Pre-breeding in Rice Development: Phenotypic-Genotypic Evaluation Associated with High Yield and Early Harvesting Traits

The breeding process involves developing techniques to create cultivars that thrive in the ever-changing global climate, allowing for early harvesting and high yield. This study aimed to screen rice genotypes with early harvesting and high yield to develop new-generation cultivars. The study was conducted in a field experiment at the Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Special Region of Yogyakarta, Indonesia, from December 2022 to April 2023. Ten genotypes were laid out using an Augmented Randomized Complete Block Design (ARCBD) with three rows and six columns. The observations were macro and micro-climate, soil quality, and morphological traits of rice. Data were analyzed using a Linear Mixed Model (LMM), correlation matrix, heatmap cluster, Principal Component Analysis (PCA), PCA-Biplot, Multiple Factor Analysis (MFA), and circular cluster. The results provided information that the rice genotypes with the early harvesting genotypes were Inbrida M70D (95.01 days), Trisakti (100.98 days), and SR Super (104.76 days). Furthermore, the rice genotypes with the highest yields were Gamagora 2 (49.82 g clump−1), Gamagora 4 (46.61 g clump−1), Gamagora 7 (37.26 g clump−1), and Gamagora 10 (29.84 g clump−1). The genetic clustering based on Simple Sequence Repeat markers linked to early flowering genes indicates that SR Super and Inbrida M70D show the most distinct characteristics compared to other genotypes. Molecular findings corroborate the morphological analysis, indicating that Inbrida M70D and SR Super are early harvesting genotypes, therefore they can be used this group of genotypes as cross-breeding material to obtain genotypes with early harvesting and high-yielding traits.