OcBSA: An NGS-based bulk segregant analysis tool for outcross populations

Abstract

Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F₁ outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F₁ populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F₁ populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F₁ population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F₁ population. Testing of OcBSA on 1800 simulated F₁ populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F₁ populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F₁ population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F₁ populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.

Keywords: BSA; F(1) population; QTL mapping; outcross; potato; self-incompatible.