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Crop Breeding for Sustainable Agriculture , Genomics Interventions in

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Encyclopedia of Sustainability Science and Technology

Definition of the Subject

There has been significant improvement in production and productivity of important cereal crops globally as a consequence of the “Green Revolution ” and other initiatives [1]. However, today the stage has reached that the available traditional methods of crop improvement are not sufficient to provide enough and staple food grains to the constantly growing world population [2]. This situation is projected to be worse by the year 2050, especially in context of climate change [3]. In other words, the conventional plant breeding practices may not be able to achieve the sustainability in today’s agriculture.

It is under such circumstances that advances in plant genomics research are opening up a new era in plant breeding , where the linkage of genes to specific traits will lead to more efficient and predictable breeding programs in future. Several initiatives have been started towards use of genomics technologies in...

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Abbreviations

Association mapping:

Association mapping is a high-resolution method for mapping quantitative trait loci (QTLs) or gene(s) for traits of interest based on linkage disequilibrium (LD) and holds great promise for the dissection of complex genetic traits.

Back cross (BC):

Back cross is a cross of the F1 with either of the parental genotype and the resultant progeny is called BC1. The progeny of the cross between BC1 and the recurrent parent is called as BC2.

Gene pyramiding:

Gene pyramiding is a process of accumulating the favorable genes/alleles from different genotypes into an elite/commercial cultivar. Gene pyramiding is often performed through marker-assisted selection (MAS).

Genome-wide selection or genomic selection (GS):

Genome-wide selection or genomic selection is a concept for accelerating genetic gain especially for complex traits in elite genotypes by utilizing genomic information and estimating their breeding values in breeding strategies. GS is becoming very popular over marker-assisted selection that was focused on few individual genes or few QTLs to improve genotypes, especially when recent advances in genomic technologies have drastically reduced the cost on marker genotyping.

Genomics-assisted breeding (GAB):

Genomics-assisted breeding is a holistic approach, where genomics technologies including molecular markers, trasncriptomics, metabolomics, proteomics, bioinformatics, and phenomics are integrated with conventional breeding strategies for breeding crop plants resistant/tolerant to biotic and abiotic stresses or improved for quality and yield.

Haplotype:

Haplotype is a set of alleles of closely linked loci on a chromosome that tend to be inherited together.

Linkage disequilibrium (LD):

Linkage disequilibrium is a nonrandom association of alleles at different loci, describing the condition with non-equal (increased or reduced) frequency of the haplotypes in a population at random combination of alleles at different loci. LD is not the same as linkage, although tight linkage may generate high levels of LD between alleles.

Marker-assisted selection (MAS):

Marker-assisted selection is a process of indirect selection for improving the traits of interest by employing morphological, biochemical, or DNA-based markers. DNA-based markers/molecular markers, in the recent past, were proven to be the markers of choice for MAS.

Narrow genetic base:

Narrow genetic base does frequently exists in modern crop cultivars or breeding lines due to the continuous use of small number of elite genotypes in breeding programs. In fact, it is a serious obstacle to sustain and improve crop productivity due to rapid vulnerability of genetically uniform cultivars to emerging biotic and abiotic stresses.

Next-generation sequencing (NGS) technologies:

Next-generation sequencing (NGS) technologies include various novel sequencing technologies for example 454/FLX (Roche Inc.), ABI SOLiD (Applied Biosystems), Solexa (Illumina Inc.), etc., that have surpassed traditional Sanger sequencing in through-put and in cost-effectiveness for generating large-scale sequence data.

Polygenes:

Polygenes are a group of non-allelic genes, each having a small quantitative effect, that together produce a wide range of phenotypic variation.

Quantitative trait loci (QTLs):

Quantitative trait loci are the loci or regions in the genome that contribute towards conferring tolerance to abiotic stresses (e.g., drought, salinity) or resistance to biotic stresses (e.g., fungal, bacterial, viral diseases) or improving agronomic traits (e.g., yield, quality) which are generally controlled by polygenes and greatly depend on gene × environmental (G × E) interactions.

Sustainable agriculture:

Sustainable agriculture refers to efficient agricultural production while maintaining the environment, farm profitability, and prosperity of farming communities.

Sustainable development:

Sustainable development is defined as balancing the fulfillment of human needs with the protection of the environment so that these needs can be met not only at the present time, but also in the future.

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Acknowledgments

We thank the Generation Challenge Program (www.generationcp.org), the Indian Council of Agriculture Research (ICAR) and the Department of Biotechnology (DBT) of Government of India for funding various research projects (RKV) on genomics applications in breeding.

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Authors and Affiliations

  1. State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri, 413722, Maharashtra, India

    Pawan L. Kulwal

  2. Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, AP, 502324, India

    Mahendar Thudi & Rajeev K. Varshney

  3. Genomics Towards Gene Discovery Sub programme, Generation Challenge Programme (GCP), Generation Challenge Programme (GCP) c/o CIMMYT, Int APDO Postal, 6-641,06600, Mexico, DF, Mexico

    Rajeev K. Varshney

  4. School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    Rajeev K. Varshney

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  1. Pawan L. Kulwal
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    Robert A. Meyers

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Kulwal, P.L., Thudi, M., Varshney, R.K. (2012). Crop Breeding for Sustainable Agriculture , Genomics Interventions in. In: Meyers, R.A. (eds) Encyclopedia of Sustainability Science and Technology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-0851-3_271

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