Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.

SUMMARYThe majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F 2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.

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The process of strong artificial selection during a domestication event is modeled, and its effect on the pattern of DNA polymorphism is investigated. The model also considers population bottleneck during domestication. Artificial selection during domestication is different from a regular selective sweep because artificial selection acts on alleles that may have been neutral variants before domestication. Therefore, the fixation of such a beneficial allele does not always wipe out DNA variation in the surrounding region. The amount by which variation is reduced largely depends on the initial frequency of the beneficial allele, p. As a consequence, p has a strong effect on the likelihood of detecting the signature of selection during domestication from patterns of polymorphism. These theoretical results are discussed in light of data collected from maize. Although the main focus of this article is on domestication, this model can also be generalized to describe selective sweeps from standing genetic variation.population genetics ͉ theory ͉ coalescent ͉ domestication selection A rtificial selection is believed to be the main evolutionary force acting on domesticated species since their origin 5,000-10,000 years ago. During domestication, humans exercised extremely strong selective pressure on ancestral gene pools to achieve desired phenotypic characteristics. These beneficial phenotypes were therefore fixed in the founder population of domesticated species in a short (probably very short) time. These fixation events differ from the fixation of an advantageous mutant in a natural population, in that artificial selection in a domestication event acts on an allele that was likely a neutral or nearly neutral variant before domestication. In other words, domestication causes some neutral polymorphisms in the ancestral population of the wild progenitor species to suddenly become very advantageous in the small founder population, the progenitor of the domesticated species. Therefore, the initial frequency of a beneficial allele (p) before domestication is not necessarily low. In contrast, the initial frequency of an advantageous mutant in a regular selective sweep model is 1͞(2N) (1), where N is the diploid population size. Hence, models developed to describe selective sweeps in natural populations may not be appropriate for cases in which alleles are fixed from standing genetic variation, such as has been described for an amino acid variant at the CAULIFLOWER gene in Brassica (2).In this article, a model for this process of strong artificial selection during a domestication event is developed. In addition to artificial selection, the model incorporates a population size bottleneck during domestication so that the level of polymorphism in the cultivated species is expected to be lower than that in its wild progenitor species (3, 4). In cultivated crops, polymorphism is typically reduced by 60-80% (5). Under this model, the patterns of DNA polymorphism both with and without selection are studied to understand the genetic ...

Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of flowering time in cultivated rice are not known. We used a core collection of 64 rice cultivars that represent the genetic diversity of 332 accessions from around the world and studied the expression levels and polymorphisms of 6 genes in the short-day flowering pathway. The RNA levels of Heading date 3a (Hd3a), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of Hd3a expression. Functional and nonfunctional alleles of Hd1 are associated with early and late flowering, respectively, suggesting that Hd1 is a major determinant of variation in flowering time of cultivated rice. We also found that the type of Hd3a promoter and the level of Ehd1 expression contribute to the diversity in flowering time and Hd3a expression level. We evaluated the contributions of these 3 factors by a statistical analysis using a simple linear model, and the results supported our experimental observations.) has evolved during the last 8,000 to 10,000 years of domestication and breeding (1, 2). A major reason for the spread of rice cultivation to a wide range of geographical regions, and for the increases in yield, is the diversification of flowering time (1). In general, rice is known as a short-day plant that induces transition from the vegetative phase to the reproductive phase when it senses a decrease in day length. The molecular genetic pathway for short-day flowering in cultivated rice (Fig. 1A) is relatively well characterized (3-5). Signals from light and circadian clocks are received by OsGI, the rice orthologue of Arabidopsis GIGANTEA, and it regulates expression of Heading date 1 (Hd1) and OsMADS51 (6-8). Hd1 and its Arabidopsis orthologue CONSTANS encode zinc-finger type transcriptional activators with the CO, CO-like, and TOC1 (CCT) domains (9). Hd1 regulates Heading date 3a (Hd3a) expression (7, 9, 10). Hd3a is a rice orthologue of Arabidopsis FLOWERING LOCUS T (FT), and these genes recently were shown to encode a mobile flowering signal (11-16). RICE FLOWERING LOCUS T1 (RFT1) belongs to the rice FT-like gene family and functions as a floral activator, acting redundantly with Hd3a (17, 18). OsMADS51 encodes a type I MADSbox gene and functions upstream of Early heading date 1 (Ehd1) (8). Ehd1 encodes a B-type response regulator and acts as an activator of Hd3a independently from Hd1 (19). No clear orthologues of Ehd1 or OsMADS51 are found in the Arabidopsis genome. Although the genetic pathway for short-day flowering in rice is relatively well understood, the molecular mechanisms generating the diversity of flowering time in cultivated rice are not known. In this study, we analyzed the expression and nucleotide sequences of genes involved in short-day flowering in rice. Our study revealed that allelic vari...