Protocol

Centre : Rubber Research Institute of India
Name of the Protocol
Application of DArT markers (SNP and silico DArT) for generating high density genetic linkage map in rubber (Hevea brasiliensis)
Nature : Modification of existing protocol
Crop / Pathogen : Hevea brasiliensis/ Phytophthora spp.

Inventors

1. C. Bindu Roy
2. T. Saha
3. Andrzej Kilian

Objectives

1. To develop high density genetic linkage map in rubber using SNP and silico DArT markers
2. Quantitative trait loci (QTL) mapping for disease resistance against abnormal leaf fall disease in rubber caused by Phytophthora spp.

Procedure / Summary

DArTsequencing represents a new implementation of sequencing of complexity reduced representations and next generation sequencing platforms generating both co-dominant (SNP) and dominant (silico DArT) markers. An interspecific cross between Hevea brasiliensis clone RRII 105 (high yielder with low level of resistance to Phytophthora spp.) and H. benthamiana (low yielder with high level of tolerance to Phytophthora spp.) was made and a progeny population of 86 individuals were used for the study. 24004 markers obtained from DArTsequencing were used for construction of genetic linkage map using DArT PL’s OCD MAPPING program. Linkage maps were produced for each parent and consensus map between the two parental maps established using common bridge markers. Phenotyping for disease resistance was carried out using zoospore suspension from a virulent isolate of Phytophthora through in vitro challenge inoculation of the progeny population. In vitro leaf disc assay quantified disease reaction and categorized individuals based on size of lesion produced. Duncan's Multiple Range Test was performed to compare means of disease intensity observed. Genotyping and phenotyping of progeny population are a necessity for QTL detection. Therefore, the genotypic and phenotypic data for disease resistance were merged together to identify marker trait relationship for identification of QTLs.

Applications

1. High density genetic linkage map construction using both dominant (silico DArT) and co-dominant (SNP) markers.
2. Genome wide association mapping for agronomic traits of interest.
3. Quantitative trait loci (QTL) analysis using genetic map.

Publications

1. Bindu Roy C., Bikku B., Anuja S., Jayasree M. and Saha T. (2016). Transgressive segregation for resistance to Phytophthora pathogen in an interspecific hybrid population of rubber (Hevea brasiliensis). In: 6th International Conference on Plant, Pathogens and People – Challenges in plant pathology to benefit humankind, jointly organized by Indian Phytopathology Society, Crop Protection Federation, Indian Council of Agricultural Research and Indian Agricultural Research Institute, New Delhi at IAR
2. Bindu Roy C. (2016). Targeting disease resistance loci conferring tolerance to major leaf diseases of rubber tree through QTL mapping using high density genetic linkage map with DArT markers. In: 38th Annual Conference and National Symposium on Challenges towards plant health under changing climate scenario for sustainable agriculture organized by Indian Society of Mycology and Plant Pathology, at Bidhan Chandra Krishi Viswavidhyalaya, Nadia, Kolkata, 24-26 November, 2016.
3. Bindu Roy C., Bikku B., Andrzej Kilian, Jayasree M. and Saha T. (2016). Construction of a high density genetic linkage map using SNP and silico DArT markers and QTL mapping for disease resistance in rubber tree (Hevea brasiliensis). In: 22nd Biennial Symposium on Plantation Crops (PLACROSYM 22), ICAR-Central Plantation Crops Research Institute, Kasaragod, 15-17 December 2016.