Characterization of Myanmar Paw San Hmwe Accessions Using Functional Genetic Markers

doi:10.1016/S1672-6308(14)60285-7

Abstract

Abstract:

Paw San Hmwe (PSM) rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions were genotypically characterized, and their physical grain and cooking quality traits were studied. We used specific gene markers associated with aroma, apparent amylose content (AAC) and alkali spreading value to determine the alleles carried by different PSM accessions. The results revealed that six PSM accessions (PSM10, PSM12, PSM13, PSM21, PSM22 and PSM30) had a 3-bp insertion in Os2AP gene. Gel consistency (GC) allele was predominant among the PSM accessions for gelatinization temperature (GT), however, the phenotype observed was between low and intermediate GT because of the combination of the GC allele with the presence of low GT allele at heterozygous state from the other loci of the SSIIa gene. Intermediate to high AAC was observed among the PSM accessions corresponding to the haplotype identified for the single nucleotide polymorphism G/T and the (CT)_n repeat in the Wx gene. The characterization and grouping data of PSM accessions posted benefits to Myanmar seed banks, and our results will help in maintaining the integrity of PSM rice variety.

Key words: Paw San Hmwe, rice, aroma, apparent amylose content, gel consistency, gelatinization temperature, alkali spreading value, functional genetic marker, grain quality, haplotype analysis

Swar Oo Kyaw, Kongjaimun Alisa, Khanthong Srisawat, Yi Myint, Tin Myint Tin, Korinsak Siriporn, Lanceras Siangliw Jonaliza, Myo Myint Khin, Vanavichit Apichart, Malumpong Chanate, Toojinda Theerayut. Characterization of Myanmar Paw San Hmwe Accessions Using Functional Genetic Markers[J]. Rice Science, 2015, 22(2): 53-64.

Figures/Tables 6

References 49

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Code	Accession No.	Local name	Region	Type
PSM1	807	Paw San Bay Kyar	Aeyawady	Indica
PSM2	870	Mee Don	Aeyawady	Japonica
PSM3	923	NgaKywe	Yangon	Japonica
PSM4	930	Paw San Hmwe	Pago	Indica
PSM5	962	Paw San Hmwe	Pago	Indica
PSM6	998	Mee Don Saba	Kayin	Indica
PSM7	1 045	ZawGyiPyan (Mee don)	Aeyawady	Indica
PSM8	1 105	NgaKywe (U To)	Aeyawady	Japonica
PSM9	1 139	Paw San Hmwe	Pago	Indica
PSM10	1 207	Paw San Hmwe	Aeyawady	Japonica
PSM11	1 495	Paw San Hmwe	Yangon	Indica
PSM12	1 627	Paw San Hmwe	Mon	Japonica
PSM13	1 641	Paw San Hmwe	Aeyawady	Japonica
PSM14	1 981	NgaKywe	Yangon	Indica
PSM15	2 117	Mee Don Hmwe	Aeyawady	Indica
PSM16	2 176	Hnan War Mee Don	Rakhine	Indica
PSM17	2 447	NgaKywe	Pago	Indica
PSM18	2 460	Paw San Bay Kyar	Aeyawady	Indica
PSM19	2 499	Paw San Hmwe	Pago	Indica
PSM20	2 500	Paw San Hmwe	Pago	Japonica
PSM21	2 501	Paw San Hmwe	Yangon	Japonica
PSM22	2 502	Paw San Hmwe	Aeyawady	Japonica
PSM23	2 522	Paw San Hmwe	Aeyawady	Japonica
PSM24	2 578	Paw San Shwe War	Aeyawady	Indica
PSM25	2 620	Paw San Hmwe	Aeyawady	Indica
PSM26	2 878	Hnan War Mee Don	Sagaing	Indica
PSM27	2 946	Paw San Hmwe	Pago	Indica
PSM28	3 225	Mee Don Yoe Sein	Aeyawady	Indica
PSM29	3 530	Bay Kyar Lay	Aeyawady	Japonica
PSM30	5 802	Paw San Hmwe	Chin	Japonica
PSM31	11 800	Paw San Hmwe	Aeyawady	Indica

Code	Accession No.	Local name	Region	Type
PSM1	807	Paw San Bay Kyar	Aeyawady	Indica
PSM2	870	Mee Don	Aeyawady	Japonica
PSM3	923	NgaKywe	Yangon	Japonica
PSM4	930	Paw San Hmwe	Pago	Indica
PSM5	962	Paw San Hmwe	Pago	Indica
PSM6	998	Mee Don Saba	Kayin	Indica
PSM7	1 045	ZawGyiPyan (Mee don)	Aeyawady	Indica
PSM8	1 105	NgaKywe (U To)	Aeyawady	Japonica
PSM9	1 139	Paw San Hmwe	Pago	Indica
PSM10	1 207	Paw San Hmwe	Aeyawady	Japonica
PSM11	1 495	Paw San Hmwe	Yangon	Indica
PSM12	1 627	Paw San Hmwe	Mon	Japonica
PSM13	1 641	Paw San Hmwe	Aeyawady	Japonica
PSM14	1 981	NgaKywe	Yangon	Indica
PSM15	2 117	Mee Don Hmwe	Aeyawady	Indica
PSM16	2 176	Hnan War Mee Don	Rakhine	Indica
PSM17	2 447	NgaKywe	Pago	Indica
PSM18	2 460	Paw San Bay Kyar	Aeyawady	Indica
PSM19	2 499	Paw San Hmwe	Pago	Indica
PSM20	2 500	Paw San Hmwe	Pago	Japonica
PSM21	2 501	Paw San Hmwe	Yangon	Japonica
PSM22	2 502	Paw San Hmwe	Aeyawady	Japonica
PSM23	2 522	Paw San Hmwe	Aeyawady	Japonica
PSM24	2 578	Paw San Shwe War	Aeyawady	Indica
PSM25	2 620	Paw San Hmwe	Aeyawady	Indica
PSM26	2 878	Hnan War Mee Don	Sagaing	Indica
PSM27	2 946	Paw San Hmwe	Pago	Indica
PSM28	3 225	Mee Don Yoe Sein	Aeyawady	Indica
PSM29	3 530	Bay Kyar Lay	Aeyawady	Japonica
PSM30	5 802	Paw San Hmwe	Chin	Japonica
PSM31	11 800	Paw San Hmwe	Aeyawady	Indica

Trait	Gene	Chromosome	Marker	Reference
Amylose content	Wx	6	Waxy (G-T)	Ayres et al, 1997
		6	Waxy (CT)_n	Bligh et al, 1995
Fragrance	Os2AP	8	Aromarker	Vanavichit et al, 2008
		8	3In2AP	Myint et al, 2012a
		8	FMbadh2-E2A	Shi et al, 2008
Gelatinization temperature	SSIIa	6	SNP2340-41	Katengam et al, 2008
		6	SNP2209	Katengam et al, 2008

Trait	Gene	Chromosome	Marker	Reference
Amylose content	Wx	6	Waxy (G-T)	Ayres et al, 1997
		6	Waxy (CT)_n	Bligh et al, 1995
Fragrance	Os2AP	8	Aromarker	Vanavichit et al, 2008
		8	3In2AP	Myint et al, 2012a
		8	FMbadh2-E2A	Shi et al, 2008
Gelatinization temperature	SSIIa	6	SNP2340-41	Katengam et al, 2008
		6	SNP2209	Katengam et al, 2008

Code	Waxy (G-T)	Waxy (CT)_n	SNP2340-41	SNP2209	3In2AP	FMbadh2-E2A	Aromarker
PSM1	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM2	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM3	T	11月19日	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM4	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM5	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM6	G	11	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM7	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM8	G	19	High GT	High GT	Non aroma (197/194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM9	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM10	G	19	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM11	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM12	G	19	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM13	G	19	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM14	G/T	11月17日	High/low GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM15	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM16	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM17	G	17	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM18	G/T	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM19	G	11月19日	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM20	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM21	T	11月19日	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM22	G	19	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM23	G	19	High GT	High GT	Non aroma (197/194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM24	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM25	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM26	G	11月17日	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM27	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM28	G	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM29	G/T	19	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM30	G	19	High GT	High GT	Aroma (197 bp)	Non aroma (207 bp)	Non aroma (400 bp)
PSM31	G	19	High GT	High/low GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)
KDML105	T	17	Low GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Aroma (392 bp)
Basmati 370	G	17	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Aroma (392 bp)
IR57514	G	11	High GT	High GT	Non aroma (194 bp)	Non aroma (207 bp)	Non aroma (400 bp)