In this study, we aimed to identify the genetic sources associated with seed characteristics in rice. The preliminary study on two genotypes (367R and RU1501139) determined significant differences between the two genotypes for four seed characteristics of SDLG, SDWD, L/W, and SWT100. Restorer line 367R is a medium-grain rice cultivar, while RU1501139 is a long-grain breeding line. The seed length-width ratio is an essential measurement for the classification of rice cultivars. The results showed a positive correlation between L/W and SDLG, But a negative correlation between L/W with SDWD. In addition, the data showed a positive correlation between SWT100 with SDLG. Although there was no significant correlation between SWT100 and SDWD, the data showed a weak negative correlation between these two traits. Furthermore, results revealed that there was a positive correlation between SDWD and SDTH. Therefore, it can be assumed that longer and thicker seeds are heavier than shorter and wider seeds.
Enhancing seed yield, milling, and eating quality of rice can be achieved by developing superior cultivars by incorporating several agronomic traits, such as seed dimension and seed weight. The majority of these traits are classified as quantitative traits and are controlled by several QTL located in different parts of the rice genome. Each QTL has a different impact on the phenotypic variation. A breeder considers only those QTL that have the more significant impact on the phenotypic variations in a breeding program. In this study, we identified 17 major QTL and several minor QTL associated with seed characteristics. Annotation analysis revealed that five detected QTL contain genes associated with seed characteristics, and 11 were co-localized with previously reported QTLs (Huang et al., 1997; Redona et al., 1998; Xing et al., 2001; Jiang 2004; Alam et al., 1998; Zhu et al., 2000; Xu et al., 2002; Mei et al., 2003; Wissuwa et al., 1998; Sato et al., 2003; Cui et al., 2002; Zuang et al., 2001; Aluka et al., 2004). It can be concluded that 1) the annotation analysis of the QTL validates our finding via previously reported genes/QTLs associated with traits, and 2) these QTLs can be incorporated into the genomes of new superior genotypes.
For example, one important detected QTL is qSDLG 7 − 1 on chr. 7 associated with SDLG. This QTL is co-localized with qL/W-1 associated with L/W. Further investigation identified two candidate genes, GL7 and OsGASR9, in this genomic region. Another important detected QTL qSDLG 3 − 2 on chr. 3 is associated with SDLG and co-localized with qL/W3-1, associated with L/W.
On chr. 11, one QTL qSDLG 11 − 1 was detected for SDLG. Two candidate genes, RBG1 and FLA were identified on chr. 11 for SDLG. The RBG1 gene is associated with seed, root development, and stress tolerance by enhancing cell division and auxin levels; thus, it helps to improve root development and stress tolerance, which are essential factors for having a greater yield. (Lo et al., 2020). The second candidate gene, FLA, is a cell membrane protein that belongs to the Ubiquitin-specific proteases. The FLA is a common amino acid for eukaryotic cells. The FLA improves seed length and yield by regulating chloroplast and flower development (Ma et al., 2019). Thus, we can summarize that the QTLs qSDLG 7 − 1 and q SDLG 11 − 1 contain several candidate genes associated with seed length and significantly impact the phenotypic variations; thus, these two QTL can be integrated into a new generation of long-seed rice cultivars.
Although the ANOVA analysis showed the significance of SDWD in this population, no major QTL were identified on chr.s. However, a total of 12 minor QTL were detected with an LOD from 2 to 3 LOD scores. Therefore, it can be assumed that SDWD is controlled by several minor QTLs that, overall, significantly enhance SDWD.
The ANOVA analysis showed there was no difference between 367R and RU1501139 for the SDTH trait, but the genotypic analysis identified three major QTLs associated with the SDTH trait. Furthermore, the genotypic analysis showed that the two QTL of qSDTH5-1 and qSDTH6-1 originated from 367R, while qSDTH8-1 originated from RU1501139. Therefore, there is a biological significance between these two genotypes despite no statistical significance due to these detected QTLs.
Rice is one of the major crops in the world, with vast marketing all around the world. The rice breeders’ goals are to address farmers’ and consumers’ expectations by improving seed yield and seed characteristics. Further study is needed to identify major genes associated with these characteristics and developing molecular markers via a multi-location/year study. The results of this study can be used for marker-assisted selection in breeding programs.