Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 16 Table 1 Domestication genes detected in RUF-SSSLs and NIV-SSSLs (Adapted from Wang et al., 2023) Trait SSSLs Identifed genes Chr Region Known genes References Tiller angle SR59, SR60, SR61, SR63 TA7-RUF 7 RM515-RM195 PROG1 Jin et al. (2008); Tan et al. (2008) SR72, SR77, SR76, SR75 TA8-RUF 8 RM515-RM195 TIG1 Zhang et al. (2019) SR78, SR79, SR80 SN136, SN139, SN143 TA11-NIV 11 RM332-PSM175 - - Spreading panicle SN22, SN28, SN29, SN33 SPR3-NIV 3 RM569-RM231 - - SN57, SN58 SPR4-NIV 4 OSR15-PSM361 OsLG1 Zhu et al. (2013) Awn SN34, SN39 AN3-NIV 3 PSM428-RM218 - - SN54, SN56 AN4-NIV 4 RM273-RM252 - - SR118, SR119 AN4-RUF 4 RM4835-PSM326 An-1 - Seed shattering SN58 SH4-NIV 4 PSM361-RM559 SH4 Li et al. (2006) Red pericarp SR64, SR65 RC7-RUF 7 PSM144-RM214 Rc Sweeney et al. (2006) SN79, SN82, SN85 RC7-NIV 7 RM180-RM6728 4 Genetic Basis of Domestication Traits 4.1 Key genes involved in domestication The Sh4 gene plays a crucial role in the domestication of rice by controlling seed shattering. The nonshattering sh4 allele was fixed in all rice cultivars, significantly reducing sequence polymorphism compared to wild progenitors (Zhang et al., 2009). The gene encodes a YABBY transcription factor, and its mutations lead to the loss of seed shattering, facilitating easier harvest (Lin et al., 2012; Lv et al., 2018). Additionally, the sh4 gene has been shown to have a single origin and was fixed by artificial selection during rice domestication (Zhang et al., 2009). However, some studies suggest that the sh4 locus might have played a minor role in Asian rice domestication, indicating the presence of other unidentified shattering loci (Zhu et al., 2012). Moreover, research has found that the single segment substitution lines (SSSL) have been developed using high-quality indica rice variety HJX74 as the background and wild rice varieties O. rufipogon and O. nivara as donors. In the SSSLs population, the broken grain domestication character SH4 was identified by substitution mapping, and locate it on chromosome 4 (Figure 1). Through sequence comparison with known genes, it was found that SH4-NIV and SH4 alleles, and SSSL became a valuable germplasm resource for understanding the regulation of character variation during domestication (Wang et al., 2023). The PROG1 gene is another significant gene involved in the domestication of rice, particularly influencing plant architecture. This gene affects the plant’s growth habit, transitioning from a prostrate to an erect form, which is more suitable for cultivation and harvesting. The domestication of rice involved selecting for mutations in the PROG1 gene that resulted in an erect growth habit, thereby improving yield and ease of harvest (Lv et al., 2018). The qSW5 gene is a quantitative trait locus (QTL) associated with grain width in rice. A deletion in this gene results in a significant increase in grain width, which was likely selected by ancient humans to increase rice yield (Shomura et al., 2008). This deletion increases the cell number in the outer glume of the rice flower, contributing to larger grain size and higher yield (Shomura et al., 2008). 4.2 Molecular pathways and networks The domestication of crops involves complex molecular pathways and networks that regulate various agronomically important traits. For instance, the Sh1 gene family, including Sh1, OsSh1, and ZmSh1, encodes YABBY transcription factors that control seed shattering in sorghum, rice, and maize, respectively (Lin et al., 2012). These genes were under parallel selection during the domestication of these cereals, indicating a conserved molecular pathway for seed shattering across different species (Lin et al., 2012). Additionally, the SH3 gene in African rice also regulates seed shattering, highlighting the involvement of multiple genes and pathways in this trait (Lv et al., 2013).
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