HTP

HTP identifies haplotype-tag polymorphisms and provides marker datasets, a searchable database, analysis algorithms, and visualization to support high-throughput genotyping, pedigree reconstruction, genetic mapping, and heterotic-pattern prediction in maize.

Key Features:

• Integration of Maize6H-60K array data: Incorporates Maize6H-60K array genotype data from 3,587 maize inbred lines and information from 6,375 blocks derived from a recombination block map.
• Highly polymorphic HTP markers: Identifies 6,163 highly polymorphic haplotype-tag polymorphisms (HTPs) evenly distributed across the maize genome via stringent filtering criteria.
• HTPtools algorithms: Implements seven algorithms including chain Bayes probability and heterotic-pattern prediction for pedigree reconstruction and heterotic-pattern inference.
• BCplot visualization engine: Provides the BCplot plotting engine for rapid visualization of background information across multiple backcross groups.
• HTP database (HTPdb): Maintains a database covering whole genomes of 3,587 maize inbred lines with 172,921 non-redundant HTP allelic variations.
• Multiplex molecular markers: Uses multiplex molecular markers to enable efficient genotyping of large breeding populations.

Scientific Applications:

• High-throughput genotyping: Generates marker data for large-scale genotyping in maize breeding populations.
• Genetic mapping: Supports genome-wide genetic mapping using HTP markers distributed across the maize genome.
• Germplasm resource analysis: Enables analysis of germplasm diversity and allelic variation across 3,587 maize inbred lines.
• Pedigree reconstruction: Reconstructs complex pedigrees using HTPtools algorithms such as chain Bayes probability.
• Heterotic-pattern prediction: Predicts maize heterotic patterns using dedicated HTPtools algorithms.
• Breeding decision support: Informs selection and background analysis in backcross and breeding programs via BCplot visualization and HTPdb allele data.

Methodology:

Integrates Maize6H-60K array genotype data with a 6,375-block recombination map; applies stringent filtering to identify 6,163 HTPs; constructs HTPdb with 172,921 non-redundant allelic variations from 3,587 inbred lines; implements seven HTPtools algorithms (including chain Bayes probability and heterotic-pattern prediction) for pedigree reconstruction and heterotic-pattern prediction; uses BCplot for background visualization and multiplex molecular markers for genotyping.