Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

doi:10.1016/j.rsci.2016.08.009

Abstract

Abstract:

Joha rice of Assam is a class of rice with aroma, good cooking qualities and excellent palatability, which are grown in different places of Assam with their adaptability to local situations. A total of 143 simple sequence repeat markers were used in this study to reveal sufficient genetic variations among the 40 Joha and 14 non-Joha rice genotypes. Polymorphism information content of these markers were from 0.17 to 0.88, where the average of 3.7 alleles were observed. The model-based population assignment and dendrogram analysis identified three distinct groups in the 54 rice accessions, which established a clear identity of Joha accessions from the Basmati accessions, indicating high diversity and strong population structure in Joha rice. Furthermore, a total of 29 significant marker-trait associations (P < 0.05) for 10 characters were detected. The QTLs related with yield and grain quality can be used effectively in crop improvement programs and for further fine mapping and validation of specific genes to develop gene-based perfect markers in rice breeding and for mining of better alleles of these genes in Joha rice collections.

Key words: Joha rice, genetic diversity, association mapping, population structure, quantitative trait locus, aroma

Rekha Talukdar Preeti, Rathi Sunayana, Pathak Khanin, Kumar Chetia Sanjay, Nath Sarma Ramendra. Population Structure and Marker-Trait Association in Indigenous Aromatic Rice[J]. Rice Science, 2017, 24(3): 145-154.

Figures/Tables 6

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51	(Managing Editor: Li Guan)

No.	Genotype	Parent	Date of heading (d)	Yield per	Aroma score ^a	No.	Genotype	Parent	Date of heading (d)	Yield per	Aroma score ^a
No.	Genotype	Parent	Date of heading (d)	plant (g)	Aroma score ^a	No.	Genotype	Parent	Date of heading (d)	plant (g)	Aroma score ^a
1	Kunkuni Joha-1	IJR	123	32.78	3	28	Bor Joha	IJR	125	42.64	1
2	Kamini Joha	IJR	131	41.487	4	29	Bhugri Joha	IJR	131	43.51	3
3	Ronga Joha-2	IJR	131	47.81	3	30	Bhaboli Joha	IJR	131	36.873	4
4	Tulsi Joha	IJR	132	39.88	2	31	Boga Joha-1	IJR	120	21.3	1
5	Monipuri Joha-2	IJR	132	60.61	3	32	Kharika Joha	IJR	121	44.467	3
6	Kon Joha-3	IJR	129	36.103	3	33	Koli Joha-2	IJR	120	21.117	1
7	Kola Joha-2	IJR	123	51.923	4	34	Siali Joha	IJR	123	42.033	1
8	Konbogi Joha	IJR	129	41.94	4	35	Kunkuni Joha-2	IJR	120	36.047	4
9	Goalporia Joha-2	IJR	127	47.763	3	36	Maniki Madhuri Joha	IJR	118	32.48	2
10	Joha	IJR	124	24.06	3	37	Monipuri Joha-1	IJR	120	35.147	1
11	Koli Joha	IJR	120	36.643	3	38	Kolajoha new	IJR	120	30.33	1
12	Joha Bora	IJR	127	53.51	3	39	Jeera Joha	IJR	120	22.56	3
13	Kon Joha-1	IJR	120	38.56	4	40	Kon Joha	IJR	120	34.7	1
14	Ronga Joha-1	IJR	122	31.92	3	41	Keteki Joha	H	136	21.993	3
15	Kola Joha-1	IJR	120	39.807	2	42	NDR6330	B	120	20.807	3
16	Goalporia Joha-1	IJR	127	42.88	3	43	Dehradun Basmati Selection-13	D	110	19.307	1
17	Chufon Joha	IJR	128	35.51	3	44	13-Selection Kamal	L	90	18.85	3
18	Cheniguti Joha	IJR	131	31.817	4	45	15-Selection Kamal	L	86	24.97	3
19	Bor Sal Joha	IJR	122	38.573	2	46	Bishnubhog	PV	130	29.793	1
20	Boga Tulsi Joha	IJR	121	24.57	4	47	Tulsi Phool	PV	131	24.43	2
21	Boga Joha	IJR	121	42.843	2	48	Kala Namak	PV	117	46.997	1
22	Bengoli Joha	IJR	122	37.06	2	49	Indrobhog	PV	120	17.817	2
23	Badshabhog	IJR	119	21.387	2	50	Jowar Pool	PV	124	27.98	4
24	Arab Joha	IJR	133	25.05	3	51	Kalijeera	PV	128	21.357	2
25	Bokul Joha	IJR	119	41.663	1	52	Harinarayan	PV	128	29.68	2
26	Boga Maniki Modhuri	IJR	120	28.78	3	53	Saheb Sali	PV	120	41.02	3
27	Bogi Joha	IJR	100	37.055	1	54	Ranjit	NH	128	24.614	1
IJR, Indigenous Joha rice; H, High-yielding aromatic rice of Assam developed from Savitri × Badshabhog; B, Selection from Bishnuparag; D, Selection from Dehradun Basmati; L, Selection from local Kamal; PV, Pure line variety; NH, Non-aromatic high-yielding variety of Assam developed from Pankajb × Mahsuri. Nos. 1-40 are Joha aromatic rice accessions, and Nos. 41-54 are Joha non-aromatic rice accessions.
^a Based on Sood and Siddiq (1978).

No.	Genotype	Parent	Date of heading (d)	Yield per	Aroma score ^a	No.	Genotype	Parent	Date of heading (d)	Yield per	Aroma score ^a
No.	Genotype	Parent	Date of heading (d)	plant (g)	Aroma score ^a	No.	Genotype	Parent	Date of heading (d)	plant (g)	Aroma score ^a
1	Kunkuni Joha-1	IJR	123	32.78	3	28	Bor Joha	IJR	125	42.64	1
2	Kamini Joha	IJR	131	41.487	4	29	Bhugri Joha	IJR	131	43.51	3
3	Ronga Joha-2	IJR	131	47.81	3	30	Bhaboli Joha	IJR	131	36.873	4
4	Tulsi Joha	IJR	132	39.88	2	31	Boga Joha-1	IJR	120	21.3	1
5	Monipuri Joha-2	IJR	132	60.61	3	32	Kharika Joha	IJR	121	44.467	3
6	Kon Joha-3	IJR	129	36.103	3	33	Koli Joha-2	IJR	120	21.117	1
7	Kola Joha-2	IJR	123	51.923	4	34	Siali Joha	IJR	123	42.033	1
8	Konbogi Joha	IJR	129	41.94	4	35	Kunkuni Joha-2	IJR	120	36.047	4
9	Goalporia Joha-2	IJR	127	47.763	3	36	Maniki Madhuri Joha	IJR	118	32.48	2
10	Joha	IJR	124	24.06	3	37	Monipuri Joha-1	IJR	120	35.147	1
11	Koli Joha	IJR	120	36.643	3	38	Kolajoha new	IJR	120	30.33	1
12	Joha Bora	IJR	127	53.51	3	39	Jeera Joha	IJR	120	22.56	3
13	Kon Joha-1	IJR	120	38.56	4	40	Kon Joha	IJR	120	34.7	1
14	Ronga Joha-1	IJR	122	31.92	3	41	Keteki Joha	H	136	21.993	3
15	Kola Joha-1	IJR	120	39.807	2	42	NDR6330	B	120	20.807	3
16	Goalporia Joha-1	IJR	127	42.88	3	43	Dehradun Basmati Selection-13	D	110	19.307	1
17	Chufon Joha	IJR	128	35.51	3	44	13-Selection Kamal	L	90	18.85	3
18	Cheniguti Joha	IJR	131	31.817	4	45	15-Selection Kamal	L	86	24.97	3
19	Bor Sal Joha	IJR	122	38.573	2	46	Bishnubhog	PV	130	29.793	1
20	Boga Tulsi Joha	IJR	121	24.57	4	47	Tulsi Phool	PV	131	24.43	2
21	Boga Joha	IJR	121	42.843	2	48	Kala Namak	PV	117	46.997	1
22	Bengoli Joha	IJR	122	37.06	2	49	Indrobhog	PV	120	17.817	2
23	Badshabhog	IJR	119	21.387	2	50	Jowar Pool	PV	124	27.98	4
24	Arab Joha	IJR	133	25.05	3	51	Kalijeera	PV	128	21.357	2
25	Bokul Joha	IJR	119	41.663	1	52	Harinarayan	PV	128	29.68	2
26	Boga Maniki Modhuri	IJR	120	28.78	3	53	Saheb Sali	PV	120	41.02	3
27	Bogi Joha	IJR	100	37.055	1	54	Ranjit	NH	128	24.614	1
IJR, Indigenous Joha rice; H, High-yielding aromatic rice of Assam developed from Savitri × Badshabhog; B, Selection from Bishnuparag; D, Selection from Dehradun Basmati; L, Selection from local Kamal; PV, Pure line variety; NH, Non-aromatic high-yielding variety of Assam developed from Pankajb × Mahsuri. Nos. 1-40 are Joha aromatic rice accessions, and Nos. 41-54 are Joha non-aromatic rice accessions.
^a Based on Sood and Siddiq (1978).

Character	Range	Mean ± SD	PCV (%)	GCV (%)	h² (%)	AGA (%)
LLB (mm)	36.80-81.00	54.70 ± 0.44	14.64	14.57	99.09	29.88
WLB (mm)	0.70-1.41	1.12 ± 0.04	14.69	13.43	83.61	25.3
PH (cm)	90.77-182.33	142.37 ± 0.85	12.64	12.6	99.33	25.87
PL (cm)	18.77-38.53	28.89 ± 0.41	13.13	12.89	96.42	26.08
PPP	7.00-25.00	15.13 ± 0.77	31.64	30.38	92.23	60.08
DH (d)	86.00-136.00	122.24 ± 0.01	7.49	7.47	99.98	15.42
GPN	69.00-272.33	161.55 ± 15.97	27.44	21.44	61.07	34.51
GL (mm)	5.17-10.03	7.62 ± 0.19	14.26	13.6	91.03	26.73
GW (mm)	1.93-4.63	2.63 ± 0.10	11.17	10.98	87.26	34.03
RLW	1.72-5.01	2.99 ± 0.13	23.99	22.81	90.42	44.69
BGL (mm)	4.00-7.47	5.71 ± 0.19	17.38	16.41	89.11	31.9
BGW (mm)	1.50-4.00	2.14 ± 0.08	18.81	17.57	87.32	33.83
RBLW	1.50-4.67	2.75 ± 0.12	25.63	24.56	91.85	48.5
TGW (g)	9.407-26.998	14.984 ± 0.118	28.49	28.45	99.77	58.55
Yield per plant (g)	17.817-60.610	34.619 ± 3.856	34.24	28.28	68.25	48.13
LLB, Length of leaf blade; WLB, Width of leaf blade; PH, Plant height; PL, Panicle length; PPP, Number of panicles per plant; DH, Date of heading; GPN, Number of grains per panicle; GL, Grain length; GW, Grain width; RLW, Ratio of grain length/width; BGL, Brown grain length; BGW, Brown grain width; RBLW, Ratio of brown grain length/width; TGW, 1000-grain weight; PCV, Phenotypic coefficient of variation; GCV, Genotypic coefficient of variation; h², Broad-sense heritability; AGA, Average genetic advance.

Character	Range	Mean ± SD	PCV (%)	GCV (%)	h² (%)	AGA (%)
LLB (mm)	36.80-81.00	54.70 ± 0.44	14.64	14.57	99.09	29.88
WLB (mm)	0.70-1.41	1.12 ± 0.04	14.69	13.43	83.61	25.3
PH (cm)	90.77-182.33	142.37 ± 0.85	12.64	12.6	99.33	25.87
PL (cm)	18.77-38.53	28.89 ± 0.41	13.13	12.89	96.42	26.08
PPP	7.00-25.00	15.13 ± 0.77	31.64	30.38	92.23	60.08
DH (d)	86.00-136.00	122.24 ± 0.01	7.49	7.47	99.98	15.42
GPN	69.00-272.33	161.55 ± 15.97	27.44	21.44	61.07	34.51
GL (mm)	5.17-10.03	7.62 ± 0.19	14.26	13.6	91.03	26.73
GW (mm)	1.93-4.63	2.63 ± 0.10	11.17	10.98	87.26	34.03
RLW	1.72-5.01	2.99 ± 0.13	23.99	22.81	90.42	44.69
BGL (mm)	4.00-7.47	5.71 ± 0.19	17.38	16.41	89.11	31.9
BGW (mm)	1.50-4.00	2.14 ± 0.08	18.81	17.57	87.32	33.83
RBLW	1.50-4.67	2.75 ± 0.12	25.63	24.56	91.85	48.5
TGW (g)	9.407-26.998	14.984 ± 0.118	28.49	28.45	99.77	58.55
Yield per plant (g)	17.817-60.610	34.619 ± 3.856	34.24	28.28	68.25	48.13
LLB, Length of leaf blade; WLB, Width of leaf blade; PH, Plant height; PL, Panicle length; PPP, Number of panicles per plant; DH, Date of heading; GPN, Number of grains per panicle; GL, Grain length; GW, Grain width; RLW, Ratio of grain length/width; BGL, Brown grain length; BGW, Brown grain width; RBLW, Ratio of brown grain length/width; TGW, 1000-grain weight; PCV, Phenotypic coefficient of variation; GCV, Genotypic coefficient of variation; h², Broad-sense heritability; AGA, Average genetic advance.

Trait	Marker	Chromosome	P value	R²(%)	Previously identified
Aroma	RM214	7	0.00231	19.61	Novel
	RM23120	8	0.0017	19.37	Sun et al (2008)
	RM152	8	0.003	18.53	Vhora et al (2013)
	RM102	10	0.00429	17.71	Novel
1000-grain weight	RM3	6	0.00341	25	Novel
	RM259	7	0.0041	24.37	Novel
	RM215	9	0.00247	14.71	Novel
	RM19	12	0.00443	21.86	Novel
Brown grain length	RM342A	8	0.00304	17.81	Temnykh et al (2000)
Ratio of grain length/width	RM346	7	0.00152	18.44	Novel
Number of grains per panicle	RM105	9	0.00382	23.82	Novel
Plant height	RM174	2	0.00063	21.4	Novel
	RM138	2	0.00335	16.25	Novel
	RM214	7	0.00471	19.36	Novel
	RM270	12	0.00468	14.59	Novel
Panicle length	RM228	2	0.00176	23.22	Novel
Number of panicles per plant	RM251	3	0.0001	31.63	Novel
Date of heading	RM218	3	0.000001	43.75	Novel
	RM251	3	0.0004	27.53	Novel
	RM267	5	0.000031	42.57	Novel
	RM346	7	0.000008	38.61	Novel
	RM337	8	0.00183	23.11	Novel
	Aro7	8	0.00381	21.32	Sun et al (2008)
	RM171	10	0.0092	17.75	Novel
	RM270	12	0.00031	23.51	Novel
Yield per plant	RM138	2	0.00089	20.33	Novel
	RM174	2	0.04757	13.67	Novel
	RM251	3	0.0015	23.74	Novel
	RM16	3	0.00324	13.81	Novel
R², Percentage of the total variation explained.