Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

/pdf/genome-wide-association-studies-of-14-agronomic-traits-in-4ds8wectal.pdf

Genome-wide association studies of 14 agronomic traits in rice landraces

Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.

/pdf/population-genomics-of-domestic-and-wild-yeasts-1incyifh0w.pdf

Population genomics of domestic and wild yeasts

There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifi es quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased signifi cantly since its debut in plants. We have seen a more concerted effort in assembling various association-mapping populations and initiating experiments through either candidategene or genome-wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics-assisted crop improvement. L arge-scale genome-wide association analyses of major human diseases have yielded very promising results, corroborating fi ndings of previous candidategene association studies and identifying novel disease loci that were previously unknown (Th e Wellcome Trust Case Control Consortium, 2007). Th e same strategy is being exploited in many plant species thanks to the dramatic reduction in costs of genomic technologies. In contrast to the widely used linkage analysis traditional mapping research in plants, association mapping searches for functional variation in a much broader germplasm context. Association mapping enables researchers to use modern genomic technologies to exploit natural diversity, the wealth of which is known to plant geneticists and breeders but has been utilized only on a small scale before the genomics era. Owing to the ease of producing large numbers of progenies from controlled crosses and conducting replicated trials with immortal individuals (inbreds and recombinant inbred lines, RILs), association mapping in plants may prove to be more promising than in human or animal genetics. In the current review,

/pdf/status-and-prospects-of-association-mapping-in-plants-h5kcg1ymdj.pdf

Status and Prospects of Association Mapping in Plants

Plants, like other eukaryotes, rely on proteolysis to control the abundance of key regulatory proteins and enzymes. Strikingly, genome-wide studies have revealed that the ubiquitin-26S proteasome system (UPS) in particular is an exceedingly large and complex route for protein removal, occupying nearly 6% of the Arabidopsis thaliana proteome. But why is the UPS so pervasive in plants? Data accumulated over the past few years now show that it targets numerous intracellular regulators that have central roles in hormone signalling, the regulation of chromatin structure and transcription, tailoring morphogenesis, responses to environmental challenges, self recognition and battling pathogens.

The ubiquitin–26S proteasome system at the nexus of plant biology

To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis.

/pdf/the-rate-and-molecular-spectrum-of-spontaneous-mutations-in-ywopsnbxvd.pdf

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ∼4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

https://science.sciencemag.org/content/sci/317/5836/338.full.pdf

Glenn Fu

Papers

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.