Study on genetic diversity in rice (oryza sativa L.) Germplasm

In 2024, the present investigation Study on Genetic Diversity in Rice (Oryza sativa L.) Germplasm. Five plants selected at random from every genotype were examined for 13 yield- related traits. ANOVA results for all traits identified considerable genetic heterogeneity favourable for fostering yield improvement through breeding. These high-yielding genotypes SHUATS DHAN-1, INDRANI, AK DHAN, D DHAN-39, and JARAVA were characterized by pronounced genetic progress, elevated heritability, and pronounced variability. Their adaptation to a variety of conditions was highlighted by the clear genetic differences found in variations in phenotypic traits, including as blooming time, maturity, plant height, and yield components. Other promising lines KHAYAM DHAN, FALGUNA, KRISHNA HAMSA, and HMT displayed outstanding performance in vital yield-related traits and are therefore recommended for direct selection and incorporation into breeding programs. Cluster analysis further emphasised the genetic diversity, noting that Cluster II possesses considerable yield potential and considerable separation from other clusters most notably from Cluster VI indicating abundant opportunity for heterotic hybrid development.

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Genetic Clustering of Rice GenotypesClose ×

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Introduction

Rice (Oryza sativa L.), a true diploid that carries 2n=24 chromosomes, has been cultivated by humankind for more than 10,000 years. Cultivated varieties are cataloged into three subspecies indica, japonica, and javanica (Vinoth et al. 2016) [30] and (Vivek et al. 2005) [31] . Indica cultivar is propagated in tropical and subtropical regions worldwide, japonica across the entire temperate zone, and javanica chiefly within Indonesia by (Veludandi Sumanth et al. 2017) [29] and (Singh et al. 2011) [22] . Rice, a day-neutral autogamous crop chiefly consumed by almost two-thirds of India's populace, plays a pivotal role in the country's economy by (Burton & Devane 1953) [5] and (Kumar et al. 2017) [13] . Rice's nutritional composition consists of mostly carbohydrates (80%) alongside 7-8% protein (an amino-acid spectrum revealing high concentrations of glutamic and aspartic acids, with lysine the highest quality amino acid in cereal proteins present at 3.8% (Juliano et al. 1985) [35] . Rice cultivation in Uttar Pradesh occupies roughly 5.9 million hectares. The cropping intensity stands at 153%. In production, the state captures the top position nationally by (Islam et al. 2015) [10] and (Sujitha et al. 2020) [27] . With production and productivity standing at respective levels of 12.27 mt and 2.7 t/ha, it becomes evident that Uttar Pradesh's rice cultivation urgently requires amplifying productivity a goal that will be fulfilled solely by cultivating high-yielding hybrid varieties (Agriculture at a Glance, 2022) [2] . India's population presently stands at 120 crores. By 2025, the population is expected to reach close to 150 crores. Accordingly, there is a necessity to create high-yielding varieties [36] .

The area experiences heavy rainfall, with most precipitation falling in the months of June to September. A considerable share of the rainfall arrives under the south-west monsoon, chiefly during July and August. Soil PH values lay between 7.3 and 7.6, whereas the aggregated rainfall amounted to 732.40 mm. The experiment had 3 replicates and employed a randomized block design (RBD). The amount of space between plants was measured to be 15 cm and the row spacing was 20 cm. Information was collected on a number of characteristics. Days to ripeness and 50% blooming Flag leaf width (cm), length (cm), and height (cm) of the plant Data from fifteen plants of each genotype were averaged replication-wise, and the data was used for statistical analysis. The data included a total number of tillers per hill, number of panicles per hill, panicle length (cm), spikelets per panicle, test weight (g), harvest index (%), biological yield per hill (g), and grain yield per hill (g).

Experiment Materials

In this study, the experimental material was 42 rice genotypes of the Department of Genetics and Plant Breeding, SHUATS Prayagraj. 1. The 42 distinct rice genotypes' mean sum of squares for the 13 distinct traits were highly significant at the 0.01 level of significance, suggesting that the genotypes differ greatly in terms of genetic makeup. The data in Table 1 indicates that there is enough room in the current gene pool to choose lines with promising yield and component characteristics. The results showed that there was significant genetic variation between genotypes, highlighting the importance of genotype differences in plant breeding.

Summary of ANOVA	—	—	—	—
Sr. No	Traits	Mean Sum of Squares (MSS)
		Replications	Genotypes	Error
		(df = 2)	(df=41)	(df=82)
1	Days to 50% flowering	3.96	322.991**	1.626
2	Days to Maturity	2.055	678.254**	1.006
3	Plant Height	22.459	953.515**	9.762
4	Flag leaf length	70.199	36.345**	9.241
5	Flag leaf width	0.288	0.029**	0.007
6	Number of tillers per hill	0.207	3.116**	0.255
7	Number of panicles per hill	1.445	2.723**	0.419
8	Panicle length	16.829	13.928**	2.796
9	Number of spikelets per panicle	834.419	4238.112**	152.507
10	Biological yield per hill	38.234	222.765**	14.225
11	Harvest Index	43.303	282.035**	23.76
12	Test Weight	0.67	66.348**	0.122
13	Grain Yield Per hill	2.973	31.747**	1.205

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Analysis of Variance for 13 Quantitative Characters of rice

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Results and Discussion

Because it provides a solid foundation for choosing superior genetic compositions, this variability explains upcoming efforts to create breeding material. The findings corroborate some of the research. The findings are in line with some of the earlier research by (Vinoth and colleagues 2016), (Dhanwani and colleagues 2013) [7] , (Sandeep and colleagues 2018) [19] , and (Satturu and colleagues 2023) [20] , which revealed significant genetic variation in each of the estimated attributes described. 2019) [1] , (Rani et al. 2019) [17] , (Sudeepthi et al. 2020) [26] , (Guptha et al. 2020) [8] , (Singh et al. 2021) [23] , (Akshay et al. 2022) [42] , and (Sravani et al. 2022) [24] reported similar results. [34] and (Yadav et al. 2024) [35] .

Heritability

Heritability

Genetic Advance

The greatest genetic advance (GA) was detected for spikelets per panicle (72.09), with plant height (35.98) and days to maturity (30.88) came next, followed by days to 50% flowering (21.16) and harvest index (16.92). Significant GA were likewise recorded for biological yield (15.65), test weight (9.65), and grain yield (6.22) evidence of a favourable response to selection and a predominance of additive genetic control. For panicle length (3.00), flag leaf length (4.35), number of tillers per hill (1.79), and number of panicles per hill (1.45), GA was comparatively lower, while the smallest GA was registered for flag leaf width (0.12), implying that limited selection opportunity arises from modest genetic variation or substantial environmental effects. [37] , (Sudeepthi et al. 2020) [26] , (Lingaiah et al. 2020) [38] , (Bhor et al. 2020) [39] , (Lakshmi et al. 2021) [40] , (Akshay et al. 2022) [42] , and (Sravani et al. 2022) [27] Yada24v. [3] and Burton (1952) [4] .

Genetic Advance as Percent Mean

Genetic Advance as Percent Mean

Intra and Inter Cluster Average Divergence (D2)

The six rice genotype clusters' average intra and inter cluster distances (D 2 ) are displayed in [18] , (Neeraja et al. 2015) [41] , (Praveen et al. 2015) [16] , (Chandramohan et al. 2016) [6] , (Sridhar et al. 2016) [25] , (Tejaswini et al. 2016) [28] , (Guru et al. 2017) [9] , (Sujitha et al. 2020) [27] , (Kumar et al. 2014) [12] , (Shaili et al, 2022) [21] and (Kumari et al. 2021) [15] also document.

Contribution of individual characters towards total divergence

The analysis of trait-based genetic divergence among 42 rice genotypes ( [18] , (Neeraja et al. 2015) [41] , (Praveen et al. 2015) [16] , (Chandramohan et al. 2016) [6] , (Sridhar et al. 2016) [25] , (Tejaswini et al. 2016) [28] , (Guru et al. 2017) [9] , (Sujitha et al. 2020) [27] , (Kumar et al. 2014) [12] , (Shaili et al, 2022) [21] and (Kumari et al. 2021) [15] also document.

Conclusion

Based on the current examination, it was determined that all of the characters had significant variation according to the analysis of variance. Due to their high heritability and genetic variability, traits including grain yield, test weight, harvest index, and biological yield identified as key markers for genetic improvement were shown to exhibit considerable genetic diversity among the rice genotypes. Marked variability in yield attributes, plant height, maturity, and flowering period all attest to the genotypes' environmental adaptability. Suggested for breeding schemes are the genotypes SHUATS DHAN-1, KHAYAM DHAN, D DHAN-39, FALGUNA, KRISHNA HAMSA, and HMT, all distinguished by their superior yield traits. Cluster II exhibited the greatest yield potential, and the cluster analysis confirmed this variety. Owing to the pronounced genetic divergence between Clusters II and VI, highyielding hybrids may be developed. The findings furnish the genetic backbone on which climate-resilient, high-yielding rice varieties can be developed.

Figures and tables from the paper

Sr. No	Genotypes	Days to 50% flowering	Days to Maturity	Plant Height	Flag leaf length	Flag leaf width	Number of tillers per hill	Number of panicles per hill	Panicle length	Number of spikelets per panicle	Biological yield per hill	Harvest Index	Test Weight	Grain Yield per hill
1	Indrani	109.00	132.00	107.69	31.92	1.10	5.87	5.67	26.07	168.47	36.67	48.07	24.53	17.61
2	AK Dhan	107.67	122.33	128.98	31.34	1.02	8.53	7.87	27.35	136.20	48.80	34.32	24.47	16.80
3	80 NLR 40024	108.33	125.33	102.71	23.71	1.04	7.03	6.73	20.27	195.93	37.07	32.54	16.47	12.05
4	JGL 3828	105.67	131.67	110.59	31.42	1.06	6.30	6.20	23.54	193.73	31.79	25.81	20.27	8.22
5	Bina Dhan-10	94.33	117.00	114.87	33.71	1.04	7.67	7.03	25.33	108.27	25.13	30.52	20.20	7.54
6	Lage Dhan	125.33	165.33	165.69	29.59	1.03	8.37	7.30	25.76	182.80	37.20	30.37	20.67	11.25
7	Talmunfar	122.00	158.00	161.09	36.47	0.85	9.17	8.37	25.60	144.00	40.34	21.10	12.27	8.45
8	Jarava	119.00	140.33	131.14	32.06	0.95	5.83	5.20	22.44	146.80	27.75	54.64	20.67	15.13
9	84-Nlr-3354	113.00	138.67	98.14	29.16	1.04	7.27	6.67	23.55	174.53	29.51	48.73	20.53	14.36
10	Gautam	95.33	117.67	99.07	30.57	0.86	8.53	7.03	23.14	119.87	24.87	51.90	16.73	12.60
11	Boichi	113.33	131.33	99.64	28.60	0.93	7.43	6.93	22.19	121.07	27.93	32.51	20.27	8.93
12	Vikramarya	114.00	131.67	102.89	33.71	0.98	7.87	7.03	23.05	138.93	27.48	53.94	24.67	14.39
13	DRRH-2	113.67	131.33	97.70	30.87	0.92	7.23	6.37	23.55	192.33	34.96	42.12	20.33	14.63
14	74-NLR-33359	113.33	130.00	100.45	28.19	0.93	8.93	8.43	22.60	154.80	36.67	34.30	16.73	12.47
15	81-NLR-33641	114.00	132.00	97.45	28.59	1.08	8.73	8.03	20.71	132.07	43.31	18.99	12.67	8.28
16	Lal Bhuna	115.00	135.00	118.71	27.68	0.76	8.70	8.13	21.53	203.13	41.13	25.26	16.47	10.40
17	Ranukasel	119.67	151.33	148.85	26.89	0.83	6.93	6.60	21.51	147.20	52.89	20.45	21.00	10.80
18	Sampada	115.67	143.00	99.55	27.89	0.85	6.77	6.20	22.43	123.20	28.08	34.14	12.53	9.46
19	Suraksha	114.67	146.67	107.47	30.81	0.87	5.47	5.33	23.53	135.60	26.73	33.14	20.93	8.80
20	Mandhya Vijaya	119.00	155.00	129.17	27.08	0.87	7.83	7.20	22.72	177.40	26.15	37.83	20.87	9.87
21	Signet-5455	110.33	131.33	111.55	22.53	1.12	6.50	5.93	22.21	134.20	27.49	33.21	20.60	8.88
22	Dhan-75	106.00	129.33	116.31	25.45	0.96	6.40	6.07	22.98	138.87	26.13	41.92	20.53	10.87
23	NLR	103.67	122.33	108.97	22.80	1.08	5.77	5.20	22.82	131.93	20.00	44.23	24.47	8.80
24	MTU-1035	119.00	149.33	93.03	24.54	1.16	7.50	7.07	21.39	156.53	24.93	38.95	12.33	9.67
25	79-NLR-30491	115.00	137.33	103.50	26.19	1.09	6.83	6.07	21.58	240.00	27.19	31.14	16.40	8.42
26	Kasturi	89.67	115.67	125.74	27.63	1.02	6.83	6.10	25.35	149.13	24.60	35.29	24.47	8.51
27	Dhan-38	105.00	122.00	130.17	30.40	1.14	6.63	6.20	24.69	126.20	40.33	34.77	20.40	14.05

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Mean performance of 42 Rice Genotypes

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Sr. No	Genotypes	Days to 50% flowering	Days to Maturity	Plant Height	Flag leaf length	Flag leaf width	Number of tillers per hill	Number of panicles per hill	Panicle length	Number of spikelets per panicle	Biological yield per hill	Harvest Index	Test Weight	Grain Yield per hill
28	Dhan-55	105.67	120.33	113.63	32.20	1.15	8.53	8.13	26.57	173.07	26.69	52.49	20.53	13.71
29	72-Dhan-59	97.00	119.00	128.44	27.09	1.11	7.53	6.80	24.31	158.67	35.47	39.51	20.73	13.92
30	NLR-34449	114.67	150.67	93.89	27.47	1.13	7.87	7.03	20.29	157.53	30.92	30.07	16.93	9.25
31	Khayam Dhan	123.33	163.67	138.26	29.25	1.02	9.00	8.30	22.53	148.13	42.45	30.89	30.60	13.03
32	MTU-1190	121.00	151.00	118.29	25.49	1.06	8.00	7.73	22.12	214.67	42.60	17.58	20.80	7.45
33	Birri Dhan-75	98.67	120.33	101.81	24.76	1.03	7.83	6.93	20.54	215.93	29.32	41.33	12.60	12.12
34	D Dhan-39	99.33	121.00	122.77	31.86	1.03	7.70	7.47	27.65	200.73	43.85	37.64	27.80	16.48
35	Sidha Sannalu	116.67	152.00	117.93	27.23	0.96	7.60	7.27	21.20	178.93	44.48	16.58	12.27	7.40
36	71-Dhan-58	115.67	148.67	92.09	22.77	1.00	7.43	6.90	21.33	114.80	33.55	33.19	13.07	11.10
37	Falguna	116.00	161.67	101.19	33.24	1.14	8.63	8.10	26.47	181.00	47.61	29.20	24.73	13.71
38	82-NLR-145	108.67	127.00	100.63	26.72	1.03	7.67	7.53	21.29	226.73	42.20	28.83	16.47	12.15
39	HMT	115.67	163.67	96.47	32.30	1.04	9.20	8.57	22.06	278.27	33.82	37.46	12.33	12.65
40	Krishna Hamsa	93.67	120.67	112.05	23.96	1.01	9.37	8.80	23.54	154.20	35.06	40.03	24.67	13.88
41	Dhan-53	118.67	159.67	88.77	25.21	0.92	8.67	8.20	22.39	211.73	38.09	22.47	12.00	8.52
42	Shuats Dhan-1 (Check)	74.00	128.33	109.30	34.25	1.10	7.97	7.56	29.33	134.87	57.60	39.39	22.60	22.36
Range	Minimum	74.00	115.67	88.77	22.53	0.76	5.47	5.20	20.27	108.27	20.00	16.58	12.00	7.40
	Maximum	125.33	165.33	165.69	36.47	1.16	9.37	8.80	29.33	278.27	57.60	54.64	30.60	22.36
Grand Mean		109.98	136.92	113.01	28.66	1.01	7.62	7.05	23.32	164.82	34.73	34.93	19.30	11.64
SEm		0.74	0.58	1.80	1.76	0.05	0.29	0.37	0.97	7.13	2.18	2.81	0.20	0.63
SEd		1.04	0.82	2.55	2.48	0.07	0.41	0.53	1.37	10.08	3.08	3.98	0.29	0.90
CD 5%		2.07	1.63	5.07	4.94	0.14	0.82	1.05	2.72	20.06	6.13	7.92	0.57	1.78
CV		1.16	0.73	2.76	10.61	8.52	6.63	9.17	7.17	7.49	10.86	13.96	1.81	9.43

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Contd.

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Sr. No	Trait	PCV	GCV	Heritability%	Genetic advance	GAM at 5%
1.	Days to 50% flowering	9.48	9.41	98.50	21.16	19.24
2.	Days to Maturity	11.00	10.97	99.56	30.88	22.56
3.	Plant Height	15.94	15.69	96.99	35.98	31.84
4.	Flag leaf length	14.92	10.49	49.44	4.35	15.19
5.	Flag leaf width	12.03	8.50	49.84	0.12	12.36
6.	Number of tillers per Hill	14.43	12.82	78.88	1.79	23.45
7.	Number of panicles per hill	15.44	12.43	64.74	1.45	20.60
8.	Panicle length	10.94	8.26	57.03	3.00	12.85
9.	Number of spikelets per panicle	23.61	22.39	89.93	72.09	43.74
10.	Biological yield per hill	26.35	24.00	83.01	15.65	45.05
11.	Harvest Index	30.01	26.57	78.37	16.92	48.45
12.	Test Weight	24.41	24.34	99.45	9.65	50.01
13.	Grain Yield Per Hill	28.98	27.41	89.42	6.22	53.39

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Estimation of Genetic Parameters for 42 Rice Genotypes

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Histogram showing genetic parameters such as GCV, PCV, Heritability and GA

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Cluster	No. of Genotypes	Genotypes
I	4	Talmunfar, falguna, lage dhan, khayam dhan
II	9	Mtu-81, nlr-33641, dhan-53, mtu-1190, sidha sannalu, ranukasel, mandhya vijaya, 74-nlr-33359, lal bhuna
III	14	Dhan-75, nlr, signet-5455, suraksha, boichi, sampada, 71- dhan-58, mtu-1035, nlr-34449, birri dhan-75, 80-nlr- 40024, 82- nlr-145, jgl-3828, 79-nlr-30491
IV	3	Shuats dhan-1 (check), ak dhan, ddhan-39,
V	5	Vikramarya, 84-nlr-3354, drrh-2, indrani, jaravia
VI	7	Dhan-38, 72-dhan-59, bina dhan-10, kasturi, gautam, dhan-55, krishna hamsa

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Distribution of 42 Rice Genotypes in different Clusters using D2 statistics

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Cluster	I	II	III	IV	V	VI
I	3.007
II	4.926	3.672
III	3.863	6.303	3.586
IV	3.767	4.416	3.943	3.872
V	5.317	5.459	5.509	5.364	4.461
VI	5.072	6.321	3.889	4.975	4.288	4.034

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Average Intra and Inter-cluster distances of 42 Rice Genotypes

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Group	Days to 50% flowering	Days to Maturity	Plant Height	Flag leaf length	Flag leaf width	Number of tillers per hill	Number of panicles per hill	Panicle length	Number of spikelets per panicle	Biological yield per hill	Harvest Index	Test Weight	Grain Yield Per hill
C I	113.73	134.8	107.51	31.54	0.996	6.81	6.19	23.73	164.21	31.28	49.5	22.15	15.23
C II	99.39	129.06	114.65	31.14	1.075	8.46	7.99	26.82	163.35	43.27	38.85	24.13	16.16
C III	101.46	123.54	118.33	27.63	1.064	6.7	6.19	23.9	142.63	28.87	35.66	21.46	10.1
C IV	120.25	153.92	137.25	28.71	0.923	8.2	7.61	22.87	174.53	40.9	25.01	19.37	9.83
C V	109.75	134.67	101.43	29.47	0.878	7.05	6.38	22.82	124.93	26.9	37.92	17.62	9.95
C VI	112.88	140.36	97.34	26.4	1.042	7.97	7.41	21.31	189.48	34.28	31.75	14.36	10.61

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Cluster Means of Different Traits in Rice

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Sr. No	Characters	Percent contribution
1.	Days to 50% flowering	10.50%
2.	Days to Maturity	56.80%
3.	Plant Height	5.30%
4.	Flag leaf length	0.30%
5.	Flag leaf width	0.30%
6.	Number of tillers per hill	0.20%
7.	Number of panicles per hill	0.30%
8.	Panicle length	0.30%
9.	Number of spikelets per panicle	1.60%
10.	Biological yield per hill	1.20%
11.	Harvest Index	0.60%
12.	Test Weight	21.70%
13.	Grain Yield Per hill	0.90%

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Percent Contribution of 13 Characters towards Genetic Divergence

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Cluster dendrogram showing the distribution of genotypes into different cluster

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