Background and Aims The C4Urochloa species (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 the 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 diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT. Methods We studied allelic diversity of 20 target genes (11 for digestibility, nine 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 RNA sequencing and then bait capture DNA sequencing 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 seven putative LOF alleles with high confidence, including those 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.

中文翻译：

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在热带草的不同种质中挖掘等位基因以提高草料质量并减少对环境的影响

背景和目的 C4Urochloa 物种（同义词 Brachiaria）和 Megathyrsus maximus（同义词 Panicum maximum）在非洲和南美洲的热带农业系统的广大地区被用作牛的牧场。品种改良的一个关键目标是草料质量：提高消化率可以减少单位产量所需的土地数量，提高脂质含量可以减少牛的甲烷排放量。对于这些性状，已知基因靶标中的功能丧失 (LOF) 等位基因预计会改善它们，从而使等位基因挖掘的反向遗传学方法可行。因此，我们开始从 CIAT 的基因库收集的不同种质的 Urochloa 物种和 Megathyrsus maximus 中寻找这些等位基因。方法 我们研究了 20 个靶基因的等位基因多样性（11 个用于消化率，9 个用于脂质含量）在 104 个种质中选择来代表 U. brizantha、U. decumbens、U. humidicola、U. ruziziensis 和 M. maximum 的遗传多样性和倍性水平。我们使用 RNA 测序，然后使用诱饵捕获 DNA 测序来改进 U. ruziziensis 参考基因组中的基因模型，从而以高置信度分配多态性。主要结果 我们在所有基因和种质中发现了 953 个非同义多态性；在这些基因中，我们以高可信度鉴定了七个推定的 LOF 等位基因，包括存在于二倍体和四倍体种质中的非冗余 SDP1 和 BAHD01 基因中的那些。如果将这些 LOF 等位基因纳入育种计划，则可以分别提高脂质含量和消化率。结论 我们展示了一部小说，使用来自单一物种的参考基因组草图在不同种质中发现等位基因的有效方法。我们用它在一系列热带草中寻找基因变异，这有助于减少养牛对环境的影响。