Genome-Wide Dissection of Novel QTLs and Genes Associated with Weed Competitiveness Traits Using a Population of Early-Backcross Selective Introgression Lines of Rice (Oryza sativa L.)
Authors: Nocito Kim Diane , Murugaiyan Varunseelan , Ali Jauhar , Pandey Ambika , Casal Carlos , de Asis Erik Jon , Dimaano Niña Gracel B. 
Published: June 2024

Background
Direct-seeded rice (DSR) system is anticipated to become the dominant rice cultivation method in the coming years due to its advantages, such as reduced water usage and labor requirements, less greenhouse gas emission, and adaptation to climate change risks. However, weeds are a significant constraint in the DSR system due to the yield losses incurred by weed infestations. Developing rice cultivars that are competitive against weeds through selective breeding has great potential to solve this challenge. Early seed germination (ESG) and seedling vigor (ESV) are important characteristics for the competitive ability of rice against weeds. This study used 181 early-backcross selective introgression-breeding lines (EB-SILs) that were generated by the process of backcrossing Weed Tolerant Rice 1 (WTR 1) with three specific donor parents (Haoannong, Cheng Hui 448, and Y134). Using the tunable genotyping-by-sequencing (tGBS®) method, we obtained 3,971 single nucleotide polymorphisms (SNPs). These SNPs were then utilized to identify and map quantitative trait loci (QTLs) associated with ESG and ESV features using their precise physical positions.
Results
High phenotypic variations among the EB-SILs and parental lines in different ESG- and ESV-related traits were observed. The association between the phenotypic and genotypic data detected 18 QTLs governing weed competitiveness, with eight and ten QTLs associated with the ESG and ESV traits, respectively. All detected QTLs were novel, except qRPH1, associated with relative plant height at 14 and 21 days after sowing (DAS). Four ESG-related QTLs (qRL2, qTDWG2, qSVI2.1, and qSVI2.1) were detected on chromosome 2, with two more QTLs governing germination rate (qGR12) and seed vigor index (qSVI12) identified on chromosome 12, and additional QTLs for seed vigor index found on chromosome 3 (qSVI3) and 6 (qSVI6). For ESV traits, qRPH1 detected on chromosome 1 was linked with relative plant height at 14 DAS and 28 DAS, while chromosome 10 harbored four QTLs (qRLC10.1, qRLC10.2, qRTN10, and qRRL10) associated with relative leaf count, relative tiller number, and relative root length at 28 DAS. Additionally, QTLs were detected for relative plant height at 21 DAS on chromosomes 5 and 9 (qRPH5 and qRPH9), relative leaf count at 28 DAS on chromosome 4 (qRLC4), relative tiller number at 28 DAS on chromosome 3 (qRTN3), and relative root length at 28 DAS on chromosome 8 (qRRL8). Candidate genes discovered within the identified QTLs were responsible for the plant’s response to various abiotic and biotic stresses.
Conclusion
This study provides a more profound comprehension of the genetic foundation of ESG and ESV traits, which are essential characteristics for the weed competitiveness of rice. The novel QTLs and candidate genes found have the potential to aid in marker-assisted and genomic selection approaches for breeding rice varieties with enhanced weed competitiveness. Simultaneously, the potential genes might be further examined to determine their expression patterns when subjected to intense weed pressure. The findings of this research will contribute to the development of rice varieties capable of competing with weeds. These varieties will be crucial in integrated weed management within the DSR system.