Genotyping strategies for plant and animal breeding range from low-throughput molecular markers, printed SNP arrays, and short-read sequencing. PacBio HiFi long-reads have traditionally been cost prohibitive for genotyping given the combined challenges of high-throughput sample preparation, per-cell multiplexing, and downstream analytics. Here we demonstrate highly multiplex pooling of HiFi libraries for several plant breeding programs - hemp, blueberry, and peanut - and the value proposition of long-read genotyping at lower sequencing coverages to accelerate plant and animal breeding with more than 50% increases in variant calls.