染色体水平单倍型解析的基因组组装为多花黑麦草(Lolium multiflorum Lam.)高度杂合的基因组提供了见解。

Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).

作者信息

Chen Yutang, Kiesbauer Jenny, Copetti Dario, Frei Daniel, Frey Jürg E, Grieder Christoph, Kölliker Roland, Studer Bruno

机构信息

Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.

Fodder Plant Breeding, Division of Plant Breeding, Agroscope, Zurich, Switzerland.

出版信息

Plant Genome. 2025 Sep;18(3):e70079. doi: 10.1002/tpg2.70079.

Abstract

Italian ryegrass (Lolium multiflorum Lam.) is an important forage grass, providing a major source of feed for ruminants in temperate regions. Due to its highly heterozygous and repeat-rich genome, high-quality chromosome-level genome assemblies are scarce for Italian ryegrass. Here, we sequenced the genome of a genotype from the Italian ryegrass cultivar 'Rabiosa' (hereafter referred to as Rabiosa), and we obtained Oxford Nanopore Technologies long reads (∼60-fold coverage), Illumina short reads (∼85-fold coverage), and high-throughput chromosome conformation capture data (∼60-fold coverage). With Rabiosa as one of the parents, we constructed an F population consisting of 304 individuals, which were genotyped by reduced representation sequencing for linkage map construction and quantitative trait locus (QTL) analysis. Using whole-genome sequencing data of Rabiosa and the genetic linkage map, we first generated a chromosome-level unphased haploid assembly (scaffold N50 of 338.75 Mb, total Benchmarking Universal Single-Copy Orthologs [BUSCO] score of 94.60%). Then, based on the unphased assembly and a reference-based phasing approach, we generated a chromosome-level haplotype-resolved assembly containing both haplotypes (scaffold N50 of ∼250 Mb and total BUSCO score of ∼90% for each haplome). Between the two haplotypes of Rabiosa, we observed a highly collinear gene order at the chromosome level and a high sequence variation at the local level. With a graph-based reference built from the unphased and the haplotype-resolved assemblies of Rabiosa, we conducted a QTL analysis, and two QTL significantly associated with stem rust resistance were detected. The genome assemblies of Rabiosa will serve as invaluable genomic resources to facilitate genomic applications in forage grass research and breeding.

摘要

意大利黑麦草(Lolium multiflorum Lam.)是一种重要的饲草,为温带地区的反刍动物提供了主要的饲料来源。由于其基因组高度杂合且富含重复序列,高质量的染色体水平基因组组装对于意大利黑麦草来说较为稀缺。在此,我们对意大利黑麦草品种‘Rabiosa’(以下简称Rabiosa)的一个基因型进行了基因组测序,获得了牛津纳米孔技术的长读长序列(约60倍覆盖度)、Illumina短读长序列(约85倍覆盖度)以及高通量染色体构象捕获数据(约60倍覆盖度)。以Rabiosa作为亲本之一,我们构建了一个由304个个体组成的F群体,并通过简化基因组测序对其进行基因分型,用于构建连锁图谱和进行数量性状位点(QTL)分析。利用Rabiosa的全基因组测序数据和遗传连锁图谱,我们首先生成了一个染色体水平的未分型单倍体组装(支架N50为338.75 Mb,基准通用单拷贝直系同源基因[BUSCO]总分94.60%)。然后,基于该未分型组装和基于参考的分型方法,我们生成了一个包含两个单倍型的染色体水平单倍型解析组装(每个单倍型的支架N50约为250 Mb,BUSCO总分约为90%)。在Rabiosa的两个单倍型之间,我们在染色体水平观察到高度共线性的基因顺序,在局部水平观察到较高的序列变异。利用基于Rabiosa的未分型和单倍型解析组装构建的基于图的参考基因组,我们进行了QTL分析,检测到两个与秆锈病抗性显著相关的QTL。Rabiosa的基因组组装将成为宝贵的基因组资源,有助于促进饲草研究和育种中的基因组应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a81a/12376112/0044d046862d/TPG2-18-e70079-g004.jpg

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