Allele Mining in Diverse Accessions ofUrochloaandMegathyrsusspp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact

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.HighlightWe found gene variants in a collection of tropical grasses that could help reduce environmental impact of cattle production.

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

“…in Aster amellus ), no mixing of ploidies is seen even in contact zones ( Mandáková and Münzbergová, 2006 ). Deliberate or accidental roadside or forage introductions (likely to be over-represented in the genebank material sampled here) may introduce different ploidies, although our accessions are genetically different ( Hanley et al , 2020 ; Higgins et al , 2021 ). Polyploids are often argued to have a competitive advantage over diploids ( Alix et al , 2017 ) and production of polyploid seeds and individuals by diploids is widespread, although subsequent establishment of whole polyploid populations and their expansion can be hindered by insufficient seed production ( Levin, 2021 ).…”

“…These activities built a global grass collection with 700 accessions of Urochloa species representing a highly diverse gene pool for breeding and systematic studies ( Keller-Grein et al , 1996 ). Valuable traits of Urochloa include biomass yield, physiological tolerance to low-fertility acid soils of the tropics ( Arroyave et al , 2011 ), digestibility and energy content ( Hanley et al , 2020 ), insect tolerance (particularly to neotropical spittlebugs; Miles et al , 2006 ) and disease resistance ( Valério et al , 1996 ; Alvarez et al , 2014 ; Hernandez et al , 2017 ). However, undesirable traits are also present, such as allelopathy (leaving bare soil; Kato-Noguchi et al , 2014 ), cold-susceptibility (hybrid Mulato II: Pizarro et al , 2013 ) and invasiveness ( Durigan et al , 2007 in the Brazilian Cerrado; Urochloa panicoides is on the US Federal Noxious Weed List https://www.aphis.usda.gov/plant_health/plant_pest_info/weeds/downloads/weedlist.pdf ; accessed on 16 February 2021).…”

The five Urochloa spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

“…Samples were ground in liquid nitrogen and lyophilised. Total RNA was extracted as described in Hanley et al (2020) with the difference that prior to DNAse treatment the pellets were dried in a rotary evaporator (Eppendorf, USA) and stored at room temperature. Another seven accessions were obtained from the United States Department of Agriculture (USDA, GA, USA) as seeds.…”

“…In another recent work (Worthington et al, 2021), we have made available a genome assembly and gene annotation of a diploid accession of U. ruziziensis (GCA_003016355), which has allowed a greater use of genomics to characterise these materials. For example, we identified loss-of-function (LOF) genes related to forage quality and environmental impact using allele mining (Hanley et al, 2020).…”

Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

“…In exploiting biodiversity in breeding, improvements in yield and nutritional quality of forages can be achieved by identifying genes increasing the digestibility of plant cell walls and the protein and lipid content in vegetative tissues, and increasing biomass production [ 4 ]. By introduction to plant breeding programmes, genetic improvement of forage lines, recurrent genetic selection of plants showing useful traits, and subsequent hybridizations and back-crossings [ 5 , 6 ], create more diverse agroecosystems resilient to climate and environmental changes [ 7 ]. The DNA amount measurement for ploidy and genome size estimation, and the characterization of genome composition are required for effective use of diploids and polyploids in breeding programs, as well as for research purposes [ 8 , 9 ].…”