SSR and morphological traits based fingerprints and DNA barcodes for varietal identification in rice

Figures & data

Table 1. List of rice varieties used for developing DNA fingerprints.

Varieties	Name of the research centre
JGL 1798, JGL 3855, JGL 11470, JGL 18047, JGL 11118, JGL 17004 and JGL 24423	Regional Agricultural Research Station, Polasa, Jagtial
KNM 118	Agricultural Research Station, Kunaram, Karimnagar District
RNR 15048, Tellahamsa, RNR 2458 and RNR 2465	Rice Research Unit, Rajendranagar, Hyderabad
WGL 44, Ramappa and WGL 32100	Regional Agricultural Research Station, Warangal
BPT 5204 and MTU 1010	Bapatla and Maruteru, ANGRAU
KPS 2874	Agricultural Research Station, Kamapasagar, Nalgonda District

Table 2. Frequency distribution of 21 differentiating traits.

S. No.	Character	Status	No. of varieties	Frequency (%)
1	Leaf: Pubescence of blade surface	Weak	9	50.00
		Medium	9	50.00
2	Leaf: Anthocyanin colouration of auricles	Colourless	13	72.22
		Light purple	5	27.77
3	Leaf: Shape of Ligule	Acute	11	61.11
		Split	7	38.80
4	Leaf: Length of blade	Short	2	11.11
		Medium	16	88.88
5	Culm: attitude	Semi erect	11	61.11
		Open	7	38.88
6	Time of heading	Very early	6	33.33
		Early	9	50.00
		Medium	3	16.66
7	Flag leaf: Attitude of blade	Erect	3	16.66
		Semi erect	15	83.33
8	Spikelet: Density of pubescence of lemma	Weak	16	88.88
		Early	2	11.11
9	Stem: Thickness	Medium	12	66.66
		Thick	6	33.33
10	Stem: Length	Very short	14	77.77
		Short	4	22.22
11	Panicle: Length of main axis	Short	12	66.66
		Medium	6	33.33
12	Flag leaf: Attitude of blade	Erect	3	16.66
		Semi erect	15	83.33
13	Panicle: Curvature of main axis	Semi straight	6	33.33
		Deflexed	8	53.33
		Dropping	4	22.22
14	Panicle: Number per plant	Few	3	16.66
		Medium	15	83.33
15	Spikelet: Colour of tip of Lemma	White	4	22.22
		Yellowish	14	77.77
16	Lemma and Palea: Colour	Straw	13	72.22
		Gold and gold furrows on straw Background	5	27.77
17	Panicle: Secondary Branching	Weak	17	94.40
		Strong	1	5.56
18	Panicle: Attitude of Branches	Semi erect	12	66.66
		Spreading	6	33.33
19	Panicle: exertion	Mostly exerted	12	66.66
		Well exerted	6	33.33
20	Time maturity (days)	Very early	1	5.55
		Early	4	22.22
		Medium	11	61.11
		Late	2	11.11
21	Leaf: Senescence	Medium	15	83.33
		Late	3	16.66

Figure 1. DUS Fingerprints of 18 rice varieties using 21 informative traits. (1) JGL1798, (2) JGL 3855, (3) JGL 11470, (4) JGL 18047, (5) JGL 11118, (6) JGL 17004, (7) JGL 24423, (8) KNM 118, (9) RNR 15048, (10) Tellahamsa, (11) RNR 2458, (12) RNR 2465, (13) WGL 44, (14) RAMAPPA, (15) WGL 32100, (16) BPT 5204, (17) MTU 1010, (18) KPS 2874.

Figure 2. DUS Fingerprints of Medium slender varieties differentiating BPT 5204 with other similar looking varieties using 20 differentiating traits.

Figure 3. DUS Fingerprints of long slender varieties differentiating Tellahamsa and MTU 1010 with other similar looking varieties using 20 differentiating traits.

Table 3. Polymorphism information content and number of alleles per 53 SSR markers.

S. No.	Marker	Chromosome no	No. of alleles	PIC value
1	RM10009	1	3	0.58
2	RM10695	1	3	0.41
3	RM10255	1	3	0.43
4	RM11449	1	4	0.64
5	RM13131	2	3	0.41
6	RM12398	2	4	0.59
7	RM12983	2	4	0.03
8	RM13209	2	4	0.06
9	RM15151	3	3	0.29
10	RM15203	3	3	0.53
11	RM14698	3	3	0.12
12	RM15379	3	3	0.32
13	RM15337	3	4	0.63
14	RM16913	4	3	0.54
15	RM16816	4	2	0.17
16	RM16760	4	2	0.37
17	RM1388	4	4	0.44
18	RM16769	4	2	0.29
19	RM6909	4	3	0.53
20	RM3524	4	2	0.22
21	RM18600	5	2	0.17
22	RM18704	5	4	0.55
23	RM18983	5	2	0.32
24	RM18516	5	2	0.17
25	RM19346	6	3	0.37
26	RM20043	6	2	0.37
27	RM19697	6	3	0.56
28	RM19417	6	3	0.42
29	RM21521	7	2	0.32
30	RM20913	7	3	0.54
31	RM22171	7	3	0.55
32	RM21069	7	2	0.32
33	RM21392	7	2	0.24
34	RM6699	8	2	0.37
35	RM22372	8	3	0.57
36	RM22585	8	3	0.45
37	RM22703	8	2	0.36
38	RM22772	8	3	0.51
39	RM23791	9	3	0.53
40	RM23819	9	4	0.59
41	RM23966	9	3	0.54
42	RM23959	9	2	0.28
43	RM25661	10	3	0.42
44	RM25181	10	3	0.58
45	RM25754	10	3	0.56
46	RM26784	11	4	0.61
47	RM26438	11	2	0.36
48	RM27183	11	3	0.56
49	RM26558	11	3	0.53
50	RM27689	12	3	0.00
51	RM28481	12	3	0.59
52	RM28067	12	2	0.34
53	RM27601	12	2	0.28

Figure 4. Amplification pattern of the rice varieties obtained using the SSR marker. RM 23819, RM 3524, RM 19346, RM25754 and 20913. Lane 1—JGL1798, Lane 2—JGL3855, Lane 3—JGL11470, Lane 4—JGL18047, Lane 5—JGL11118, Lane 6—JGL17004, Lane 7—JGL24423, Lane 8—KNM118, Lane 9—RNR15048, Lane 10—Tellahamsa, Lane 11—RNR2458, Lane 12—RNR2465, Lane 13—WGL44, Lane 14-Ramapa, Lane 15—WGL32100, Lane 16—BPT5204, Lane 17—MTU1010, Lane 18—KPS2874.The unique alleles amplified by the varieties are indicated by arrow.

Table 4. Seventeen Unique markers for the nine varieties.

S.No.	Genotypes	Unique markers
1	JGL 1798	RM19417
2	JGL 3855	RM 12398, RM18704, RM25661, RM 19697
3	JGL 11470	RM21392
4	JGL 18047	RM22171
5	JGL 11118	RM16760, RM25754
6	Tellahamsa	RM 12983, RM14698, RM23819
7	RNR 2458	RM22585
8	WGL 32100	RM20913
9	KPS 3754	RM 15151, RM3524, RM19346

Figure 5. Microsatellites-based DNA barcodes for 18 varieties of rice.

Figure 6. Barcode for multiplex assay.

Data availability statement

The authors confirm that the data supporting the findings of this study are available within the article (and/or) its supplementary materials.