RAD sequencing for the development of microsatellite markers for identification of Malaysian taro cultivars

Figures & data

Table 1. List of SSR markers used to characterise taro cultivars.

SSR ID	Primer sequence	Acc. number*
CesSSR1	F: TGAGGAGTTGTTGTGCCTC	LC484345
	R: AATAACGGCGCGAGTTTGG
CesSSR2	F: GAAATGATGTGAAGACAGCGG	LC484346
	R: ATTCCAGCCCAGGTGACAG
CesSSR3	F: GGGAGAAGGGCTCGGAAG	LC484347
	R: TACCCAACCCAAATACGGC
CesSSR4	F: AACGACTATAAGGAGATTTGATAGC	LC484348
	R: TGAGAAGGGTCAGCAGTTC
CesSSR5	F: CCCAGAAACTCTCAGCGAAG	LC484349
	R: AGCCCAATCAAGAGAACCC
CesSSR6	F: TGGGCTAAGTTCTTGGGTTAG	LC484350
	R: CCACATGTCTCGGTTGCAG
CesSSR7	F: ACGGGTCTTACTGTGTGGAC	LC484351
	R: TTCCTACGGCCGCTTTCTG
CesSSR8	F: CCACAATATTTGTTATGGTTAGTCCC	LC484352
	R: CGCTCTGACTTTGGGCTATG
CesSSR9	F: CGCGATCGAGCCATAGCC	LC484353
	R: TGTACTAGTGTCTGGTTACTATTGAG
CesSSR10	F: TCTTGAACGCGAAACATGAAAG	LC484354
	R: GCTCCTAAGTCCTAACCGTACC
CesSSR11	F: AGAGATTAGCAAGTTTGGATATGG	LC484355
	R: TCTAACTCAGATCTCTAATGCCAC
CesSSR12	F: GCTCTAGGTGACAAAGGATGC	LC484356
	R: ACCCTGCACAATGTATTTCAGC
CesSSR13	F: CTGCCTCAGTCATGCCAAC	LC484357
	R: TCTCACCAAAGGTATACTAAAGAAGG
CesSSR14	F: CCTTCATTTCACATAGCCTCTCAAG	LC484358
	R: TATAGCTCGAGGACACGGG

* GenBank accession number, NCBI/DDBJ.

Table 2. Statistical summary of RAD sequencing data for microsatellites.

Clean bases	2,479,455,351
Clean reads	8,490,604
Total Contig	222,445
Contigs containing repeats	3280
Total repeats found	3454
Total successfully design Primer	1790
No. of selected SSR for cultivar identification	14

Table 3. The abundance of repeat motifs type found in this study.

Repeat types	No. of repeats	% No. of repeats
Dinucleotide	2,760	79.9
Trinucleotide	631	18.3
Tetranucleotide	40	1.2
Pentanucleotide	15	0.4
Hexanucleotide	8	0.2
Total	3,454	100.00

Table 4. Abundance of the motif.

Repeat motif	Frequency	% Frequency
CT	707	20.5
AG	701	20.3
AT	612	17.7
AC	414	12.0
GT	311	9.0
CG	15	0.4
AAG	103	3.0
CTT	99	2.9
AGC	51	1.5
GCT	49	1.4
CCT	42	1.2
AAT	41	1.2
AGG	41	1.2
ATT	39	1.1
AAC	37	1.1
GAT	35	1.0
ACC	21	0.6
GTT	21	0.6
ATC	20	0.6
GGT	10	0.3
CGG	8	0.2
CCG	5	0.1
ACT	3	0.1
CGT	3	0.1
AGT	2	0.1
ACG	1	0.0
Others	63	1.8
Total	3454	100.0

Table 5. Characterisation of novel microsatellite markers.

Marker	Major allele frequency	Allele number	Gene diversity	Heterozygosity	PIC
CesSSR1	0.64	6	0.54	0.24	0.51
CesSSR2	0.82	5	0.32	0.05	0.31
CesSSR3	0.93	4	0.13	0.13	0.12
CesSSR4	0.89	3	0.19	0.00	0.18
CesSSR5	0.97	2	0.06	0.00	0.05
CesSSR6	0.50	5	0.63	0.68	0.56
CesSSR7	0.57	5	0.62	0.18	0.59
CesSSR8	0.86	3	0.25	0.08	0.23
CesSSR10	0.75	3	0.40	0.03	0.36
CesSSR12	0.75	4	0.41	0.16	0.38
CesSSR13	0.67	7	0.50	0.37	0.45
CesSSR14	0.89	3	0.19	0.16	0.18
Mean (polymorphic only)	0.77	4.17	0.35	0.17	0.33

Figure 1. UPGMA dendrogram generated based on shared allele genetic distance of studied cultivar.

Table 6. Pairwise genetic distance of studied cultivars based on 12 novel microsatellite marker.

OTU	BADAK_A7	CINA_A16	MAWAR_A11	MAWAR_B2	MERAH_60	MINYAK_C17	PUTIH_20	PUTIH_58	PUTIH_G_MUSANG	TELUR	UDANG_C17	WANGI _A1	WANGI_B4
BADAK_A7	0.00	0.07	0.25	0.25	0.12	0.06	0.06	0.06	0.06	0.70	0.61	0.40	0.52
CINA_A16	0.07	0.00	0.27	0.27	0.10	0.02	0.02	0.02	0.02	0.72	0.62	0.43	0.52
MAWAR_A11	0.25	0.27	0.00	0.00	0.29	0.25	0.25	0.25	0.25	0.71	0.67	0.50	0.52
MAWAR_B2	0.25	0.27	0.00	0.00	0.29	0.25	0.25	0.25	0.25	0.71	0.67	0.50	0.52
MERAH_60	0.12	0.10	0.29	0.29	0.00	0.10	0.10	0.10	0.10	0.71	0.53	0.39	0.51
MINYAK_C17	0.06	0.02	0.25	0.25	0.10	0.00	0.00	0.00	0.00	0.71	0.63	0.43	0.52
PUTIH_20	0.06	0.02	0.25	0.25	0.10	0.00	0.00	0.00	0.00	0.71	0.63	0.43	0.52
PUTIH_58	0.06	0.02	0.25	0.25	0.10	0.00	0.00	0.00	0.00	0.71	0.63	0.43	0.52
PUTIH_G_MUSANG	0.06	0.02	0.25	0.25	0.10	0.00	0.00	0.00	0.00	0.71	0.63	0.43	0.52
TELUR	0.70	0.72	0.71	0.71	0.71	0.71	0.71	0.71	0.71	0.00	0.62	0.75	0.70
UDANG_C17	0.61	0.62	0.67	0.67	0.53	0.63	0.63	0.63	0.63	0.62	0.00	0.50	0.62
WANGI_A1	0.40	0.43	0.50	0.50	0.39	0.43	0.43	0.43	0.43	0.75	0.50	0.00	0.55
WANGI_B4	0.52	0.52	0.52	0.52	0.51	0.52	0.52	0.52	0.52	0.70	0.62	0.55	0.00

Data availability

All data that support the findings reported in this study are available from the corresponding author upon reasonable request.