Phenotypic variation of local rice in West Java, Indonesia

Rice is the leading staple food in Indonesia and one of the largest production centers in West Java Province. Of the wide local varieties of rice in West Java, only a few have been inventoried and characterized for their morphological characteristics. This study aims to determine West Java’s phenotypic diversity of rice plants. Inventory and morphological characterization of local rice plants was carried out from 2018 to 2021 in seven districts in West Java (Sukabumi, Subang, Cianjur, Sumedang, Bogor, Tasikmalaya, and Bandung). A total of 30 accessions of local rice were observed based on Rice Descriptors. Data analysis used Principal Component Analysis (PCA) and Cluster Analysis with Minitab 21. The results showed that the seven main components contributed to the proportion of diversity of 83.7%. The local rice varieties in the five groups had a degree of similarity of 30%. The characters of leaf blade length, ligule length, ligule color, stem diameter, panicle extrusion, and the presence of awn contributed the most to the total diversity.


Introduction
Rice (Oryza sativa L.) is the main food crop in the world and provides 60% of the food intake in Southeast Asia [1].Most of Indonesia's population consumes rice as a staple food.In addition, there are many other processed products, such as rice flour as raw material for snacks, bran as animal feed, rice husks as compost material, and straw used as mulch.Indonesia has a very diverse potential for rice genetic resources.At this time, 3,169 rice germplasm accessions have been characterized and collected by the Indonesian Center for Rice Research.The germplasm comprises 2,095 local variety accessions, 804 introduced varieties, and 270 new superior varieties [2].
Indonesia has diverse local rice varieties as one of the broad plant genetic resources [3], including the center of origin of wild rice plants [4].Before 1970, most farmers in Indonesia used local varieties, numbering thousands or even tens of thousands of accessions and spreading over a relatively large 1230 (2023) 012051 IOP Publishing doi:10.1088/1755-1315/1230/1/012051 2 area [5] and climate conditions (agroecosystems) [6].In addition, local varieties have naturally been tested for their resistance to various stresses, both biotic stress (pests and diseases/plant-disturbing organisms) and abiotic (environmental) stress [7].Suboptimal agroecosystem conditions include drought, acid soil, flooded land, and iron poisoning.Will form local varieties tolerant to these suboptimal conditions.Allseason farmers choose rice varieties with good taste so that local varieties generally have high quality [6,8,9].So local varieties are priceless plant genetic resources (PGR).
Local rice is a plant cultivated for generations, so the genotype has adapted well to various specific land and climate conditions where rice is cultivated [10].In 2013, 98 local rice accessions were identified and collected, consisting of white rice, brown rice, black rice, white glutinous rice, black sticky rice, and aromatic rice [8,11].
Local rice has a higher phenotype diversity than modern varieties or numerous superior varieties [12].High genetic diversity is utilized in rice breeding programs and for improving hybrid rice parents.Identifying essential traits in local rice needs to be continued to know its potential in breeding programs [13].Several local varieties of rice germplasm have been identified as resistant and tolerant to biotic and abiotic stresses and have good rice quality.Over 53 years, 39 varieties have been released against the background of local varietal elders [10].This study aims to determine the phenotype diversity of rice plants in West Java.

Materials and methods
Inventory and morphological characterization of local rice plants was carried out from 2018 to 2021 in seven sub-districts in West Java (Sukabumi, Subang, Cianjur, Sumedang, Bogor, Tasikmalaya, and Bandung) (Table 1).The descriptive and multivariate analysis variables were phenological and agroquantitative, including leaf, ligule, culm, panicle, grain, and endosperm type.The materials used were rice plant parts, color charts, scales, vernier calipers, and cameras.The research used exploratory methods and direct observation of several morphological characters under the guidelines of the General Guidelines for The Preparation of Descriptions of Food Crop Varieties [14,15]

Principal component analysis
According to principal component analysis, four of the thirteen components had eigenvalues greater than two for 64.2% of the total variation.The first principal component had 3,228 values, contributing to 24.8% of diversity (PC1), the second principal component (PC2) had 17.3%, and PCA3 accounted for 13.1% of diversity (Table 2).The character influences diversity if the characteristic vector value exceeds 0.3 (Table 2).While the PC3 was loaded with blade leaf width (0.31), leaf flag attitude (0.376), ligule color (0.495), and grain color, the PCA1 and PC2 were loaded strongly with a vector value by panicle extrusion (0.40), grain color (0.35), length of flag leaf (0.33), and ligule length (0.48) and blade leaf length (0.47), presence of awns (0.46), which are observable, load PC4.PC1 and PC2 factor scores were used to create a scatter plot, and the factor plane revealed a distinct pattern of genotype clustering (Figure 1).These genotypes occupied the upper area, namely Kawung Cicadas, Jago Campaka Warna, Tampeuy Beureum, and Hideung Cibeusi, as these genotypes were placed at the highest point on the scatter plot.These genotypes had the most variance.They can be utilized as heterogeneous parents in a crossing scheme to maximize heterosis [16].This vector line is drawn from the origin to the area of trait mapping.Based on the vector's length, the attributes, namely panicle exertion, leaf blade length, ligule length, and leaf flag length, possess long vectors; these attributes could play a role as essential criteria for characterization.
Pearson correlation coefficients were calculated for 13 different morphological traits, and 13 pairwise correlations were significant (Table 3).The flag leaf length strongly correlated with the flag leaf's width and the presence of awns in PC1; this is similar to the past study for 80 regional rice varieties from Asia and America, leaf flag width and length was linked as the phenotypic association is consistent [16].The length of the leaf blade significantly correlated with the flag leaf length and ligule length in PC2, whereas the ligule's color positively correlated with the grain color.However, panicle extrusions are negatively significant with the flag leaf's attitude and the culm's diameter.The sustainability of the existing landraces and farmer varieties should take precedence.Once characterized, these landraces are advantageous to developing modern plant varieties because they are relatively simple to preserve without modifying their genetic makeup [17,18].Morphological characterization is necessary for a successful breeding program to generate crop varieties through hybridization; one of the helpful techniques and a crucial element in determining parents is the study of genetic diversity [19].Cluster analysis using all 13 morphological traits grouped the 30 accessions into five major groups at the genetic similarity level of 30%.Additionally, it was discovered that, out of the five clusters, cluster III was the most extensive and had 15 genotypes, including three from Sukabumi, two from Cianjur, four from Tasikmalaya, two from Bandung, one from Sumedang, and three from Bogor.The Second largest group was cluster IV, with six genotypes: two from Subang and four from Sukabumi.In the following cluster I had four varieties dominated by Sukabumi.Then, cluster II, with three varieties, including two from Sukabumi and one from Subang.The smallest group was cluster V, containing two local varieties: Marahmay Jawara from Subang and Tebar Kiarasari 1 from Bogor.

Cluster analysis of landraces rice phenotypic in West Java
Thirteen morphological variables used in a clustering study to divide 30 landrace rice genotypes into five groups revealed significant genetic differences among the 30 rice genotypes in terms of morphological attributes.As a result, the classification in this study based on morphological features concurs with the earlier report.The formation of different numbers of clusters using morphological characters in diverse rice genotypes was also reported [16, [20][21][22][23][24][25].The dendrogram tends to cluster various landraces with related morphological features together can seen in Figure 2. The morphologicalcharacter of cluster III was panicle extrusion with a negative value.Cluster IV consisted of the attributes of endosperm type.Cluster I consisted of the characteristics of the length of the leaf blade, the width of the leaf blade, the length of the flag leaf, the width of flag leaf length of a ligule, and the extrusion of the panicle; however, the negative value character of the attitude of the flag leaf.The last had three characters: the attitude of the leaf, ligule color, and panicle exertion.There were few differences in the number of genotypes used in cluster construction when the dendrogram and PCA methods were used for cluster analysis [19,21].In order to produce enormous heterosis, the hybridization procedure could use genotypes with distant clusters as parents [16].The dendrogram and PCA graph indicated that cluster V was far from four other clusters.Therefore, the varieties from cluster III could be used for a hybridization program with landrace from cluster V.

Conclusion
The main objective of plant breeding is to develop new genotypes from the existing ones while improving plant traits.The current study showed that among the newly created 30 landraces genotypes of rice from West Java, there was substantial diversity for thirteen agro-morphological traits.By component analysis, most of the traits showed positive correlations with each other, which will assist in the combined improvement of these traits by selecting only highly heritable and easily measurable phenotypic traits.In addition, correlation indicated that the length of the leaf blade, length of a ligule, the color of the ligule, presence of awns, and color of the grain contributed significantly to the diversity.Cluster analysis grouped the accessions into 5 clusters.

Table 1 .
Accession and sources local rice in West Java.Data were analyzed using a scoring system, Principal Component Analysis (PCA) [16], and cluster analysis on the Minitab 21 Multivariate Software Program.
3. Results and discussionsThe survey results in 7 sub-districts in West Java showed 30 accessions of rice with phenotypic morphology variations.The PVPPP Center registered the rice accessions.Local farmers always grow local rice because of the taste or aroma of rice, the availability of seeds, and the high selling price.The occurrence of phenotypic diversity in local rice plants was caused by genetic factors and the environment in which rice plants grow.Phenotypic diversity is used in rice breeding programs to improve hybrid rice parents, which improves breeding efficiency, including quantitative, and is quickly impacted by the environment[14].Breeders select for overall phenotypic expression and high tolerance to various biotic and abiotic stresses[15].

Table 2 .
Principal component analysis (PCA) of morphological characters of local rice in West Java, Indonesia.

Table 3 .
Pearson correlation of morphological characters of several local rice genotypes in West Java, Indonesia.