QTL Mapping and Functional Analysis Reveal Candidate Genes, Including BrSRR1, Involved in Negative Regulation of Shade-Induced Hypocotyl Elongation in Brassica rapa

Abstract

Shade avoidance response (SAR) is an important adaptive mechanism that enables plants to optimize light capture in dense canopies, but excessive shade-induced hypocotyl elongation can negatively affect plant architecture, yield, and quality in Chinese cabbage. In this study, we investigated the genetic basis of SAR using an advanced intercross recombinant inbred line (AI RIL) population derived from a cross between the oil type Chinese cabbage ‘R500’ with significantly longer hypocotyls and the vegetable type Chinese cabbage ‘L58’ with shorter hypocotyls. Quantitative trait locus (QTL) mapping under simulated shade, represented by a low red/far-red light ratio of 0.5, and non-shade conditions, represented by a high red/far-red light ratio of 2.0, identified several candidate genes associated with hypocotyl elongation, including COP1, XTH17, HYH and SRR1. Among these genes, BrSRR1 was selected for functional validation by introducing two alleles of BrSRR1 coding sequences into the Arabidopsis srr1 mutant. Under simulated shade, the srr1 mutant exhibited significantly longer hypocotyl than wild-type Col-0, whereas the BrSRR1-L58 restored hypocotyl length to a level statistically indistinguishable from that of wild-type Col-0. In contrast, the BrSRR1-R500 failed to complement the mutant phenotype, indicating ecotype-specific and allele-dependent functional divergence. Collectively, these findings indicate that BrSRR1 is implicated as a candidate gene involved in negative regulation of shade-induced hypocotyl elongation, though pending validation in the native species, providing insights into the genetic regulation of SAR in Chinese cabbage and a potential target for breeding varieties with reduced shade-induced hypocotyl elongation suited to high-density planting.