Dataset Information

Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum.

ABSTRACT: To study the genetic architecture of anther exsertion, a trait under stabilizing selection in wild radish, artificial selection on anther exsertion was applied for 11 generations. Two replicate lines each of increased and decreased exsertion plus two randomly-mated controls were included. Full pedigree information is available from generation five. To estimate correlated responses to selection, 571 plants from all lines and matrilines were grown in the greenhouse and a number of floral, growth, and phenology traits were measured. To create an outbred F2 mapping population, all possible crosses among the two high and two low exsertion lines were made, using a multiple-family design to capture the genetic variance still present after 11 generations of selection. Six floral traits were measured on 40 parents, 240 F1, and 4,868 F2 offspring. Opportunities for reuse of these data include traits not previously analyzed, other analyses, especially using the pedigree and fitness data, and seeds from all generations and photos of flowers in the later generations are available.

SUBMITTER: Conner JK

PROVIDER: S-EPMC4322571 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum.

Conner Jeffrey K JK Mills Cynthia J CJ Koelling Vanessa A VA Karoly Keith K

Scientific data 20140902

To study the genetic architecture of anther exsertion, a trait under stabilizing selection in wild radish, artificial selection on anther exsertion was applied for 11 generations. Two replicate lines each of increased and decreased exsertion plus two randomly-mated controls were included. Full pedigree information is available from generation five. To estimate correlated responses to selection, 571 plants from all lines and matrilines were grown in the greenhouse and a number of floral, growth, ...[more]

PMID: 25977784

Similar Datasets

Project description:BackgroundRadish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized.ResultsIn this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred.ConclusionComprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.

Project description:Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.

Dataset Information

Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum.

Publications

Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets