Relationships between differential gene expression and heterosis in cotton hybrids developed from the foundation parent CRI-12 and its pedigree-derived lines.

CRI-12, an Upland cotton variety with high yield, elite fiber quality and disease resistance, is further characterized by its high heritability, combining ability and genetic stability. CRI-12 and its pedigree-derived lines were used to develop increased heterosis cotton hybrids, including CRI-28, CRI-29, XZM 2 and Jimian18. CRI-12 was chosen as the cotton foundation parent and analyzed by gene differential expressions between hybrids and their corresponding parents at seedling, squaring and flowering stages. The following approaches were considered the most viable candidates to elucidate the molecular basis of CRI-12: cDNA-amplified fragment length polymorphisms (cDNA-AFLPs), gene differential expression ratios, and vegetative growth heterosis and yield heterosis for correlation analysis. The results indicated that CRI-12 plays a predominant role in vegetative heterosis in CRI-28, CRI-29 and Jimian18 hybrids at the seedling and squaring stages; the percentage of dominant expression in single parents was greater than other patterns; downregulated expression in single parents was higher than upregulated expression in hybrids, and downregulated expression in hybrids was the lowest of the four patterns in the three growth stage cumulative totals. The gene differential expression ratio of hybrids and parents varied for the three growth stages, suggesting gene differential expression changes over time. Further analysis of differential gene expression ratios, vegetative growth and yield heterosis correlation revealed upregulated expression in hybrids were correlated with vegetative heterosis at the seedling and squaring stages, which play an important role in yield heterosis at the flowering stage. Downregulated expression in the maternal parent (CRI-12 and its pedigree-derived lines) suggested benefits in vegetative heterosis at the squaring stage, but a possible hybrid yield decrease at the flowering stage. These results provided evidence that CRI-12 and its pedigree-derived lines express genes integral for heterosis in CRI-28, CRI-29 and Jimian18.