Trait-based differentiation and agro-morphological profiling in Germplasm accessions of Rice (Oryza sativa L.)
 
ABSTRACT

Agro-morphological characterization of a total of 2,879 rice germplasm accessions was conducted during 2023. This large-scale evaluation aimed to document phenotypic variability among accessions for Nineteen qualitative agro-morphological traits following standard descriptors, with emphasis on visually distinguishable and agronomically relevant characteristics. The analysis revealed categorical variation across all 19 traits, indicating broad phenotypic diversity within the germplasm pool. High variability was observed in traits such as early plant vigour, leaf blade colour, leaf pubescence, panicle exertion, flag leaf angle, threshability, and leaf senescence—traits closely associated with early-stage plant establishment, reproductive success, and ease of harvest. Moderate diversity was noted in coleoptile colour, basal leaf sheath colour, stigma colour, apiculus colour, kernel colour, and hull colour, which, while less conspicuous, remain relevant for taxonomic differentiation and potential marker development. The remaining traits exhibited relatively limited variation, suggesting a degree of uniformity in those phenotypic expressions across accessions. The comprehensive documentation of these agro-morphological traits contributes significantly to the understanding of phenotypic diversity in rice germplasm. Such traits can serve as diagnostic markers in germplasm management, varietal identification, and breeding program design. Moreover, the presence of highly variable and easily observable traits among the accessions offers valuable opportunities for trait-based selection and genetic enhancement aimed at improving rice productivity, adaptability, and grain quality in diverse agro-ecological contexts.

Key word: Rice, germplasm accession, morphological traits, markers, diversity, variability.

INTRODUCTION

Rice (Oryza sativa L.), a member of the family Poaceae (Gramineae), is one of the most important staple food crops globally and holds exceptional significance in India’s agricultural and socio-economic landscape. With a chromosome number of 2n = 24, rice is primarily represented by two cultivated species: Oryza sativa and Oryza glaberrima. Of these, Oryza sativa (2n = 24, genome AA) is the most widely cultivated species worldwide, whereas Oryza glaberrima (2n = 24, genome AA) is predominantly cultivated in West Africa (Kanwar et al., 2017). Among the three major cereal crops—rice, wheat, and maize—rice ranks first in terms of global production and consumption.
As one of the oldest domesticated cereal crops, rice has played a crucial role in sustaining human civilizations and continues to be the primary dietary source for more than half of the world’s population. It thrives across a broad spectrum of agro-ecological environments, including upland, lowland, irrigated, and rain-fed systems, making it a highly adaptable crop. The genus Oryza encompasses 24 species, including 2 cultivated and 22 wild species, with genome compositions such as AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ (2n = 24 or 48), representing extensive genetic diversity.
Rice is not only vital in terms of caloric intake, accounting for approximately 20% of global dietary energy and 15% of protein intake, but also contributes essential minerals and dietary fibre, reinforcing its role as a nutrient-dense cereal. Particularly in Asia, where about 90% of the world's rice is produced, it serves as a dietary staple for approximately 2.7 billion people (Salim et al., 2003).
Agro-morphological characterization aids in rice breeding projects by identifying superior genes for restoration and transfer, explaining the phenotypic diversity in germplasms. (Sivakumar et al., 2021).The conservation, classification, and characterization of rice germplasm are critical for sustainable crop improvement. Germplasm collections serve as reservoirs of genetic diversity, including wild relatives, landraces, obsolete cultivars, and improved varieties. These collections are housed in global and national gene banks, representing invaluable resources for breeding programs. The strategic evaluation of these accessions enables the identification of donors with desirable traits, such as abiotic and biotic stress resistance, yield potential, and grain quality, which are essential for varietal development and long-term conservation efforts (Bisen and Sarawgi, 2008). Effective utilization of this genetic diversity is imperative not only for enhancing productivity and resilience but also for safeguarding unique rice genotypes from genetic erosion and eventual extinction. Rice is prioritized for improvement on salt-contaminated soils due to its negative impact on various components like stand establishment, leaf area index, panicle and tiller number, spikelet, floret sterility, heading time, and grain size (Xu et al., 2024 and Meng et al., 2021). The selection of high-variability genotypes is crucial for successful hybridization programs, enabling the incorporation of desirable character combinations to enhance grain quality and yield (Singh et al., 2021).
Agro-morphological characterization is the primary method used to provide essential data for plant breeding programs (Das and Ghosh, 2011). Historically, agro-morphological features have been utilized to assess the correlations between genotypes, both qualitatively and quantitatively (Goodman, 1972). Morphological characterization is crucial for understanding the unique traits of rice varieties, which can help create a genetic database for breeding program strategies, and agro-morphological markers are used for this purpose 
(Islam et  al.,  2017 and  Akter et  al.,  2018).

MATERIALS AND METHODS
The materials for the study comprised 2,879 germplasm accessions of rice received from the gene bank of ICAR-NBPGR (National Bureau of Plant Genetic Resources), New Delhi, including 6 checks: Annada, IR 64, Pusa Basmati-1, Swarna, NDR-97, and Jaya. The experimental materials were grown in Kharif (wet season), 2022 in Augmented Block Design. The 21-day-old seedlings of each genotype were transplanted manually in 2 rows, each 2m in length, with a spacing of 20cm between rows and 15cm between plants within each row. Observations were recorded on 3 random plants for each genotype for 19 qualitative traits.
RESULTS  AND DISCUSSION
            For plant descriptions, qualitative characteristics are important (Kurlovich, 1998) and mainly influenced by the consumer's preference, socioeconomic scenario and natural selection (Hien et al., 2007). The most crucial characteristics to distinguish one plant variety from another are said to be their qualitative characteristics. Because they are largely genetically determined, qualities are less dependent on how the environment reacts (Sinha and Mishra, 2013). When identifying rice landraces, qualitative traits are thought of as marker traits, since they are less dependent on environmental fluctuation (Singh et al., 2014). The most crucial characteristics to identify a plant variety are its qualitative traits, which are genetically governed.
              Qualitative characteristics are important for describing plants and are mainly related to their distinguishing feature. Results of the present investigation on Agro-morphological characterization revealed that, frequency distribution for 19 qualitative traits I presented in Table No. 1. The characteristics were recorded as the shape of ligules: split (100%). The traits coleoptiles colours were found 73% show green colouration and 26 % purple colour, auricle colour were observed light green 87% followed by 13 % purple colour, Decorticated grain aroma two alternative form of traits were observed Presence (8 %) and Absence (91 %), The character sterile lemma colour were found straw 94 %, Red 1 % and purple 5%. Whereas character panicle type 94% genotype shows intermediate, shows open panicle type 3 % and 2% genotype shows compact. The traits awning observed were 92% others, 4% long and fully partly, 2% short and partly, and followed by 1% long awned, 0.17% short and fully partly awned. Farmer prefers awnless grain because awns are objectionable in threshing and milling (Singh et al.,2014). There was no variation for a few characters among the accessions. Similar findings have also been reported by Sarawgi et al. (2013) and Thete et al. (2023).
There has been a moderate difference in character basal leaf sheath colour 71% of germplasm found green, 11% purple line colouration, and 2% showed light purple colouration. Following the stigma colour, white and purple colours were found at 72% and 27%, respectively. Most of the genotype 78% showed straw apiculus colour, 2% red and the rest of the characters 1% (red and purple apex apiculus colour). Seed coat/ Kernel colour (79% white, 10% light brown, 6% red, 5% brown and rest of the genotype lack kernel colour and the traits hull colour were found 73% straw, 9% golden, 8% brown furrow on straw, 4% golden brown, 3% purple furrow on straw and rest of the traits lack showed on hull colour.
 The following characteristics show a high variation in experimental materials the traits early plant vigor 40% very good, 37% good and 22% show poor plant vigour, The character leaf blade colour (33% green, 24% light green, 20 % purple margins, 19% dark green and rest of the genotypes few colourtaion of leaf blade colour). The traits leaf pubescence were observed 68% pubescent, 32% intermediate and lack pubescent rest of the genotype (Umarani et al., 2017), panicle exsertions (65% well, 21% moderate, 12% just and 2% partly exserted) The character flag leaf angle( 48% erect, 29% intermediate, 21% horizontal and others 2%), threshability were observed early 56%, intermediate 32% and 12% difficult threshability and  The character leaf senescence were found 63% intermediate, 24% early and fast and 13% late and slow. The distinguishable variation among the accessions is used as markers for the identification of genotypes. Table No. 2 shows the list of important genotypes for different characters and Fig. 1 depicts the agro-morphological variation among the rice accessions. The study characterized seventy-one aromatic rice germplasm from IGKV, Raipur, based on anthocyanin pigmentation, plant habit, and awning character. Twelve groups were formed based on pigmentation distribution, and three groups were formed for plant habit and awning character (Parikh, et al., 2012 and Subedi et al., 2024).

Table.1: Frequency distribution of 19 qualitative traits as per DUS descriptor of rice

	Characters	Descriptions with code	Frequency	Frequency %	
1.	Early plant vigour	1- Poor	633	21.98	
		2- Good	1087	37.75	
		3-Very good	1159	40.25	
2.	Coleoptile colour	1-Green	2120	73.63	
		2-Purple	759	26.36	
3.	Basal leaf sheath colour	1-Green	2069	71.86	
		2-Purple lines	317	11.01	
		3-Light purple	60	2.08	
4.	Leaf blade colour	1-Light green	716	24.86	
		2-Green	960	33.34	
		3-Dark green	561	19.48	
		4-purple tips	14	0.48	
		5-Purple margins	570	19.79	
		6-Purple blotch	19	0.65	
		99-others	39	1.35	
5.	Leaf pubescence	1-Glabrous	1	0.034	
		2-Intermediate	912	31.67	
		3-Pubescent	1966	68.28	
6.	Ligules shape	2-Split	2879	100	
7.	Auricle colour	1-Light green	2513	87.28	
		2-Purple	366	12.71	
8.	Stigma colour	1-White	2084	72.38	
		5-Purple	787	27.33	
9.	Panicle exsertion	1-Well exserted	1862	64.67	
		3-Moderate exserted	602	20.91	
		5-Just exserted	345	11.98	
		7-Partly exserted	62	2.15	
10.	Apiculus colour	2-Straw	2237	77.70	
		4-Red	20	0.69	
		6-Purple	593	20.59	
		5-Purple apex	21	0.72	
11.	Panicle type	1-Compact	65	2.25	
		5-Intermediate	2694	93.57	
		9-Open	99	3.34	
		99-Others	13	0.45	
12.	Flag leaf angle	1-Erect	1386	48.14	
		3-Intermediate	837	29.07	
		5-Horizontal	598	20.77	
		99-Others	50	1.73	
13.	Awning	1-Short and partly awned	70	2.43	
		5-Short and fully awned	5	0.17	
		7-Long awaned	32	1.11	
		9-Long and fully awned	126	4.37	
		99-Others	2638	91.62	
14.	Seed coat colour/ kernel colour	1-White	2272	78.91	
		2-Light brown	277	9.62	
		4-Brown	142	4.93	
		5-Red	178	6.18	
		7-Purple	1	0.03	
		99-Others	1	0.03	
15.	Hull colour	1-Straw	2089	72.55	
		2-Golden	271	9.41	
		3-Golden brown	107	3.71	
		4-Brown furrows on straw	218	7.57	
		5-Purple	19	0.65	
		6-Purple furrow on straw	83	2.88	
		8-Black	27	0.93	
		99-Others	57	1.97	
16.	Threshability	1-Easy	1618	56.20	
		2-Intermediate	918	31.88	
		3-Difficult	335	11.63	
17.	Aroma	0-Absent	2630	91.35	
		1-Present	241	8.37	
18.	Leaf senescence	9-Early & Fast	677	23.51	
		5-Intermediate	1808	62.79	
		1-Late & Slow	386	13.40	
19.	Sterile lemma colour	1-Straw	2703	93.88	
		3-Red	34	1.18	
		4-Purple	134	4.65	

Fig.1.Frequency distributions of important morphological characters

Table 2:  List of unique accessions identified based on morphological characters
S. No.	Name of Acc.	Specific character	
1.	IC0216428, IC0217487, IC0217954, IC0604072, IC0252052	Long-seedling height	
	IC0211206 IC0463684, IC0465371, IC0211206, IC0215759	Short-seedling height	
2.	IC0217552, IC0462562, IC0217040, IC0249229, IC0246879	Long-plant height	
	IC0215612, IC0219298, IC0245774, IC0245998	Short- plant height, Panicle type	
3.	IC0245777, IC0245734, IC0245922, IC0246521, IC0245923	Days to 50% flowering- early	
	IC0216070, IC0215441, IC0215557, IC0245656, IC0246402	Days to 50% flowering- Late	
4.	IC0219340, IC0246537, IC0246556, IC0246643, IC0246554	Long, cluster and cluster open- panicle type	
5.	IC0245729, IC0463199, IC0252056, IC0604014, IC0245722	High- number of effective tillers	
6.	IC0217247, IC0463077, IC0463212, IC0217591, IC0463460	High-grain yield	
7.	IC0249211	Glabrous-leaf pubescence	
8.	IC0464591, IC0462809	Kernel colour- black and purple	
9.	IC0463683, IC0462847, IC0463683	Kernel colour- white glumes and glumes	
10.	IC0604024, IC0125139, IC0215177, IC0215792, IC0216872	Hull colour- brown towning	
11.	IC0463739, IC0214552, IC0246477, IC0216110, 	Long bold seeded	
12.	IC0124726, IC0462221, IC0219226, IC0466663-X	Small seeded	

CONCLUSONS
In conclusion, the qualitative characteristics evaluated in this study play a pivotal role in the morphological description and differentiation of plant genotypes. The moderate variation observed in traits such as basal leaf sheath colour, stigma colour, seed coat/kernel colour, and hull colour indicates a level of phenotypic consistency among accessions, while still offering discernible markers for classification. Conversely, the high degree of variation in traits including early plant vigour, leaf blade colour, leaf pubescence, panicle exertion, flag leaf angle, threshability, and leaf senescence underscores their potential utility in distinguishing genotypic diversity. These highly variable traits serve as reliable morphological markers for genotype identification, contributing to the effective characterization and selection of plant accessions in breeding programs and genetic resource management.

Disclaimer (Artificial intelligence)
Option 1: 
Author(s) hereby declare that NO generative AI technologies such as Large Language Models (ChatGPT, COPILOT, etc.) and text-to-image generators have been used during the writing or editing of this manuscript. 

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