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Questions have arisen about the genomics focus of The Plant Genome. What is the meaning of genomics? The common definition is that Genomics is the study of an organism's entire genome. This is distinguished from investigations of single genes and their roles and functions. The latter is in the realm of molecular biology. The emphasis of this journal is genomics, but as we will see, the line between molecular biology and genomics may become blurred. The papers presented in this issue depart from molecular biology and enter the realm of genomics.
Mohan et al. physically mapped wheat and rye EST-SSRs using a combination of deletion stocks and bioinformatics. The authors were able to assign putative functions to 216 ESTs through database searches. They also determined that distribution of the genic loci was non-random, with more loci mapping to the distal regions of chromosomal arms. More than 100 of the ESTs were also placed to the rice chromosomes, thus facilitating additional comparative genomic analyses and map-based cloning.
The Omega-6 fatty acid desaturase of soybean is responsible for conversion of oleic acid to linoleic acid, and, thus is important in oil quality. The work of Schlueter et al. identified BAC clones containing five members of the FAD2 gene family. This included two new members never previously reported. This work extended beyond molecular biology by characterizing the structure and organization of the physical regions surrounding the members of the gene family. Two BAC clones with very high degrees of homeology and identity mapped to two linkage groups with known polyploidy relationships. Two others showed no relationships to any other BAC, except for the FAD2 gene. This work showed that the soybean genome is a mosaic of conserved and non-conserved regions, and is important as the soybean community begins to address the ongoing whole-genome sequencing effort.
The article by McGrath et al. reports the construction of a genetic linkage map in sugar beet. This, in itself, is not new, nor is the use of relatively population-specific AFLP markers. Alone, these would not warrant publication in The Plant Genome. However, the authors made some interesting use of markers to resolve details of the sugar beet genome. They integrated their map with other maps through common markers and they used UTR regions to map members of a large gene family to eight of nine linkage groups. They showed that duplicate SSRs clustered to the same linkage group. And they demonstrated the association of their markers to a publicly available BAC library, thus providing a basis for a genetically anchored physical map.
The final Original Research article by Jia et al. addresses the complexity of pleiotropy and maize protein quality. The opaque2 mutant in maize increases nutritional quality in mutant kernels through elevated levels of lysine and other essential amino acids. However, pleiotropic effects of the mutant have negative agronomic value. The work of Jia et al. addresses the potential bases for the variety of pleiotropic effects of this mutant. These authors used microarray analyses to test two hypotheses for these effects. They carried out novel analyses in an attempt to determine the extent each proposed mechanism functions to control phenotype in different genetic backgrounds. Not so easy, it seems. Up-regulated genes supported one hypothesis, while down-regulated genes supported the other.
Forward genetics resources such as TILLING populations will play a crucial role in determining the function of genic sequences in crops. In this issue's Activities and Resources report, Weil and Monde discuss The Maize Tilling Project. The authors not only describe the mechanics of the project, but provide an excellent and concise review of TILLING and EcoTILLING. This report is timely since forward genetics will become increasingly important as the whole-genome sequence of maize is expected to be available in 2008.
Each of the papers in this issue takes a uniquely different approach to creating resources, resolving genome structure, dissecting quantitative traits, or understanding the genetics and biology of crops. As we all know, research results can sometimes be exhilarating but they always leave us with more questions to answer. If crop improvement were easy, all the problems would already be solved.
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