ISSR and SRAP for assessing genetic variability of Indonesian local rice genotypes (<i>Oryza sativa L</i>.)

Rini, Dwi Setyo; Budiyanti, Yashinta; Valentine, Meyta; Permana, Rega

doi:10.1590/1984-70332023v23n4a46

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Crop Breeding and Applied Biotechnology

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ARTICLE • Crop Breed. Appl. Biotechnol. 23 (4) • 2023 • https://doi.org/10.1590/1984-70332023v23n4a46 copy

ISSR and SRAP for assessing genetic variability of Indonesian local rice genotypes (Oryza sativa L.)

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

This study evaluated the genetic variability of 34 local rice genotypes from Simeulue Island and Sumba Island, Indonesia, using ISSR and SRAP markers. The amplification of ISSR and SRAP primers produced high percentages of polymorphism, with values of 98.17% and 99.75%, respectively. The result of the UPGMA dendrogram analysis classified the rice genotypes into three groups by ISSR and two groups by SRAP. The ISSR had a higher Resolving Power (RP = 14.66) and Marker Index (MI = 4.61) than the SRAP (RP = 9.13, MI = 3.8). However, the results of the UPGMA dendrogram corresponded to the STRUCTURAL data analysis. The ΔK of STRUCTURAL analysis performed its maximum value when K = 3 by ISSR and K = 2 by SRAP. This study pointed out that ISSR markers were more effective than SRAP markers in evaluating the degree of genetic variability of rice genotypes.

Keywords:
ISSR; genetic variability; Oryza sativa L.; SRAP

No	Genotype code	Geographic Origin	Latitude (S)	Longitude (E)	Group*
1	M1_A(G)	Seubah Village, Simeulue Island	2⁰28’35.98”	96⁰22’33.82’’	A
2	M2_A	Latitik Village, Simeulue Island	2⁰38’34.12”	95⁰59’47.52’’	A
3	M3_A	Lambaya Village, Simeulue Island	2⁰37’59.50”	96⁰1’59.23’’	A
4	M4_A**	Serdang Village, Bangka Island	2⁰53’49.19”	10⁰22’10.03’’	A
5	M5_A	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
6	M6_A	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
7	M7_A	Padang Unoi Village, Simeulue Island	2⁰41’12.52”	95⁰48’41.83’’	A
8	M8_A	Lambaya Village, Simeulue Island	2⁰37’59.5”	96⁰1’59.23’’	A
9	M9_A(G)	Lambaya Village, Simeulue Island	2⁰37’59.5”	96⁰1’59.23’’	A
10	M10_A(G)	Lafaha Village, Simeulue Island	2⁰44’7.37”	95⁰46’20.36’’	A
11	M11_AI(G)	Langi Village, Simeulue Island	2⁰48’7.84”	95⁰46’41.8’’	A
12	M12_AII(G)	Padang Unoi Village, Simeulue Island	2⁰41’12.52”	95⁰48’41.83’’	A
13	M13_A	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
14	M14_A	Air Pinang Village, Simeulue Island	2⁰33’58.67”	96⁰14’19.54’’	A
15	M15_A	Latitik Village, Simeulue Island	2⁰38’34.12”	95⁰59’47.52’’	A
16	M16_A	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
17	M17_A(G)	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
18	M18_A	Leubang Hulu Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
19	M19_A	Labuhan Bukti Village, Simeulue Island	2⁰28’5.19”	96⁰17’53.79’’	A
20	M20_A(G)	Seubah Village, Simeulue Island	2⁰28’35.98”	96⁰22’33.82’’	A
21	M21_A	Seubah Village, Simeulue Island	2⁰28’35.98”	96⁰22’33.82’’	A
22	M22_A	Padang Unoi Village, Simeulue Island	2⁰41’13.23”	95⁰48’41.94’’	A
23	M23_A	Latitik Village, Simeulue Island	2⁰38’34.12”	95⁰59’47.52’’	A
24	M24_A(G)	Lafaha Village, Simeulue Island	2⁰34’59.99”	96⁰4’59.99’’	A
25	M25_B	Praingkareha Village, Sumba Island	10⁰1’12.28”	120⁰4’4.87’’	B
26	M26_B(GH)	Wudipandak Village, Sumba Island	9⁰58’30.86”	120⁰3’18.97’’	B
27	M27_B	Wahang Village, Sumba Island	10⁰4’42.64”	120⁰3’17.88”	B
28	M28_B	Pinduhurani Village, Sumba Island	10⁰1’24.36”	120⁰0’31.45’’	B
29	M29_B(GH)	Praing Kareha Village, Sumba Island	10⁰1’12.28”	120⁰4’4.87’’	B
30	M30_B	Praing Kareha Village, Sumba Island	10⁰1’12.28”	120⁰4’4.87’’	B
31	M31_B	Matawai La Pau Village, Sumba Island	10⁰11’46.31”	120⁰21’59.79”	B
32	M32_B(G)	Praing Kareha Village, Sumba Island	10⁰1’12.28”	120⁰4’4.872’	B
33	M33_B	Ramuk Village, Sumba Island	10⁰4’29.02”	120⁰8’18.038’’	B
34	M34_B(G)	Wahang Village, Sumba Island	10⁰4’42.64”	120⁰3’17.88”	B

	Primers	Sequences (5´ - 3´)	Number of nucleotides
ISSR primers
1	UBC 807	AGA GAG AGA GAG AGA GT	17
2	UBC 808	AGA GAG AGA GAG AGA GC	17
3	UBC 809	AGA GAG AGA GAG AGA GG	17
4	UBC 810	GAG AGA GAG AGA GAG AT	17
5	UBC 813	CTC TCT CTC TCT CTC TT	17
6	UBC 814	CTC TCT CTC TCT CTC TA	17
7	UBC 815	CTC TCT CTC TCT CTC TG	17
8	UBC 817	CAC ACA CAC ACA CAC AA	17
9	UBC 819	GTG TGT GTG TGT GTG TA	17
10	UBC 820	GTG TGT GTG TGT GTG TC	17
11	UBC 823	TCT CTC TCT CTC TCT CC	17
12	UBC 825	ACA CAC ACA CAC ACA CT	17
13	UBC 826	ACA CAC ACA CAC ACA CC	17
14	UBC 862	AGC AGC AGC AGC AGC AGC	18
15	UBC 880	GGA GAG GAG AGG AGA	18

SRAP primers
1	Me1 (forward)	TGAGTCCAAACCGGATA	17
2	Me2 (forward)	TGAGTCCAAACCGGAGC	17
3	Me3 (forward)	TGAGTCCAAACCGGACC	17
4	Me4 (forward)	TGAGTCCAAACCGGTAG	17
5	Me5 (forward)	TGAGTCCAAACCGGTGT	17
6	Em1 (reverse)	GACTGCGTACGAATTTGC	18
7	Em2 (reverse)	GACTGCGTACGAATTGCA	18
8	Em3 (reverse)	GACTGCGTACGAATTAGC	18
9	Em4 (reverse)	GACTGCGTACGAATTTAG	18
10	Em5 (reverse)	GACTGCGTACGAATTGGT	18

No	Primers	NTB	NPB	PP	PIC	RP	MI
ISSR
1	UBC 807	18	18	100	0.23	RP	MI	11.71	4.14
2	UBC 808	23	23	100	0.36	24.71	8.28
3	UBC 809	15	14	93.33	0.25	17.88	3.50
4	UBC 810	16	14	87.5	0.21	16.65	2.94
5	UBC 813	15	15	100	0.32	8.76	4.80
6	UBC 814	12	12	100	0.23	6.35	2.76
7	UBC 815	21	21	100	0.30	11.00	6.30
8	UBC 817	23	23	100	0.29	21.41	6.67
9	UBC 819	16	16	100	0.18	3.94	2.88
10	UBC 820	17	17	100	0.22	8.41	3.74
11	UBC 823	14	14	100	0.25	12.18	3.50
12	UBC 825	23	23	100	0.28	16.47	6.44
13	UBC 826	24	24	100	0.22	32.59	3.74
14	UBC 862	12	11	91.67	0.20	7.18	2.20
15	UBC 880	22	22	100	0.33	20.65	7.26
	Total	271	267
	Mean	18.07	17.8	98.17	0.26	14.66	4.61

SRAP
1	Me1-Em1	17	17	100	0.44	14.47	7.48
2	Me1-Em2	14	14	100	0.42	12.29	5.88
3	Me1-Em3	14	14	100	0.44	12.71	6.16
4	Me1-Em4	12	12	100	0.42	9.53	5.04
5	Me1-Em5	6	6	100	0.4	5.59	2.4
6	Me2-Em1	14	14	100	0.2	4.35	2
7	Me2-Em2	10	10	100	0.26	4.47	2.6
8	Me2-Em3	16	15	94	0.17	5.76	2.38
9	Me2-Em4	19	19	100	0.25	6.53	4.25
10	Me2-Em5	11	11	100	0.2	6.35	1.8
11	Me3-Em1	14	14	100	0.17	2.82	2.38
12	Me3-Em2	16	16	100	0.21	5.12	3.36
13	Me3-Em3	17	17	100	0.24	5.65	4.08
14	Me3-Em4	19	19	100	0.17	3.82	3.23
15	Me3-Em5	19	19	100	0.3	8.29	5.7
16	Me4-Em1	15	15	100	0.22	11.53	3.3
17	Me4-Em2	14	14	100	0.33	13.35	4.62
18	Me4-Em3	7	7	100	0.33	7.24	2.31
19	Me4-Em4	13	13	100	0.23	10.00	2.99
20	Me4-Em5	11	11	100	0.3	11.71	3.3
21	Me5-Em1	16	16	100	0.35	18.65	5.6
22	Me5-Em2	13	13	100	0.3	14.24	3.9
23	Me5-Em3	11	11	100	0.23	8.29	2.53
24	Me5-Em4	14	14	100	0.26	11.59	3.64
25	Me5-Em5	20	20	100	0.2	13.88	4
	Total	352	351
	Mean	14.08	14.04	99.75	0.2816	9.13	3.80

Population	Sample size	Number of loci	% polymorphic loci	Ne	I	h
ISSR marker
Simeulue	24	225	90.59	1.340 a	0.358 a	0.222 a
Sumba	10	225	63.92	1.313 b	0.303 b	0.195 b

SRAP marker
Simeulue	24	309	88.35	1.337 a	0.350 a	0.218 a
Sumba	10	309	73.75	1.326 b	0.310 b	0.201 b

Mean				Ne	I	h
ISSR marker				1.326 a	0.331 a	0.209 a
SRAP marker				1.332 a	0.330 a	0.210 a

Source	df	SS	MS	Est. Var.	%
ISSR marker
Among populations	1	74.12	74.12	3.19	10
Within populations	32	928.90	29.02	29.02	90
Total	33	1003.02		32.22	100
Stat	Value	ρ
PhiPT	0.099	0.001

SRAP marker
Among populations	1	99.68	99.68	4.58	12
Within populations	32	1119.25	34.97	34.97	88
Total	33	1218.94		39.56	100
Stat	Value	ρ
PhiPT	0.116	0.001

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