Genetic Relationships based on Qualitative Characters Differences of Several Yam bean (Pachyrhizus erosus) Lines

Yam bean serves strategically as food, medicine and cosmetics (Ningsih et al., 2019). Market demand for yam bean is substantial (Pudyastuti et al., 2022), yet its production is seasonal, failing to meet off-season needs. Additionally, its productivity as a functional food remains low. Productivity is influenced by variety and growing agroecosystem. The number of released yam bean varieties is minimal, with only one released variety, Kota Padang. Farmers often use uncertified seeds, leading to inconsistent seed development across regions, presenting a challenge and an opportunity for breeding new, superior yam bean lines (Ningsih et al., 2019). Utilizing genetic resources/germplasm for selection is vital in plant breeding (Fransisko and Bainamus, 2020).
       
The goal of plant breeding is to obtain genetically superior traits preferred by consumers. The success of breeding superior varieties depends on genetic diversity reflected in qualitative phenotypic characteristics. Breeding can involve collecting germplasm, crossing and mutating. The resulting lines are characterized and analyzed for similarities to facilitate evaluation. In 2019, a yam bean line, Line X, was purified through selection. The characteristics of Line X need comparison with existing varieties to identify distinguishing features. Conventional breeding can develop new lines. This requires phenotypic and genotypic diversity information (Rihadi et al., 2021). Potential lines are obtained through selection, which focuses on permanent traits from a population to define variety identity (Rihadi et al., 2021). Genetic variation is observable through morphological traits.
               
Similarity assessments of lines/varieties are based on morphological and phenotypic characteristics (Akinyosoye, 2022; Hamdi et al., 2024; Noviana et al., 2023) and genetics (Nugraha et al., 2017). Similarity is evaluated based on genetic and phenotypic relationships (Shikha and Narayan, 2020). Genetic diversity indicates the genetic distance of a line from its parent and dendrogram results show clusters due to geographic differences (Sari et al., 2017). Cluster analysis determines relationships, with greater genetic distance offering more opportunities for genetic purification (Nugraha et al., 2017). Morphological character-based cluster analysis helps obtain genetic resources for new varieties. Krisnawati et al., (2018) grouped 73 yam bean varieties into three clusters. Cluster analysis groups lines based on morphological similarities. Developing new varieties/lines can yield more attractive and superior seed products (Olomitutu et al., 2022). These morphological characters were shown to effectively differentiate genotypes and were recommended as selection indices for breeding programs aimed at improving chickpea adaptability and yield potential (Yadav et al., 2025). The utility of morphological traits in revealing genetic diversity and guiding parental selection for the development of high-yielding Phaseolus vulgaris L. varieties (Hussain et al., 2025). This study aims to identify differences in qualitative phenotypic characteristics and relatedness among bred yam bean lines and local lines, hoping that newly bred lines could potentially become new varieties.

The research was conducted in Kutasari Village, Baturraden District, Banyumas Regency, Central Java, from February to June 2023. Randomized Block Design (RBD) with four replicates was used. Treatments included six yam bean lines: Banyumas Line, Binjai Line, Kediri Line, Madura Line, Padang Variety and Line X.
       
The experiment began with creating beds measuring 1.25 m x 2.0 m. The beds were prepared and fertilized with organic manure. Seeds were soaked for 12 hours before planting at a depth of 2.5 cm with a spacing of 25 cm x 30 cm, planting 20 plants per bed. Fertilization with NPK 16-16-16 was applied at 30 and 70 days after planting (DAP) at a rate of 3 g/plant using a tugal system. Observations were made on five randomly selected plants per plot, focusing on qualitative traits of plant type, stem, leaf, flower, seed and tuber. Morphological observation as detailed in Table 1 (Tjitrosoepomo, 2009).


       
The qualitative phenotypic data were analyzed descriptively and through cluster analysis using OriginPro software, with results presented as a dendrogram. Quantitative data on productivity traits were analyzed using the 5% Honestly Significant Difference (HSD) test.

Qualitative phenotypic characteristics of yam bean were measured across parameters including plant growth type, stem, leaf, flower, seed and tuber. The study compared the characteristics of the bred line (Line X) with other lines. Table 2 presents the qualitative phenotypic characteristics of Line X and other lines. Morphological diversity is one trait that can be utilized to enhance plant superiority (Abdulkareem et al., 2015).


       
The bred yam bean line (Line X) has a climbing growth type, similar to the Banyumas, Kediri, Madura lines and the Kota Padang variety, but differs from the Binjai line, which has an upright growth type. The growth type is largely influenced by genetic factors. Line X has the same stem shape (round) as the other lines. The stem color of Line X is the same as the Banyumas line but differs from the other lines. The stem color of Line X and Banyumas is RHS Greyed Purple-N186-B, while the stem color of Binjai, Kediri and Madura lines is RHS Yellow Green Group-144-A and Padang is RHS Greyed Purple-N186-A (Table 2). The stem appearance of Line X is similar to that of Banyumas. Differences in stem color are due to pigment changes resulting from chlorophyll expression mutation, as seen in African yam beans (Abdulkareem et al., 2015).
       
The leaf characteristics of Line X are similar to other lines, particularly in leaf shape (diamond), leaf tip (pointed), leaf edge (smooth) and leaf surface (hairy). Leaf shape is an essential distinguishing character in yam beans (Karuniawan, 2006). The leaf color of Line X is similar to Banyumas (RHS 147-A) but differs from Binjai, Kediri, Madura and Padang lines (RHS NN137-A). The petiole color of Line X is the same as Kota Padang (RHS 147-A) but differs from Banyumas (RHS 202-A), Binjai, Madura (RHS 144-A) and Kediri (RHS 146-A) lines. Differences in leaf color are due to pigment changes in chlorophyll, which alter qualitative traits (Abdulkareem et al., 2015).
       
The flower petal shape of Line X is the same as Banyumas, Kediri, Madura and Padang lines (moderately raised) but differs from Binjai (highly raised). The flower petal color of Line X is RHS Violet Blue Group-91-A, distinct from all other yam bean lines. The sepal color of Line X is the same as Banyumas and Padang (RHS N199-B) but differs from Binjai, Kediri and Madura lines. The stigma and stamen color of Line X match Madura (RHS 11-A) but differ from Banyumas, Binjai, Kediri and Padang lines. The style color of Line X is the same as Banyumas (RHS 157-D) but differs from Binjai, Kediri, Madura and Padang lines. These color changes are due to protein content variations from physiological processes (Hayati et al., 2022) and chlorophyll pigment formation (Zakiyah et al., 2018). Chlorophyll is the green pigment in plants, influenced by environmental factors such as light, temperature and humidity (Zakiyah et al., 2018).
       
The tuber shape of Line X is the same as other yam bean lines (top-shaped). The skin color of Line X is the same as Binjai (RHS 163-D) but differs from Banyumas, Kediri, Madura and Padang lines. The flesh color of Line X matches Madura and Padang (RHS 155-D) but differs from Banyumas, Binjai and Kediri lines. Tuber color is determined by the content of natural pigments like carotenoids, tannins, anthocyanins and flavonoids. Changes in tuber color are influenced by flavonoid components, which can impart color to leaves, flowers, fruits and tubers (Priska et al., 2018). The seed shape of Line X is the same as Padang (elongated round) but differs from Banyumas, Binjai, Kediri and Madura lines. The seed color of Line X is the same as Kediri and Madura (RHS 165-B) but differs from Banyumas, Binjai and Padang lines.
       
The relationship test was conducted using morphological (phenotypic) characterization data scored with MS Excel and organized into a dendrogram using the UPGMA (Unweighted Pair Group Method with Arithmetic Averages). The dendrogram was based on various parameters including plant type, stem color, leaf color, petiole color, flower petal shape, flower petal color, sepal color, stigma color, stamen color, style color, tuber skin color, tuber flesh color, seed shape and seed color. The scoring results for each parameter of the yam bean lines are presented in Table 3.


       
Cluster analysis utilizing morphology parameters revealed distinct population groupings, reflecting inherent genetic divergence. These results confirm that morphological characteristics serve not only as valuable tools for taxonomic classification but also provide critical insights for plant breeding programs, particularly during initial selection and domestication phases targeting economically important traits in neem (Swati et al., 2025).

The extent of genetic diversity among parental lines influences the number of clusters formed during breeding programs (Chandra et al., 2024). The relatedness among the yam bean lines was measured based on the similarity of the observed parameters. The six observed lines exhibited identical similarities in stem shape, leaf shape, leaf tip, leaf edge, leaf surface and tuber shape. Cluster analysis of the six lines revealed two major clusters: Cluster 1 consisting of the Banyumas line and Cluster 2 consisting of the Binjai, Kediri, Madura, Padang and X lines (Fig 1). The Banyumas line had 0% similarity with the lines in Cluster 2. Cluster 2 was further divided into three subgroups: Subgroup 1 (Binjai), Subgroup 2 (Madura and Kediri) and Subgroup 3 (Padang and X). The Binjai line showed 13.79% similarity with Subgroup 2 and 21.03% similarity with Subgroup 3. Line X showed 34.27% similarity with the Padang line.


       
The assessment of a bred line can be evaluated through changes in qualitative phenotypic characteristics, which differentiate it from other lines. The changes in plant characteristics can be measured by morphological appearance. The evaluation of genotypic changes using morphological parameters is crucial (Nusifera and Kurniawan, 2016; Silva et al., 2016). Morphological parameters, including stem, leaf, flower, seed and tuber, are vital for determining the yield of yam beans (Aina et al., 2021). Selecting lines/varieties in yam bean cultivation is challenging due to the long lifespan of the plants (Aina et al., 2021). Each line/accession has specific morphological characteristics (Baiyeri et al., 2022). Environmental conditions, such as climate and soil, influence changes in morphological characteristics. According to Sebayang et al., (2023), growth environments have shaped different morphological characteristics in cassava.
       
This study revealed that the breeding of the yam bean hopeful line resulted in Line X, which exhibited various differences in qualitative characteristics. The main differences between Line X and the comparison lines/varieties lay in the growth type, color of various parts (stem, leaf, flower, seed and tuber). Yam bean growth types are classified into two categories: 1) upright and 2) climbing. Line X has a climbing growth type, unlike the Binjai line, which has an upright growth type. This growth type is influenced by genetic factors and is not affected by environmental conditions such as climate and soil.
       
The stem, which translocates nutrients to various plant parts, shows differences in Line X compared to the Binjai, Madura, Kediri and Padang lines. Stem color differences are influenced by chlorophyll pigment content. According to Nurchayati et al., (2019), color differences are due to variations in pigment content within the plant tissue. Leaf color is a distinguishing feature of yam bean lines. Line X differs in leaf color from all comparison lines due to the presence of chlorophyll. Danniswari et al., (2019) noted that leaf color changes are due to chlorophyll content and nutrient supply to the leaves. Ai and Banyo (2011) mentioned that pigment formation in plants is influenced by genetic factors.
       
Seed characteristics, particularly color and shape, show notable differences. Line X has different seed colors compared to the Banyumas and Padang lines and different seed shapes compared to the Banyumas, Binjai and Kediri lines. Seed color changes are influenced by soil nutrient support (Ikhajiagbe and Kwesi Mensah, 2012).
       
Line X shows differences in tuber characteristics compared to the Banyumas, Kediri, Madura and Padang lines. Tuber color changes are influenced by mineral content. Yam bean tubers contain iron, calcium and protein, affecting tuber appearance (Ibirinde et al., 2019). Additionally, yam beans contain flavonoids and phenolic acids (George et al., 2020).
       
Qualitative character analysis serves as a reference for determining plant relatedness. Morphological identification, observing the plant type, leaf, stem, flower, tuber and seed, is used to determine phenotypic characteristics (Hartati et al., 2015). Morphological characterization involves observing qualitative plant characteristics. Phenotypes are used to detect morphological plant characteristics.
       
The distance in relatedness among species is influenced by differences in morphological characteristics, one of which is qualitative traits (Kinasih et al., 2017), describing phenotypic characteristics. This study shows that yam bean lines exhibit similarities in stem shape, leaf shape, leaf tip, leaf edge, leaf surface and tuber shape. The dendrogram is based on different parameters: plant type, stem color, leaf color, petiole color, flower petal shape, flower petal color, sepal color, stigma color, stamen color, style color, tuber skin color, tuber flesh color, seed shape and seed color. The Kediri and Madura lines exhibit 44.83% similarity across all qualitative parameters except petiole color, sepal color, style color, stigma color, stamen color, tuber skin color and tuber flesh color.
       
The Padang and Line X exhibit 34.27% similarity across all qualitative parameters except stem color, leaf color, flower petal color, style color, stigma color, stamen color, seed color and tuber skin color. The Binjai line shows 13.79% similarity with differences in plant type, stem color, petiole color, leaf color, flower petal shape, sepal color, flower petal color, style color, stigma color, stamen color, seed shape, seed color, tuber skin color and tuber flesh color, but is characterized by an upright plant type and highly raised flower petal shape. Banyumas line exhibits 0% similarity with other lines. The Banyumas line shows differences in petiole color, stigma color, stamen color and seed color, with the most distinct scoring from other lines. Line X has a distant relatedness to all lines. The similarity indicates that phenotypic character similarity among yam bean lines genetically suggests a close relationship. According to Purnomo et al., (2017), a similarity level of ³ 70% indicates a close genetic relationship among lines.
               
Quantitative data on productivity traits were analyzed using Honestly Significant Difference (HSD) test. The analysis for the productivity variable indicate that Line X has the highest productivity compared to the Banyumas, Kediri, Madura and Padang lines (Table 4). However, the productivity of Line X is not significantly different from that of the Binjai line. Productivity is one of the key criteria in plant breeding for developing superior varieties with improved yield and adaptation to specific environments. Knowing the productivity of a line can facilitate the selection of high-yielding lines for further development as elite varieties.

Line X shows the highest similarity with the Padang variety, followed by the Madura and Kediri lines, Binjai and the Banyumas line. The differences in qualitative characteristics between Line X and Binjai encompass 12 parameters (60%), Kediri 11 parameters (55%), Madura 9 parameters (45%), Banyumas 7 parameters (35%) and the Padang variety 6 parameters (30%). Line X has distinctive qualitative characteristics, including the flower petal color RHS Violet Blue Group-91-A and the tuber skin color RHS 163-D. The results of the 5% HSD analysis for the productivity variable indicate that Line X has the highest productivity compared to the Banyumas, Kediri, Madura and Padang lines. However, the productivity of Line X is not significantly different from that of the Binjai line. 

The authors would like to express their sincere gratitude to Politeknik Pembangunan Pertanian Yogyakarta Magelang for invaluable support and contributions to this research.
 
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There are no animal procedures for experiments during data collection of this study.

The authors declare that there are no conflicts of interest regarding the publication of this article. No funding or sponsorship influenced the design of the study, data collection, analysis, decision to publish, or preparation of the manuscript.