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

Stansell, Zachary; Hyma, Katie E.; Fresnedo-Ramírez, Jonathan; Sun, Qi; Mitchell, Sharon E.; Björkman, Thomas; Hua, Jian

doi:10.1038/s41438-018-0040-3

Cited by 41 publications

(41 citation statements)

References 31 publications

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“…The traces of these events can be seen in both oat and wheat where varieties available prior to the 1960's have higher genetic diversity than cultivars released later (Fu, et al, 2003;Roussel, et al, 2005;Cavanagh, et al, 2013). Similarly, landrace broccoli (Brassica oleracea var italica) has been shown to carry 8.4 times as many unique alleles as its improved counterpart (Stansell, et al, 2018). This pattern is less clear in barley, where reduced diversity can only be found to affect certain traits, whereas overall diversity has not changed significantly when comparing 19 th century and modern varieties of Nordic and Baltic materials (Kolodinska Brantestam, 2005).…”

Section: Landracesmentioning

confidence: 99%

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Lundström

2018

Linköping Studies in Science and Technology. Dissertations

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Crop plants have undergone a multitude of genetic changes during and following their domestication. The spread of agriculture brought the crops to new geographic regions exposing them to new environments and selection pressures along the way. This gave rise to many local variants with traits favoured both by agricultural practices and the environment. Agriculture was introduced in Fennoscandia (Norway, Sweden, Finland and Denmark) around 4000 BC. The composition of the archaeobotanical record gives some clues as to which species were cultivated, but macroscale analyses rarely reach beyond that. Therefore, methods like genetic analysis are necessary to expand our knowledge about the history of crop cultivation. Under optimal conditions, DNA can survive in biological samples for several hundred thousand years. The preservation of plant specimens in the Fennoscandian climate has, however, rarely been explored. This thesis therefore attempts to dive deeper into the Fennoscandian cultivation history through genetic analyses of aged plant materials from both museum collections and archaeological sources. Cereal grains from a range of preservation conditions were evaluated to find which ones might be of interest for genetic investigations. Desiccated materials gave the highest success rates, in agreement with previous studies. Waterlogged materials appeared to contain small amounts of endogenous DNA, whereas genetic analysis of charred cereals failed completely in all samples. Population structure was investigated in 17-19 th century materials of both barley and rye from Sweden and Finland. Northern and southern populations of Finnish six-row barley were distinct from one another. In southern Sweden, genetic analysis suggested conserved population structure extending over 200 years. The genetic composition of rye also seemed mostly conserved, but rye did not show geographic population structure across the investigated region in Sweden and Finland. A long-standing question in Fennoscandian crop history has been the interpretation of historical written records mentioning Brassica (cole crops, turnips and mustards), as well as the species identity of archaeobotanical finds of Brassica seeds. Thus, Next Generation Sequencing (NGS) was applied to identify which Brassica types that were cultivated in 17 th century Kalmar, Sweden. The analysis corroborated morphological species classification in two of the investigated subfossil seeds, whereas no conclusions could be drawn from the remaining samples. The genome coverages were too low to allow subspecies identification. Wheat has been cultivated in Fennoscandia since the introduction of agriculture but has increased dramatically in importance over the last century. The functional allele of the wheat nutrition gene NAM-B1 was found to be particularly prominent in Fennoscandian wheats, likely associated with its effect on grain maturation time. Here the evolutionary history of NAM-B1 was investigated to see if it could truly be considered a domestication gene as suggested in a pr...

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Section: Landracesmentioning

confidence: 99%

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Lundström

2018

Linköping Studies in Science and Technology. Dissertations

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“…In recent years, considerable progress understanding the B. oleracea crop group has been made. Specifically, several key objectives have been accomplished: parsing fundamental genomic architecture [3][4][5] , publication of high-quality reference genomes [6][7][8] , evaluating diversity and domestication processes [9][10][11][12][13][14][15][16][17][18][19][20][21] , and identifying genomic regions or candidate genes associated with horticultural quality [22][23][24][25][26][27] and biotic/abiotic stress resistance [28][29][30][31][32][33][34][35] .…”

Section: Introductionmentioning

confidence: 99%

“…While modern broccoli cultivars are distinct from their landrace precursors in heading induction requirement, time to maturity, crown size and architecture, and secondary metabolic profile 14,17,[36][37][38][39][40][41][42][43][44] , the basis for these dramatic changes remains largely unexplored using genomics era tools, such as genotype-by-sequencing. Here, we build on previous work by clarifying the relationship of elite broccoli germplasm within a larger pool of italica germplasm, and characterize the genomic and phenotypic changes that occurred during this improvement process 16 .…”

Section: Introductionmentioning

confidence: 99%

“…The tropical cauliflower type was first bred in 19 th century India and is now common in Southeast Asian markets, typically producing cauliflower-like heads above 22°C and broccoli-like heads below 16°C 36,60,61 . Violet and tropical cauliflower vegetables appear as italica/botrytis intermediates in morphologic and population structure analyses 16,29,47 . It is currently unclear if these intermediates exist as recent hybrids or are derived from an ancestral breeding pool.…”

Section: Introductionmentioning

confidence: 99%

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From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection

Stansell

Björkman

2020

Hortic Res

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Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.

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“…There might appear some mistakes in sampling error, mutation and complex bioinformatics analysis, making it hard to apply to deeper timescale studies. But nonetheless, NGS has still successfully helped many researchers to understand the phylogeny for some representative family members of plants [20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Application of genotyping-by-sequencing data on inferring the phylogeny of Curcuma (Zingiberaceae) from China

Liang¹,

Yan²,

Deng³

et al. 2019

Preprint

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Background: Genotyping-by-sequencing (GBS), as one of the next generation sequences, has been applied to large scale genotyping in plants, which is poor in morphological differentiation and low in genetic divergence among different species. Curcuma is a significantly medicinal and edible genus. Improvement efforts of phylogenetic relationships and disentangling species are still a challenge due to poor morphology and lack in a reference genome. Result: A high-throughput genomic sequence data which was obtained through GBS protocols was used to investigate the relationships among 8 species with 60 total samples of Curcuma. Through the use of the ipyrad software, 437,061 loci and 997,988 filtered SNPs without reliance upon a reference genome were produced. After quality control (QC) of the filtered SNPs, 1,295 high-quality SNPs were used to clarify the phylogenetic relationships among Curcuma species. Based on these data, a supermatrix approach was used to speculate the phylogeny, and the phylogenetic trees and the relationships were inferred . Conclusions: Varying degrees of support can be explained, as well as the diversification events for Chinese Curcuma. The diversification events showed that the third intense uplift of Qinghai–Tibet Plateau (QTP) and formation of the Hengduan Mountains may speed up Curcuma interspecific divergence in China. The PCA suggested the same topology of the phylogenetic tree. The genetic structure analysis revealed that extensive hybridization may exist in Chinese Curcuma. Additionally, the GBS will be a promising approach for the phylogenetic and systematic study in the future.

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

Cited by 41 publications

References 31 publications

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection

Application of genotyping-by-sequencing data on inferring the phylogeny of Curcuma (Zingiberaceae) from China

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