Figure 4. Pattern of linkage decay. Red dots highlight the SNP pairs that are significantly associated with plant height and seed weight.
Linkage disequilibrium decay analysis showed that genes in genomic block within 1 Mb are likely linked in inheritance (if anr 2 of 0.02 and below suggesting random segregation). Of the 23 immediate neighbouring SNPs pairs with one SNP being associated with plant height, and other with seeds weight, 12 pairs were within the distance of 5 Mb in the same chromosome, a further seven pairs within 5 Mb of linkage block (Figure 4), disproportional higher than expected random distribution on the chromosome (Chi-squarep < 0.05).
Common factor analysis on the pleiotropic effect of SNPs on both traits revealed as a general trend of positive correlation of SNPs effects on both traits (r = 0.138, p = 0.0001) (Fig. 2C). Further outlier analysis revealed 20 SNPs with significant pleiotropic effects in both plant height and seed size. Their effect on each trait are significantly correlated with r = 0.926 and p =0.0001. (Figure 5). Noticeably, three SNPs, among the 20 found to have pleiotropic effects through common factor analysis, were associated with both trait as revealed in the above GWAS analysis. The SNPs that were identified as being associated with both traits in GWAS analysis and common factor analysis, the variant description and the gene where the SNP is located were shown in Table 1.
Current literature links the responsible SNPs to several genes, including an Hsp70-Hsp90 organising protein gene, an Expansin B3 gene, an Elongation factor G gene, and a Vacuolar protein sorting-associated protein 18 gene (Table 1).