Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

Hendre, Prasad Suresh; Phanindranath, Regur; Annapurna, V; Lalremruata, Albert; Aggarwal, Ramesh K

doi:10.1186/1471-2229-8-51

Table 4 Allelic diversity attributes of new SSR markers as revealed across elite genotypes of arabica and robusta, and related coffee taxa

From: Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

Primer Id	C. arabica (n = 8)						C. canephora (n = 8)						Coffea spp. (n = 12)			Psilanthus spp. (n = 2)
	N_A	PA^$	Allele range	H_o	H_e	PIC	N_A	PA^$	Allele range	H_o	H_e	PIC	N_A	PA^$	Allele range	N_A	PA^$	Allele range
CaM02	2	0	252–262	Duplicated loci			2	0	256–268	0.71	0.69	0.67	8	4^a,c,k,l	252–278	2	0	262–272
CaM03	6	1⁶	164–184	0.38	0.74*	0.70	6	0	171–194	0.63	0.88	0.83	12	5^c,e,f,j,l	165–201	1	1^m	187
CaM06	3	0	285–327	Duplicated loci			2	0	275–277	1.00	0.53*	0.56	4	1^j	275–289	2	0	275–281
CaM08	1	0	210	Monomorphic			3	1¹⁶	201–205	0.50	0.43	0.40	4	2^b,l	142–201	1	1ⁿ	254
CaM09	1	0	135	Monomorphic			3	1¹⁶	135–139	0.50	0.43	0.40	7	5^a,b,g,l	124–211	NA	--	--
CaM11	1	0	286	Monomorphic			1	0	286	Monomorphic			4	2^c,h	278–295	NA	--	--
CaM12	1	0	137	Monomorphic			4	1¹⁰	122–137	1.00	0.65**	0.61	4	1^g	124–137	2	0	131–137
CaM13	2	1⁵	281–286	0.00	0.23	0.23	1	0	286	Monomorphic			7	3^j,k	278–336	2	1ⁿ	255–283
CaM15	2	0	167–170	Duplicated loci			1	0	167	Monomorphic			2	1^l	164–167	2	2^m,n	153–156
CaM16	3	0	187–198	0.63	0.51	0.49	4	1¹¹	181–198	0.75	0.74	0.72	9	2^c,l	177–198	2	0	191–193
CaM17	2	0	175–181	0.88	0.53	0.55	2	0	175–181	0.63	0.46	0.48	3	1^l	162–181	2	0	175–181
CaM18	5	0	180–189	Duplicated loci			5	0	178–186	0.38	0.79**	0.75	12	5^d,e,j,k	174–189	1	0	175
CaM20	2	0	184–192	0.13	0.46	0.48	3	0	192–200	0.13	0.42*	0.40	3	1^d	192–198	NA	--	--
CaM21	2	0	158–164	Duplicated loci			4	1¹⁰	158–162	0.25	0.64**	0.62	9	3^a,j,l	154–178	3	3^m,n	161–172
CaM22	1	0	103	Monomorphic			6	2^9,16	99–110	0.43	0.86**	0.80	8	2^c,l	82–122	1	0	88
CaM23	1	0	154	Monomorphic			1	0	154	Monomorphic			3	1^l	140 154	2	2^m,n	152–158
CaM24	2	0	191–197	0.00	0.50**	0.52	4	0	191–198	0.43	0.71	0.67	8	4^a,b,g,l	178–204	2	2^m,n	177–189
CaM25	4	0	182–185	0.13	0.53**	0.5	3	0	182–184	0.63	0.51	0.48	5	0	182–186	2	0	182–186
CaM26	3	0	252–259	0.00	0.43**	0.42	5	0	247–255	0.25	0.80**	0.76	11	3^g,h,k	241–262	1	0	254
CaM27	3	0	150–169	0.13	0.34	0.33	3	0	161–169	0.88	0.68	0.64	8	2^a,c	150–169	2	0	161–168
CaM30	2	0	216–229	0.13	0.13	0.12	2	0	216–218	0.63	0.46	0.48	7	2^f,j	212–229	4	3^m,n	210–225
CaM31	3	0	258–261	Duplicated loci			4	0	258–262	0.38	0.59	0.57	6	2^h,k	258–267	1	1^m	265
CaM32	4	0	127–145	0.88	0.69	0.68	5	1¹⁴	145–158	0.75	0.72	0.68	10	2^a,e	127–164	3	1^m	133–145
CaM33	3	2^1,6	230–233	0.13	0.34	0.32	7	2^12,13	226–241	0.71	0.88	0.83	11	5^b,d,f,i,k	213–143	1	1^m	217
CaM34	2	0	194–199	Duplicated loci			2	0	198–200	0.00	0.23	0.23	5	2^e,l	194–209	2	2^m,n	166–171
CaM35	3	0	192–211	Duplicated loci			4	0	198–211	0.63	0.69	0.66	7	1^g	186–211	1	0	204
CaM36	5	3^3,7,8	228–253	0.00	0.85**	0.78	7	6^{except 10,15}	230–268	0.17	0.92**	0.86	10	8 ^{a,c,e,f,h,i,h,l}	181–262	1	1ⁿ	190
CaM38	6	14	214–226	0.38	0.86**	0.81	5	2^9,10,^12,15	227–235	0.17	0.80**	0.74	6	2^b,d	220–241	2	0	223–227
CaM39	2	0	174–186	Duplicated loci			3	0	180–194	1.00	0.59*	0.60	9	2^b,h	174–205	3	3^m,n	208–229
CaM40	5	15	230–240	0.40	0.82	0.75	7	1¹⁶	226–242	0.50	0.91*	0.86	8	2^d,e	232–246	3	0	233–239
CaM41	6	4^5,6,8	232–243	0.25	0.68**	0.65	5	1⁹	234–242	0.25	0.81**	0.77	4	0	235–242	2	1ⁿ	237–244
CaM42	2	0	192–196	0.75	0.50	0.52	2	0	190–192	0.00	0.53*	0.56	7	2^e,l	173–199	2	2^m,n	191–195
CaM43	3	0	196–211	Duplicated loci			4	2^11,15	198–203	0.63	0.64	0.64	10	4^b,c,e,f	188–224	2	1ⁿ	192–196
CaM44	2	16	215–217	0.00	0.23	0.23	2	0	224–226	0.00	0.23	0.23	10	3^c,h,l	194–227	3	1ⁿ	221–227
CaM45	3	0	151–182	0.50	0.43	0.42	5	2^10,13	151–235	0.75	0.6	0.57	8	3^d,i,k	147–214	3	1^m	145–193
CaM46	4	2^3,6	208–228	0.38	0.69	0.65	6	1¹⁴	208–223	0.38	0.82**	0.78	7	1^e	208–234	2	1ⁿ	208–212
CaM49	3	0	191–194	0.38	0.68**	0.66	4	0	190–194	0.71	0.76	0.72	8	3^g,j,k	186–194	NA	--	--
CaM52	2	0	157–159	0.00	0.23	0.23	3	0	148–158	0.13	0.34	0.33	5	0	148–158	1	0	155
CaM53	1	0	172	Monomorphic			3	2²	167–190	0.13	0.24	0.23	5	3^i,j,l	125–197	2	2^m,n	170–184
CaM54				No amplification			2	0	176–184	0.57	0.44	0.45	1	0	184	1	1ⁿ	164
CaM55	2	0	144–151	Duplicated loci			6	2^15,16	159–178	0.75	0.84	0.79	9	0	144–178	1	0	160
CaM57	3	0	146–188	Duplicated loci			5	0	102–176	0.63	0.77	0.73	9	2^a,l	102–174	3	1^m	102–156
CaM58	2	0	189–191	Duplicated loci			2	0	183–191	0.75	0.5	0.52	8	2^b,l	181–224	2	0	192–193
CaM59	2	0	224–226	0.13	0.13	0.12	3	0	222 –225	0.88	0.69	0.67	4	0	222–228	3	0	222–228
Range	0–6	0–4	--	0–0.88	0.13–0.86	0.12–0.81	1–7	0–6	--	0–1.00	0.23–0.88	0.23–0.83	1–13	0–8	--	0–4	0–3	--
Mean	2.7	0.37	--	0.29	0.5	0.49	3.78	0.67	--	0.52	0.63	0.62	7.07	2.42	--	1.98	0.87	--
SD (±)	1.4	0.87	--	0.28	0.22	0.21	1.73	1.13	--	0.29	0.19	0.18	2.87	1.72	--	0.79	0.95	--
SE (±)	0.3	0.13	--	0.06	0.05	0.04	0.26	0.17	--	0.04	0.03	0.03	0.43	0.26	--	0.12	0.14	--

^$: Represents the genotype(s) as per Table 7, wherein the private allele is observed; *: Significant HW dis-equilibrium at P < 0.05; **: Highly significant HW dis-equilibrium at P < 0.01; Markers showing 100% H_o values in arabicas, which are expected to be the result of duplicated loci were not considered for various estimates.

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