant similarity found
PMA49^§	CGG​GTT​CGT​CGA​TAA​AAG​AAA​GA/TCC​TTT​CTC​TGT​TGT​TGT​TTC​TCT	59.08/58.25	216	CA837106.1	PREDICTED: tubulin alpha-3 chain-like, partial (Raphanus sativus)
PMA50	AGG​AAA​CAA​AGG​AGC​GGC​TC/GGT​TGA​CCT​CCC​AAT​CTC​GT	60.61/59.39	244	AW266506.1	BEL1-like homeodomain protein 1 (Chenopodium quinoa)
PMA51	ATT​GTG​TTA​TGA​GCT​TAT​GTG​TTC​A/TCC​TCC​TTA​TAT​GGG​CCA​GTT​G	57.31/59.29	230	BE035895.1	PREDICTED: peamaclein-like (Juglans regia)
PMA52	ACA​AAC​AAC​AAA​CAA​CAA​ACA​ACA​CT/GCC​CTT​GTT​CTT​GAT​GCG​GA	59.91/60.96	249	BF479882.1	Hypothetical protein BVRB_3g062460 (Beta vulgaris subsp. vulgaris)
PMA53	CCC​GGG​CTG​CAG​GAA​TTC/TGA​CAC​TCA​ATC​ACT​CGG​CG	60.83/60.39	190	BE033624.1	No significant similarity found
PMA54	CCA​ATT​CAA​GAG​CCG​CAC​TG/GGT​GGA​AGG​AGA​GAG​GGT​GA	59.83/60.25	347	BE034293.1	gibberellin 2-beta-dioxygenase 2-like (Chenopodium quinoa)
PMA55^§	CAA​GCT​GGG​ATA​ATG​GTG​TCA/AGG​ATG​GAA​GAG​AAA​GAG​AGA​AAA	58/57.31	241	BE037070.1	PREDICTED: triosephosphate isomerase, chloroplastic (Beta vulgaris subsp. vulgaris)
PMA56	GAG​ATA​AGC​ACC​TGG​GCC​TG/TAA​TGC​TTG​GGT​GGT​GGT​GG	60.18/60.25	214	BF480398.1	Hypothetical protein VITISV_000212 (Vitis vinifera)
PMA57^§	TCT​GGA​ACT​AGT​ATG​TTG​ATG​GAG​T/ATA​AGG​GGA​AAT​TGG​GGC​CG	59.04/60.11	242	BE035959.1	No significant similarity found
PMA58	AGG​GAG​TTT​GTA​TGT​CAG​CCA/CTC​ACT​AGG​CAA​TGG​ACC​GG	59.01/60.18	239	BE035417.1	No significant similarity found
PMA59	TGG​TTG​GAG​AAG​ATG​GAA​GAC​A/CTC​ATC​AAA​TCA​TGC​TGC​CTC​A	59.02/59.05	248	CA840173.1	No significant similarity found
PMA60	TGT​TCT​AGT​CCC​GTC​CGC​AT/AAG​GAG​GGA​AGG​AGG​GAA​GG	60.97/60.25	598	BE034770.1	No significant similarity found
PMA61	CTC​TCG​CTG​CTC​CAT​CCC​TT/TGA​GTT​GGA​TTG​GAA​ATT​AGG​GA	61.68/57.47	203	BE577610.1	No significant similarity found
PMA62^§	CCC​GGT​GTT​GGT​GGT​AGA​TAG/TGC​CGA​GAA​ATA​GGA​AAG​AAC​A	59.86/57.72	343	BE035340.1	No significant similarity found
PMA63^§	TCG​ACC​TCC​ATC​TCC​ACT​GT/TTT​TAC​CCA​AGA​GCC​GAA​CG	59.96/58.48	823	BE033728.1	No significant similarity found
PMA64^§	CAG​AAT​CCA​TCC​CAT​ACT​TCC​CA/AGG​ATA​ATG​ATG​ATT​TTG​GGT​TTG​GA	59.6/59.1	212	BM302080.1	Uncharacterized protein LOC110734179 (Chenopodium quinoa)
PMA65	AGA​AAT​TAT​TGG​AAA​TTG​TTT​GGC​C/CAA​TCT​GAA​GGG​AGA​GCG​CC	57.31/60.81	208	BE036649.1	No significant similarity found
PMA66	TTT​GGG​CTG​CTT​CTG​GGA​TT/ACC​ACA​CCT​TCA​TTT​ACA​CCC	59.89/58.13	487	BE036567.1	No significant similarity found
PMA67^§	AGG​TCA​GAA​GGA​ATC​GGC​AC/AGT​AAA​TTT​GTG​TTT​TGA​AAG​GGG​A	59.75/57.81	233	BE035280.1	No significant similarity found
PMA68	CCC​TCG​TTG​ACA​CTG​GCA​TA/TCT​AGG​GGT​TTT​GGG​CGT​TG	59.75/60.25	488	BE036046.1	No significant similarity found
PMA69^§	TGT​GGT​GCA​ATT​CTC​TCA​TTC​A/TGT​TCT​GTC​CCG​GCC​TTT​T	58.25/59.47	300	BE036153.1	No significant similarity found
PMA70	AGA​GCA​GCT​GAA​CCA​ACC​AA/TTG​GAA​TTC​TGC​ATC​TGG​GC	59.82/58.52	284	CA840329.1	PREDICTED: probable protein phosphatase 2C 27 (Beta vulgaris subsp. vulgaris)
PMA71	GGA​AGA​GGG​ATG​TTC​GCC​AA/GGG​AAA​ATT​TGG​GGA​AGG​GG	60.04/58.71	359	BE034955.1	No significant similarity found
PMA72	CCT​CTG​CCA​ATC​TTC​TTC​CCC/GCA​GCT​TGA​GGG​AGA​GAG​AA	60.41/59.1	244	BF479953.1	No significant similarity found
PMA73	AAT​CCA​TGG​CCT​TGT​GAA​GC/TGT​GTT​TTG​GGA​GGG​GTG​TT	58.81/59.66	297	BE033627.1	No significant similarity found
PMA74	CTT​CTA​GCT​GCA​GGA​ATT​CGG/GCA​AAG​AAA​CAC​ACC​CTC​CG	58.79/59.69	287	BE037450.1	Salt-inducible zinc finger 1 (Sesuvium portulacastrum)
PMA75	GCC​GAA​TTT​GGG​ACG​AGG/AAA​GGA​GAC​CGC​CCC​GAG	58.5/61.39	250	BE035632.1	No significant similarity found
PMA76^§	GGA​GGA​GAG​GAG​AGG​AGA​GG/AAT​TGG​GCG​CGG​GAA​ATA​AC	59.52/59.54	400	BE035976.1	Hypothetical protein M569_05046, partial (Genlisea aurea)
PMA77^§	AAA​CCC​TTT​TAC​CAC​CCA​AAT​C/GGA​CTT​TCC​CGG​TGG​TTG​G	57.03/60.6	494	BE036766.1	No significant similarity found
PMA78	CCA​GGC​CTT​AAG​ATG​CTG​CA/CAA​AAG​CAC​ACG​GGG​AAC​AA	60.39/59.54	393	BE036806.1	Polyadenylate-binding protein (Medicago truncatula)
PMA79^§	GAC​TGA​AGT​AAT​TCG​CGG​CC/CGC​GCT​TTG​TGT​TTC​TCT​CC	59.35/60.11	398	BE033686.1	No significant similarity found
PMA80^§	ATA​GGT​CTG​CAG​GCA​TTC​G/GGG​TTA​AGG​GGC​GCG​TAA	57.31/59.73	460	BE034828.1	No significant similarity found
PMA81	AAC​GCT​CAT​CTC​CTG​CTG​TC/TTG​GTG​GTT​GTG​TTG​GGG​TT	60.11/60.25	500	BE033954.1	No significant similarity found
PMA82	TCC​CAC​GAC​TGC​AGG​AAT​TC/CTA​GCG​GGG​TAT​GAG​TGA​GC	60.04/59.68	471	BE033727.1	No significant similarity found
PMA83^§	ATG​CGC​CGA​CAC​TCC​GAG/GCT​TTC​TGT​GCG​TGT​GTG​C	62.5/60.66	600	BE033402.1	No significant similarity found

^§Selected for diversity analysis.