DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.

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Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. This variety, the recurrent parent in the MABC, had not previously been used for quantitative trait locus (QTL) mapping. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits (root length and thickness) and the fifth carried a recessive QTL for aroma. Some selection was made at non-target regions for recurrent parent alleles. We describe the selection made in three backcross (BC) generations and two further crosses between BC3 lines to pyramid (stack) all five target segments. Pyramids with four root QTLs were obtained in eight generations, completed in 6 years using 3,000 marker assays in a total of 323 lines. Twenty-two near-isogenic lines (NILs) were evaluated for root traits in five field experiments in Bangalore, India. The target segment on chromosome 9 (RM242-RM201) significantly increased root length under both irrigated and drought stress treatments, confirming that this root length QTL from Azucena functions in a novel genetic background. No significant effects on root length were found at the other four targets. Azucena alleles at the locus RM248 (below the target root QTL on chromosome 7) delayed flowering. Selection for the recurrent parent allele at this locus produced early-flowering NILs that were suited for upland environments in eastern India.

Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.

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Breeding for abiotic stresses for sustainable agriculture.

This paper reviews and discusses how studies on (i) on-farm diversity assessment, (ii) access to diversity and information, (iii) extent of use of available materials and information, and (iv) benefits obtained by the farmer or farming community from their use of local crop diversity, are necessary to identify the different ways of supporting farmers and farming communities in the maintenance of traditional varieties and crop genetic diversity within their production systems. Throughout this paper two key themes are emphasized. First, any description or analysis within the four main areas (assessment, access, use and benefit) can, and most probably will, lead to a number of different actions. Second, the decision to implement a particular action, and therefore its success, will depend on farmers and the farming community having the knowledge and leadership capacity to evaluate the benefits that this action will have for them. This in turn emphasizes the importance of activities (whether by local, national...

https://www.tandfonline.com/doi/pdf/10.1080/07352689.2011.554358

An Heuristic Framework for Identifying Multiple Ways of Supporting the Conservation and Use of Traditional Crop Varieties within the Agricultural Production System

Field evaluation of upland rice lines selected for QTLs controlling root traits

Conventional methods for quantitative trait locus (QTL) mapping require the selection of particular traits to be measured based on assumptions as to their importance. We have tested an alternative approach for the location of QTLs-marker-evaluated selection-that makes no prior assumptions as to which traits are important. The results of phenotype selection were evaluated in the products of modified bulk-population breeding that was replicated across a range of rice ecosystems. Selection was carried out in close collaboration with farmers in bulk populations that were all derived from a cross between an Indian upland variety (Kalinga III) and a high-yielding semi-dwarf variety (IR64).Twenty-seven diverse bulks were produced that were screened with molecular markers in order to determine whether shifts could be detected in marker allele frequency as a result of selection and if such changes varied by genomic region across ecosystems. Marker loci linked to important traits for adaptation to specific environments were identified without making any prior assumptions about which traits might be important. Genomic regions from Kalinga III were strongly selected in the upland environments and regions from IR64 in the lowland ones.However, exceptions occurred where the upland parent contributed positively to lowland adaptation and vice versa. The results can be used as a basis for the development of second-cycle varieties, using marker-assisted selection to produce genotypic ideotypes for specific target environments. The very strong selection for genomic regions from the adapted parents of the wide(upland x lowland) cross indicates that, in non-marker-assisted breeding, where genetically distant parents have been used, modified backcross breeding should be efficient. A single backcross to the adapted parent for aspecific ecosystem will result in a higher frequency of segregants with the desired high genetic contribution from the adapted parent.

Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding.

Participatory plant breeding (PPB), like conventional breeding, is predicted to give a low response to selection for traits with low heritability. These include many traits that farmers consider desirable, such as drought resistance. The technology of marker-assisted selection (MAS) can be used to make selection for traits with low heritability more effective. We describe how MAS can be used to assist in the breeding of drought tolerance in upland rice. Abstract

Combining molecular marker technology and participatory techniques: A case study for drought-tolerant rice in eastern India II: Molecular breeding strategy

G. Edwards

Papers

Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding.

Combining molecular marker technology and participatory techniques: A case study for drought-tolerant rice in eastern India II: Molecular breeding strategy