| Summary: | C<sub>4</sub> photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C<sub>4</sub> photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C<sub>3</sub> and C<sub>4</sub> species have elucidated the genetic diversity underpinning the C<sub>4</sub> photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C<sub>4</sub> crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Here, we present the first genetic diversity survey of 8 known C<sub>4</sub> gene families in an important C<sub>4</sub> crop, <i>Sorghum bicolor</i> (L.) Moench, using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C<sub>4</sub> gene families varied more than 20-fold from the NADP-malate dehydrogenase (MDH) gene family (θπ = 0.2 × 10<sup>−3</sup>) to the pyruvate orthophosphate dikinase (PPDK) gene family (θπ = 5.21 × 10<sup>−3</sup>). Genetic diversity of C<sub>4</sub> genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C<sub>4</sub> photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C<sub>4</sub> PPDK and carbonic anhydrase (CA) genes, and balancing selection signals on C<sub>4</sub> PPDK-regulatory protein (RP) and phosphoenolpyruvate carboxylase (PEPC) genes. Allelic distribution of these C<sub>4</sub> genes was consistent with selection signals detected. A better understanding of the genetic diversity of C4 pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.
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