Rice landraces from haor areas of Bangladesh possess greater genetic diversity as revealed by morpho-molecular approaches along with grain quality traits

Figures & data

Table 1. List of the 40 landraces of rice

Sunamganj (24 genotypes)			Netrokona (16 genotypes)
Porbotzira	Kalomotashail	Notiguarchara	Birui	Kalojira
Ailaguta	Chengermuri	Paijom	Chinishail-3	Boroabji
Guabari	Putibirun	Faijam	Chinishail-2	Mukta
Maloti	Kalo Biron	Ajanabirun	Chinishail-1	Chanmoni
Deshi32	Hasa(Kalo)	Moynashail	Hashem irri	Chinigura
Chakloshi	Lalcheng	Hasa(sada)	Binni dhan	Govindo
Soragotobirun	Biroi dhan	Sonajuri	Lal paijam	Kashiabinni
Kutimurabirun	Guarchara	Vedabiron	Sada paijam	Lal kumri

Table 2. Analysis of variance (ANOVA) for different phenotypic attributes of 40 landraces of rice

	Replication	Genotypes	Error
Degrees of freedom	2	39	78
Sources of variation
Days to 50% flowering	54.80	139.46**	11.17
Days to maturity	84.93	94.27**	23.77
Flag leaf area (cm^2)	104.01	1815.91**	15.32
Plant height (cm)	5.97	373.43**	15.24
Total tillers/hill	2.70	28.78**	3.76
Effective tillers/hill	0.30	27.94**	0.85
Pollen fertility (%)	8.23	768.36**	17.81
Panicle length (cm)	1.81	13.19**	1.39
Grains/panicle	472.32	9763.91**	619.82
Filled grains/panicle	2095.18	7371.85**	385.88
Unfilled grains/panicle	10.54	725.25**	13.77
100 seed weight (g)	0.008	0.71**	0.004
Yield/plant (g)	0.39	81.65**	4.65

**very significant difference (P < 0.01)

Table 3. Phenotypic performance of the studied landraces for different agro-morphological attributes

Genotypes	DF (50%)	DM	FLA (cm^2)	PH (cm)	TT	ET	PF (%)	PL (cm)	GPP	FG	UG	100 SW (g)	YPP (g)
Porbotzira	89	142	52	124	11	9	92	25	216	149	67	1.0	12
Ailaguta	107	140	71	137	10	9	49	20	129	90	39	2.3	11
Birui	99	142	97	125	13	11	93	23	288	249	40	1.8	18
Chinishail-3	107	142	89	128	15	13	96	25	155	131	25	1.1	18
Chinishail-2	105	144	127	121	17	15	91	24	123	110	13	1.3	23
Chinishail-1	109	141	66	117	17	16	97	24	128	116	12	1.0	18
Notiguarchara	107	145	65	144	15	14	89	28	288	248	40	1.1	24
Govindo	117	154	123	127	12	11	88	22	250	197	53	1.7	19
Paijom	105	150	71	122	15	13	94	22	170	118	52	2.4	22
Binni dhan	100	143	105	161	10	8	88	31	246	198	46	2.3	17
Faijam	106	143	101	119	12	11	87	23	221	173	48	1.7	22
Ajanabirun	93	143	91	96	14	11	88	23	181	134	46	1.8	16
Lal paijam	81	130	85	107	10	8	37	24	112	59	53	3.4	8
Moynashail	105	140	80	128	18	15	56	26	146	114	31	1.8	24
Soragoto birun	103	138	52	116	14	12	60	23	110	79	31	2.3	15
Kutimurabirun	100	136	79	115	18	16	72	24	117	84	33	1.7	14
Kashiabinni	101	141	58	125	18	15	92	26	138	123	26	2.1	17
Chakloshi	103	138	74	117	16	14	93	25	134	105	29	1.9	16
Deshi 32	101	136	74	115	12	11	67	25	117	77	40	2.1	15
Chengermuri	107	147	74	130	12	10	92	26	152	117	34	1.4	17
Putibirun	106	141	57	139	13	11	95	26	159	144	15	2.4	16
Hashem irri	120	161	158	132	16	15	81	24	296	231	64	1.7	29
Guabari	107	139	59	134	18	17	90	26	150	122	28	1.9	25
Hasa(Kalo)	112	150	72	141	10	9	93	25	270	229	42	1.2	12
Kalomotashail	108	146	92	137	17	17	96	24	129	113	16	2.7	27
Mukta	110	144	91	121	13	11	57	23	280	199	81	2.0	19
Genotypes	DF (50%)	DM	FLA (cm^2)	PH (cm)	TT	ET	PF (%)	PL (cm)	GPP	FG	UG	100 SW (g)	YPP (g)
Sada paijam	99	137	90	121	11	9	87	23	180	123	57	1.4	19
Hasa(sada)	106	138	93	125	22	20	92	23	153	118	35	1.6	18
Biroi dhan	110	141	75	127	16	13	96	25	114	85	28	1.9	13
Guarchara	104	137	52	124	14	12	67	22	93	69	24	2.0	9
Maloti	107	149	62	137	12	12	68	22	173	148	25	2.0	16
Lalcheng	107	144	69	127	15	13	91	24	166	150	16	1.8	19
Sonajuri	108	141	90	123	17	13	65	28	129	113	16	1.7	14
Lal Kumri	106	144	73	135	17	16	92	25	162	129	33	1.9	30
Kalo Biron	107	143	83	136	12	10	53	28	169	137	33	2	17
Chinigura	105	148	49	139	16	15	65	27	158	104	54	1.7	17
Vedabiron	110	145	99	135	20	18	96	27	219	189	30	1.9	28
Kalojira	110	147	45	137	16	14	75	24	185	156	29	1.2	17
Boroabji	106	143	131	132	20	19	76	24	121	87	34	2.2	15
Chanmoni	113	153	46	134	12	11	96	24	109	80	29	2.3	15
Least significant difference (0.05)	5.43	7.92	6.36	6.34	3.15	1.5	6.86	1.91	40.47	31.93	6.03	0.102	3.51
Mean	105.19	143.14	80.53	127.73	14.62	12.89	81.28	24.60	170.85	134.88	36.20	1.88	18.05
SE (±)	1.08	0.89	3.89	1.76	0.49	0.48	2.53	0.33	9.02	7.84	2.46	0.08	0.82
SD	6.82	5.61	24.60	11.16	3.10	3.05	16.00	2.10	57.05	49.57	15.55	0.49	5.22
Minimum	80.67	130.3	45.41	96.00	9.60	7.87	37.00	20.40	93.07	58.87	12.07	1.07	8.00
Maximum	120.33	160.67	157.7	160.57	22.40	20.23	96.67	31.40	295.50	248.57	80.93	3.45	30.73
Level of significance	**	**	**	**	**	**	**	**	**	**	**	**	**
CV (%)	3.18	3.41	4.86	3.06	13.28	7.16	5.19	4.80	14.57	14.56	10.25	3.32	11.96

SE = Standard error, SD = Standard deviation, CV = Co-efficient of variation, ** = Significant at 1% level of probability (p < 0.01).

DF (50%) = Days to 50% flowering, DM = Days to maturity, FLA = Flag leaf area, PH = Plant height, TT = Total tillers/hill, ET = Effective tillers/hill, PF = Pollen fertility, PL = Panicle length, GPP = Grains/panicle, FG = Filled grains/panicle, UG = Unfilled grains/panicle, 100 SW = 100 seed weight, YPP = Yield/plant

Figure 1. Clustering of 40 landraces from haor areas in Bangladesh based on phenotypic attributes.

Table 4. Intra-inter cluster distance (D = $\sqrt{D^2}$) in 40 rice genotypes

Cluster	I	II	III	IV	V
I	14.41	23.60	18.68	18.24	19.83
II		18.54	21.94	28.44	22.39
III			16.80	21.72	17.27
IV				20.39	21.33
V					15.41

* Diagonally bold figures indicate the intra cluster distance

Table 5. Cluster mean for yield and yield contributing characters of 40 rice landraces

Characters	Cluster I	Cluster II	Cluster III	Cluster IV	Cluster V
Days to 50% flowering	99.50	99.07	106.41	111.27	107.28
Days to maturity	141.78	136.00	143.72	150.60	142.50
Flag leaf area (cm^2)	87.07	66.92	71.96	104.44	91.13
Plant height (cm)	117.75	119.86	127.81	140.94	133.06
Total tillers/hill	12.19	12.01	15.16	12.62	19.25
Effective tillers/hill	10.47	10.23	13.23	11.35	17.77
Pollen fertility (%)	84.00	56.00	82.59	87.60	90.44
Panicle length (cm)	23.39	22.81	25.06	25.98	24.78
Grains/panicle	227.83	112.09	145.77	269.78	155.64
Filled grains/panicle	171.27	74.68	118.56	220.49	126.27
Unfilled grains/panicle	56.53	37.41	27.82	48.96	29.37
100 seed weight (g)	1.67	2.44	1.80	1.62	2.08
Yield/plant (g)	17.60	11.50	17.46	20.36	23.79

Figure 2. Loading plot of principal component analysis (PCA) showing diversity of yield and yield attributes of 40 landraces from haor areas in Bangladesh.

Table 6. Principal components (PCs) for morphological traits of 40 rice genotypes

	PC1	PC2	PC3	PC4	PC5
Eigen value	3.59	2.69	1.52	1.23	1.16
% Variance	25.7	19.2	10.9	8.8	8.3
% Cumulative variance	25.7	44.9	55.8	64.6	72.9
Variable	Coefficient vectors
Days to 50% flowering	0.328	−0.131	0.084	0.489	−0.212
Days to maturity	0.339	0.076	0.024	0.455	−0.163
Flag leaf area (cm^2)	0.230	0.022	−0.466	−0.130	−0.291
Plant height (cm)	0.259	0.044	0.539	−0.027	−0.312
Total tillers/hill	0.112	−0.522	−0.175	−0.196	0.002
Effective tillers/hill	0.159	−0.518	−0.181	−0.127	−0.054
Pollen fertility (%)	0.274	−0.182	0.104	0.081	0.444
Panicle length (cm)	0.124	−0.024	0.486	−0.519	−0.164
Grains/panicle	0.388	0.341	−0.094	−0.202	0.096
Filled grains/panicle	0.421	0.260	0.001	−0.158	0.119
Unfilled grains/panicle	0.073	0.420	−0.364	−0.150	−0.032
100 seed weight (g)	−0.248	0.030	−0.051	−0.106	−0.644
Yield/plant (g)	0.365	−0.194	−0.154	−0.195	−0.158

Figure 3. Banding pattern of 40 landraces from haor areas in Bangladesh for SSR marker RM 25.

Table 7. SSR markers analysis of 40 rice genotypes for 6 microsatellites (SSR) markers

Locus	Allele ranges (bp)		Number of alleles	Rare alleles	Null alleles	Major allele		GD	H	PIC
						Size (bp)	F (%)
RM 5	99–121		14	7	1	110	22.5	0.883	0	0.872
RM 25	130–153		16	6	1	147	12.5	0.923	0	0.917
RM 44	99–115		12	3	0	101	30	0.855	0	0.841
RM 169	163–202		11	8	1	170	37.5	0.788	0	0.764
RM 286	95–135		14	8	1	97	22.5	0.869	0	0.856
RM 519	120–140		13	3	1	136	12.5	0.91	0	0.901
80
Mean	——–	14.17		5.83	0.83	126.83 22.92		0.871	0	0.859

F (%) = Frequency; GD = Gene diversity; H = Heterozygosity; PIC = Polymorphism information content

Figure 4. UPGMA (Unweighted Pair Group Method of Arithmetic means) Phylograph showing clustering of 40 landraces from haor areas in Bangladesh based on 6 SSR marker analysis.

Figure 5. Pie chart showing categorization of 40 landraces from haor areas in Bangladesh for grain quality traits.

Table 8. Performance of the 40 rice landraces considering grain quality traits

	GL (mm)	GB (mm)	L/B Ratio	Aroma score	Chalkiness score	ASV score	AC (%)	Fe (ppm)	Zn (ppm)
Max.	7.05 (Kutimurabirun)	2.77 (Kalomotashail & Paijom)	3.82 (kutimurabirun)	4	9	7	34.39 (Govindo & Lalcheng)	172.23 (Lal paijam)	33.43 (Lal paijam)
Min.	3.41 (Chinishail-3)	1.70 (Hasa(Kalo))	1.66 (Sonajuri)	1	0	1	10.58 (Hashem irri)	7.12 (Chakloshi)	8.97 (Deshi 32)
Mean	5.30	2.05	2.62	1.45	1.55	3.10	24.62	48.05	20.41
SD	0.89	0.29	0.48	1.01	2.69	1.95	6.12	36.42	4.29
% CV	16.71	14.14	18.40	69.76	173.45	62.76	24.87	75.79	21.00

GL = Grain length, GB = Grain breadth, L/B ratio = Length to breadth ratio, ASV = Alkali spreading value, AC = Amylose content, Fe = Iron content, Zn = Zinc content

Table 9. Correlation among the studied grain quality traits

	GL (mm)	GB (mm)	L/B Ratio	Aroma	Chalkiness (%)	ASV score	AC (%)	Fe (ppm)
GB (mm)	0.269
L/B Ratio	0.755 **	−0.420 **
Aroma	−0.647 **	−0.375 *	−0.360 *
Chalkiness (%)	0.258	0.413 **	−0.042	−0.244
ASV score	0.138	−0.092	0.190	−0.141	−0.075
Amylose (%)	0.187	−0.086	0.219	−0.106	0.055	−0.046
Fe (ppm)	−0.049	0.150	−0.150	0.071	0.235	−0.004	−0.007
Zn (ppm)	0.259	0.277	0.014	−0.179	0.329 *	−0.012	0.250	0.363*

GL = Grain length, GB = Grain breadth, L/B ratio = Length to breadth ratio, ASV = Alkali spreading value, AC = Amylose content, Fe = Iron content, Zn = Zinc content.

* and ** indicate significance at 5% and 1% level of probability.