Multi-parental populations are becoming important genetic resources in plant breeding. GAPL (Genetic Analysis Software of Pure Line Populations) is freely-available public software, capable of building high-density genetic linkage maps and mapping quantitative trait loci (QTL) in pure line populations derived from four-way or eight-way crosses. Four functionalities are implemented in GAPL Version 1.2: (1) SNP, SNP genotypic data conversion; (2) BIN, binning of redundant markers; (3) PLM, map construction in multi-parental derived pure-line populations; (4) PLQ, gene detection in multi-parental pure-line populations. Three methods are available in QTL, i.e., (1) SMA: Single Marker Analysis; (2) IM: the conventional Interval Mapping; (3) ICIM: Inclusive Composite Interval Mapping.

What’s new in version 1.2?

1. SNP functionality was added for SNP genotypic data conversion.

2. Interface and algorithm of PLM functionality was improved.