Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

Pomper, Kirk W.; Lowe, Jeremiah D.; Lu, Li; Crabtree, Sheri B.; Dutta, Shandeep; Schneider, Kyle J.; Tidwell, James H.

doi:10.21273/jashs.135.2.143

Cited by 16 publications

(9 citation statements)

References 40 publications

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“…and are pollinated by weak‐flying beetles and flies (Muscidae and Sacrophagidae) (Goodrich et al., 2006; Kral, 1997; Willson & Schemske, 1980). Asimina triloba is strongly self‐incompatible (Pomper et al., 2010) and produces the largest (5–16 cm long, 3–7 cm wide) edible fruits (berries) of any native North American tree. It is hypothesized that seeds were formerly dispersed by now extinct megafauna while today seeds are typically dispersed by raccoons, coyotes and foxes (Cypher & Cypher, 1999; Willson, 1993; Yeager & Elder, 1945; Wyatt, pers.…”

Section: Methodsmentioning

confidence: 99%

Ecological niche modelling and phylogeography reveal range shifts of pawpaw, a North American understorey tree

Wyatt

Hamrick

Trapnell

2021

Journal of Biogeography

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Aim Predictions of species' responses to accelerating global climate change require an understanding of historical range shifts. However, large‐scale phylogeographical studies of Eastern North American understorey plant taxa are relatively scarce. Here we employ ecological niche modelling and genetic analyses for inference of optimal pawpaw habitat in the past and future. Location In all, 26 states in the eastern United States. Taxon Asimina triloba (L.) Dunal (Annonaceae). Methods The present‐day niche of Asimina triloba was modelled in Maxent using seven bioclimatic variables, elevation and location data from field samples and herbarium specimens. To model historically optimal habitats, the present‐day model was projected onto rasters of seven bioclimatic variables and elevation representing the last glacial maximum (~22,000 years before present [YBP]) and the mid‐Holocene (~6,000 YBP). Predicted habitat suitability for 2070 was also modelled. Additionally, 62 populations were genotyped with nine nuclear microsatellite loci and statistically analysed. Levels and partitioning of genetic variation within and among populations were estimated within a geographical context. Results Models indicate that optimal habitat 22,000 YBP was severely restricted to mostly now‐submerged Gulf of Mexico and southeastern US coastlines. By 2070, models suggest that optimal habitat will expand substantially northward relative to the present. Species‐level genetic diversity (HE = 0.765) is high and genetic structure among populations is moderate (GST = 0.202). Structure indicates that there are two population clusters straddling the Appalachian Mountains. Main conclusions Models suggest that 22,000 YBP A. triloba was restricted to two major refugia in narrow bands of mostly now‐submerged habitat and possibly several small inland refugia. Molecular data are consistent suggesting that the eastern refugia expanded to give rise to the eastern cluster which is characterized by higher genetic diversity. The Gulf of Mexico refugium likely gave rise to populations in the western cluster, which is characterized by lower genetic diversity.

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Section: Methodsmentioning

confidence: 99%

Ecological niche modelling and phylogeography reveal range shifts of pawpaw, a North American understorey tree

Wyatt

Hamrick

Trapnell

2021

Journal of Biogeography

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“…Both inter-simple sequence repeat (ISSR) and SSR markers based on the polymerase chain reaction (PCR) are commonly used for measuring genetic diversity [ 16 , 17 ] and for cultivar identification [ 18 , 19 ]. ISSR analyses are easy to perform, are inexpensive, and do not require prior genetic information [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

Jia

Wang

Zhai³

et al. 2011

Molecules

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Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

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“…Supplemental Table S3. SSR data values for 5 loci from 2010 Asimina triloba (Pawpaw) study of Pomper et al [32]. Suffix _.F refers to forward SSR primer, _.R to reverse.…”

Section: A Topological Approachmentioning

confidence: 99%

Untitled

2022

IJCSA

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Hardly a week seems to go by without encountering a new genetics study that contains a diagram of specimen genetic similarities and clades. For these diagrams, biologists have long relied on universitybased and/or commercial computational packages which are not only prone to pilot errors but also contain "analysis" methods which should never be used for genetic distance or clustering. Not that all the software is poorit appears there is a mixture of good and bad in each package. The troublesome methods, however, have enjoyed acceptable use for so long that serious errors are published on a frequent basis. What follows is a list of concerns that will hopefully be useful to authors and reviewers alike. The report concludes with a graph-theoretical alternative to the current status quo in genomics.

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Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

Cited by 16 publications

References 40 publications

Ecological niche modelling and phylogeography reveal range shifts of pawpaw, a North American understorey tree

Ecological niche modelling and phylogeography reveal range shifts of pawpaw, a North American understorey tree

Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

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