Trends in Biotechnology
Volume 24, Issue 11, November 2006, Pages 490-499
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Review
Advances in cereal genomics and applications in crop breeding

https://doi.org/10.1016/j.tibtech.2006.08.006Get rights and content

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.

Section snippets

Potential of cereal genomics

Cereals, including rice, maize, wheat, barley, rye, sorghum, oats and millets, have constituted the staple food of the world since their domestication ∼10 000 years ago. Cereals are also the most important group of cultivated plants for food production and acreage covered, providing >60% of the calories and proteins in our daily diet. In the past, cereals have been the subject of intensive cytogenetic investigations, and these are now further extended using the powerful tools of molecular

Molecular markers and applications

Owing to advances in the area of molecular genetics and automation, dense molecular genetic maps are now available for the major cereal species [1]. However, there is still a need to integrate more markers in the genetic maps of rye, oats and millet species. Furthermore, among the different classes of molecular markers (see Glossary), simple sequence repeat (SSR or microsatellite) markers (see Glossary) have proven to be the marker of choice for a variety of applications, particularly in

Marker-assisted selection

Marker-assisted selection (MAS) is a powerful tool for the indirect selection of difficult traits at an early stage before production of the next generation, thus speeding up the process of conventional plant breeding and facilitating the improvement of traits that cannot be improved easily by conventional methods [9]. Using MAS, a large number of genes and QTLs controlling agronomic traits and conferring tolerance to both abiotic and biotic stresses in cereals have been identified and tagged

Association mapping

Another approach to identify molecular markers for use in MAS is association mapping, which is based on linkage disequilibrium (LD) (see Glossary). Unlike conventional bi-parental mapping populations (see Glossary) – such as DH, F2 or RILs, which have been used in the past for identifying genes or QTLs for the trait of interest, the natural populations are the products of many cycles of recombination and have the potential to show enhanced resolution of QTLs. Association mapping might offer

Map-based cloning (MBC)

The MBC approach involves the use of molecular markers for preparing a high-density genetic map around the region harbouring the gene of interest and, ultimately, the local physical map to isolate the gene [23]. In fact, several MBC projects were started in the mid-1990s, and several genes or QTLs for disease resistance or other traits have been isolated in many cereal species (Table 1). These examples involved long-term efforts (up to 10 years), depending on the availability of resources and

Whole-genome and/or gene-space sequencing

Because the rice genome is the smallest among the cereal genomes, it was proposed as a target for whole-genome sequencing. Because of international collaborative public and private sector efforts, four drafts 27, 28, 29 (http://rgp.dna.affrc.go.jp/IRGSP/) and the complete sequence of the whole genome [30] became available for rice: one study was done with indica rice and three studies were completed with japonica rice [29]. The complete sequence of the rice genome was obtained from 3401 PAC

Functional genomics

Functional genomics involves the identification of the function of genes per se or those derived from a known allelic difference conferring an improved phenotype. In the latter approach, the objective is to identify the sequence change conferring the improved phenotype; such a sequence change can then become the basis for a molecular marker that is specific for that allele. Thus, functional genomics in the true sense can be linked or associated with plant breeding for crop improvement

Comparative genomics for orphan cereal crops

Besides the major cereal crops (maize, wheat and rice), many cereal crops such as sorghum, pearl millet, small millets and tef (Eragrostis tef) are regionally or locally important for nutrition and income, particularly in developing countries [44] (http://www.cgiar.org/impact/research/millet.html). Because of relatively low returns in terms of gross economic and welfare impacts, the ‘orphan crops’ have not received adequate investment in terms of research [45]. Given that significant genomic

Interdisciplinary genomics approach for crop improvement

Significant progress in the field of cereal genomics has already been made in many cereals. For example, the availability of a variety of molecular markers facilitated the preparation of high-density maps, which proved useful in the identification of molecular markers linked with genes and/or QTLs for a variety of economic traits, including those conferring tolerance to biotic and abiotic stresses. Development of functional molecular markers as a by-product of available sequence data will be

Acknowledgements

The research of authors at ICRISAT (RKV, DAH) is supported by grants from Generation Challenge Programme (GCP) of Consultative Group on International Agricultural Research (CGIAR) and Syngenta Foundation for Sustainable Agriculture (SFSA), whereas AKT acknowledges the support of Department of Biotechnology (DBT), Government of India for supporting research activities at ICPG. Thanks are due to Mahendar Thudi and Spurthi Nayak for their help in formatting and editing references for the article.

Glossary

Association mapping
also known as LD (linkage-disequilibrium) mapping or association analysis is a population-based survey used to identify trait–marker relationships based on linkage disequilibrium.
Binning
sorting and/or compiling of haplotypes, based on data obtained by sequencing (which is expensive) or EcoTILLING (which is inexpensive).
Bi-parental mapping populations
are the progenies derived after crossing two genotypes used as male and female parents, for example, F2 lines generated from

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