Genome-Wide Dissection of Novel QTLs and Genes Associated with Weed Competitiveness in Early-Backcross Selective Introgression-Breeding Populations of Rice (Oryza sativa L.)

Abstract

The direct-seeded rice (DSR) system is poised to become the dominant rice cultivation method due to its advantages, including reduced water usage, less labor requirements, decreased greenhouse gas emissions, and improved adaptation to climate change. However, weeds, particularly jungle rice (Echinochloa colona), significantly hinder DSR and cause substantial yield losses. This study aimed to develop rice cultivars competitive against jungle rice through selective breeding, focusing on early seed germination (ESG) and seedling vigor (ESV). We utilized 181 early-backcross selective introgression breeding lines (EB-SILs) developed using Green Super Rice (GSR) technology by backcrossing Weed Tolerant Rice1 (WTR1) with three donor parents, Haoannong, Cheng Hui 448, and Y134. Using the tunable genotyping-by-sequencing (tGBS^®, Data2Bio Technologies, Ames, IA, USA) method, we identified 3971 common single nucleotide polymorphisms (SNPs) that facilitated the mapping of 19 novel quantitative trait loci (QTLs) associated with weed competitiveness-eight linked to ESG traits and eleven to ESV traits. Notably, all QTLs were novel except qRPH1, linked to relative plant height at 14 and 21 days after sowing. Key QTLs were located on chromosomes 2, 3, 5, 6, 8, 9, 10, and 12. Candidate genes identified within these QTLs are implicated in the plant's response to various abiotic and biotic stresses. Our findings enhance the understanding of the genetic basis for ESG and ESV traits critical for weed competitiveness, supporting marker-assisted and genomic selection approaches for breeding improved rice varieties. Furthermore, this research lays the groundwork for employing gene expression, cloning, and CRISPR editing strategies to combat jungle rice, with potential applications for other weed species and contributing to effective integrated weed management in the DSR system.

Keywords: Green Super Rice; candidate genes; direct-seeded rice; jungle rice; quantitative trait loci; seedling vigor; single nucleotide polymorphisms; weed competitiveness.

Figure 1

Mean performance of parental lines and Early Backcross Selective-Introgression Lines (EB-SILs) was assessed under germination assay for early seed germination (ESG) traits. The vertical bars in the graph represent the mean phenotypic performance of these lines. Traits with no letter above the bars indicate no significant difference among the lines, while the presence of letters above the bars indicates significant differences among the lines. Different letters denote significantly different means.

Figure 2

Mean performance of parental lines and Early Backcross Selective-Introgression Lines (EB-SILs) was assessed under both non-weedy and weedy conditions for early seedling vigor (ESV). The vertical bars in the graph represent the mean phenotypic performance of these lines. Traits with no letter above the bars indicate no significant difference among the lines, while letters above the bars indicate significant differences among the lines. Different letters denote significantly different means.

Figure 3

The heat map displays the correlation coefficients for traits related to weed competitiveness. Heat map (A) shows the correlation coefficients for early seed germination (ESG) traits, while heat map (B) illustrates the correlation coefficients for early seedling vigor (ESV) traits. Significant * 0.05 ≥ p-value ≥ 0.01; ** 0.01 ≥ p-value ≥ 0.001; *** p-value ≤ 0.001.

Figure 4

Principal Component Analysis (PCA) was conducted to determine traits related to rice competitiveness against weeds. Plot (A) shows the score plot for the first two principal component (PC) scores, PC1 versus PC2, depicting the measurements for early seed germination (ESG) traits across all genotypes. Plot (B) displays the score plot for PCA of early seedling vigor (ESV) traits, again showing PC1 versus PC2 for all genotypes.

Figure 5

Five selected early backcross selective-introgression lines (EB-SILs) along with their recipient and donor parents showing early seedling vigor (ESV) traits—abbreviations: NW, non-weedy condition; W, weedy condition.

Figure 6

Chromosomal distribution of Low Missing Data 50 (LMD50) single nucleotide polymorphisms (SNPs) and identified quantitative trait loci (QTLs) associated with early seed germination (ESG) and early seedling vigor (ESV) traits. QTLs were located on the chromosome based on the physical position of the SNP marker.