Comparisons On Properties Of Marker Linkage And Qtl Mapping Between Two Methods Of Recombinant Inbred Line Development

Four global algorithms maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation SER (SER) were used to compare the marker ordering efficiencies for giving correct linkage groups for doubled haploid (DH) population. The Monte Carlo simulation results indicated the marker ordering powers for five methods were almost identical. High correlation coefficients of greater than 0.99 between grouping power and ordering power indicated that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power.Since the SER approach provided the advantages of fast speed without losing ordering power, this approach was used for more detailed simulations. For more generality, multiple linkage groups were employed, and in addition, population size, linkage cutoff criterion, marker spacing pattern (evenly or unevenly), and marker spacing distance (closely or loosely) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, large population size could provide higher grouping power than small population size, closely linked loci could provide higher grouping power than that for loosely-linked loci for both evenly and unevenly-spaced loci. Appropriate cutoff criterion range for achieving peak grouping power was different for different population sizes and marker spacing distances. For a given population size, a wider cutoff criterion range was applicable for closely linked loci than for loosely linked loci. On the other hand, for given marker spacing distance, large populations could utilize wider appropriate cutoff criterion range than small population size, however, combining all situations in this study, common appropriate cutoff criterion ranging from 50~60cM was determined. Closely linked loci may result in high grouping power but may not show higher ordering power, especially if population size is small. These closely linked loci may cause inverted loci order due to sampling error.Two types of recombinant inbred (RI) populations, one developed by bulk selfing and individual selection (bulk-based) method and the other by the traditional single seed descent (SSD) method, were used to compare the linkage mapping properties by the SER approach. These comparisons were also based on various population sizes (orfamily number, and line number per family), marker spacing patterns, and cutoff criterion. Monte Carlo simulations indicated that the grouping power and ordering power were commonly influenced by population size, marker spacing pattern, and cutoff criterion for both SSD RI population and bulk-based RI population. In addition, cutoff criterion also played an important role in linkage mapping. The cutoff criterion range could be different for obtaining high grouping power and, correspondingly, ordering power for different population sizes and different marker spacing patterns. Wider range of cutoff criterion could be used for larger population size or closely linked loci than for small population size or loosely linked loci. The simulation results also indicated that the grouping power and ordering power were generally higher for SSD RI populations than those for bulk-based RI populations for a given population size and marker spacing patterns. Additionally, narrower cutoff criterion range could be used to achieve peak grouping power and ordering power for bulk-based RI lines. Increasing the number of lines from each family while decreasing family number not only resulted in lower mapping power, but also lowered the cutoff criterion range for better mapping power. However population with 150 RI lines or above (75 families and 2 lines each family) provided acceptable genetic variation for marker mapping for different marker spacing patterns. A minimum number of 75 F2 -derived families...