Utilizing "Connected Populations" for QTL Discovery

Bi-parental populations have been used to identify quantitative trait loci (QTL) using a combination of genotypic and phenotypic information taken from carefully constructed populations.   This population structure requires comparatively low allelic richness, but produces a low resolution map.  Association mapping may also be utilized to identify QTL.  These populations generally contain diverse germplasm, which can increase applicability to relevant genetic materials.  This method results in high resolution linkage maps and the ability to detect rare alleles.  Relationships between these genetic materials must be known to avoid false QTL detection.  The utilization of ‘connected populations’ integrates the benefits of both bi-parental and association mapping populations. Connected populations are constructed using common parents to create related individuals for use in QTL mapping and gene discovery.  This creates inherent replication with the expression of alleles in multiple backgrounds, which increases the statistical power of QTL detection and additionally enables the testing of epistatic interactions.  Additionally, the use of multiple parents increases the probability of QTL polymorphism.  QTL congruency in various populations has been low to moderate using traditional mapping population structures.  Connected populations have the ability to detect QTL in multiple populations and allow global comparison of alleles, enabling QTL associated markers to be utilized in a broader range of genetic materials.  Typically, use of connected populations facilitates detection of nearly all QTL detected in single population analysis as well as many QTL not detected in bi-parental populations.  Furthermore, higher levels of explained variance have been detected and QTL are defined with greater precision, resulting in reduced confidence intervals for QTL position.  Increased genetic gain utilizing marker assisted selection (MAS) is realized in multiple-parent design over bi-parental populations, which multiplies across additional generations of selection.  The construction of connected populations also ensures confidence in genetic relationships, which is an advantage over association mapping populations where hidden population structure can induce false positives.  Examples of different population designs for connected population structures will be examined.