Rice Genetics IV - IRRI books - International Rice Research Institute

Table 1 continued.Trait QTL a Flanking markers LOD Var (%) A f D ILgp5 G193-RZ649 2.3 8.6 –0.2 8.8 3gp6b R1014-G200 2.5 5.5 5.0 0.9 0gp7 C1023-R1440 4.7 9.5 –5.2 6.5 2gp11 C950-G389b 3.1 5.9 –0.7 7.3 0Grain weight (g) gw1 R753-C161 2.6 9.7 0.5 1.3 0gw3a C944-C746 9.5 16.8 –1.4 0.2 3gw3b R1966-G144 11.4 22.5 –1.7 –0.7 9gw5 RG360-R1674 12.9 24.1 1.6 –0.3 0gw6b R565-R902 4.7 8.6 1.0 0.3 5gw7 RG128-C1023 5.2 17.7 –1.4 –0.4 9gw8 C1121-RG333 2.7 6.7 0.7 –0.7 5gw9 R2638-RG570 4.0 8.5 1.1 –0.4 1gw11 RM4-RG98 3.5 8.6 –0.9 0.6 0aNumbers following the two letters represent the chromosomal locations of the QTLs. Var = variationexplained by each QTL, A = additive effect, D = dominance effect, IL = number of loci with which the QTLinteracts. b, c, d, e Pairs of interacting loci within a trait. f Positive values of the additive effect indicate thatalleles from Zhenshan 97 increase the trait scores and negative values indicate that alleles from Minghui63 increase the score.Correlations between overall heterozygosity of the F 2 individuals and the F 3 familymeans were very small for all four traits (data not shown). They were significant atP ≤ 0.05 only for grain weight (correlation coefficients 0.17 in 1994 and 0.16 in 1995).Thus, the overall heterozygosity made a very small contribution to trait expression.Digenic interactions between loci in the entire genomeThe entire genome was searched for digenic interactions for each trait with two-wayanalyses of variance using all possible two-locus combinations of the marker genotypes.The interaction, often referred to as epistasis, was further partitioned into fourterms each specified by a single degree of freedom: additive (first locus) × additive(second locus) (AA), additive × dominance (AD), dominance × additive (DA), anddominance × dominance (DD). Table 2 presents the number of two-locus combinationsshowing significant (P < 0.01) interactions resulting from testing all possibletwo-locus combinations and also the number of various types of interactions determinedby orthogonal contrast tests. Only data sets formed of two codominant lociwith each class of the marker genotypes containing five or more individuals wereincluded in the calculation, resulting in 7,585 tests for 1994 and 7,681 for 1995. Withα = 0.01 for individual tests, the 99% confidence intervals for the expected numbersof spurious interactions (false positive) would be 75.85 ± 20.02 for 1994 and 76.81 ±20.14 for 1995. It is clear from Table 2 that the number of interactions detected in bothyears for all the traits far exceeded expectations based on spurious interactions, indicatingthe existence of real interactions in the genome of this population.Significant interactions were detected simultaneously in both years for many of thetwo-locus combinations (Table 2). These interactions, referred to as common interactionsfor ease of description, can be taken as the minimum of statistically significant176 Qifa Zhang et al