Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1

Abstract

Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient’s genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.

Characterization of chromosomal segment substitution lines developed in the genetic background of rice variety K 343

“…In addition to the target genes, CSSL populations exhibit introgression of segments from donor lines; thus, each line in a CSSL library has a specific marker-defined large donor segment [4]. The successful application of novel QTLs in rice improvement via CSSLs is well documented [5,6,7]. The CSSLs are powerful tools for investigating large-scale gene discovery in wild rice, which could be adapted for rice quality improvement.…”

“…The CSSLs are powerful tools for investigating large-scale gene discovery in wild rice, which could be adapted for rice quality improvement. The successful application of novel QTL in rice improvement via CSSLs is well documented [5,6,7]. In addition, certain distinct morphological characteristics of wild rice that are derived from CSSLs were utilized as useful phenotypic markers in rice breeding programs [8].…”

Root attributes governing drought stress adaptation and the associated molecular markers in chromosome segment substitution lines in rice (Oryza sativa L.)

“…Exploring these favorable alleles of wild rice, through the development of CSSLs from crosses between wild species and cultivated varieties might be a powerful tool by identifying naturally occurring favorable alleles and to overcome yield limitations. CSSL libraries have been developed for many wild rice species, helping identify many quantitative trait loci (QTLs) of biological and economic interest (Subudhi et al 2015;Zhao et al 2022). These QTLs have been utilized for their important agronomic traits by effective mapping, cloning, and identification of gene interactions (Bimpong et al 2011;Li et al, 2023).…”