Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints

@article{Stansell2018GenotypingbysequencingOB,
  title={Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints},
  author={Zachary Stansell and Katie E. Hyma and Jonathan Fresnedo-Ram{\'i}rez and Qi Sun and Sharon E. Mitchell and Thomas Bj{\"o}rkman and Jian Hua},
  journal={Horticulture Research},
  year={2018},
  volume={5}
}
Brassica oleracea forms a diverse and economically significant crop group. Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm. Here, we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved B. oleracea broccoli, cauliflower, and Chinese kale entries. Ultimately, 21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among B… Expand
From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection
TLDR
This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars. Expand
Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China
TLDR
This first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli is evaluated. Expand
The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)
TLDR
The authors' analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region and several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. Expand
The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)
TLDR
The authors' analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region and identifying several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. Expand
Survey and genetic diversity of wild Brassica oleracea L. germplasm on the Atlantic coast of France
TLDR
The absence of a domestication bottleneck invited the wild French populations as the likely source of original domestication events to be excluded, and the level of genetic diversity of the wild populations was similar to, or lower than that of the cultivated crops. Expand
Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification
TLDR
High-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage, and the important roles of SVs in diversification of different morphotypes are revealed, providing insights into the regulatory network of curd development. Expand
On genetic diversity in caraway: Genotyping of a large germplasm collection
TLDR
A broad overview of population structure and genetic diversity of caraway is reported and it is suggested that the genome size of the plant should be significantly smaller than stated in literature. Expand
Feral populations of Brassica oleracea along Atlantic coasts in western Europe
TLDR
Interestingly, there were no indications of isolation by distance; several geographically close populations were genetically more distinct from each other than to distant populations, but there were signals of local adaptation to different environments, including a possible relationship between genetic diversity and soil pH. Expand
Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population
TLDR
The BolTBDH population provides a framework for B. oleracea improvement by targeting key genomic loci contributing to high horticultural quality broccoli and enabling de novo mapping of currently unexplored traits. Expand
Opening the Treasure Chest: The Current Status of Research on Brassica oleracea and B. rapa Vegetables From ex situ Germplasm Collections
TLDR
This review covers recent reports on the utilization of germplasm material to isolate genotypes of Brassica oleracea and B. rapa vegetables, focusing on high nutrient use efficiency, accumulation of biologically active metabolites, pest resistance, and favorable phenotypic appearance. Expand
...
1
2
...

References

SHOWING 1-10 OF 40 REFERENCES
Genetic Diversity and Population Structure of Collard Landraces and their Relationship to Other Brassica oleracea Crops
TLDR
The previous placement of collard with the cabbage family was confirmed through phylogenetic analysis and principal coordinates analysis (PCoA), allowing for sufficient coverage of the genome for GWAS using the physical positions of the 8273 SNPs polymorphic among the landraces. Expand
Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs)
TLDR
Molecular evidence for an ascending order of chromosome numbers in the evolution of Brassica and allied genera was obtained on the basis of RFLP data and phylogenetic analysis, suggesting that two basic evolutionary pathways exist for the diploid species examined. Expand
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
TLDR
Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture, and epigenetic mechanisms play a role in the functional diversification of duplicate genes. Expand
Genetic relationships of Brassica vegetables determined using database derived simple sequence repeats
TLDR
Polymorphism information content (PIC) values and number of alleles produced per marker ranged between 0.25 to 0.86 and 1 to 8, respectively, for database derived SSR markers. Expand
The distribution of BoCAL-a alleles in Brassica oleracea is consistent with a genetic model for curd development and domestication of the cauliflower
TLDR
A genetic model based on segregation of recessive alleles at specific, mapped loci of the candidate genes BoCAL and BoAP1 suggests that the cauliflower curd arose in southern Italy from a heading Calabrese broccoli via an intermediate Sicilian crop type. Expand
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
TLDR
This study developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS) of switchgrass, and revealed the fundamentally diploid nature of tetraploid switchgrass. Expand
Generation of a Brassica oleracea composite RFLP map: linkage arrangements among various populations and evolutionary implications
TLDR
The genealogy of chromosomes sharing duplicated segments was formulated and indicates that B. oleracea is a secondary polyploid species derived from ancestral genome(s) of fewer chromosomes. Expand
Genetic structure and domestication history of the grape
TLDR
It is proposed that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. Expand
Taxonomy and evolution of broccoli (Brassica oleracea var. italica)
TLDR
Calabrese has been the most intensively developed, being currently represented by many cultivars, including F1 hybrids, and the need to conserve existing genetic variability of existing cultivars within Cape and sprouting broccoli is stressed. Expand
Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)
TLDR
A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average, suggesting that genome-wide surveys for association analyses require SNPs every 100–200 bp. Expand
...
1
2
3
4
...