Mapping the genetic basis of natural variation in Arabidopsis thaliana using a heterogenous stock

Most traits of economical and evolutionary interest are complex. Complex traits are usually the product of the interaction of many genes of small effect, and tend to be affected by environmental effects. Thus, traditional genetic approaches used to identify single genes of large effect are not appropriate. Currently, the best approach to map and identify these genes is through quantitative trait locus (QTL) analysis. This analysis uses statistical associations between genetic markers and traits to identify chromosomal segments that contain genetic factors (QTL) affecting the trait being studied. Most QTL mapping studies use designs that involve a cross between two inbred parental lines that differ for the trait being studied. While this approach has been successful, it usually allows the identification of only a few QTL for which the two lines differ. In addition, the confidence intervals associated with these QTL tend to be large, requiring further studies to identify the QTL before it can be cloned. More importantly, QTL are identified in a simple background which may not be relevant to the usual complex genetic background in which gene expression occurs in plants. The goal of this proposal is to identify the genetic factors that underlie life-history traits (such as germination rate, growth, flowering time, and fruit production) with precision, in a complex genetic background (as in real plant populations). To achieve this goal, we propose to develop a set of Recombinant Inbred Lines from a Heterogeneous Stock (RIHS) in the plant Arabidopsis thaliana. These lines will be derived from a cross between 19 parental lines. Because these lines will have higher genetic and phenotypic diversity than current resources, they can be used to detect a larger number of genetic factors for a larger number of traits. In addition, RIHS allow the localization of these factors with more precision (i.e. smaller confidence intervals), facilitating the cloning of the actual gene from the QTL results. A. thaliana, the primary model system for the study of plant genetics, is an ideal plant in which to develop these new mapping lines. Extensive genomic tools will facilitate cloning QTL. In addition, because A. thaliana is in the same family as a number of important crops (rape seed, cabbage, broccoli and other mustards), genes identified in this model species will allow the identification of homologous genes that can be used to improve crop quality and productivity. Seeds from the RIHS being produced here, together with data on their genotypes and phenotypes will be made publicly available, improving the ability of the scientific community to study the genetic basis of complex traits in plants.

The goal of this proposal is to fine-map QTL that affect life-history traits in a genetically complex background. Most traits of economical and evolutionary interest, such as yield, disease resistance and growth are complex. Complex traits are usually the product of the interaction of many genes of small effect, and tend to be affected by environmental effects. Currently, the best approach to map and identify these genes is through Quantitative trait locus (QTL) analysis. Most QTL mapping studies use designs that involve a cross between two homozygous parental lines. Here, we propose to develop Recombinant Inbred Lines from a Heterogeneous Stock of A. thaliana (RIHS), which will be derived from a heterogeneous stock formed by the intermating of 19 accessions. Because RIHS include alleles from 19 different accessions, they capture higher allelic and phenotypic diversity than traditional recombinant inbred lines (RIL). Thus, RIHS has the potential to identify a larger number of QTL and their genetic interaction. In addition, due to the increased number of recombination events, RIHS allow the localization of QTL with more precision (i.e. smaller confidence intervals) than current RIL, facilitating future QTL cloning. More importantly, RIHS allow the detection of QTL in a complex background, uncovering gene functions in conditions that more similarly mimic the natural populations. The development of this mapping panel in A. thaliana, the primary model system for the study of plant genetics, will further expedite QTL cloning, and subsequent identification of homologous genes in crop species. Mapping will be accomplished using multipoint analysis, and will be implemented using a modification of the HAPPY software. Seeds from the RIHSs, together with their genotype and phenotype data will be made publicly available, improving the ability of scientific community to study the genetic basis of complex traits in plants and their response to the environment.