Effects of SNP or haplotypes and their distribution among different variety types

We investigated the significance of effects on related traits of alleles of each pleiotropic SNP (pSNP; that is, a SNP simultaneously associated with two different traits), haplotypes of pQTLs, and interactive genes (iGenes, the genes that simultaneously control different traits of interest by interaction among those genes) by multiple comparison analysis of GLM in SPSS (version 19.0). Alleles with significantly higher effect on some traits such as HD were denoted as increased effect alleles for that trait, and those with significantly lower effect were denoted as decreased effect alleles. For pSNPs or haplotypes, for example, pleiotropy between HD and GNP, we classified their effects into four types: the same direction (SD) with both increased effect on HD and GNP, or SD with both decreased effect on HD and GNP, the opposite direction (OD) with increased effect on HD but decreased effect on GNP, or OD with decreased effect on HD but increased effect on GNP. We then calculated the distribution of alleles with different kinds of effects among four types of varieties, including indica landraces, improved indica varieties, japonica landraces, and improved japonica varieties.