Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
G3 (Bethesda). 2021 Sep 6;11(9). doi: 10.1093/g3journal/jkab232.
The sustainability of many crops is hindered by the lack of genomic resources and a poor understanding of natural genetic diversity. Particularly, application of modern breeding requires high-density linkage maps that are integrated into a highly contiguous reference genome. Here, we present a rapid method for deriving haplotypes and developing linkage maps, and its application to Mentha suaveolens, one of the diploid progenitors of cultivated mints. Using sequence-capture via DNA hybridization to target single nucleotide polymorphisms (SNPs), we successfully genotyped ∼5000 SNPs within the genome of >400 individuals derived from a self cross. After stringent quality control, and identification of nonredundant SNPs, 1919 informative SNPs were retained for linkage map construction. The resulting linkage map defined a total genetic space of 942.17 cM divided among 12 linkage groups, ranging from 56.32 to 122.61 cM in length. The linkage map is in good agreement with pseudomolecules from our preliminary genome assembly, proving this resource effective for the correction and validation of the reference genome. We discuss the advantages of this method for the rapid creation of linkage maps.
许多作物的可持续性受到基因组资源的缺乏和对自然遗传多样性认识不足的阻碍。特别是，现代育种的应用需要高密度的连锁图谱，这些图谱整合到一个高度连续的参考基因组中。在这里，我们提出了一种快速衍生单倍型和构建连锁图谱的方法，并将其应用于薄荷属植物中的二倍体祖先之一——留兰香。我们使用通过 DNA 杂交靶向单核苷酸多态性 (SNP) 的序列捕获，成功地对来自自交的 400 多个个体的基因组中的约 5000 个 SNP 进行了基因分型。经过严格的质量控制和非冗余 SNP 的鉴定，保留了 1919 个信息性 SNP 用于连锁图谱构建。由此产生的连锁图谱定义了一个总遗传空间，分为 12 个连锁群，长度从 56.32 到 122.61 cM。连锁图谱与我们初步基因组组装的拟南芥假分子很好地吻合，证明了该资源可有效用于参考基因组的校正和验证。我们讨论了这种方法在快速构建连锁图谱方面的优势。
