Genotyping of Single Nucleotide Polymorphisms (SNP) in photosynthetic genes of Sorghum bicolor

Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, usually coupled with excessive light, and that greatly affects the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for eight photosynthesis and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28°C/24°C), cold (15°C/15°C) and recovery (28°C/24°C). Cold stress significantly reduced the photosynthetic capacity of sorghum plants and a total of 204 genomic regions were discovered associated with at least one trait in a particular treatment or in the time integrated response to cold. If no GBS markers were available for the targeted candidate genes, new SNPs were developed and genotyped using a SNPtype™ Assay (Fluidigm) on the Fluidigm BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm. 98 SNPtype™ Assay were designed to genotype 24 photosynthesis-related genes in 359 diverse sorghum accessions. 82 SNPs were finally genotyped in all accessions using BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm.