Identification of loci and candidate genes related to SPAD via SNP- and InDel-GWAS

Chlorophyll is an essential component for capturing light energy to drive photosynthesis, and its content is crucial for leaf photosynthetic capacity and crop yield. SPAD, as a chlorophyll content-related parameter, has been widely applied. In this study, GWAS was performed on SPAD at the R2 stage of 219 accessions using 5,410,112 SNPs and 634,106 InDels, identifying 511 SNPs, 67 InDels and a candidate gene GmPMI1 associated with SPAD. GmPMI1 divided the natural population into three haplotypes, with Hap2 exhibiting higher SPAD values. The SNP in its promoter region (Chr08-3973347) may account for this phenomenon. This gene is regulated by the MYB transcription factor Glyma.05g013000 and functions in the ABA signaling pathway. Its effect on SPAD is likely mediated through the regulation of chloroplast movement rather than chlorophyll content. While most researchers consider "optimizing photosynthesis by regulating chlorophyll content to improve crop yield" as a breeding objective, maximizing photosynthetic potential under different environmental conditions by modulating chloroplast movement provides an alternative viable strategy for yield enhancement.

The online version contains supplementary material available at 10.1007/s11032-026-01662-9.