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

doi:10.1016/j.rsci.2016.05.003

摘要/Abstract

. [J]. Rice Science, 2016, 23(6): 317-325.

图/表 6

参考文献 50

1	Ahmadi J, Fotokian M H.2011. Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza sativa) using SSR markers. Iran J Biotechnol, 9(1): 21-30.
2	All India Coordinated Rice Improvement Project (AICRIP). 2012. Annual Progress Report 2011-2012. Hyderabad, India: Directorate of Rice Research.
3	All India Coordinated Rice Improvement Project (AICRIP). 2013. Annual Progress Report 2012-2013. Hyderabad, India: Directorate of Rice Research.
4	Babu N N, Vinod K K, Krishnan S G, Bhowmick P K, Vanaja T, Krishnamurthy S L, Nagarajan M, Singh N K, Prabhu K V, Singh A K.2014. Marker based haplotype diversity ofSaltol QTL in relation to seedling stage salinity tolerance in selected genotypes of rice. Ind J Genet Plant Breeding, 74(1): 16-25.
5	Bimpong I K, Manneha B, Sock M, Diawa F, Amoah N K A, Ismail A M, Gregoriob G, Singh R K, Wopereis M.2016. Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa.Plant Sci, 242: 288-299.
6	Bonilla P S, Dvorak J, Mackill D, Deal K, Gregorio G.2002. RFLP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philipp Agric Sci, 85: 64-74.
7	Das P, Nutan K K, Singla-Pareek S L, Pareek A.2015. Understanding salinity responses and adopting ‘omics-based’ approaches to generate salinity tolerant cultivars of rice.Front Plant Sci, 6: 712.
8	Dellaporta S L, Wood J, Hicks J B.1983. A plant DNA minipreparation: Version II.Plant Mol Biol Rep, 1(4): 19-21.
9	Eliades N G, Eliades D G.2009. Haplotype analysis: Software for analysis of haplotype data. Goettingen, Germany: Forest Genetics and Forest Tree Breeding, Georg-August University.
10	Emon R M, Islamb M M, Halderb J, Fan Y.2015. Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces.Crop J, 3(5): 440-444.
11	Ganeshan P, Jain A, Parmar B, Rao A R, Sreenu K, Mishra P, Mesapogu S, Subrahmanyam D, Ram T, Sarla N, Rai V.2016. Identification of salt tolerant rice lines among interspecific BILs developed by crossingOryza sativa × O. rufipogon and O. sativa × O. nivara. AJCS, 10(2): 220-228.
12	Ganie S A, Borgohain M J, Kritika K, Talukdar A, Pani D R, Mondal T K.2016. Assessment of genetic diversity ofSaltol QTL among the rice(Oryza sativa L.) genotypes. Physiol Mol Biol Plants, 22(1): 107-114.
13	Gregorio G B.1997. Tagging salinity tolerance genes in rice using amplified fragment length polymorphism (AFLP). Los Baños, the Philippines: University of the Philippines.
14	Gregorio G B, Senadhira D, Mendoza R D.1997. Screening Rice for Salinity Tolerance. Los Baños, the Philippines: International Rice Research Institute.
15	Hossain H, Rahman M A, Alam M S, Singh R K.2015. Mapping of quantitative trait loci associated with reproductive-stage salt tolerance in rice.J Agron Crop Sci, 201(1): 17-31.
16	Huyen L T N, Cuc L M, Ismail A M, Ham L H.2012. Introgression the salinity tolerance QTLsSaltol into AS996, the elite rice variety of Vietnam. Am J Plant Sci, 3(7): 981-987.
17	Huyen L T N, Cuc L M, Ham L H, Khanh T D.2013. Introgression theSaltol QTL into Q5DB, the elite variety of Vietnam using marker-assisted-selection (MAS). Am J BioSci, 1: 80-84.
18	IRRI (International Rice Research Institute). 1997. Rice almanae. In: Maclean J L. Rice Geographical Distribution. 2nd edn. Los Baños, Laguna, the Philippines: International Rice Research Institute (IRRI)-West Africa Rice Development Association (WARDA)-Centre for Tropical Agriculture (CIAT).
19	Islam M R, Gregorio G B, Salam M A, Collard B C Y, Tumimbang-Raiz E, Adorada D L, Mendoza R D, Singh R K, Hassan L.2011. Validation of a major QTL for salinity tolerance on chromosome 1 of rice in three different breeding populations.Agrochimica, 55: 355-366.
20	Islam M R, Gregorio G B, Salam M A, Collard B C Y, Singh R K, Hassan L.2012. Validation ofSaltol linked markers and haplotype diversity on chromosome 1 of rice. Mol Plant Breeding, 3(10): 103-114.
21	Ismail A M, Heuer S, Thomson M J, Wissuwa M.2007. Genetic and genomic approaches to develop rice germplasm for problem soils.Plant Mol Biol, 65(4): 547-570.
22	Ismail A M, Thomson M J, Vergara G V, Rahman M A, Singh R K, Gregorio G B, Mackill D J.2010. Designing resilient rice varieties for coastal deltas using modern breeding tools. In: Hoanh C T, Szuster B W, Pheng K S, Ismail A M, Nobel A D. Tropical Deltas and Coastal Zones: Food Production, Communities and Environment at the Land-Water Interface. Wallingford, UK: CAB International: 154-165.
23	Krishnamurthy S L, Sharma S K, Kumar V, Tiwari S, Batra V, Singh N K.2014. Assessment of genetic diversity in rice genotypes for salinity tolerance usingSaltol markers of chromosome 1. Ind J Genet Plant Breeding, 74(2): 243-247.
24	Krishnamurthy S L, Sharma S K, Kumar V, Tiwari S, Singh N K.2015. Analysis of genomic region spanningSaltol using SSR markers in rice genotypes showing differential seedlings stage salt tolerance. J Plant Biochem Biotechnol, 25(3): 331-336.
25	Kumar V, Singh A, Amitha Mithra S V, Krishnamurthy S L, Parida S K, Jain S, Tiwari K K, Kumar P, Rao A R, Sharma S K, Khurana J P, Singh N K, Mohapatra T.2015. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Res, 22(2): 133-145.
26	Lakshmi V J, Swamy B P M, Kaladhar K, Sarla N.2010. BPH resistance in introgression lines of Swarna/Oryza nivara and KMR3/O. rufipogon. Direct Rice Res Newsl, 8: 4.
27	Lang N T, Yanagihara S, Buu B C.2000. Quantitative trait loci for salt tolerance in rice via molecular markers.Omonrice, 8: 37-48.
28	Lang N T, Li Z K, Buu B C.2001. Microsatellite markers linked to salt tolerance in rice.Omonrice, 9: 9-21.
29	Linh L H, Linh T H, Xuan T D, Ham L H, Ismail A M, Khanh T D.2012. Molecular breeding to improve salt tolerance of rice (Oryza sativa L.) in the red river delta of Vietnam. Int J Plant Genom, 2012: 1-9.
30	Liu K, Muse S V.2005. Power marker: An integrated analysis environment for genetic marker analysis.Bioinformatics, 21(9): 2128-2129.
31	Liu S, Anderson J A.2003. Targeted molecular mapping of major wheat QTL forFusarium head blight resistance using wheat ESTs and synteny with rice. Genome, 46(5): 817-823.
32	McCartney C A, Sommers D J, Fedak G, Cao W.2004. Haplotype diversity atFusarium head blight resistance QTLs in wheat. Theor Appl Genet, 109(2): 261-271.
33	Mishra S, Singh B, Panda K, Singh B P, Singh N, Misra P, Rai V, Singh N K.2016. Association of SNP haplotypes of HKT family genes with salt tolerance in Indian wild rice germplasm.Rice, 9: 15.
34	Mohammadi-Nejad G, Arzani A, Rezai A M, Singh R K, Gregorio G B.2008. Assessment of rice genotypes for salt tolerance using microsatellite markers associated with theSaltol QTL. Afr J Biotechnol, 7(6): 730-736.
35	Rahman M A, Thomson M J, Shah-E-Alam M, de Ocampo M, Egdane J, Ismail A M.2016. Exploring novel genetic sources of salinity tolerance in rice through molecular and physiological characterization.Ann Bot: 1-15.
36	Rai V, Sreenu K, Pushpalatha B, Babu A P, Brajendra, Sandhya G, Sarla N.2010. Swarna/Oryza nivara and KMR3/O. rufipogon introgression lines tolerant to drought and salinity. Direct Rice Res Newsl, 8: 4.
37	Ren Z H, Gao J P, Li L G, Cai X L, Huang W, Chao D Y, Zhu M Z, Wang Z Y, Luan S, Lin H X.2005. A rice quantitative trait locus for salt tolerance encodes a sodium transporter.Nat Genet, 37: 1141-1146.
38	Samal R, Roy P S, Dash A K, Rao G J N. Bharathkumar S, Subudhi H N, Reddy J N.2016. Genetic diversity in the rice landraces (Oryza sativa L.) of coastal Sundarbans (India) and their adaptation to the local saline condition investigated both at molecular and physiological level. Acta Physiol Plant, 38: 56.
39	Singh A K, Gopala Krishnan S, Singh V P, Prabhu K V, Mohapatra T, Singh N K, Sharma T R, Nagarajan M, Vinod K K, Singh D, Singh U D, Chander S, Atwal S S, Seth R, Singh V K, Ellur R K, Singh A, Anand D, Khanna A, Yadav S, Goel N, Singh A, Shikari A B, Singh A, Marathi B.2011. Marker assisted selection a paradigm shift in Basmati breeding.Ind J Genet Plant Breeding, 71(2): 120-128.
40	Singh R K, Gregorio G B, Jain R K.2007. QTL mapping for salinity tolerance in rice.Physiol Mol Biol Plant, 13(2): 87-99.
41	Singh R K, Flowers T J.2010. The physiology and molecular biology of the effects of salinity on rice. In: Pessarakli M. Handbook of Plant and Crop Stress. 3rd edn. Boca Raton, Florida, USA: Taylor and Francis: 901-942.
42	Singh R, Singh Y, Xalaxo S, Verulkar S, Yadav N, Singh S, Singh N, Prasad K S N, Kondayya K, Ramana Rao P V, Rani M G, Anuradha T, Suraynarayana Y, Sharma P C, Krishnamurthy S L, Sharma S K, Dwivedi J L, Singh A K, Singh P K, Nilanjay, Singh N K, Kumar R, Chetia S K, Ahmad T, Rai M, Perraju P, Pande A, Singh D N, Mandal N P, Reddy J N, Singh O N, Kataral J L, Marandi B, Swain P, Sarkar R K, Singh D P, Mohapatra T, Padmawathi G, Ram T, Kathiresan R M, Paramsivam K, Nadarajan S, Thirumeni S, Nagarajan M, Singh A K, Vikram P, Kumar A, Septiningshih E, Singh U S, Ismail A M, Mackill D, Singh N K.2016. From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.Plant Sci, 242: 278-287.
43	Tiwari S, Krishnamurthy S L, Kumar V, Singh B, Rao A R, Amitha Mithra S V, Rai V, Singh A K, Singh N K.2016. Mapping QTLs for salt tolerance in rice (Oryza sativa L.) by bulked segregant analysis of recombinant inbred lines using 50K SNP chip. PLoS One, 11(4): e0153610.
44	Thomson M J, de Ocampo M, Egdane J, Rahman M A, Sajise A G, Adorada D L, Tumimbang-Raiz E, Blumwald E, Seraj Z I, Singh R K, Gregorio G B, Ismail A M.2010. Characterizing theSaltol quantitative trait locus for salinity tolerance in rice. Rice, 3(2): 148-160.
45	van Berloo R.2008. GGT2.0: Versatile software for visualization and analysis of genetic data.J Hered, 99(2): 232-236.
46	Vinod K K, Gopala Krishnan S, Naresh Babu N, Nagarajan M, Singh A K.2013. Improving salt tolerance in rice: Looking beyond the conventional. In: Ahmad P, Azooz M M, Prasad M N V. Salt Stress in Plants: Signalling, Omics and Adaptations. New York, USA: Springer: 219-260.
47	Walia H, Wilson C, Condamine P, Liu X, Ismail A M, Zeng L, Wanamaker S I, Mandal J, Xu J, Cui X, Close T J.2005. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage.Plant Physiol, 139(2): 822-835.
48	Yoshida S, Forno D A, Cock J H, Gomez K A.1976. Laboratory Manual for Physiological Studies of Rice. Los Baños, the Philippines: International Rice Research Institute.
49	Zhou Y, Yang P, Cui F L, Zhang F T, Luo X D, Xie J K.2016. Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.). PLoS One, 11: e0146242.
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

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