Abstract
Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products.
Highlights
Maize is a widely grown C4 crop with a high rate of photosynthetic activity leading to high grain and biomass yield potential
These alleles may never have been found via simple phenotypic screens, either because it is not possible to grow and measure every plant in a large germplasm collection under all possible environmental conditions, because their effect may be masked in certain genetic backgrounds, or because the effect may be so small that it will not be found unless sought in carefully controlled phenotypic screens
The MAGIdb contains Maize Assembled Genomic Islands (MAGIs) using almost four billion genome survey sequences generated through the Consortium for Maize Genomics (CMG) which can be viewed and used to BLAST against other sequences with basic local alignment search tool (BLAST)
Summary
Maize is a widely grown C4 crop with a high rate of photosynthetic activity leading to high grain and biomass yield potential. Changes in the DNA sequence, corresponding to new alleles of this locus, will be identified in this manner, and individuals carrying the new alleles can be evaluated for the target trait to determine the associated change in phenotype and the value for subsequent use in breeding programs These alleles may never have been found via simple phenotypic screens, either because it is not possible to grow and measure every plant in a large germplasm collection under all possible environmental conditions, because their effect may be masked in certain genetic backgrounds, or because the effect may be so small that it will not be found unless sought in carefully controlled phenotypic screens. These results demonstrated that 454-based transcriptome sequencing is a method of choice for the high-throughput acquisition of gene-associated SNPs
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