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Many Aspects of Genome Research

Many Aspects of Genome Research

By TA News Bureau:

In this final and concluding part of the interview with renowned plant breeder Dr Mallinath Priyadarshan, he talks about genomic research innovations to develop Hevea clones and the measures that should be in place to fight a potential leaf blight disasters. Author of Biology of Hevea Rubber published by Springer, he shares in this interview his research experience spanning over four decades. The first part of the interview appeared in the Feb-March 2018 issue of Tyre Asia

Development of Asian rubber plantations has come a long way since the set of 22 Hevea rubber seedlings originally collected from Brazil by Sir Henry Wickham arrived in Singapore Botanical Gardens in 1877 which became the gene repository of modern Hevea clones. What are the genomic research innovations that are going on in the region and what is their results/impact?

Sir Henry Wickham collected 70,000seedsfrom the RioTapajoz region of the Upper Amazon (Boim district) and transported the collection to Kew Botanic Gardens during June1876. Of the 2,899 seeds germinated, 1911were sent to the Botanic Gardens in Ceylon – now Sri Lanka –during1876. And 90 per cent of them survived at the Henarathgoda Botanical Gardens, one of the six botanical gardens in Sri Lanka. It is about 29 km from the country’s capital of Colombo.
DuringSeptember1877, 100 Hevea plants specified as ‘Cross material’ were also sent to Ceylon. In June 1877, 22seedlings not specified either as Wickham or Cross were sent from Kew to Singapore, which were distributed in Malaya and formed the prime source of 1000 seedlings tappable trees found by Ridley during1888. All modern Hevea clones are believed to have arisen from the so called 22 Wickham seedlings.
The IIRDB expedition during 1981 collected 10,000 odd accessions from Brazil. Till to date, no clones got derived from this collection. The secret is that Wickham collections underwent several rounds of natural selections at several places to end up in 22 seedlings from the original collection of 70,000 seeds.
Genomic research is many fold. Association mapping, subtractive hybridization, reverse genetics and draft genome analysis are some of them. A comparative evaluation between self-rooting juvenile clones (JCs) and bud-grafted (donor) clones (DCs) at transcriptome level is one of the most recent research breakthroughs. Genes, especially encoding epigenetic modifications, are differentially expressed in JCs and DCs.
Genes involved in carbohydrate metabolism, hormone metabolism and reactive oxygen species scavenging were up-regulated in JCs of CATAS 7-33-97 and Haiken 2, indicating that the JCs provide sufficient molecular basis for the increased rubber yield. Comparative trial between self-rooting JCs and DCs has proved self-rooting JCs exhibited better performance in rubber yield.
Such investigation clearly indicates the intricateness of stock-scion interactions. No doubt, such investigations can gain a perfect juvenile selection system in Hevea in the years to come. Scientists at Chinese Academy of Tropical Crops at Haikou must be congratulated for such advancements.
Scientists of RIKEN team of Japan, working in collaboration with Universiti Sains Malaysia (USM), Chinese Academy of Tropical Agricultural Sciences (CATAS) are the claimers of draft genome of Hevea. It is noteworthy that the CATAS assembly captures practically all the USM sequences contained in a purportedly larger draft genome. It appears that CATAS has done a better job of fitting contiguous sequences into a smaller number of scaffolds. Despite three published Hevea genomes now in the public domain, the discrepancies between the reports have the logic that the last word is still not yet in.
The Beijing Genomics Institute, China; RIKEN, Japan; Universiti Sains Malaysia; Malaysia Genome Institute; Centre for Genetic Engineering and Biotechnology, Bangkok and CIRAD , France and Tun Abdul Razak Research Centre, UK are the leading institutions involved in genomics research.

Leaf blight exterminated rubber plantations in Brazil. From this historical experience, what are the strategic initiatives that Asian rubber growing nations should take to promote and protect the Hevea plantations from similar disasters that could happen again? Are we doing enough in this field as mere quarantine policies might not be enough to fight a potential leaf blight disaster?

South American Leaf Blight is a potential threat to all rubber growing areas. Certainly, mere quarantine may not be sufficient enough to check the entry of the disease. SALB is recognized as a biological weapon by the United Nations. Spores of Microcyclusulei (casual fungi of SALB) can remain on transport. Mass production of conidiospores and the rapid build-up of inoculum is the causal step in the epidemiological development of fungal infection in flushing canopies. The conidia are short lived, whereas the ascospores produced in black stromatic structures survive for several months. These ascospores can initiate new infection cycles as soon as susceptible young leaf tissues are produced by the host.
The physiological tolerance of the isolates to temperature and relative humidity, as well as to complex environmental factors, suggests that the potential for adaptation of fungal isolates to new environments is high. This variability underscores the potential threat of this fungus to new rubber growing areas outside South and Central America. Spores can grow well at 23o C. Some of the resistance clones are: FX 3864, RRIM 725, RRIM 711, IAC 300, IAN 873, FDR 5597, FDR 4575, PMB 1, CDC 312, CDC 308, CDC 56, FDR 5240 and FDR 5788. The level of resistance differs from clone to clone. Introduction of clones from SALB area is risky. If the infection escapes Southeast Asian nations, we are lucky.

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