Development of microsatellites from <i>Fothergilla</i> ×<i>intermedia</i> (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae

Hatmaker, E. Anne; Wadl, Phillip A.; Mantooth, Kristie; Scheffler, Brian E.; Ownley, Bonnie H.; Trigiano, Robert N.

doi:10.3732/apps.1400123

Cited by 7 publications

(5 citation statements)

References 9 publications

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“…eSSRs commonly display greater cross-transferability than gSSRs because they are more likely to be within functional gene sequences and therefore are typically more conserved [ 35 , 36 ]. eSSRs and gSSRs have both transferred to closely related species within and outside of their genus, including well-studied economically important agronomic crops [ 34 , 37 ] as well as a number of woody ornamental species including Cercis canadensis [ 38 ], Cornus species [ 39 ], and Fothergilla species [ 40 ].…”

Section: Introductionmentioning

confidence: 99%

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Hamm

Nowicki

Boggess

et al. 2021

Plants

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The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA sequencing and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.

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Section: Introductionmentioning

confidence: 99%

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Hamm

Nowicki

Boggess

et al. 2021

Plants

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“…Small from Tennessee (USA) was used as a negative control for amplification. Ten µl reaction amplifications were completed as described in Hatmaker et al (2015) using 75 primer pairs. The thermal cycler conditions consisted of 94°C for 3 min and 35 cycles of 94°C for 40 s, 55°C for 40 s and 72°C for 30 s, followed by 72°C for 4 min.…”

Section: Methodsmentioning

confidence: 99%

“…The thermal cycler conditions consisted of 94°C for 3 min and 35 cycles of 94°C for 40 s, 55°C for 40 s and 72°C for 30 s, followed by 72°C for 4 min. Allelic products were separated via electrophoresis using the QIAxcel Capillary Electrophoresis System (Qiagen, Valencia, California USA) and the data binned into allelic classes according to the protocols described by Hatmaker et al (2015). Data was analysed for number of alleles/locus, observed heterozygosity, expected heterozygosity, probability of deviation from HardyWeinberg equilibrium at P<0.05, Shannon's information index, and genetic differentiation (F ST ) using the program GenALEx 6.5 (Peakall and Smouse, 2012).…”

Section: Methodsmentioning

confidence: 99%

Characterization of thirteen microsatellite loci from the Ghanian antimalarial plant Cryptolepis sanguinolenta

Amissah¹,

Wadl²,

Hadziabdic³

et al. 2016

J. Med. Plants Res.

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Cryptolepis sanguinolenta (Lindl.) Schlechter (Periplocaceae) is an herbaceous plant used in traditional medicine to treat malaria and populations of the species are diminishing due to overharvesting and lack of conservation. Codominant microsatellite markers that can be used to characterize genetic diversity and population structure are currently not available. Therefore, the study isolated 75 microsatellite loci from genomic sequence data, which were then screened for the ability to reveal polymorphisms. From the 75 candidate loci, 13 polymorphic microsatellite loci were optimized for future population genetics studies. Twenty-two C. sanguinolenta samples were collected from eight different geographical locations in Ghana. Alleles per locus ranged from 3 to 7 with a mean of 4.4. Expected heterozygosity ranged from 0.24 to 0.77, and all but one locus deviated significantly from Hardy-Weinberg equilibrium. Genetic differentiation mean was 0.06 among all loci, indicating relatively low genetic diversity in these samples. These microsatellite loci should be useful to study genetic diversity, gene flow and population structure as well as in a project involving breeding and conservation of C. sanguinolenta.

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“…For subfam. Hamamelidoideae, some simple sequence repeat (SSR) markers have been developed for Fothergilla × intermedia Ranney & Fantz (Hatmaker et al., ), Chunia bucklandioides H. T. Chang (Meng et al., ), Distylium lepidotum Nakai (Sugai and Setsuko, ), and Sinowilsonia henryi Hemsl. (Li et al., ), yet PCR amplifications have showed low transferability of these SSR markers to H. mollis (Q. Yin, S. Chen, Q.…”

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confidence: 99%

Identification and development of microsatellite markers in Hamamelis mollis (Hamamelidaceae)

Yin

Huang

et al. 2018

Appl Plant Sci

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Premise of the Study Hamamelis mollis (Hamamelidaceae) is a Tertiary relict species endemic to southern China. Polymorphic microsatellite markers were developed to reveal the genetic diversity of this species.Methods and ResultsThe genome of H. mollis was sequenced and de novo assembled into 642,351 contigs. A total of 72,097 paired primers were successfully designed from 80,282 simple sequence repeat (SSR) markers identified in 63,419 contigs. PCR amplification showed that 96 of the 136 synthesized primers could be successfully amplified, and 22 demonstrated polymorphism. The mean number of alleles, levels of observed heterozygosity, and levels of expected heterozygosity were 4.602 ± 0.140, 0.632 ± 0.020, and 0.696 ± 0.010, respectively. The majority of the 96 primer pairs could be amplified in at least one other Hamamelidaceae species, including Distylium myricoides (60), Loropetalum chinense (39), Exbucklandia populnea (24), and E. tonkinensis (24).ConclusionsThese microsatellite loci provide abundant genomic SSR markers to evaluate genetic diversity of this woody ornamental plant.

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Development of microsatellites from Fothergilla ×intermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae

Cited by 7 publications

References 9 publications

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Characterization of thirteen microsatellite loci from the Ghanian antimalarial plant Cryptolepis sanguinolenta

Identification and development of microsatellite markers in Hamamelis mollis (Hamamelidaceae)

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