Unraveling the Complex Trait of Crop Yield With Quantitative Trait Loci Mapping in <i>Brassica napus</i>

TLDR

Yield is a critical yet complex trait in crops, with its genetic architecture remaining ambiguous and heavily influenced by gene–environment interactions. The study aims to estimate indicator QTL for yield and identify candidate genes, advancing methodology for complex traits. Researchers mapped 85 seed‑yield QTL and 785 trait QTL across two rapeseed populations and ten environments, then performed a trait‑by‑trait meta‑analysis to identify consensus and pleiotropic QTL. The analysis uncovered 401 consensus QTL, of which 111 were pleiotropic and 47 influenced seed yield, underscoring the complex, pleiotropic, and plastic genetic architecture of yield.

Abstract

Abstract Yield is the most important and complex trait for the genetic improvement of crops. Although much research into the genetic basis of yield and yield-associated traits has been reported, in each such experiment the genetic architecture and determinants of yield have remained ambiguous. One of the most intractable problems is the interaction between genes and the environment. We identified 85 quantitative trait loci (QTL) for seed yield along with 785 QTL for eight yield-associated traits, from 10 natural environments and two related populations of rapeseed. A trait-by-trait meta-analysis revealed 401 consensus QTL, of which 82.5% were clustered and integrated into 111 pleiotropic unique QTL by meta-analysis, 47 of which were relevant for seed yield. The complexity of the genetic architecture of yield was demonstrated, illustrating the pleiotropy, synthesis, variability, and plasticity of yield QTL. The idea of estimating indicator QTL for yield QTL and identifying potential candidate genes for yield provides an advance in methodology for complex traits.