Allele Mining in Diverse Accessions of Urochloa and Megathyrsus spp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact

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Hanley, S. J., Pellny, T. K., De Vega, J. J., Castiblanco, V., Arango, J., Eastmond, P. J., Heslop-Harrison, J. S. and Mitchell, R. A. C. 2021. Allele Mining in Diverse Accessions of Urochloa and Megathyrsus spp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact. Annals of Botany. https://doi.org/10.1093/aob/mcab101

AuthorsHanley, S. J., Pellny, T. K., De Vega, J. J., Castiblanco, V., Arango, J., Eastmond, P. J., Heslop-Harrison, J. S. and Mitchell, R. A. C.
Abstract

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.

KeywordsUrochloa brizantha; Urochloa decumbens; Urochloa humidicola; Urochloa ruziziensis,; Megathyrsus maximum; cell wall digestibility; ecotilling; reverse genetics; forage energy content
Year of Publication2021
JournalAnnals of Botany
Digital Object Identifier (DOI)https://doi.org/10.1093/aob/mcab101
Open accessPublished as green open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codes5633
BB/R022828/1
Output statusPublished
Publication dates
Online28 Jul 2021
PublisherOxford University Press (OUP)
ISSN0305-7364

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Under embargo until 28 Jul 2022

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