Genomics and Molecular Breeding

Abstract

Scientific developments over the last two decades have led to a new phase of genetics—the plant genomics. This is the application of a wide range of novel methods and technologies for analysing the structure of the genome and its interaction with cell metabolism for protein synthesis and the use of this knowledge for better understanding of the functioning of plants or improving them into new varieties. Plant genomes are more complex than other eukaryotic genomes, and analysis reveals many evolutionary flips and turns of the DNA sequences over time. One spectacular result achieved at the beginning of this century was the entire genomic DNA sequencing of Arabidopsis (The Arabidopsis Genome Initiative 2000) (see Bevan and Walsh 2005) and Oryza (rice—International Rice Genome Sequencing Project (IRGSP)) (Eckardt 2000; Jackson 2016), the main dicotyledon and monocotyledon plant models used due to their small genomes. Some recent powerful technologies are:

• (i) automatic DNA sequencing, where one machine can read two million base pairs a day (Egan et al. 2012);

• (ii) microarrays and DNA chips where tens of thousands of genes can be scanned for activity levels at the same time (Pflieger et al. 2001); and

• (iii) automated genoty** machines that can assay tens of thousands of DNA diagnostic points a day (Li et al. 2001).

In fact, it will soon be possible to monitor whole genomes by the use of DNA molecular genetic markers (MGMs) or analysis of gene expression on single chips. Two main fields must be distinguished: (i) MGMs, which are non-coding DNA fragments independent from the variation of the environment, and (ii) expressed genes. Genomic technologies were taken up by various research groups working with Hevea, in order to increase knowledge and also to identify new targets for breeding and/or complement genetic transformation and assist rubber breeders in various strategies. The group led by Huasun at the Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS) (in collaboration with Bei**g Institute of Genomics, Chinese Academy of Science), Danzhou, China (see Tang et al. 2016) and Centre for Chemical Biology, Universiti Sains Malaysia (Rahman et al. 2013) and the group led by Sithichoke Tangphatsornruang at the National Center for Genetic Engineering and Biotechnology, Bangkok, are the prominent schools working on Hevea genomics. Tun Abdul Razak Research Centre (TARRC) (Malaysian Rubber Board) and The Genome Analysis Centre (TGAC), Norwich Research Park, UK, are also actively participating in this research. The latest advancement was during 2013, when Rahman et al. reported the draft genome sequence of H. brasiliensis. The assembly spans to ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. This was refined by Lau et al. (2016).