GenoTypeMapper

GenoTypeMapper visualizes and compares genotypic data on genetic and physical maps to present genome organization at a physical scale and identify chromosomal introgressions in species with large genome assemblies such as bread and durum wheat and barley.

Key Features:

• Graphical presentation: Provides graphical illustration of genomic data on a physical scale to reveal genome organization and regions where genetic maps are distorted, including centromeres and telomeres.
• Comparison across scales: Compares genotypic data on both genetic and physical scales to enable direct cross-scale interpretation of marker positions.
• Allele-matching algorithm: Implements an allele-matching algorithm to compare offspring with parents within crossing schemes accommodating up to four parental genomes.
• Handling large data sets: Analyzes up to 500 individuals and datasets containing up to 50,000 markers, with example performance of a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers processed in under five seconds on modern computing hardware.
• Identification of chromosomal introgressions: Detects additional chromosomal introgressions to support pre-breeding decisions aimed at minimizing linkage drag and managing desirable and undesirable traits.

Scientific Applications:

• Plant breeding and genetics: Analysis of near-isogenic lines (NILs) and QTL regions to map introgressions and their phenotypic effects.
• Case study—wild emmer wheat QTLs: Applied to NILs carrying QTL regions for drought stress tolerance from wild emmer wheat on chromosomes 2BS and 7AS to identify introgressions associated with increased drought tolerance and delayed heading time.
• Pre-breeding marker selection: Supports selection of molecular markers for breeding by comparing genetic and physical map positions and identifying introgressed segments.

Methodology:

Analyzes genotypic data from offspring and parents within crossing schemes using an allele-matching algorithm to compare genetic and physical maps and identify chromosomal introgressions and suitable molecular markers.