Molecular genetic analysis of a tropical synthetic (TropicS) population of maize developed for a parallel selection experiment
University of Delaware
The genetic diversity present within U.S. maize represents a small fraction of the total diversity available globally for maize. The lack of genetic diversity within U.S. maize may constrain the potential for trait improvement and it raises concerns about the vulnerability of the U.S. maize crop to biological and environmental stresses. Utilizing germplasm with unique, putatively useful variation would help to mitigate these issues, and a rich source of diversity is available in tropical maize germplasm. Adapting tropical material to temperate climates can be highly inefficient due to major genetic barriers including photoperiod sensitivity. As part of a national collaboration (Maize ATLAS project), a tropical synthetic (TropicS) population was developed from seven tropical inbred lines with the goal of using it to study the genetics of response to artificial selection on flowering time across multiple environments. Development of this resource led to two main questions: Do the parental lines contain the novel genetic diversity expected of tropical germplasm? And, how does the TropicS population relate to expectations about genetic diversity as defined by those parents? To examine genetic diversity among the parental lines, nucleotide diversity was compared to that of a tropical subpopulation of a diversity panel. Additionally, differentiation between the parental lines and a representative sample of temperate germplasm was examined using the fixation index ( FST ). Measures of nucleotide diversity showed that the parental lines contained less diversity than other subpopulations (0.271 for the parental lines vs. 0.293 for the temperate group and 0.284 for the tropical group). FST between the TropicS parents and temperate germplasm ranged from 0 to 0.8 with an average of 0.11, suggesting moderate differentiation between the two groups, with some highly differentiated regions of the genome. To examine the structure of genetic diversity in the TropicS population, tests on the expectation for allele frequencies in the population were performed and linkage disequilibrium was characterized. Allele frequencies in the TropicS were very close to the parental lines with the average shift in frequency being less than 10% and well in line with expectations due solely to genetic drift. The LD present in the TropicS was markedly reduced from that present in the parental lines with few marker pairs at long distance with a high r2 , and r 2 decaying to a rate well below 0.1 within distances of 50 Mb.