Soybean is one of the most important grain legumes in the world in terms of production. It is also a promising source of vegetable oil, nutraceuticals and protein. Cultivation of soybean in India is recorded to be below average than the rest of the world. One of the major limitations for increasing the productivity of soybean is non-availability of resistant varieties for disease and pest. Soybean rust is a fungal disease caused by Phakopsora pachyrhizi, commonly known as Asian soybean rust. Under conducive condition it causes yield loss up to 80%. Defoliation and early maturation are symptoms shown by infected plants. Application of fungicide is the only available treatment, but the fungus tends to develop resistance over it. Thus, there is need for developing soybean resistant varieties.
DNA molecular markers would prove to be powerful tool in developing soybean resistant varieties by selecting target traits for breeding. For this a mapping population would be develop by crossing a soybean rust resistance parent with a susceptible parent. The population will be artificially infected by rust inoculum and after few days’ disease score would be recorded on F2 population. Prior to infection, leaf samples will be collected to extract the DNA. The SSR markers linked to rust resistance would be identified by Bulked segregant analysis method. Over 500 primers will be screened on parents and F2 bulks. The identified putative markers would be screened on entire F2 mapping population for linkage analysis. Phenotypic and genotypic data would be corelated with the help of software based on recombinant frequency. Finally, the identified markers would be validated on rust resistance and susceptible soybean cultivars. Tightly linked molecular markers identified in this study would serve as an important tool for marker assisted selection of rust resistant soybean genotypes in soybean breeding programs.
1. Details of the Project:
i. Origin of Proposal
Human communities are greatly impacted by plant pathogens that cause serious epidemics in crop plants 1. One such example is an obligate fungus Phakopsora pachyrhizi Syd. & P. Syd which causes soybean rust 2. Rust has been one of the most destructive diseases affecting the most important economic crop, soybean (Glycine max (L) Merr.). Soybean is a promising source of vegetable oil, nutraceuticals and protein.10 to 80% of yield losses are reported worldwide under the conducive environmental conditions for the development of disease 3. Defoliation and early maturation are observed in infected plants which ultimately lead to reduction of weight and quality of grains. To combat this, resistant varieties of soybean should be planted but due to their limited availability, application of fungicides the only option left out for farmers. Nonetheless, fungicide treatments are high-priced and cause contamination of the environment. Over a period of time pathogens also tend to develop tolerance to certain fungicide, endangering the cultivation of soybean. Thus, the strategy adopted to sustain economically and environmentally is to search for resistant varieties 4. For this purpose phenotypic screening of segregating population can be carried out but it is time-consuming and laborious. Hence, resistance genotypes in segregating population must be identified in the early breeding stages for successful breeding and cultivation of disease resistant varieties. This can be done with DNA marker-assisted selection. Microsatellites and SNPs (Single Nucleotide Polymorphism) are the most commonly used DNA markers for mapping the genomic regions in soybean 5. Microsatellite markers (SSR) have a higher advantage over SNPs due to their high polymorphism, reproducibility, co-dominance and distributed across the genome 6.
ii. a) Rationale of the Study supported by cited literature
Most of the soybean growing countries have reported the presence of rust. Amongst which Japan is the first country to report in 1903 7. During mid-century rust was confined to East Asia and Australia. But the disease started spreading to different countries since it disperses in the form of urediniospores through wind 8. In India, it was first accounted in 19709, in Puerto Rico in 1956 10, and in Hawai in 1994 11. By the beginning of the twentieth century, it was detected in Brazil, Paraguay, and Argentina 12 13. And by 2004, pathogen showed up in South America14 followed by North America in 200515.
Some P. pachyrhizi populations have exhibited tolerance to fungicides16. Therefore the development of high yielding cultivars resistant to rust pathogen will be a sustainable approach to control rust. Worldwide researchers have screened for resistance or tolerance to rust 17 and identified seven different loci carrying dominant alleles: Rpp1 18, Rpp2 19, Rpp3 20, Rpp4 21, Rpp5 22, Rpp6 23and Rpp1-b 24. However, these genes are not effective for all population of P. pachyrhizi 25. Some researchers have identified recessive genes in association with rust resistance 26.
Molecular markers are an essential tool to monitor the transfer alleles of interest for the development of resistant varieties 27. SSR’s have been used for mapping specific genes in soybean to determine the traits, QTLs, resistance to diseases and pest etc. 28. However, some P. pachyrhizi population have evolved the ability to prevail over single-gene resistance 29 30. Therefore, there is a need for identification of novel genes linked to rust resistance for the development of resistant cultivars.
SSR markers linked to rust resistance gene would be identified.
c) Key Questions
· Establishing of mapping population.
· Assessing mapping population for rust.
· Identifying Molecular markers.
· Assessing mapping population with putative molecular markers.
· Generating linkage map.