Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium and chromosomal rearrangements across chromosomes, sexes and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultra-dense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (~6 markers/cM) linkag...高密度遗传连锁图谱（high-density linkage maps）是基因组生物学与进化遗传学领域的重要工具，可量化不同染色体、性别及种群间的重组程度、连锁不平衡水平与染色体重排事件。其是验证与优化从头基因组组装的最优手段之一，且组装错误的识别效率会随标记密度提升而增强。然而受限于现有软件的技术瓶颈，构建高密度遗传连锁图谱仍面临诸多挑战。本文介绍Lep-MAP2，一款用于构建超高密度全基因组遗传连锁图谱的软件。该软件可适配多种家系结构，并可通过考量无交叉减数分裂（achiasmatic meiosis）过程提升遗传连锁图谱的构建精度。模拟实验结果表明，Lep-MAP2在计算效率与作图精度上均优于当前已有的其他连锁图谱构建软件。当将其应用于两个九刺鱼（Pungitius pungitius）种群间的两个大型F2代重组杂交群体时，该软件可生成两张高密度（约6个标记/厘摩）的连锁...