Enhancement of genetic gain for early seedling vigor traits through marker-assisted pedigree selection in rice (Oryza sativa L.).

Early Seedling Vigor (ESV) is a critical trait for direct-seeded rice (DSR), as it promotes rapid seedling establishment and effective weed suppression. Enhancing ESV is therefore essential for developing varieties adapted to DSR conditions. This study aimed to accelerate genetic gain for ESV traits through Marker-Assisted Pedigree Selection (MAPS) by leveraging reported quantitative trait loci (QTLs). Markers associated with ESV and grain size (GS) traits were validated using bulked segregant analysis (BSA) and haplotype analysis. These validated markers were then applied to select progenies carrying different combinations of the targeted QTLs from the F4 to F7 generations derived from a cross between MTU3626 (an ESV donor) and BPT5204 (a medium-slender grain size) variety. Using MAPS, 20 promising lines were identified, with QTL combinations ranging from nine QTLs in line BM3 to three QTLs in lines BM284 and BM410. Notably, the presence of qSV-3-1, qSDW-2, and qVI contributed substantially to improved ESV. MAPS achieved genetic gain enhancements of 45.87% in the F5 generation and 86.47% in the F6 generation compared to phenotypic selection alone. These results highlight that integrating molecular markers into pedigree breeding enables precise selection and significantly improves genetic gain for ESV traits. The identified promising lines could either be advanced for varietal release after rigorous yield evaluation or serve as donor parents in breeding programs targeting DSR adaptation.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-025-01635-w.