Genetic structure and diversity of India hybrid tea

The most important evolutionary event in the success of commercial tea cultivation outside China in ~30 countries came about by the origin of India hybrid tea in India, derived from the extensive spontaneous hybridization that took place between the Assam type tea growing in the forest regions of Assam, North-East India and China type tea introduced from China in ~1875 to many regions of North-East India. The release of an enormous pool of vigorous and highly variable plants of India hybrid tea in North-East India was a significant step forward for the origin and evolution of tea as a highly successful crop plant. The 1,644 accessions and clones of India hybrid tea, representatives of known 15 morphotypes, were screened by 412 AFLP markers amplified by 7 AFLP primer pair combinations. All the 412 genetic loci were polymorphic across the 1,644 accessions and clones. The analysis was done with distance (PCoA and NJ) methods, and the STRUCTURE (Bayesian) model. Both PCoA and NJ analysis clustered 1,644 tea accessions and clones into six major groups with one group in each, constituted mostly by China hybrid, Assam China hybrid and Assam hybrid morphotypes, of distinct genetic identity. No group was exclusive for any particular morphotype. The accessions and clones belonging to morphotypes, Assam type, Assam hybrid, China hybrid and China Cambod were distributed in all the groups. It is the Assam type/Assam hybrid morphotypes which exhibit much broader genetic variability than in China type/China hybrid/Cambod type/Cambod hybrid morphotypes. The STRUCTURE analysis inferred 16 populations (K = 16), for which the greatest values of probability were obtained. Nine of the 16 clusters were constituted by the tea accessions and clones of ‘pure’ ancestry. The remaining clusters were of ‘mixed’ ancestry. This analysis provides evidence that the accessions and clones of the same morphotype are not always of same genetic ancestry structure. The tea accessions and clones obtained from outside North-East India shared the same groups (distance method) and clusters (STRUCTURE model) which were constituted by North-East India accessions. The present study also demonstrates very narrow genetic diversity in the commercial tea clones vis-à-vis the profound genetic diversity existing in the tea accessions. These clones were distributed in hardly two of the six groups in NJ tree. The identified 105 core accessions and clones, capturing 98% diversity, have their origin from almost all groups/subgroups of NJ tree.     

Alterations in inheritance pattern and level of cytosine DNA methylation,and their relationship with heterosis in rice

Novel hybrid-specific/heterotic gene expression patterns observed from expression studies suggest the need to characterize the underlying regulatory mechanism(s) to reveal the biological basis of heterosis in crop plants. To gain an insight into the molecular basis of heterosis in rice, we investigated the inheritance pattern and level of cytosine methylation, a major epigenetic regulatory mechanism, in the leaf tissue of an elite Indian rice hybrid KRH2 and its parents at three stages (15 day-old, 35 day-old seedling and flag leaf) and their correlation with heterosis using methylation-sensitive amplification polymorphism (MSAP) technique. In contrast to parents, the level of methylation was high during initial growth stages and reduced as the hybrid grew. Even though, a majority of cytosine methylation profiles were transmitted to hybrid at all stages, a considerable level (25.4%) of cytosine methylation pattern was observed to be novel in hybrid and some of these altered loci were identified to code for known/hypothetical proteins. It was also observed that demethylation events occurred more predominantly during early stages than hypermethylation while the frequency of demethylation events decreased in flag leaf with a remarkable increase in hypermethylation in the hybrid. These bi-directional events in methylation in KRH2 were validated in six hybrids with different levels of grain yield heterosis and the level of cytosine methylation in the hybrid was observed to be significantly correlated with heterosis.