David L. Remington

Structure of linkage disequilibrium and phenotypic associations in the maize genome

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r2 < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.

Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families

The complete genomic sequence for Arabidopsis provides the opportunity to combine phylogenetic and genomic approaches to study the evolution of gene families in plants. The Aux/IAA and ARF gene families, consisting of 29 and 23 loci in Arabidopsis, respectively, encode proteins that interact to mediate auxin responses and regulate various aspects of plant morphological development. We developed scenarios for the genomic proliferation of the Aux/IAA and ARF families by combining phylogenetic analysis with information on the relationship between each locus and the previously identified duplicated genomic segments in Arabidopsis. This analysis shows that both gene families date back at least to the origin of land plants and that the major Aux/IAA and ARF lineages originated before the monocot-eudicot divergence. We found that the extant Aux/IAA loci arose primarily through segmental duplication events, in sharp contrast to the ARF family and to the general pattern of gene family proliferation in Arabidopsis. Possible explanations for the unusual mode of Aux/IAA duplication include evolutionary constraints imposed by complex interactions among proteins and pathways, or the presence of long-distance cis-regulatory sequences. The antiquity of the two gene families and the unusual mode of Aux/IAA diversification have a number of potential implications for understanding both the functional and evolutionary roles of these genes.

Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda

Abstract  De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.

A genetic map of maritime pine based on AFLP, RAPD and protein markers

Abstract TheAFLP (amplified fragment length polymorphism) technique was adapted to carry out genetic analysis in maritime pine, a species characterized by a large genome size (24 pg/C). A genetic linkage map was constructed for one F1 individual based on 239 AFLP and 127 RAPD (randomly amplified polymorphic DNA) markers. Markers were scored on megagametophytes (1n) from 200 germinated F2 seedlings. Polymorphism rate, labour time and cost of both AFLP and RAPD techniques were compared. The AFLP technique was found to be twice as fast and three-times less costly per marker than the RAPD technique. Thirteen linkage groups were identified with a LOD score ≥6 covering 1873 cM, which provided 93.4% of genome coverage. Proteins were extracted from needles (2n) of the F2 progeny and revealed by 2-DE (two-dimensional electrophoresis). Thirty one segregating proteins were mapped using a QTL detection strategy based on the quantification of protein accumulation. Two framework maps of the same F1 individual are now available. The first map (Plomion et al. 1996) uses RAPD markers and the second map, presented in this study, uses mostly AFLP markers. Although the total genetic length of both maps was almost identical, differences among homologous groups were observed.

Candidate genes, quantitative trait loci, and functional trait evolution in plants

Two key characteristics of the neo‐Darwinian synthesis in evolutionary biology have been its emphasis on the importance of mutations of small effect (micromutationism) and the view that studies of individual gene function shed relatively little light on evolutionary processes. Recent advances in molecular biology, however, have broken down many of the barriers between functional and evolutionary inquiry, opening the door to detailed studies of the genetic basis of functional trait evolution in plants. In this article, we review the insights into plant evolution that have been provided by molecular methods and address future research needs. Quantitative trait locus (QTL) mapping in crop and model plants has shown that individual loci often have large effects on trait variation, at variance with the micromutationist perspective. Evidence so far indicates that QTLs with large effects are also important in wild populations, underlying interspecific differences as well as intraspecific variation. Isolation of some of these QTLs, in particular for flowering time variation, has revealed a prominent role for regulatory genes known to function in regulation of flowering and exposed the complexity of regulatory processes. Preliminary evidence indicates that plant growth variation may be directly regulated rather than primarily the indirect result of selection on constituent processes. Future research should expand the number of traits that are intensively studied and make greater use of QTL mapping in wild plant taxa, especially those undergoing adaptive radiations, while continuing to draw on insights from model plants. Promising techniques include testing of candidate gene‐trait associations in wild populations, genetic mapping in hybrid zones, and microarray analyses of gene expression.

Paths to Selection on Life History Loci in Different Natural Environments Across the Native Range of Arabidopsis thaliana

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment‐specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2‐5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.

Genetic Basis of Local Adaptation and Flowering Time Variation in Arabidopsis lyrata

Understanding how genetic variation at individual loci contributes to adaptation of populations to different local environments is an important topic in modern evolutionary biology. To date, most evidence has pointed to conditionally neutral quantitative trait loci (QTL) showing fitness effects only in some environments, while there has been less evidence for single‐locus fitness trade‐offs. At QTL underlying local adaptation, alleles from the local population are expected to show a fitness advantage. Cytoplasmic genomes also can have a role in local adaptation, but the role of cytonuclear interactions in adaptive differentiation has remained largely unknown. We mapped genomic regions underlying adaptive differentiation in multiple fitness components and flowering time in diverged populations of a perennial plant Arabidopsis lyrata. Experimental hybrids for this purpose were grown in natural field conditions of the parental populations in Norway and North Carolina (NC), USA, and in the greenhouse. We found QTL where high fitness and early flowering were associated with local alleles, indicating a role of different selection pressures in phenotypic differentiation. At two QTL regions, a fitness component showing local adaptation between the parental populations also showed signs of putative fitness trade‐offs. Beneficial dominance effects of conditionally neutral QTL for different fitness components resulted in hybrid vigour at the Norwegian site in the F2 hybrids. We also found that cytoplasmic genomes contributed to local adaptation and hybrid vigour by interacting with nuclear QTL, but these interactions did not show evidence for cytonuclear coadaptation (high fitness of local alleles combined with the local cytoplasm).

Map-based cloning of quantitative trait loci: progress and prospects

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.

Local adaptation, phenotypic differentiation and hybrid fitness in diverged natural populations of Arabidopsis lyrata

Selection for local adaptation results in genetic differentiation in ecologically important traits. In a perennial, outcrossing model plant Arabidopsis lyrata, several differentiated phenotypic traits contribute to local adaptation, as demonstrated by fitness advantage of the local population at each site in reciprocal transplant experiments. Here we compared fitness components, hierarchical total fitness and differentiation in putatively ecologically important traits of plants from two diverged parental populations from different continents in the native climate conditions of the populations in Norway and in North Carolina (NC, U.S.A.). Survival and number of fruits per inflorescence indicated local advantage at both sites and aster life‐history models provided additional evidence for local adaptation also at the level of hierarchical total fitness. Populations were also differentiated in flowering start date and floral display. We also included reciprocal experimental F1 and F2 hybrids to examine the genetic basis of adaptation. Surprisingly, the F2 hybrids showed heterosis at the study site in Norway, likely because of a combination of beneficial dominance effects from different traits. At the NC site, hybrid fitness was mostly intermediate relative to the parental populations. Local cytoplasmic origin was associated with higher fitness, indicating that cytoplasmic genomes also may contribute to the evolution of local adaptation.

Complex Data Produce Better Characters

Two studies were conducted to explore the use of complex data in character description and hybrid identification. In order to determine if complex data allow the production of better characters, eight groups of plant systematists were given two classes of drawings of plant parts, and asked to divide them into character states (clusters) in two separate experiments. The first class of drawings consisted only of cotyledons. The second class consisted of triplets of drawings: a cotyledon, seedling leaf, and inflorescence bract. The triplets were used to simulate complex data such as might be garnered by looking at a plant. Each experiment resulted in four characters (groups of clusters), one for each group of systematists. Visual and statistical analysis of the data showed that the systematists were able to produce smaller, more precisely defined character states using the more complex drawings. The character states created with the complex drawings also were more consistent across systematists, and agreed more closely with an independent assessment of phylogeny. To investigate the utility of complex data in an applied task, four observers rated 250 hybrids of Dubautia ciliolata X arborea based on the overall form (Gestalt) of the plants, and took measurements of a number of features of the same plants. A composite score of the measurements was created using principal components analysis. The correlation between the scores on the first principal component and the Gestalt ratings was computed. The Gestalt ratings and PC scores were significantly correlated, demonstrating that assessments of overall similarity can be as useful as more conventional approaches in determining the hybrid status of plants.