MVQTLCIM

MVQTLCIM implements a multivariate extension of composite interval mapping (CIM) to map quantitative trait loci (QTL) in outbred full-sib forest hybrid F1 populations, accommodating non-fixed linkage phase and segregation patterns and enabling analysis of multiple or longitudinal traits.

Key Features:

• Multivariate Trait Analysis: Handles multiple and longitudinal traits for QTL analysis across time points or trait dimensions.
• Adaptation to Outbred Populations: Models diverse segregation types and non-fixed linkage phases characteristic of outbred full-sib F1 populations.
• Takeuchi's Information Criterion (TIC): Uses TIC to discriminate among different QTL segregation types.
• Parallel Computing for Permutation Tests: Supports parallel permutation testing to assess significance of QTL signals.
• Flexible Parameter Options: Provides configurable parameters to tailor analysis settings.

Scientific Applications:

• Forest tree genetics: QTL mapping in forest tree species using outbred full-sib hybrid populations.
• Populus hybrid mapping: Application to hybrid populations of Populus deltoides and P. simonii, including identification of 12 QTLs for tree height across six time points.
• Integration with high-density linkage maps: Applied in studies using next-generation sequencing technologies to construct high-density genetic linkage maps for QTL discovery.

Methodology:

Implements a multivariate extension of composite interval mapping (CIM), employs Takeuchi's Information Criterion (TIC) to distinguish QTL segregation types, and conducts permutation tests using parallel computing.