Genetic Basis of Seedling Root Traits in Common Wheat (Triticum aestivum L.) Identified by Genome-Wide Linkage Mapping

Common wheat production is significantly influenced by abiotic stresses. Identifying the genetic loci for seedling root traits and developing the available molecular markers are crucial for breeding high yielding and stable varieties. In this study, five wheat seedling root traits, including root length (RL), root surface area (RA), root volume (RV), number of root tips (RT), and root dry weight (RW), were measured in the Wp-072/Wp-119 recombinant inbred line (RIL) population. Genotyping was conducted for the RIL population and their parents using the wheat 90K single-nucleotide polymorphism (SNP) chip. In total, three quantitative trait loci (QTLs) for RL (<i>QRL.gau-1DS</i>, <i>QRL.gau-1DL</i> and <i>QRL.gau-4AL</i>), two QTLs for RA (<i>QRA.gau-1D</i> and <i>QRA.gau-2DL</i>), one locus for RV (<i>QRV.gau-6AS</i>), two loci for RW (<i>QRW.gau-2DL</i> and <i>QRW.gau-2AS</i>), and two loci for RT (<i>QRT.gau-3AS</i> and <i>QRT.gau-6DL</i>) were identified, with each explaining 4.5-8.4% of the phenotypic variances, respectively. Among these, <i>QRT.gau-3AS</i>, <i>QRL.gau-4AL</i>, and <i>QRV.gau-6AS</i> overlapped with the previous reports, whereas the other seven QTLs were novel. The favorable alleles of <i>QRL.gau-1DS</i>, <i>QRL.gau-1DL</i>, <i>QRL.gau-4AL</i>, <i>QRA.gau-1D</i>, <i>QRW.gau-2AS</i>, <i>QRV.gau-6AS</i>, <i>QRT.gau-3AS</i>, and <i>QRT.gau-6DL</i> were contributed by Wp-072, whereas the other two loci originated from Wp-119. Additionally, five kompetitive allele-specific PCR (KASP) markers, <i>KASP-RL-1DL</i> for RL, <i>KASP-RA-1D</i> and <i>KASP-RA-2DL</i> for RA, <i>KASP-RW-2AS</i> and <i>KASP-RW-2DL</i> for RW, were developed and validated successfully in 149 wheat accessions. Furthermore, seven candidate genes mainly for plant hormones were selected and validated by quantitative real-time PCR (qRT-PCR). This study provides new loci, new candidate genes, available KASP markers, and varieties for optimizing wheat root system architecture.