Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact

Abstract

Background and Aims 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 therefore set out to look for such alleles in a diverse Urochloa spp and Megathyrsus maximus accessions from the genebank collection held at CIAT. Methods 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. Key results 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. Conclusions We demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production.

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits inUrochloa ruziziensis

“…Recent advances in omics approaches and computational methods for polyploid species have enabled the emergence of studies in important Urochloa breeding areas. These include genome assembly (Pessoa-Filho et al, 2019; Worthington et al, 2021), contaminant identification (Martins et al, 2021), transcriptomics (Vigna et al, 2016a; Salgado et al, 2017; Worthington et al, 2021; Jones et al, 2021; Hanley et al, 2021), linkage and QTL mapping (Vigna et al, 2016b; Thaikua et al, 2016; Ferreira et al, 2016; Worthington et al, 2016; Worthington et al, 2019; Worthington et al, 2021), GWAS (Matias et al, 2019b), and GS/GP (Matias et al, 2019a; Aono et al, 2022). Even with the recent progress, there are no studies employing integrative methodologies in the genus.…”

“…Previous RNA-Seq data of 11 genotypes of U. ruziziensis were used to assess gene expression (Hanley et al, 2021; NCBI BioProject PRJNA513453). Raw data were quality-trimmed using Trimmomatic v0.39 (Bolger, Lohse & Usadel, 2014).…”

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis

“…Recent advances in omics approaches and computational methods for polyploid species have enabled the emergence of studies in important Urochloa breeding areas. These include genome assembly ( Pessoa-Filho et al., 2019 ; Worthington et al., 2021 ), contaminant identification ( Martins et al., 2021 ), transcriptomics ( Vigna et al., 2016a ; Salgado et al., 2017 ; Hanley et al., 2021 ; Jones et al., 2021 ; Worthington et al., 2021 ), linkage and QTL mapping ( Ferreira et al., 2016 ; Thaikua et al., 2016 ; Vigna et al., 2016b ; Worthington et al., 2016 ; Worthington et al., 2019 ; Worthington et al., 2021 ), GWAS ( Matias et al., 2019b ), and GS/GP ( Matias et al., 2019a ; Aono et al., 2022 ). Even with the recent progress, there are no studies employing integrative methodologies in the genus.…”

“…Previous RNA-Seq data of 11 genotypes of U. ruziziensis were used to assess gene expression ( Hanley et al., 2021 ; NCBI BioProject PRJNA513453). Raw data were quality-trimmed using Trimmomatic v0.39 ( Bolger et al., 2014 ).…”

Genome-editing opportunities to enhance cattle productivity in the tropics

“…Also in elephant grass, 39 markers were associated with eight feed quality traits, including acid detergent lignin and in vitro organic matter digestibility (Muktar et al 2022). In U. ruziziensis, three genes associated with cell wall components were found to be highly confident loss-of-function alleles that may confer increased digestibility (Hanley et al 2021). After confirming the role of such genes, GnEd may target them to improve the digestibility of tropical forage grasses.…”