Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines

Labate, Joanne A.; Robertson, Larry D.

doi:10.1007/s11032-015-0302-9

Cited by 10 publications

(10 citation statements)

References 33 publications

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“…Leaf tissue samples were stored at −80°C until DNA was isolated. Total genomic DNA isolation was conducted using the DNeasy 96 plant kit (Qiagen, USA) with minor modifications of the protocol (Labate and Robertson, 2015 ). DNA concentration was quantified using PicoGreen reagent (Thermo Fisher Scientific, Waltham, MA) and a TECAN Infinite 200 PRO (Tecan US, Morrisville, NC) microplate reader.…”

Section: Methodsmentioning

confidence: 99%

“…To serve as a quality check for genotyping, 17 plants were sampled twice as technical replicates for GBS. Before removing duplicated samples for downstream analyses, all samples were used to generate a Neighbor-Joining tree in PHYLIP v. 3.6 (Felsenstein, 1989 ) as in Labate and Robertson ( 2015 ). All duplicated samples clustered sister to each other in the Neighbor-Joining tree with bootstrap values ranging from 87 to 100%.…”

Section: Methodsmentioning

confidence: 99%

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Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Bird

Gazave

et al. 2017

Front. Plant Sci.

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The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Bird

Gazave

et al. 2017

Front. Plant Sci.

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“…We ligated uniquely identifying barcode adapters to DNA fragments for each individual fish sequenced so that locality and biological metadata could be matched to sequence data, and we analyzed each species separately. We first removed individuals with low SNP coverage using a threshold of 0.01 proportion of sites present for each species (i.e., individuals with <1% of possible reads were removed; Labate & Robertson, ). We then filtered SNP occurrence for each species and retained only those genotyped in at least 75% of individuals (we also assessed SNP occurrences using 50% of individuals but only analyzed the more conservative 75% threshold).…”

Section: Methodsmentioning

confidence: 99%

Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning

Malone

Perkin

Leckie

et al. 2018

Global Change Biology

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Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.

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“…Although P. philadelphica has been categorized as a selfincompatible species, it is possible to find some self-compatible individuals in husk tomato crops and wild populations (Pandey, 1957;Labate and Robertson, 2015). This may be attributed to a mutation in the S locus (Mulato-Brito et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Changes in Reproductive Traits in Physalis philadelphica; An Unexpected Shift Toward Self-Incompatibility in a Domesticated Annual Fruit Crop

et al. 2021

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Domestication is an evolutionary process with an impact on plant reproduction. Many domesticated plants are self-compatible (i.e., they lack mechanisms to reject their own pollen), but few domesticated plants are fully or partially self-incompatible. We used the husk tomato, Physalis philadelphica, as a study model to investigate changes in the reproductive strategy of an annual partially self-incompatible plant during the process of domestication. Wild and cultivated populations of this species coexist in close proximity. These different populations present a high level of morphological and genetic variation associated with different degrees of domestication. We hypothesized that artificial selection favors self-compatibility in cultivated plants through changes in their reproductive strategy and some reproductive parameters associated with domestication. To test this hypothesis, we characterized the floral morphology and some reproductive parameters of weedy plants (wild plants), landraces (semi-domesticated plant), and commercial plants (domesticated plants). We conducted an artificial crossing experiment, germinated the seeds, and recorded seedling growth. Commercial plants had the largest flowers and the highest number of ovules. Yet, they did not differ in other reproductive parameters (e.g., herkogamy, size of pollen grains, stigmatic area, and pollen:ovule ratio) from landraces and weedy plants. Physalis philadelphica produced fruits by autonomous autogamy in the artificial crossing experiment. These fruits were the smallest and lightest fruits at all degrees of domestication; however, fruit set of autonomous autogamy was higher in weedy plants. In addition, fruit production was higher when weedy plants donated pollen to commercial plants. Although seeds produced by autonomous autogamy of weedy plants had a low germination percentage, their cotyledons and the embryonic foliage leaves appeared earlier than in landraces and commercial plants. In conclusion, the domestication syndrome in this plant was manifested as increments in flower size and ovule production. Contrary to expectations, there was higher fruit production by autonomous autogamy in weedy plants than in cultivated plants. It seems that artificial selection in P. philadelphica favors self-incompatibility in cultivated plants. Nonetheless, spontaneous self-pollination seems to be advantageous in weedy populations because they produced viable seeds from which cotyledons and the embryonic foliage leaves emerged earlier than in cultivated plants.

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Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines

Cited by 10 publications

References 33 publications

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning

Changes in Reproductive Traits in Physalis philadelphica; An Unexpected Shift Toward Self-Incompatibility in a Domesticated Annual Fruit Crop

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