A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

5 7Carrot (Daucus carota subsp. carota L.; 2n = 2x = 18) is a globally important root crop whose production has quadrupled between 1976 and 2013 (FAO Statistics; see URLs), outpacing the overall rate of increase in vegetable production and world population growth (FAO Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions 1 .The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago 2,3 , with orange carrots not reliably reported until the sixteenth century in Europe 4,5 . The popularity of orange carrots is fortuitous for modern consumers because the orange pigmentation results from high quantities of alpha-and beta-carotene, making carrots the richest source of provitamin A in the US diet 6 . Carrot breeding has substantially increased nutritional value, with a 50% average increase in carotene content in the United States as compared to 40 years ago 6 . Lycopene and lutein in red and yellow carrots, respectively, are also nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation.Carrot is the most important crop in the Apiaceae family, which includes numerous other vegetables, herbs, spices, and medicinal plants that enhance the epicurean experience 7 , including celery, parsnip, arracacha, parsley, fennel, coriander, and cumin. The Apiaceae family belongs to the euasterid II clade, which includes important crops such as lettuce and sunflower 8 . Genome sequences of euasterid I species have been reported, but only two genomes 9,10 have been published among the other euasterid II species.Here we report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions caro...

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“…GBS libraries were prepared as described by Elshire et al 71 , with minimal modification. TASSEL version 4.3.11 (ref.…”

Section: Methodsmentioning

confidence: 99%

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

et al. 2016

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“…A total of 558 DNA samples that fulfilled the quality and quantity criteria (DNA of high molecular weight, with at least 40 μl of DNA available at a concentration >10 ng/μl) were then sequenced. Individuals were genotyped using genotyping‐by‐sequencing technique (GBS) based on the use of restriction enzyme digestion to sequence a reduced portion of the genome (Elshire et al., 2011). Libraries were constructed using restriction enzyme ApeKI (recognition site: GCWGC) following a protocol modified from Elshire et al.…”

Section: Methodsmentioning

confidence: 99%

“…Libraries were constructed using restriction enzyme ApeKI (recognition site: GCWGC) following a protocol modified from Elshire et al. (2011). Six 96‐plex GBS libraries were prepared and sequenced at the Institute of Genomic Diversity at Cornell University using the Illumina HiSeq 2500 (100 bp, single‐end reads).…”

Section: Methodsmentioning

confidence: 99%

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Dalongeville

Andrello

Mouillot

et al. 2018

Evolutionary Applications

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Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db‐MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000 km), while larval dispersal was the major predictor at smaller spatial scale (<1,000 km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping‐stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.

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“…2011). Briefly, a total of 190 A. artemisiifolia genomic DNA extracts were digested with the restriction enzyme ApeKI (4.5‐bp recognition site 5′ ‐GCWGC ‐3′ ).…”

Section: Methodsmentioning

confidence: 99%

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Martin

Olsen

Samaniego

et al. 2016

Ecology and Evolution

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Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind‐pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native‐range populations has been described as rapid evolution. However, a recent study demonstrated major human‐mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native‐range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine‐scale population genetic structure across the species' native range, we characterized diallelic SNP loci via a reduced‐representation genotyping‐by‐sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.

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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

Cited by 5,346 publications

References 39 publications

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

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