Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

Kpatènon, Mariano Joly; Salako, Kolawolé Valère; Santoni, Sylvain; Zekraoui, Leila; Latreille, Muriel; Tollon-Cordet, Christine; Mariac, Cédric; Jaligot, Estelle; Beulé, Thierry; Adéoti, Kifouli

doi:10.1186/s12863-020-00955-y

Table 8 Characteristics of the palm SSR markers tested for transferability to B. aethiopum

From: Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

Marker name	Primer sequences (5′-3′ orientation)	T_a (°C)	Source palm species	Successful transfer to other palm species	References
mEgCIR0230	CCCTGGCCCCGTTTTTC	57.0	E. guineensis	E. oleifera Syragus sp. C. nucifera P. roebelinii P. canariensis P. reclinata	[62]
mEgCIR0230	AGCGCTATATGTGATTCTAA	57.0
mEgCIR0326	GCTAACCACAGGCAAAAACA	59.0
mEgCIR0326	AAGCCGCACTAACATACACATC	59.0
mEgCIR0465	TCCCCCACGACCCATTC	63.1
mEgCIR0465	GGCAGGAGAGGCAGCATTC	63.1
mEgCIR0476	TTCCTCGGCCCCTTCTC	61.6
mEgCIR0476	TCGCCGACCTTCCACTG	61.6
EgCSSR-5781	TTCACGCTACTGATGGTTGG	59.4	E. guineensis	B. flabellifer	[49]
EgCSSR-5781	TCGATCCCTTCTCTGGAAAC	59.4
EgCSSR-1461	GTCCTCTCCTACGCCTCCTC	60.3
EgCSSR-1461	ATGCGATCCGAGTTCAGAAG	60.3
mEgCIR2332	GAAGAAGAGCAAAAGAGAAG	55.0	E. guineensis.	B. flabellifer	[44, 45]
mEgCIR2332	GCTAGGTGAAAAATAAAGTT	55.0
mEgCIR3295	TGCCTCCAGACAATCAC	55.0
mEgCIR3295	GTAAGGCTTAACCAGATAAC	55.0
mEgCIR3311	AATCCAAGTGGCCTACAG	55.0
mEgCIR3311	CATGGCTTTGCTCAGTCA	55.0
mEgCIR3413	AAAGCTATGGGGTGAAAGAT	55.0
mEgCIR3413	TGGATAAGGGCGAGAAGAGA	55.0
mEgCIR3477	CCTTCAAGCAAAGATACC	55.0
mEgCIR3477	GGCACCAAACACAGTAA	55.0
mEgCIR3592	GAGCCAAAACAGACTTCAA	55.0
mEgCIR3592	ACCGTATATGACCCCTCTC	55.0
mEgCIR3755	GCTCACCAAAAAGTGTTAAGTC	55.0
mEgCIR3755	AGTTTCAACGGCAGGTATAT	55.0
mEgCIR3788	TTGTATGACCAAAGACAGC	55.0
mEgCIR3788	AGCGCAACATCAGACTA	55.0
ESSR75	AGATGGTTGGAGATTTCATGGT	60.0	E. guineensis	B. flabellifer	[44, 45, 47]
ESSR75	AACTTGAGGGTGCCATTACAAG	60.0
ESSR76	CCATACCAGCAGAAGAGGATGT	60.0
ESSR76	CTGAAGGTCATAGGGGTCTCTG	60.0
ESSR82R	CCCTCGACACCCATAGTTATTT	60.0
ESSR82R	CTCGATTTCTGGCCTCTCATAC	60.0
ESSR332	AGTTAATGTGTCAGGGCCAGTT	60.0
ESSR332	CTTGGTTCACTTGGGTGTGTC	60.0
ESSR553	ATAAATTGTGCGAGGGGAAAAC	60.0
ESSR553	AGATCCGCGACAGGTCTTAAC	60.0
ESSR566	GTGTCATCAAATTCGGTCCTTT	60.0
ESSR566	CGGTTCTTCTGCTGCTCTACTT	60.0
ESSR609	AGGCGGTGATGAAGATGAAG	59.0
ESSR609	CTCCTCTCAAACAGAGTGGGAT	59.0
ESSR650	GCCTTTTCTGGTTAATGGACTG	59.0
ESSR650	GTTTGTCTATGGATGATTGTGAGG	59.0
ESSR652	CATACCGTCACCACTCAGAAAC	60.0
ESSR652	GCCGTCATTCTACCAGTTGAG	60.0
ESSR673	TTCTGGCTACGAGCATAAGGA	59.0
ESSR673	TCAATAACCCTGGCTAAACACA	59.0
ESSR681	TCTGAATTGTCGGAGTGGC	59.0
ESSR681	CATCCTTGCGTAAACAAAAGAG	59.0
CNZ34	CATGTCGATAATTATACCCAA	55.0	C. nucifera	B. flabellifer K.laciniosa Z. zalacca D.kurzianus C.simplicifolia C. mannan C. thwaitesii C. erectus C. palustris	[46, 63]
CNZ34	TGCAAATATGAATGCAAACAC	55.0
CN2A5	AAGGTGAAATCTATGAACACA	53.2
CN2A5	GGCAGTAACACATTACACATG	53.2
CNZ 12	TAGCTTCCTGAGATAAGATGC	54.6	C. nucifera	B. flabellifer P. dactylifera E. guineensis	[46, 64]
CNZ 12	GATCATGGAACGAAAACATTA	54.6
CNZ 24	TCCTAAGCTCAATACTCACCA	55.0
CNZ 24	CGCATTGATAAATACAAGCTT	55.0
CNZ 18	ATGGTTCAGCCCTTAATAAAC	60.3
CNZ 18	GAACTTTGAAGCTCCCATCAT	60.3
CNZ 42	TGATACTCCTCTGTGATGCTT	55.5
CNZ 42	GTAGATTGTGGGAGAGGAATG	55.5
CN2A4	CAGGATGGTTCAAGCCCTTAA	61.0
CN2A4	GGTGGAAGAGGGAGAGATTGA	61.0
CAC 21	AATTGTGTGACACGTAGCC	54.1	C. nucifera	B. flabellifer	[65, 66]
CAC 21	GCATAACTCTTTCATAAGGGA	54.1
CAC 71	ATAGCTCAAGTTGTTGCTAGG	54.2
CAC 71	ATATTGTCATGATTGAGCCTC	54.2
CAC 84	TTGGTTTTTGTATGGAACTCT	54.4
CAC 84	AAATGCTAACATCTCAACAGC	54.4
CN1H2	TTGATAGGAGAGCTTCATAAC	53.2	C. nucifera	B. flabellifer P. dactylifera	[65]
CN1H2	ATCTTCTTTAATGCTCGGAGT	53.2	C. nucifera	B. flabellifer P. dactylifera	[65]
PdAG-SSR	TCTGATTTCGTTTACTTCTTAGGA	58.0	P. dactylifera		[44]
PdAG-SSR	TTCATATTCAGTTGTCGGGTGTA	58.0
mPdCIR015	AGCTGGCTCCTCCCTTCTTA	59.1
mPdCIR015	GCTCGGTTGGACTTGTTCT	59.1
mPdCIR063	CTTTTATGTGGTCTGAGAGA	52.5
mPdCIR063	TCTCTGATCTTGGGTTCTGT	52.5
mPdIRD1	CTCGGAAGGGTATGGACAAA	59.6	P. dactylifera	P. reclinata P. roebelenii P. rupicola P. theophrasti H. thebaica L. carinensis C. humilis	[67]
mPdIRD1	TTGCCTTCGACGTGGTAGTA	59.6
mPdIRD3	CATTGATCCAACACCACCAC	60.3
mPdIRD3	GCCAAAACCAGCTCTGGTAAC	60.3
mPdIRD4	TTGGTGGCCTTTCTCAGAGT	59.8
mPdIRD4	TGGGATCAAAGTAGGGTTGG	59.8
mPdIRD5	CTATCAGGATGGGGGTGATG	60.2
mPdIRD5	ACCCATCTGCATAGCTCCAG	60.2
mPdIRD7	TGCAATACGATGGCAGAGTC	60.2
mPdIRD7	CCTTGCAAGTTTTCCACACC	60.2
mPdIRD8	CTATTGGGTCCCTTGGTGAG	59.7
mPdIRD8	TGACTGCTCGTCATCAGGTC	59.7
mPdIRD10	ATGCGTTCATCTCCCTTGAG	59.7
mPdIRD10	GCTGCAAACATCATCCTCAC	59.7
mPdIRD11	GAGTTGGAGGCAAAACCAGA	59.8
mPdIRD11	CCACAAAACCCTTGTCTTCC	59.8
mPdIRD14	GAGGGGTTCACGTTTGTGTC	60.9
mPdIRD14	GCACCAAGCACAAGAGCAAT	60.9
mPdIRD15	CCGAGTCTGGCGAAGTAAAC	60.0
mPdIRD15	CTCCCCTTCCTCATCCTCTC	60.0
mPdIRD16	CTGTCCGATCGAATTCTGC	50.7
mPdIRD16	GGACATCTCTTTGCGGTCAT	50.7
mPdIRD17	GTGGGAGAAACCCGAAGAAT	60.2
mPdIRD17	CTGCTGCCTCATCTGCATT	60.2
mPdIRD20	TTGAATGGTCCCCTGTAGGT	59.5
mPdIRD20	GTCCCAGCATGATTGCAGTA	59.5
mPdIRD22	GGCTGTATGGGAAAGACCTG	59.5
mPdIRD22	CCTGCTGCATATTCTTCGTG	59.5
mPdIRD24	GCTCCTGCAGAACCTGAAAC	59.9
mPdIRD24	GGACATCACCGTCCAATTCT	59.9
mPdIRD25	CACTGGAAATTCAGGGCCTA	59.9
mPdIRD25	CCCAATTTCTCAGCCAAGAC	59.9
mPdIRD26	CCTCCAGTTCATGCTTCTCC	60.0
mPdIRD26	GAGCAGACCCGACAGACAAT	60.0
mPdIRD28	GAAACGGTATCGGGATGATG	59.7
mPdIRD28	TTAACGACGCCGTTTCCT	59.7
mPdIRD29	GGCTCCACCATCATTGACA	60.3
mPdIRD29	AACAGCATCGACTGCCTTCT	60.3
mPdIRD30	GCAGATGGTTGAAAGCTCCT	59.8
mPdIRD30	CCCCATTAACAGGATCAACG	59.8
mPdIRD31	GCAGGTGGACTGCAAAATCT	60.0
mPdIRD31	CTATTGGGGTGCTGATCCAT	60.0
mPdIRD32	AAGAAGACATTCCGGCTGGT	59.9
mPdIRD32	GCGGGTGTGTGATATTGATG	59.9
mPdIRD33	GGAGCATACAGTGGGTTTGC	60.1
mPdIRD33	CAGCCTGGGAATGAGGATAG	60.1
mPdIRD35	CAGCCCCTTACTCAGACTGG	59.6
mPdIRD35	CCCATAAGCTGATTGTGCTG	59.6
mPdIRD36	GACACGTTGACGATGTGGAA	60.7
mPdIRD36	CCATTGCTGTTGAGGAGGAG	60.7
mPdIRD37	TTTCCTGCTCGAAAGACACC	60.2
mPdIRD37	CTTAGCCAGCCTCCACACTC	60.2
mPdIRD40	GAGAGATGCGTCAGGGAATC	59.2
mPdIRD40	CCAGAATCTTCCAAGCAAGC	59.2
mPdIRD42	GAGGCAAAACTATGGGAAGC	59.5
mPdIRD42	TTCACTGGAGCAAGGGTAGG	59.5
mPdIRD43	GCAGCCATTGCTTACAGTGA	60.2
mPdIRD43	TAAACTGCTGCCTTCCTTGG	60.2
mPdIRD44	CAGATCCGGGAGATGATGAA	60.4
mPdIRD44	AGCAGGAGCAGCTGCATAA	60.4
mPdIRD45	TAGCCTGTGCATGTTCGTTG	60.4
mPdIRD45	AACAGCAGCTGATGGTGATG	60.4
mPdIRD46	ATGGGTCCATTGGAGGAACT	60.2
mPdIRD46	GACGGAGACCTTGACTGCTC	60.2
mPcCIR10	ACCCCGGACGTGAGGTG	62.8	P. dactylifera		Cherif, Castillo and Aberlenc-Bertossi, unpublished data.
mPcCIR10	CGTCGATCTCCTCCTTTGTCTC	62.8
mPcCIR20	GCACGAGAAGGCTTATAGT	51.7
mPcCIR20	CCCCTCATTAGGATTCTAC	51.7
mPcCIR32	CAAATCTTTGCCGTGAG	53.3
mPcCIR32	GGTGTGGAGTAATCATGTAGTAG	53.3
mPcCIR35	ACAAACGGCGATGGGATTAC	60.8
mPcCIR35	CCGCAGCTCACCTCTTCTAT	60.8
mPcCIR50	CTGCCATTTCTTCTGAC	50.6
mPcCIR50	CACCATGCACAAAAATG	50.6
mPcCIR57	AAGCAGCAGCCCTTCCGTAG	62.0
mPcCIR57	GTTCTCACTCGCCCAAAAATAC	62.0
mPcCIR85	GAGAGAGGGTGGTGTTATT	51.8
mPcCIR85	TTCATCCAGAACCACAGTA	51.8
mPdIRD41	ATCTTCCATGCAGCCTCAAG	60.3
mPdIRD41	CAGGTCGTCCCGTCTCTAAA	60.3
mPdIRD47	GTTGGCATCACTTCAGAGCA	60.1
mPdIRD47	GCTCTTTCGGTGCTAGTTGC	60.1

For each marker, forward (top) and reverse primers (bottom) are provided
T_a: average annealing temperature for each primer pair
Species names are abbreviated as follows: P. roebelinii: Phoenix roebelinii; P. canariensis: Phoenix canariensis; Phoenix reclinata; H. thebaica: Hyphaene thebaica; L. carinensis: Livistona carinensis; C. humilis: Chamaerops humilis; K. laciniosa: Korthalsia laciniosa; Z. zalacca: Zalacca zalacca; D. kurzianus: Daemonorops kurzianus;C. simplicifolia: Calamus simplicifolia;C. mannan: Calamus mannan; C. thwaitesii: Calamus thwaitesii; C. erectus: Calamus erectus; C. palustris: Calamus palustris; P. rupicola: Phoenix rupicola; P. theophrasti: Phoenix theophrasti

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