SUMMARYWe explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species-and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.

Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach.

BackgroundRecently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution.ResultsWe perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis.We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.ConclusionsOur analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0415-1) contains supplementary material, which is available to authorized users.

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Abstract-Dopamine and angiotensin II negatively interact to regulate sodium excretion and blood pressure. D 3 dopamine receptors downregulate angiotensin type 1 (AT 1 ) receptors in renal proximal tubule cells from normotensive Wistar-Kyoto rats. We determined whether AT 1 receptors regulate D 3 receptors and whether the regulation is different in cultured renal proximal tubule cells from normotensive and spontaneously hypertensive rats. Angiotensin II (10 Ϫ8M/24 hours) decreased D 3 receptors in both normotensive (control, 36Ϯ3; angiotensin II, 24Ϯ3 U) and hypertensive (control, 30Ϯ3; angiotensin II, 11Ϯ3 U; nϭ9 per group) rats; effects that were blocked by the AT 1 receptor antagonist, losartan (10 Ϫ8 M/24 hours). However, the reduction in D 3 expression was greater in hypertensive (60Ϯ10%) than in normotensive rats (32Ϯ9%). In normotensive rats, angiotensin II (10 Ϫ8 M/24hr) also decreased AT 1 receptors. In contrast, in cells from hypertensive rats, angiotensin II increased AT 1 receptors. AT 1 and D 3 receptors coimmunoprecipitated in renal proximal tubule cells from both strains. Angiotensin II decreased D 3 /AT 1 receptor co-immunoprecipitation similarly in both rat strains, but basal D 3 /AT 1 co-immunoprecipitation was 6 times higher in normotensive than in hypertensive rats. Therefore, AT 1 and D 3 receptor interaction is qualitatively and quantitatively different between normotensive and hypertensive rats; angiotensin II decreases AT 1 expression in normotensive but increases it in hypertensive rats. In addition, angiotensin II decreases D 3 expression to a greater extent in hypertensive than in normotensive rats. Aberrant interactions between D 3 and AT 1 receptors may play a role in the pathogenesis of hypertension. Key Words: receptors, dopamine Ⅲ receptors, angiotensin II Ⅲ rats, spontaneously hypertensive Ⅲ kidney T he proximal tubule is a major site of salt and water reabsorption in the mammalian nephron, with up to 60% of the filtrate reabsorbed in this segment. 1,2 Renal proximal tubule (RPT) function is under hormonal control, with angiotensin II stimulating sodium reabsorption via activation of apical Na ϩ /H ϩ exchanger and basolateral [Na ϩ ]/[K ϩ ]ATPase, and with dopamine inhibiting reabsorption by inhibiting these proteins. [3][4][5] The paracrine regulation of sodium reabsorption in the proximal tubule by the renin-angiotensin system occurs via several angiotensin receptor subtypes (AT 1 , AT 2 , and AT 4 ). [5][6][7][8] The activation of AT 1 receptors by angiotensin II increases sodium transport, whereas the activation of AT 2 and AT 4 receptors decreases sodium reabsorption in this nephron segment. [5][6][7][8] However, under physiological conditions, the major effect of angiotensin II on sodium transport is stimulatory, via AT 1 receptors. [5][6][7][8] The dopaminergic system also exerts a paracrine regulatory role on renal sodium transport in the proximal tubule via several receptor subtypes. Dopamine receptors, pharmacologically grouped into D 1 -like (D 1 and D 5 ) and D 2 -like...

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