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International Team Develops Corn Genetics Resource

NEW YORK (GenomeWeb News) – An international research team has developed a new resource for mapping the genetics underlying complex traits in corn.

The researchers created the collection of maize varieties, dubbed the maize Nested Association Mapping, or NAM, population, by crossing the corn genetic reference strain with dozens of other corn varieties and then self-crossing the offspring for several generations to create thousands more lines. They then used genetic mapping in the NAM population to delve into the genetics behind corn flowering time, demonstrating that many loci contribute to the process. The work appears in a pair of papers appearing online today in Science.

Together, their results suggest that identifying quantitative trait loci, or QTLs, for corn may not be as simple as once imagined, since many small changes contribute to traits in the plant. Even so, those involved in the new research say that developing a new mapping population in corn opens the door for improved corn genetics and breeding programs.

"These findings will be a big help in the future," James Holland, a crop science researcher affiliated with NC State and the US Department of Agriculture, said in a statement. "We can now take a complicated trait, identify gene regions involved in the trait, and then use that information in breeding to ensure the best combinations of genes from different sources or varieties."

In the first of the papers, lead author Michael McMullen, a geneticist affiliated with the USDA's Agricultural Research Service and the University of Missouri, and his colleagues described how they developed the NAM population by crossing the B73 corn reference line, which was used for the Maize Sequencing Project, with 25 inbred maize lines. The effort ultimately generated 4,699 recombinant inbred lines belonging to 25 corn families.

Within this population, McMullen and his co-workers identified roughly 136,000 recombination events (about three crossovers per gene, on average, though there were differences in recombination rates between corn families). The population contains at least 1,106 SNPs, the team reported. And of these, between 63 percent and 74 percent were polymorphic in any given family tested.

The researchers also explored a potential relationship between recombination heterozygosity patterns near centrosomes and a phenomenon called heterosis, or hybrid vigor, in which crosses between different strains result in improvements in offspring compared with either parent strain.

Meanwhile, for the second paper, lead author Edward Buckler, a genetics researcher affiliated with USDA-ARS and Cornell University, and his colleagues used the new corn population set to examine the QTLs involved in corn flowering time.

By looking at nearly a million plants grown in four different locations over two years, the researchers found that between 29 and 56 QTLs — each of small effect — contribute to flowering time. That's far more than detected in Arabidopsis, in which flowering is thought to be controlled by just a few QTLs.

Among the flowering QTLs detected, the researchers did not see any large effects related to geography or environmental interactions. "Our results suggest that for the outcrossing species, the genetic architecture of flowering time is dominated by small additive QTLs with few genetic or environmental interactions (within the tested range of environments)," Buckler and his co-authors wrote.

In a perspectives paper also appearing in Science, North Carolina State University geneticist Trudy Mackay, who was not involved with either study, likened the corn NAM population to genetic analysis resource populations generated by projects such as the mouse collaborative cross, the Drosophila Genetic Reference Panel, and the Arabidopsis 1001 Genomes Project.

"This NAM population can be used for initial QTL detection using linkage mapping with moderate numbers of markers, followed by a second stage of high-resolution association mapping in QTL regions that capitalizes on a high-density marker map within each diverse strain," Mackay explained.

Nevertheless, Mackay noted, more work is needed to genotype the parental strains using a dense panel of molecular markers before the new mapping population can be used for high-resolution studies of corn genetics. And, she noted, "The large numbers of QTLs, small effects, and likelihood of identifying novel genes affecting quantitative traits from dissection of natural genetic variation pose a challenge for functional validation."