Highly polygenic control of photosynthetic responses to nighttime temperature in Arabidopsis studied by genomic prediction

Rising nighttime temperature (T _night ) can reduce crop yields, while low T _night may restrict plant growth and development. Despite these quantifiable effects of T _night , the genetic basis underlying plant responses to T _night remains unclear. We investigated natural variation in long-term response of effective photosynthetic efficiency (F _q ’/F _m ’) to T _night among Arabidopsis accessions.

Genome-wide association study (GWAS) was conducted for F _q ’/F _m ’ of the accessions grown under 15°C or 20°C T _night . The associated single nucleotide polymorphisms (SNPs) were identified and incorporated in genomic prediction (GP) models to assess the improvement of prediction accuracy. The predictions were experimentally validated in an independent, genetically diverse population.

GWAS revealed highly polygenic architecture of F _q ’/F _m ’, with associated SNPs varying across T _night conditions and measurement days. Notably, 15°C T _night stabilized the contributions of a subset of associated SNPs, whereas 20°C T _night enhanced day-to-day variations in SNP-trait associations. The GWAS-derived SNPs significantly improved the prediction accuracy of GP models, indicating their collective influence. The validation experiment confirmed the identification of low-F _q ’/F _m ’ accessions in 15°C T _night .

The results uncover the genetic underpinnings of long-term F _q ’/F _m ’ response to cool vs warm nights and establish a framework for leveraging GWAS and GP to explore complex traits, such as photosynthesis, toward breeding climate-resilient crops.