Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F₂ populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F₃ populations offering notable advantages over F₂ populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F₃ population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F₃ populations and multi-environment experiments can achieve high power, resolution, and reliability.

Plant trichomes are a specialized cellular tissue that functions in resistance to biotic and abiotic stresses. In rice, three transcription-factor genes: OsWOX3B, HL6, and OsSPL10, have been found to control trichome development. Although studies have shown interactions between the three genes, their full relationship in trichome development is unclear. We found that the expression levels of OsWOX3B and HL6 were both reduced in OsSPL10-knockout plants but increased in OsSPL10-overexpression plants, suggesting that OsSPL10 positively regulates their expression. Physical interaction between OsSPL10 and OsWOX3B was found both in vivo and in vitro and attenuated their abilities to bind to the promoter of HL6 to activate its transcription. This mechanism may regulate trichome length by adjusting the expression of HL6. A rice gene network regulating trichome development is proposed.