Association Analysis of Quantitative Traits in F_1 Families Derived from Two Maize Landraces

[ Objective] The objective of this study was to evaluate the genetic diversity and characterization of special maize population consisting of 135 Fl fami- lies. [ Method ] In this study, association analysis was conducted in 135 F1 families derived from two maize landraces, and the efficiency of this method was evalua- ted through simulation. [ Result] Association analysis with different kinds of families showed that large population size and robust phenotypic data were required for association mapping. For all the phenotypic traits, the model controlling beth population structure and relative kinship （ Q ＋ K） performed better than the model controlling relative kinship （K）, and similarly to the model controlling population structure （Q）. Across 100 simulation runs in QULINE, the average power of QTL detection for the two models were 88.64% and 83.64% respectively, and the number of false QTL was reduced from 399 with GLM model to 199 with K mod- el. Our simulation results suggested that these F1 families can be used for association analysis, and the power of the QTL detection was related to the maximum al- lele frequency （MAF）and the phenotypic variation （PVE） explained by QTL. [ Conclusion] The results from this study suggest that association analysis using the F1 families is an effective approach to study maize landraces for discovering elite genes which we are interested in from these special populations.

Molecular evolution of the rice miR395 gene family

MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.