Selection is practically ubiquitous during marker-QTL linkage analysis with an experimental population.
They were subjected to preliminary linkage analysis with 83 DNA markers distributed on the whole rice genome (for details, see Materials and methods).
For detecting the precise location of the target QTL, a total of 95 F2 plants were subjected to linkage analysis with 4 and 6 SSR markers on the target regions of chromosomes 1 and 3, respectively (McCouch et al. [2002]).
The genes of milk proteins and hormones are excellent candidate genes for linkage analysis with quantitative trait loci (QTL) because of their biological significance on the quantitative traits of interest.
The first round of linkage analysis with 750 viable F2 plants revealed that there were 64 and 37 recombinants, respectively, at RM487 and RM16 loci on the centromere side, 35 and 22 distinct recombinants, respectively, at RM168 and RM55 loci on the telomere side, indicating that the four candidate markers were indeed linkage markers with the target Pi gene (Fig. 2a).
In each mapping population, six typical weak plants and six typical normal plants were selected and subjected to preliminary linkage analysis with DNA markers, with the result that the linkage of HWA1 and HWA2 with RM5349 (McCouch et al. 2002) and RM224 (Chen et al. 1997) was visible on the long arm of chromosome 11.
Six typical weak plants and six typical normal plants that had been selected from the three-way cross population were subjected to preliminary linkage analysis with 84 DNA markers distributed throughout the rice genome (see Materials and methods), indicating that HWA2 was also linked with RM5349 and RM224.
Several studies have employed linkage analysis with QTL mapping to identify genomic regions regulating EAE in rats [52], [53], [54], [55], [56].
We performed multipoint linkage analysis with dense marker coverage over all autosomes: nearly 4000 unlinked SNPs at an average distance of 1 cM.
The markers with more than three missing genotype data were excluded, and the remaining marker data were used in linkage analysis with JoinMap program version 3.0 [24].
In linkage analysis with dense SNP maps particular attention must be paid to the LD between SNPs, because it can be responsible for a bias.
