Screening plant genetic resources for novel alleles in cereals
Authors: Sundeep Kumar1, Amit K. Singh1, Ruchi Bansal1, Jyoti Kumari1, Sheel Yadav1 and Monendra Grover2

1National Bureau of Plant Genetic Resources, New Delhi-110012
2Indian Agricultural Statistical Research Institute, New Delhi-110012

Agriculture scientists face uphill task to ensure food security as the climate change has started impacting crop production and productivity. Hence, the development of climate resilient cultivars to mitigate the effect of various biotic and abiotic stresses is essentially required to meet the demand of growing population of the world. Development of climate resilient varieties depends upon the availability of diverse genetic resources which possess genes tolerant to abiotic and biotic stresses. Nearly a century has been spent collecting and preserving genetic diversity in plants. Germplasm banksâ€"living seed collections that serve as repositories of genetic variationâ€"have been established as a source of genes for improving agricultural crop production. However, only a part of this has been utilized in the varietal development programs. The molecular tools still not played significantly to unleash the genetic potential of our wild and cultivated germplasm resources for the benefit of the society. In India, National Genebank is located at NBPGR, New Delhi where approximately 4 lacs accessions comprising of wild relatives and landraces of different cop species are conserved. Genebanks were setup in different countries with the main objective to conserve the wild relatives and landraces of the crop plants are now looked upon as a reservoir of novel sources of the alleles and genes conferring resistance to different stresses. However, the pity situation is that a large number of the accessions conserved in the various genebanks are yet to be characterized and evaluated for different traits for their proper utilization in developing climate resilient cultivars. Therefore, there is an urgent need to characterize them through precised phenotyping and molecular tools. Recently, In India, National Agricultural Research System (NARS) has taken up new initiatives to characterize gene bank material for various economically important traits and also for identification and isolation of novel genes/alleles. Broadly, these programs are based on the following aspects.

1. Extensive phenotyping of accessions under controlled and field conditions to identify a core/minicore
2. Evaluation of these cores at various locations/hot spots for validation and reference set development
3. Genotyping and marker trait association.

How the gene pool become more useful to the mankind?

It is clearly understood that these gene pools are the reservoir of thousands of useful genes which can be of much use specially under changing climatic conditions. In India, a mega trial was conducted by ICAR-NBPGR scientists to characterize the entire set of around 22,000 wheat accessions for terminal heat tolerance and biotic stresses including leaf, stem and stripe rusts and spot blotch diseases so that some useful germplasm lines can be identified and used in national crop improvement program. In this collection, some of the germplasm lines were age old and lying in National Genebank of India for more than 30-40 years, need to be revived, multiplied and characterized. Similar situation is persisting in almost every Genebank of the world. These entire collection is like goldmine as numerous useful genes are present in these unused/unexploited collections that might be the solution for the current unsolved issues like rising temperature during the month of February-March and new pathogen races like Ug99 of stem rust in case of wheat, drought tolerance in case of rice, resistance to blast of paddy, developing nutrient rich or input efficient variety etc.

Evaluation of germplasm for biotic and abiotic stress tolerance in cereals

This is the need of hour, to look forward the new sources of resistance to biotic and abiotic stresses as existing sources of resistance has been exploited up to much higher extent and a saturation point has been felt by the scientists working in the cereals. To find the solution of existing threats like biotic and abiotic stresses, problem of malnutrition, yield enhancement etc, evaluation of our old unexploited germplasm lines is essentially required. Further, for identification of promising donors, precise phenotyping is required with the help of NARS partners under controlled/hot spot conditions using new phenotyping tools. Pyramiding of minor genes in combination of major genes might be advantageous to have better control of the diseases like rusts. Likewise pyramiding of genes for other useful traits can pay dividend and lesser risk to the food security of the millions of the poor peoples living in developing countries.

Can molecular markers play a vital role in characterizing cereal germplasm to make them more useful?

In the era of modern science, this would be injustice with economic growth if we do not take the advantage of advancement taking place in the field of molecular biology. Molecular markers can play a significant role in the characterization of wheat and rice germplasm for various useful traits. Rice genome has been decoded; information of all the useful genes is now available in the public domain that can be used in characterizing wild relatives, landraces and obsolete varieties to make them more useful for breeding purpose. Likewise in wheat, blueprint of wheat genome is available now, information about many useful genes is also available and complete genome information is expected to come within 4-5 years. However, the available wheat genome information is sufficient enough to be used in marker assisted selection for various biotic and abiotic stress tolerance lines. Information about 68 lr (leaf rust resistance),49 sr (stem rust resistance) and 48 Yr (yellow rust resistance) genes and various transcription factors involved in pathways of abiotic stress tolerance is known that can be used to characterize age old potential wheat germplasm lines.

Further, due to global warming and changes in the climate pattern, development of heat, drought and salinity tolerant varieties and generation of pre-breeding material is the priority for future breeding for achieving improved crop productivity and greater food security. The existing germplasm lines are not much promising as far as abiotic stresses are concerned. Hence, there is a need to develop trait based cores/reference sets that will be exploited in different ways to identify the genetic factors (gene/QTLs) for various abiotic stresses like heat, drought and salinity tolerance. The purposes of this kind of programs are to strengthen our conventional breeding program by providing valuable characterized germplasm with identified gene/QTLs information.

Can new promising genetic resources be generated? Yes, it is possible by following a systematic crossing program like wide crossing and mutation breeding etc. new breeding lines, pre-breeding material, advanced crossing material, mapping populations can be generated. Mutation breeding can generated good TILLING population in wheat as being hexaploid, wheat crop can sustain the lethality due to mutation and it will be a good resource for allele mining. This kind of material is of much use to mobilize the useful traits from wild relative or landraces to cultivated one. By following such approach, a set of useful genes can be accumulated in few germplasm lines that can be used as parent material in developing new improved cultivars in much lesser time comparison to conventional breeding methods. Possibility of new useful QTLs for biotic and abiotic stress tolerance is also much higher especially when some unexploited material has been used as parent material in developing mapping populations.

Is exploration still required for specific traits?

In the gene banks, it has been seen that a big part of the collection of a particular crop lay in the genebank uncharacterized. Hence, before going for any exploration gap analysis should be done so that to have the idea about geographical region covered or not in previous exploration. However, due to drastic changes in climatic conditions in last few decades, sometimes it is important to do trait based explorations even those regions which have been explored in the past. For that focussed identification can be followed for collection of germplasm from climatically known hot spots.

Exploration of plant genetic resources can be useful for identifying novel allele/QTL:

As it has been discussed in the first part of this manuscript, we all realize that majority of germplasm lines are still lying uncharacterized in genebank for last 30-40 years. These lines might be having some novel alleles/QTLs which have the potential to provide durable disease resistance and a satisfactory answer to abiotic stresses. Hence, there is an urgent need to characterize gene banks material of major cereal crops and include superior germplasm lines in breeding programs for the betterment of human being and to ensure

"Food to all"


1. Amit Kumar Singh, Sundeep Kumar, Jameel Akhtar, M K Rana, Rajesh Kumar and Rakesh Singh (2013). Biotechnological Approaches for Conservation and Sustainable Utilization of Plant Genetic Resources. C.R. Prajapati et al.(eds.). Plant Disease Management for Food Security: Role of Plant Diseases in Global Food Security, Pp 72-84 (Published by LAMBERT Academic Publishing, Germany).
2. Rakesh Singh, Sundeep Kumar, Amit Kumar Singh, Monendra Grover and Rajesh Kumar (2012). Biotechnological Approaches for Plant Biodiversity Conservation and Utilization. Biotech Today 2(2):35-38.
3. Sundeep Kumar, Amit K. Singh, Monendra Grover and Rakesh Singh (2013). Climate change-Needs to develop climate resilient wheat cultivars. In: Proc. International Conference on Impact of Technological Tools on Food Security under Global Warming Scenario (ITTFS-2012), 11-12 May 2013, Meerut, India.

About Author / Additional Info:
I am Senior Scientist at ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi.