Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Biselli, Chiara; Cavalluzzo, Daniela; Perrini, Rosaria; Gianinetti, Alberto; Bagnaresi, Paolo; Urso, Simona; Orasen, Gabriele; Desiderio, Francesca; Lupotto, Elisabetta; Cattivelli, Luigi; Valè, Giampiero

doi:10.1186/1939-8433-7-1

Rice

Table 1 Germplasm collection of 127 rice accessions

From: Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

Accession	AAC (%)	EU Classification	Group	Origin	Maturity time (days)	Grain length (mm)^a	Grain width (mm)^a	Length to width ratio	RM190	T/G intron 1	A/C exon 6	_1514 G/T promoter	1801 T/C exon 9	2282 A/G intron 10	2806 C/T intron 12
CALMOCHI 101	-	Medium	Jap	USA	158	5,26	2,97	1,77	17	T	A	G	T	A	C
PREVER	14,92	Long B	Jap	ITA	141	7,22	2,16	3,34	18	T	A	G	T	A	C
MEJANES 2	15,21	Long B	Jap	FRA	144	8,24	2,28	3,61	18	T	A	G	T	A	C
YRL 196	15,55	Medium	Jap	AUS	142	5,90	2,61	2,26	19	T	A	G	T	A	C
DELTA	15,60	Long A	Jap	FRA	139	8,16	2,90	2,81	18	T	A	G	T	A	C
LOMELLINO	15,77	Medium	Jap	ITA	129	5,67	3,22	1,76	18	T	A	G	T	A	C
SOURE	15,86	Long A	Jap	PRT	149	7,56	2,88	2,63	18	T	A	G	T	A	C
CAMPINO	15,90	Medium	Jap	PRT	145	6,19	3,39	1,83	18	T	A	G	T	A	C
EUROSIS	16,11	Long A	Jap	ITA	149	6,73	2,52	2,67	18	T	A	G	T	A	C
FAMILIA 181	16,27	Long A	Jap	PRT	159	7,05	2,85	2,47	18	T	A	G	T	A	C
TAICHUNG 65	16,29	Long A	Jap	TWN	149	6,58	2,66	2,47	18	T	A	G	T	A	C
SMERALDO	16,34	Long A	Jap	ITA	159	6,89	2,64	2,61	18	T	A	G	T	A	C
YRM 6-2	16,40	Medium	Jap	AUS	160	5,93	2,90	2,04	19	T	A	G	T	A	C
TIMICH 108	16,42	Round	Jap	ROM	127	4,92	3,13	1,57	17	T	A	G	T	A	C
GIOVANNI MARCHETTI	16,53	Medium	Jap	ITA	140	5,76	3,29	1,75	18	T	A	G	T	A	C
TOPAZIO	16,55	Medium	Jap	PRT	138	5,70	3,31	1,72	18	T	A	G	T	A	C
ZENA	16,57	Long B	Jap	ITA	144	7,49	2,16	3,47	18	T	A	G	T	A	C
RIBE 253	16,71	Long A	Jap	ITA	149	6,91	2,88	2,40	18	T	A	G	T	A	C
PIEMONTE	16,98	Long A	Jap	ITA	149	6,21	3,25	1,91	19	T	A	G	T	A	C
RPC 12	17,03	Round	Jap	CHN	141	5,01	3,11	1,61	18	T	A	G	T	A	C
RONCOLO	17,06	Medium	Jap	ITA	144	5,69	3,22	1,77	18	T	A	G	T	A	C
SLAVA	17,23	Medium	Jap	BGR	144	6,14	3,38	1,82	18	T	A	G	T	A	C
SELN 244 A6-20	17,29	Medium	Jap	AUS	154	5,34	3,17	1,68	18	T	A	G	T	A	C
BONNI	17,47	Long A	Jap	ITA	143	7,72	2,83	2,73	19	T	A	G	T	A	C
OSCAR	17,56	Long A	Jap	PRT	166	7,12	2,40	2,97	18	T	A	G	T	A	C
PERLA	17,67	Round	Jap	ITA	150	5,14	2,88	1,78	18	T	A	G	T	A	C
ROXANI	17,72	Long A	Jap	GRC	162	7,01	2,96	2,37	18	T	A	G	T	A	C
SELENIO	17,75	Round	Jap	ITA	155	5,01	2,90	1,73	17	T	A	G	T	A	C
ARBORIO	17,79	Long A	Jap	ITA	149	7,21	3,50	2,06	18	T	A	G	T	A	C
GRITNA	17,83	Long A	Jap	ITA	140	7,21	2,94	2,45	18	T	A	G	T	A	C
S 101	17,85	Medium	Jap	USA	153	5,28	2,93	1,80	18	T	A	G	T	A	C
AUGUSTO	18,06	Long A	Jap	ITA	143	6,86	2,69	2,55	18	T	A	G	T	A	C
ARIETE	18,08	Long A	Jap	ITA	145	6,81	2,64	2,58	18	T	A	G	T	A	C
GIZA 177	18,10	Medium	Jap	EGY	158	5,36	2,90	1,85	17	T	A	G	T	A	C
SAVIO	18,11	Long A	Jap	ITA	151	6,57	2,60	2,53	18	T	A	G	T	A	C
LOTO	18,20	Long A	Jap	ITA	139	6,51	2,95	2,21	18	T	A	G	T	A	C
KORAL	18,27	Long A	Jap	ITA	151	6,89	2,74	2,51	18	T	A	G	T	A	C
T 757	18,30	Long A	Jap	IND	162	6,22	3,20	1,94	18	T	A	G	T	A	C
SHSS 53	18,44	Long A	Jap	ESP	158	6,63	2,96	2,24	18	T	A	G	T	A	C
SCUDO	18,49	Long B	Jap	ITA	163	7,53	2,29	3,29	18	T	A	G	T	A	C
CHACARERO	18,55	Long A	Jap	USA	164	7,84	3,00	2,61	18	T	A	G	T	A	C
M 202	18,55	Medium	Jap	USA	152	6,00	2,82	2,13	18	T	A	G	T	A	C
MELAS	18,61	Long B	Jap	GRC	154	7,04	2,34	3,01	18	T	A	G	T	A	C
GUITA	18,62	Medium	Jap	PHL	162	5,90	2,98	1,98	18	T	A	G	T	A	C
IR56381-139-2-2	18,65	Long A	Jap	ARG	160	6,34	3,05	2,08	18	T	A	G	T	A	C
LA PLATA GUANEJAN	18,65	Long A	Jap	PHL	161	7,53	3,01	2,50	18	T	A	G	T	A	C
MARATELLI	18,66	Medium	Jap	ITA	145	5,61	3,13	1,79	18	T	A	G	T	A	C
KULON	18,76	Long A	Jap	RUS	147	6,55	2,91	2,25	18	T	A	G	T	A	C
ESTRELA IRRADIADO	18,80	Long A	Jap	PRT	154	6,50	2,93	2,22	18	T	A	G	T	A	C
BENGAL	18,81	Long A	Jap	USA	163	6,11	2,74	2,23	18	T	A	G	T	A	C
CENTAURO	18,86	Round	Jap	ITA	155	5,60	3,36	1,67	18	T	A	G	T	A	C
LUXOR	18,88	Long A	Jap	ITA	158	6,48	3,02	2,15	18	T	A	G	T	A	C
CIGALON	18,92	Medium	Jap	FRA	140	5,38	3,14	1,71	18	T	A	G	T	A	C
ERCOLE	19,00	Long A	Jap	ITA	157	7,02	2,88	2,44	19	T	A	G	T	A	C
THAIPERLA	19,09	Round	Jap	USA	161	5,55	3,25	1,71	18	T	A	G	T	A	C
S. ANDREA	19,14	Long A	Jap	ITA	157	6,92	3,29	2,10	18	T	A	G	T	A	C
SIS R215	19,17	Long A	Jap	ITA	153	7,30	2,57	2,84	18	T	A	G	T	A	C
COLINA	19,25	Round	Jap	ESP	161	5,18	3,06	1,69	18	T	A	G	T	A	C
FLIPPER	19,28	Medium	Jap	ITA	152	5,99	3,01	1,99	18	T	A	G	T	A	C
ITALPATNA 48	19,34	Long A	Jap	ITA	151	7,12	2,60	2,74	17	T	A	G	T	A	C
M 204	19,42	Long A	Jap	USA	156	6,19	2,85	2,17	18	T	A	G	T	A	C
SAKHA 102	19,43	Medium	Jap	EGY	166	5,59	2,90	1,93	17	T	A	G	T	A	C
CENTURY PATNA	19,52	Long A	Jap	USA	157	8,00	3,15	2,54	18	T	A	G	T	A	C
SALVO	19,67	Long B	Jap	ITA	154	7,36	2,12	3,47	18	T	A	G	T	A	C
PECOS	19,77	Medium	Jap	USA	161	5,62	2,81	2,00	18	T	A	G	T	A	C
89 AXHVA-6	19,97	Round	Jap	ARG	166	5,69	3,13	1,82	18	T	A	G	T	A	C
Upla 104	19,97	Long A	Jap	ARG	168	7,95	3,02	2,63	18	T	A	G	T	A	C
CT 23	20,03	Long B	Jap	COL	157	7,93	2,45	3,24	18	T	A	G	T	A	C
FIDJI	20,05	Long B	Jap	PHL	163	7,88	2,23	3,53	18	T	A	G	T	A	C
S 102-2	20,09	Long A	Jap	USA	164	5,62	3,23	1,74	18	T	A	G	T	A	C
MAIORAL	20,18	Long A	Jap	PRT	154	7,96	2,83	2,81	18	T	A	G	T	A	C
BELOZEM	20,21	Medium	Jap	BGR	157	6,04	3,25	1,86	18	T	A	G	T	A	C
SUWEON 280	20,34	Long A	Jap	KOR	-	6,00	2,64	2,72	18	T	A	G	T	A	C
GRAAL	20,40	Long B	Jap	FRA	149	7,63	2,23	3,42	18	T	A	G	T	A	C
CAPATAZ	20,53	Long A	Jap	ESP	157	6,31	3,23	1,95	18	T	A	G	T	A	C
UPLA 80	20,54	Long B	Jap	ARG	142	7,81	2,12	3,68	18	T	A	G	T	A	C
ROTUNDUS	20,65	Long A	Jap	HUN	139	8,75	3,46	2,53	17	G	C	T	T	A	C
ITALPATNA X MILYANG	20,96	Long A	Jap	PRT	150	6,69	2,72	2,46	18	T	A	G	T	A	C
UPLA 91	21,21	Long A	Jap	ARG	140	7,11	2,43	2,93	18	T	A	G	T	A	C
ANTONI	21,27	Long A	Jap	BGR	131	6,49	2,91	2,23	17	G	C	T	T	A	C
GOOLARAH	21,30	Long B	Jap	AUS	174	7,62	2,16	3,53	19	T	A	G	T	A	C
UPLA 68	21,56	Long B	Jap	ARG	149	8,02	2,29	3,50	18	T	A	G	T	A	C
JEFFERSON	22,21	Long A	Jap	USA	157	6,79	2,44	2,78	20	G	C	G	T	A	C
SAFARI	22,37	Long A	Jap	PRT	149	6,60	2,72	2,43	17	G	C	T	T	A	C
A 301	22,44	Long B	Jap	USA	163	7,78	2,26	3,44	20	G	C	G	T	A	C
OTA	22,55	Long A	Jap	PRT	161	6,15	2,90	2,12	13	G	C	T	T	A	C
UPLA 64	22,57	Long B	Jap	ARG	148	7,87	2,16	3,64	17	G	C	T	T	A	C
LORD	22,60	Long A	Jap	ITA	144	6,93	2,60	2,67	20	G	C	G	T	A	C
SANDORA	22,75	Long A	Jap	HUN	135	7,39	2,62	2,82	17	G	C	T	T	A	C
DELLROSE	22,83	Long A	Jap	USA	163	6,58	2,27	2,90	20	G	C	G	T	A	C
BOMBA	22,84	Medium	Jap	ESP	159	5,45	2,99	1,82	21	G	C	T	T	A	C
N 3	22,86	Long A	Jap	ESP	167	6,64	2,58	2,57	20	G	C	G	T	A	C
KARNAK	22,90	Long A	Jap	ITA	156	7,45	3,43	2,17	17	G	C	T	T	A	C
GIGANTE VERCELLI	23,05	Long A	Jap	ITA	149	6,95	3,32	2,09	17	G	C	T	T	A	C
MARTA	23,06	Long B	Jap	ITA	183	7,40	2,29	3,23	20	G	C	G	T	A	C
COCODRIE	23,10	Long B	Jap	USA	155	7,01	2,10	3,34	20	G	A	G	T	A	C
DREW	23,26	Long B	Jap	USA	160	6,81	2,16	3,15	14	G	C	T	T	A	C
DELLMONT	23,33	Long B	Jap	USA	160	6,96	2,27	3,07	20	G	C	G	T	A	C
IR 5549-1-2	23,47	Long B	Jap	PHL	173	6,98	2,25	3,10	20	G	C	G	T	A	C
L 205	23,57	Long B	Jap	USA	156	7,47	2,21	3,38	10	G	A	T	C	G	T
BLUEBONNET	23,60	Long B	Jap	USA	-	8,16	2,66	3,07	20	G	C	G	T	A	C
TEJO	23,63	Long A	Jap	ITA	156	6,71	2,63	2,55	20	G	C	G	T	A	C
GOLFO	23,75	Long A	Jap	ITA	181	7,39	2,47	2,99	20	G	C	G	T	A	C
LAGRUE	23,76	Long A	Jap	USA	160	6,50	2,20	2,95	20	G	C	G	T	A	C
DORADO	23,79	Long B	Jap	GRC	164	7,29	2,23	3,27	14	G	C	T	T	A	C
PLUS	23,84	Long B	Jap	ITA	159	7,02	2,26	3,11	14	G	C	T	T	A	C
MAYBELLE	23,87	Long B	Jap	USA	155	6,65	2,19	3,04	20	G	C	G	T	A	C
L 204	23,90	Long B	Jap	USA	153	7,81	2,37	3,30	20	G	C	G	T	A	C
GIADA	23,93	Long B	Jap	ITA	151	7,45	2,08	3,58	17	G	C	T	T	A	C
BOND	23,96	Long B	Jap	USA	157	7,08	2,24	3,16	20	G	C	G	T	A	C
MERLE’	24,18	Long B	Jap	FRA	151	7,08	2,23	3,17	9	G	A	T	C	G	T
REXMONT	24,19	Long B	Jap	USA	161	6,72	2,19	3,07	10	G	A	T	C	G	T
LACASSINE	24,21	Long B	Jap	USA	162	7,03	2,21	3,18	20	G	C	G	T	A	C
ALAN	24,30	Long B	Jap	USA	154	6,86	2,03	3,38	14	G	A	T	T	A	C
DIXIEBELLE	24,35	Long A	Jap	USA	167	6,28	2,21	2,84	11	G	A	T	C	G	T
ARIANA	24,42	Long B	Jap	ROM	168	7,34	2,41	3,04	20	G	C	G	T	A	C
CNA 4081	24,44	Long B	Ind	BRA	149	6,64	2,19	3,03	9	G	A	T	C	G	T
A 201	24,50	Long B	Jap	USA	165	7,83	2,11	3,71	20	G	A	G	T	A	C
GLADIO	24,73	Long B	Jap	ITA	129	7,28	2,19	3,32	20	G	A	G	T	A	C
THAIBONNET	24,83	Long B	Jap	USA	159	7,81	2,37	3,30	20	G	A	G	T	A	C
ORIONE	24,85	Long A	Jap	ITA	173	6,90	2,65	2,60	9	G	A	T	C	G	T
IR 47686-9-4-1	25,03	Long B	Jap	PHL	172	7,14	2,19	3,26	20	G	A	G	T	A	C
FRAGRANCE	25,16	Long B	Jap	ITA	154	7,74	2,42	3,20	20	G	A	G	T	A	C
L.202	25,21	Long B	Jap	USA	155	7,52	2,18	3,45	20	G	A	G	T	A	C
ZHEN SHANG 47	25,40	Long A	Ind	CHN	152	6,10	2,92	2,09	11	G	A	G	C	G	T
ARROYOGRANDE	25,46	Long B	Jap	ESP	159	7,74	2,20	3,52	20	G	A	G	T	A	C
ALINANO C	26,03	Long A	Jap	FRA	151	7,38	2,57	2,87	11	G	A	G	C	G	T

The Apparent Amylose Content (AAC), with the EU classification, the group, the origin, the maturity time, the seed biometric characteristics and the alleles for the GBSSI molecular markers considered are indicated for each genotype.
^adata are referred to decorticated grains.

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