Molecular Marker-Assisted Pyramiding of SCM3, Wx, and BADH2 Genes for the Development of High-Yield, Superior-Quality, and Lodging-Resistant Rice Varieties

Utilizing the functional divergence sites of SCM3 , we established a molecular marker and performed SCM3 genotyping along with an evaluation of lodging resistance traits in 78 rice germplasm resources. Fourteen accessions with the SCM3⁹³¹¹ genotype demonstrated exceptional lodging resistance. In particular, Yangchan 93033 and Yangchannuo 1 exhibited strong stems, high bending resistance, and a significant number of grains per panicle, indicating their potential as elite donor parents for breeding lodging-resistant rice. Resequencing analysis revealed a rare variant site in the SCM3 gene of both Yangchan 93033 and Yangchannuo 1, and the derived KASP marker SCM3_k_28430214 was confirmed as an effective tool for molecular marker-assisted selection. A hybrid population was created by crossing Yangchan 93033 with Wuxiangjing 5245, a high-quality japonica cultivar known for its superior taste, to form a segregating breeding population. KASP markers targeting SCM3 , Wx , and BADH2 were utilized for genotypic screening of the progeny. Among 44 F₆ stable lines carrying SCM3⁹³¹¹ , there was a significant enhancement in lodging resistance compared to Wuxiangjing 5245, validating the effective selection capability of the SCM3_k_28430214 marker in improving lodging resistance. Through molecular marker-assisted selection, we rapidly developed a new breeding line, 24HD134, which integrates favorable alleles of SCM3 , Wx , and BADH2 . This line demonstrates high yield potential, superior grain quality, and improved lodging resistance, offering valuable genetic resources for rice breeding programs.