A genetic diversity analysis of South African sorghum genotypes using SSR markers

Figures & data

Table 1: List of sorghum genotypes used in the study

Number	Genotype		Source/origin^Table Footnotea	Number	Genotype		Source/origin^Table Footnotea
	Code	Name/pedigree			Code	Name/pedigree
1	SA-1	5405	North-West	53	SA-53	5233	KwaZulu-Natal
2	SA-2	5451	North-West	54	SA-54	5258	KwaZulu-Natal
3	SA-3	5333	North-West	55	SA-55	AS66	ACCI
4	SA-4	5464	North-West	56	SA-56	5237	KwaZulu-Natal
5	SA-5	5436	North-West	57	SA-57	4722	KwaZulu-Natal
6	SA-6	5454	North-West	58	SA-58	5246	KwaZulu-Natal
7	SA-7	5430	North-West	59	SA-59	4606	KwaZulu-Natal
8	SA-8	5393	North-West	60	SA-60	4531	KwaZulu-Natal
9	SA-9	5337	North-West	61	SA-61	5274	KwaZulu-Natal
10	SA-10	2167	Eastern Cape	62	SA-62	5281	KwaZulu-Natal
11	SA-11	3416	Eastern Cape	63	SA-63	4547	KwaZulu-Natal
12	SA-12	3414	Eastern Cape	64	SA-64	5097	KwaZulu-Natal
13	SA-13	3262	Eastern Cape	65	SA-65	5245	KwaZulu-Natal
14	SA-14	3319	Eastern Cape	66	SA-66	4952	Free State
15	SA-15	2922	Eastern Cape	67	SA-67	4909	Free State
16	SA-16	3364	Eastern Cape	68	SA-68	4905	Free State
17	SA-17	3403	Eastern Cape	69	SA-69	4891	Free State
18	SA-18	2975	Eastern Cape	70	SA-70	Motlerane	ARC-GCI
19	SA-19	3184	Eastern Cape	71	SA-71	Mammopane	ARC-GCI
20	SA-20	2934	Eastern Cape	72	SA-72	Macia-SA	ARC-GCI
21	SA-21	2985	Eastern Cape	73	SA-73	M153	ARC-GCI
22	SA-22	3217	Eastern Cape	74	SA-74	05 Potch-151	ARC-GCI
23	SA-23	4154	Mpumalanga	75	SA-75	Maseka-a-swere	ARC-GCI
24	SA-24	4276	Mpumalanga	76	SA-76	Mammolokwane	ARC-GCI
25	SA-25	5476	Mpumalanga	77	AR-2	05 Potch-138	ARC-GCI
26	SA-26	4265	Mpumalanga	78	AR-3	M48	ARC-GCI
27	SA-27	4052	Mpumalanga	79	AR-4	05 Potch-115	ARC-GCI
28	SA-28	2055	Mpumalanga	80	AR-5	05 Potch-167	ARC-GCI
29	SA-29	5518	Mpumalanga	81	AR-6	Manthate	ARC-GCI
30	SA-30	4259	Mpumalanga	82	AR-7	AS 82	ACCI
31	SA-31	5502	Mpumalanga	83	AR-8	AS13	ACCI
32	SA-32	5541	Mpumalanga	84	AR-9	AS 1	ACCI
33	SA-33	1990	Mpumalanga	85	AR-10	AS 4	ACCI
34	SA-34	4277	Mpumalanga	86	AR-11	AS 18	ACCI
35	SA-35	2048	Mpumalanga	87	AR-12	AS 19	ACCI
36	SA-36	4161	Mpumalanga	88	AC-1	AS 17	ACCI
37	SA-37	1455	Limpopo	89	AC-2	AS 16	ACCI
38	SA-38	1450	Limpopo	90	AC-3	AS 16 Cycl	ACCI
39	SA-39	4312	Limpopo	91	AC-4	AS 11	ACCI
40	SA-40	1948	Limpopo	92	AC-5	AS 6	ACCI
41	SA-41	1390	Limpopo	93	AC-6	AS 1 M2 Ctrl	ACCI
42	SA-42	4441	Limpopo	94	AC-7	AS 16 M2 Ctrl	ACCI
43	SA-43	3132	Limpopo	95	AC-8	AS 21	ACCI
44	SA-44	4442	Limpopo	96	AC-9	AS 8	ACCI
45	SA-45	1413	Limpopo	97	AC-10	AS 2	ACCI
46	SA-46	1394	Limpopo	98	AC-11	N13 Striga resistant	ACCI
47	SA-47	1481	Limpopo	99	AC-12	#32 2384443	ACCI
48	SA-48	1473	Limpopo	100	AC-13	#14 235929	ACCI
49	SA-49	4303	Limpopo	101	AC-14	SRN39 FRAMIDA	ACCI
50	SA-50	4311	Limpopo	102	AC-16	HORMAT	ACCI
51	SA-51	5088	KwaZulu-Natal	103	AC-18	#21237289	ACCI
52	SA-52	5287	KwaZulu-Natal

a North West, Eastern Cape, Mpumalanga, Limpopo, KwaZulu-Natal, and Free State are administrative provinces in South Africa; ARC-GCI, Agricultural Research Council-Grain Crops Institute; ACCI-African Centre for Crop Improvement

Table 2: Descriptions of the 30 SSR markers used in the study. Chr. = Chromosome

No.	Marker	Chr.	Motif	Forward primer	Reverse primer	Annealing	No. alleles
						Tm	Min.	Max.
1	gpsb067	8	(GT)10	TAGTCCATACACCTTTCA	TCTCTCACACACATTCTTC	49	160	190
2	gpsb123	8	(CA)7+(GA)5	ATAGATGTTGACGAAGCA	GTGGTATGGGACTGGA	50	284	304
3	Isep0107	3	(TGG)4	GCCGTAACAGAGAAGGATGG	TTTCCGCTACCTCAAAAACC	59	199	206
4	Isep0310	2	(CCAAT)4	TGCCTTGTGCCTTGTTTATCT	GGATCGATGCCTATCTCGTC	60	159	214
5	mSbCIR223	2	(AC)6	CGTTCCAATGACTTTTCTTC	GCCAATGTGGTGTGATAAAT	55	104	124
6	mSbCIR240	8	(TG)9	GTTCTTGGCCCTACTGAAT	TCACCTGTAACCCTGTCTTC	55	104	180
7	mSbCIR246	5	(CA)7+(GA)5	TTTTGTTGCACTTTTGAGC	GATGATAGCGACCACAAATC	55	86	114
8	mSbCIR248	10	(GT)7	GTTGGTCAGTGGTGGATAAA	ACTCCCATGTGCTGAATCT	56	81	121
9	mSbCIR262	7	(CATG)3	GCACCAAAATCAGCGTCT	CCATTTACCCGTGGATTAGT	57	208	446
10	mSbCIR276	3	(AC)9	CCCCAATCTAACTATTTGGT	GAGGCTGAGATGCTCTGT	53	222	252
11	mSbCIR283	7	(CT)8(GT)8	TCCCTTCTGAGCTTGTAAAT	CAAGTCACTACCAAATGCAC	54	111	157
12	mSbCIR286	1	(AC)9	GCTTCTATACTCCCCTCCAC	TTTATGGTAGGATGCTCTGC	55	110	150
13	mSbCIR300	5	(GT)9	TTGAGAGCGGCGAGGTAA	AAAAGCCCAAGTCTCAGTGCTA	61	74	118
14	mSbCIR306	1	(GT)7	ATACTCTCGTACTCGGCTCA	GCCACTCTTTACTTTTCTTCTG	55	118	126
15	mSbCIR329	10	(AC)8	GCAGAACATCACTCAAAGAA	TACCTAAGGCAGGGATTG	54	73	121
16	SbAGB02	5	(AG)35	CTCTGATATGTCGTTGTGCT	ATAGAGAGGATAGCTTATAGCTCA	55	96	160
17	Xcup02	6	(GCA)6	GACGCAGCTTTGCTCCTATC	GTCCAACCAACCCACGTATC	54	189	207
18	Xcup53	1	(TTTA)5	GCAGGAGTATAGGCAGAGGC	CGACATGACAAGCTCAAACG	54	182	198
19	Xgap206	6	(AC)13+(AG)20	ATTCATCATCCTCATCCTCGTAGAA	AAAAACCAACCCGACCCACTC	55	100	162
20	Xgap72	9	(AG)16	TGCCACCACTCTGGAAAAGGCTA	CTGAGGACTGCCCCAAATGTAGG	55	175	211
21	Xgap84	2	(AG)14	CGCTCTCGGGATGAATGA	TAACGGACCACTAACAAATGATT	55	171	227
22	Xtxp012	4	(CT)22	AGATCTGGCGGCAACG	AGTCACCCATCGATCATC	55	143	213
23	Xtxp015	10	(TC)16	CACAAACACTAGTGCCTTATC	CATAGACACCTAGGCCATC	55	199	235
24	Xtxp021	4	(AG)18	GAGCTGCCATAGATTTGGTCG	ACCTCGTCCCACCTTTGTTG	60	163	223
25	Xtxp057	9	(GT)21	GGAACTTTTGACGGGTAGTGC	CGATCGTGATGTCCCAATC	55	213	285
26	Xtxp136	10	(GCA)5	GCGAATAGCATCTTACAACA	ACTGATCATTGGCAGGAC	55	240	246
27	Xtxp141	7	(GA)23	TGTATGGCCTAGCTTATCT	CAACAAGCCAACCTAAA	55	127	175
28	Xtxp265	9	(GAA)19	GTCTACAGGCGTGCAAATAAAA	TTACCATGCTACCCCTAAAAGTGG	55	168	246
29	Xtxp320	1	(AAG)20	TAAACTAGACCATATACTGCCATGATAA GTGCAAATAAGGGCTAGAGTGTT	54	251	329
30	Xtxp321	8	(GT)4+(AT)6+(CT)21	TAACCCAAGCCTGAGCATAAGA	CCCATTCACACATGAGACGAG	55	182	240

Table 3: Genetic information generated by 30 SSR markers on 103 sorghum genotypes. PIC = Polymorphic information content

Marker	Allele number	Allele size range (bp)	Heterozygosity	PIC value
gpsb123	5	284.79-293.88	0.6423	0.5754
gpsb067	4	172.53-183.07	0.3101	0.2917
mSbCIR246	4	93.33-100.00	0.2690	0.2543
mSbCIR262	5	214.26-224.37	0.5885	0.5379
Xtxp321	14	187.85-223.94	0.7740	0.7366
Xtxp320	10	253.92-283.17	0.8524	0.8351
Xtxp141	9	143.56-165.99	0.8223	0.8046
Xtxp136	3	236.48-239.58	0.5960	0.5288
Xtxp057	10	234.38-263.28	0.7022	0.6657
Xtxp021	10	159.46-196.19	0.6007	0.5791
Xtxp015	5	175.50-203.45	0.5212	0.4835
Xtxp012	15	162.28-210.23	0.7545	0.7224
Xisep0310	2	175.75-203.45	0.0194	0.0192
Xgap265	10	174.75-218.61	0.8038	0.7764
Xgap84	7	185.01-202.98	0.7362	0.7020
Xgap72	7	182.11-192.39	0.5355	0.5073
Xcup53	4	182.57-199.11	0.0756	0.0746
Xcup02	4	191.41-199.92	0.4257	0.3619
mSbCIR329	4	108.27-114.26	0.5417	0.4379
mSbCIR306	3	119.92-124.17	0.5167	0.4013
mSbCIR300	3	102.16-108.60	0.4065	0.3535
mSbCIR286	7	103.94-125.15	0.6721	0.6245
SbAGB02	11	97.87-157.55	0.5034	0.4786
mSbCIR283	6	115.47-145.52	0.4975	0.4518
mSbCIR276	3	229.26-233.20	0.5423	0.4484
mSbCIR240	6	104.95-104.95	0.3377	0.3165
mSbCIR248	3	90.09-100.78	0.6540	0.5798
mSbCIR223	3	104.55-113.09	0.5677	0.4927
Xgap206	13	105.40-147.45	0.7437	0.7081
Isep107	2	220.82-227.15	0.4377	0.3419
Average	6.4	163.755-183.516	0.5483	0.50305

Figure 1: Dendrogram revealing genetic relationships among 103 sorghum genotypes from South Africa based on SSR analysis of Euclidian similarity coefficients with UPGMA clustering. Ia, Ib, IIa and IIb are subgroups within the clusters