Indian Wheat Rust Pathogen Genome Cracked by ICAR Scientists

A major scientific breakthrough of ICAR Scientists lead to  the decoding of  genomes of 15 strains of wheat rust fungus Puccinia triticina. It will aid in understanding the dynamic nature of this notorious wheat pathogen causing disease epidemics in various parts of the world including India. The paper "Draft genome of the wheat rust pathogen (Puccinia triticina) unravels genome-wide structural variations during evolution" has been recently published in an International Journal, Genome Biology and Evolution(

Indian Wheat Rust Pathogen Genome Cracked by ICAR Scientists

Wheat, a staple food of more than 50% of world’s population and is important food security crops of India is severely affected by three types of rust diseases. Among these, leaf rust is of worldwide occurrence, more frequent and, therefore, results into more yield losses than any other wheat rust. Leaf rust (Puccinia triticina) can cause grain yield losses higher than 50% under severe epidemics, if fungicides are not applied. The wheat production in India has faced serious problems during 1970 to 1980 because of rust epidemics which were later managed effectively by growing rust resistant varieties. Most of the resistant varieties released in India carried only race specific resistance.  Therefore, evolution of new races and biotypes of  P. triticina had been going on in nature and this issue still remains a matter of concerns for  Indian wheat breeders and policy makers.

Wheat Leaf rust symptom, fungal spores and comparative analysis of rust genomesDr. T. R. Sharma, Director of ICAR-NRCPB, New Delhi,  coordinated a Department of Biotechnology, Govt. of India funded project on De Novo genome sequencing of Puccinia triticina  (Leaf rust pathogen)across three ICAR institutes consisting of  National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, Indian Institute of Wheat and Barley Research, Flowerdale Centre, Shimla, Indian Agricultural Research Institute,  Regional Station Wellington, and two State Agricultural Universities,   Punjab Agricultural University, Ludhiana &Tamil Nadu Agricultural University, Coimbatore. In this consortium, the main focus was to understand the molecular basis of variability in rust fungus by decoding the genomes of a highly variable Race77 and its 13 biotypes and a stable Race 106. Race106 was first identified in 1930 and preserved in the National collection at Shimla and did not mutate during the past more than eighty five  years, whereas race 77 was first detected in 1954 from Pusa (Bihar) and evolved into thirteen biotypes affecting wheat breeding programme in the country.   Therefore, it is very important to understand the molecular mechanism for virulence and adaptability within Race77, and unravelling the molecular basis of its fast evolution and stability of race 106 genome.

At ICAR-NRCPB, Next generation sequencing (NGS) technology was used to decode the genomes of 15 strains (~1500 MB data) of wheat leaf rust fungus. We generated a high quality draft genome (~100Mb) sequence of Race 77  with 33X genome coverage and predicted 27678 protein coding genes responsible for various functions. Genome wide comparative analysis revealed   that P. triticina genome is 37.49 % and 39.99% repetitive in case of Race77 and Race106, respectively and    Race77 substantially differs from Race106 at segmental duplication (SD), repeat elements and SNP/InDel levels. We found certain "host spot regions" in the genomes of Race 77 which are vulnerable for reshuffling, leading to variability in it. This study provides an insight about P. triticina plant fungal pathogen, with emphasis on the genome structure, organization, molecular basis of variation and pathogenecity.   This genome information will be an important landmark research in India and will facilitate wheat improvement programme in the country.

It is important to mention that ICAR-NRCPB has already decoded the complete genome sequence of   plants species   like Rice, Tomato, Pigeonpea, Wheat and Mango under various International and National Genome Sequencing Programmes.  The genome sequence information is being used for the identification of agriculturally important genes, DNA markers and QTLs which are being used by the breeders in their crops improvement programmes.

(Source: ICAR- National Research Centre on Plant Biotechnology, Pusa Campus , New Delhi)