PT - JOURNAL ARTICLE AU - SJ Hanley AU - TK Pellny AU - JJ de Vega AU - V Castiblanco AU - J Arango AU - PJ Eastmond AU - JS Heslop-Harrison AU - RAC Mitchell TI - Allele Mining in Diverse Accessions of <em>Urochloa</em> and <em>Megathyrsus</em> spp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact AID - 10.1101/2020.12.09.418087 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.12.09.418087 4099 - http://biorxiv.org/content/early/2020/12/09/2020.12.09.418087.short 4100 - http://biorxiv.org/content/early/2020/12/09/2020.12.09.418087.full AB - The C4 Urochloa spp (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease amount of land required per unit production and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We studied allelic diversity of 20 target genes (11 for digestibility, 9 for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNAseq and then bait-capture DNA-seq to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified 7 putative LOF alleles with high confidence, including ones in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme.Highlight We found gene variants in a collection of tropical grasses that could help reduce environmental impact of cattle production.