Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

doi:10.1016/j.rsci.2016.05.003

Abstract

Abstract:

Salt stress is a major problem in most of the rice growing areas in the world. A major QTL Saltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice. This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated with salt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1 to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding lines including three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 and can be good sources of new genes/alleles for salt tolerance. Simple sequence repeat (SSR) marker RM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information content value varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54 lines were clearly separated into two major clusters. Fourteen haplotypes were identified based on Saltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminate between the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assisted selection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 on chromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

Key words: haplotype, rice, salt tolerance, Saltol, simple sequence repeat marker

D. Chowdhury A., Haritha G., Sunitha T., L. Krishnamurthy S., Divya B., Padmavathi G., Ram T., Sarla N.. Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance[J]. Rice Science, 2016, 23(6): 317-325.

Figures/Tables 6

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50	(Managing Editor: Li Guan)

Score	Observation	Tolerance
1	Normal growth, no leaf symptoms	Highly tolerant
3	Nearly normal growth, only the tips of few leaves whitish and rolled	Tolerant
5	Growth severely retarded, most leaves rolled, the two youngest leaves were still elongating	Moderately tolerant
7	Complete cessation of growth, all lower leaves dried out, the two youngest leaves started to wilt	Susceptible
9	The whole plant dried out and dead	Highly susceptible

Score	Observation	Tolerance
1	Normal growth, no leaf symptoms	Highly tolerant
3	Nearly normal growth, only the tips of few leaves whitish and rolled	Tolerant
5	Growth severely retarded, most leaves rolled, the two youngest leaves were still elongating	Moderately tolerant
7	Complete cessation of growth, all lower leaves dried out, the two youngest leaves started to wilt	Susceptible
9	The whole plant dried out and dead	Highly susceptible

Genotype	Designation	Source	Score	Reaction to salinity	Genotype	Designation	Source	Score	Reaction to salinity
IRSSTN25 (CK)	FL478 (IR66946-3R-178-1-1)	IRRI	3	T	KMR3	KMR3	India	9	HS
IRSSTN24 (CK)	IR28	IRRI	7	S	IET19543	DRRH3	India	5	MT
IET22631	RP Bio 4919-13-5 (KMR3 × O. rufipogon)	India	5	MT	IET23124	RP Bio 4918-7-1 (Swarna × O. nivara)	India	9	HS
IET22625	RP Bio 4918-250 (Swarna × O. nivara)	India	7	S	IET21542	RP Bio 4918-248 (Swarna × O. nivara)	India	9	HS
IET21943	RP Bio 4919-50-13 (KMR3 × O. rufipogon)	India	3	T	IET21944	RP Bio 4919-13-7 (KMR3 × O. rufipogon)	India	3	T
IET22636	RP Bio 4919-86-18 (KMR3 × O. rufipogon)	India	5	MT	IET21940	RP Bio 4919-463 (KMR3 × O. rufipogon)	India	3	T
IET23183	RP Bio 4918-230 (Swarna × O. nivara)	India	9	HS	IET22628	RP Bio 4919-50-12 (KMR3 × O. rufipogon)	India	5	MT
IET22627	RP Bio 4919-50-10 (KMR3 × O. rufipogon)	India	7	S	IET22633	RP Bio 4919-495 (KMR3 × O. rufipogon)	India	7	S
IET22624	RP Bio 4918-24 (Swarna × O. nivara)	India	7	S	IET22626	RP Bio 4919-50-7 (KMR3 × O. rufipogon)	India	5	MT
IET3116	Vikas	India	5	MT	IRSSTN19	IRT11173	IRRI	5	MT
IET19487	DRR Dhan 39	India	5	MT	IRSSTN5	IRT11237	IRRI	7	S
IET9341	CST7-1	India	5	MT	IRSSTN14	IRT11160	IRRI	5	MT
IRSSTN15	IRT11176	IRRI	5	MT	IRSSTN3	IRT11239	IRRI	5	MT
IRSSTN29	IR45427-2B-2-2B-1-1	IRRI	3	T	IRSSTN21	Pokkali (ACC108921)	IRRI	3	T
IRSSTN6	BR11-Saltol	IRRI	9	HS	IRSSTN1	IRT11169	IRRI	5	MT
IRSSTN11	IRT11236	IRRI	7	S	IRSSTN9	IRT11149	IRRI	5	MT
IRSSTN13	IRT11260	IRRI	5	MT	IRSSTN22	Nonabokra	IRRI	3	T
IRSSTN10	IRT11133	IRRI	7	S	IET18076	DRRH2	India	5	MT
IRSSTN17	IRT11174	IRRI	5	MT	IRSSTN16	IRT11172	IRRI	5	MT
IRSSTN30	A69-1	India	5	MT	IET5656	Swarna	India	9	HS
IET19046	Sambha Mahsuri	India	9	HS	IET17340	CSR36	India	3	T
IRSSTN28	AT401	India	3	T	IRSSTN8	IRT11252	IRRI	7	S
IRSSTN12	IRT11254	IRRI	5	MT	IRSSTN7	IRT11170	IRRI	7	S
IRSSTN27	IR55179-3B-11-3	IRRI	3	T	IET15420	Jarava	India	5	MT
IRSSTN2	IRT11158	IRRI	5	MT	IRSSTN18	IRT11141	IRRI	3	T
IRSSTN4	IRT11247	IRRI	5	MT	IRSSTN20	IRT11175	IRRI	5	MT
IRSSTN23	IR29	IRRI	7	S	IET13765	CSR27	India	3	T
T, Tolerant; MT, Moderately tolerant; S, Susceptible; HS, Highly susceptible; IRRI, International Rice Research Institute.

Genotype	Designation	Source	Score	Reaction to salinity	Genotype	Designation	Source	Score	Reaction to salinity
IRSSTN25 (CK)	FL478 (IR66946-3R-178-1-1)	IRRI	3	T	KMR3	KMR3	India	9	HS
IRSSTN24 (CK)	IR28	IRRI	7	S	IET19543	DRRH3	India	5	MT
IET22631	RP Bio 4919-13-5 (KMR3 × O. rufipogon)	India	5	MT	IET23124	RP Bio 4918-7-1 (Swarna × O. nivara)	India	9	HS
IET22625	RP Bio 4918-250 (Swarna × O. nivara)	India	7	S	IET21542	RP Bio 4918-248 (Swarna × O. nivara)	India	9	HS
IET21943	RP Bio 4919-50-13 (KMR3 × O. rufipogon)	India	3	T	IET21944	RP Bio 4919-13-7 (KMR3 × O. rufipogon)	India	3	T
IET22636	RP Bio 4919-86-18 (KMR3 × O. rufipogon)	India	5	MT	IET21940	RP Bio 4919-463 (KMR3 × O. rufipogon)	India	3	T
IET23183	RP Bio 4918-230 (Swarna × O. nivara)	India	9	HS	IET22628	RP Bio 4919-50-12 (KMR3 × O. rufipogon)	India	5	MT
IET22627	RP Bio 4919-50-10 (KMR3 × O. rufipogon)	India	7	S	IET22633	RP Bio 4919-495 (KMR3 × O. rufipogon)	India	7	S
IET22624	RP Bio 4918-24 (Swarna × O. nivara)	India	7	S	IET22626	RP Bio 4919-50-7 (KMR3 × O. rufipogon)	India	5	MT
IET3116	Vikas	India	5	MT	IRSSTN19	IRT11173	IRRI	5	MT
IET19487	DRR Dhan 39	India	5	MT	IRSSTN5	IRT11237	IRRI	7	S
IET9341	CST7-1	India	5	MT	IRSSTN14	IRT11160	IRRI	5	MT
IRSSTN15	IRT11176	IRRI	5	MT	IRSSTN3	IRT11239	IRRI	5	MT
IRSSTN29	IR45427-2B-2-2B-1-1	IRRI	3	T	IRSSTN21	Pokkali (ACC108921)	IRRI	3	T
IRSSTN6	BR11-Saltol	IRRI	9	HS	IRSSTN1	IRT11169	IRRI	5	MT
IRSSTN11	IRT11236	IRRI	7	S	IRSSTN9	IRT11149	IRRI	5	MT
IRSSTN13	IRT11260	IRRI	5	MT	IRSSTN22	Nonabokra	IRRI	3	T
IRSSTN10	IRT11133	IRRI	7	S	IET18076	DRRH2	India	5	MT
IRSSTN17	IRT11174	IRRI	5	MT	IRSSTN16	IRT11172	IRRI	5	MT
IRSSTN30	A69-1	India	5	MT	IET5656	Swarna	India	9	HS
IET19046	Sambha Mahsuri	India	9	HS	IET17340	CSR36	India	3	T
IRSSTN28	AT401	India	3	T	IRSSTN8	IRT11252	IRRI	7	S
IRSSTN12	IRT11254	IRRI	5	MT	IRSSTN7	IRT11170	IRRI	7	S
IRSSTN27	IR55179-3B-11-3	IRRI	3	T	IET15420	Jarava	India	5	MT
IRSSTN2	IRT11158	IRRI	5	MT	IRSSTN18	IRT11141	IRRI	3	T
IRSSTN4	IRT11247	IRRI	5	MT	IRSSTN20	IRT11175	IRRI	5	MT
IRSSTN23	IR29	IRRI	7	S	IET13765	CSR27	India	3	T
T, Tolerant; MT, Moderately tolerant; S, Susceptible; HS, Highly susceptible; IRRI, International Rice Research Institute.

Marker	Chromosome	Frequency of major allele	Number of alleles	PIC value
RM493	1	0.46	3	0.96
RM3412	1	0.53	3	0.96
RM7075	1	0.26	5	0.97
RM8094	1	0.24	7	0.99
RM10694	1	0.57	3	0.97
RM10720	1	0.43	3	0.95
RM10793	1	0.32	5	0.97
RM10843	1	0.39	3	0.95
RM10852	1	0.35	3	0.94
RM289	5	0.70	2	0.55
RM413	5	0.56	5	0.96
RM264	8	0.70	3	0.90
RM149	8	0.20	4	0.77
RM222	10	0.35	5	0.96