Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Center for Plant Science Innovation, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
Sci Rep. 2018 Jul 4;8(1):10088. doi: 10.1038/s41598-018-28294-0.
F and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F and RIL populations. Genotype-Corrector is publicly available on GitHub at https://github.com/freemao/Genotype-Corrector .
F 和重组近交系 (RIL) 群体在植物遗传图谱研究中非常常用。虽然全基因组遗传标记，如单核苷酸多态性 (SNP)，可以通过多种方法轻松识别，但基因型的准确呼叫仍然具有挑战性，特别是对于杂合位点和由于每个个体的测序覆盖度低而导致的缺失数据。因此，我们开发了 Genotype-Corrector，这是一个可以纠正基因型呼叫并对缺失数据进行插补以提高遗传图谱准确性的程序。Genotype-Corrector 可应用于基于低覆盖度全基因组测序 (WGS) 或测序 (GBS) 相关技术的广泛的遗传图谱研究中。我们的结果表明，Genotype-Corrector 在应用于合成和真实基因型数据时都具有很高的准确性。与使用原始或仅插补的基因型呼叫相比，通过校正基因型数据构建的连锁群噪声更小，并且可以校正明显的扭曲。此外，Genotype-Corrector 在 F 和 RIL 群体中均优于流行的插补软件 LinkImpute 和 Beagle。Genotype-Corrector 可在 GitHub 上公开获得，网址为 https://github.com/freemao/Genotype-Corrector 。
