Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific

Payacán, Claudia; Moncada, Ximena; Rojas, Gloria; Clarke, Andrew; Chung, Kuo‐Fang; Allaby, Robin G.; Seelenfreund, Daniela; Seelenfreund, Andrea

doi:10.1093/aob/mcx062

Cited by 15 publications

(33 citation statements)

References 42 publications

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“…A total of 158 contemporary specimens collected between 2008 and 2016 under projects FONDECYT 1080061 and 1120175 were obtained from New Caledonia, Fiji, Samoa, Wallis and Tonga in West Remote Oceania (WRO); 121 were collected from East Remote Oceania (ERO) locations (Hawaii, Tahiti, the Marquesas Archipelago, Rapa in the Austral Islands, Rapa Nui and Pitcairn); 34 samples were collected from China, Taiwan and Vietnam, all in the native range, and from Japan; with one sample from South America (Santiago de Chile). Herbarium samples were taken from 67 specimens (S2 Table)] collected between 1882 and 2006 following the protocol designed by Payacán et al [27]. Samples were provided by the following Institutions: Herbarium Pacificum (BISH), B.P.…”

Section: Methodsmentioning

confidence: 99%

“…Genomic DNA from contemporary samples was extracted following a CTAB extraction protocol as reported previously [23, 31, 27] based on Lodhi et al [32]. The herbarium sample extractions were carried out in the ancient DNA laboratory of the University of Otago, following stringent ancient DNA contamination control protocols as described in Payacán et al [27]. DNA quality from all samples was determined by the 260 nm/280 nm absorbance ratio using Nanodrop 2000 and DNA concentration was determined by fluorescence using the Quant-iTtM PicoGreen dsDNA Assay Kit (#7589) as indicated by the provider (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

“…Also, using microsatellites on a limited set of paper mulberry herbarium samples, we were able to detect genetic diversity within Near and Remote Oceania, in spite of the vegetative propagation of this species in Oceania. Genotypes were structured into two major groups, separating West and East Remote Oceania and placing Pitcairn in a pivotal position between these regions, suggesting pulses during the dispersal history [27]. A fundamental question that remained unanswered with the previous studies is whether the genetic diversity of paper mulberry detected with microsatellites within Remote Oceania can be used as an effective proxy of past human movements.…”

Section: Introductionmentioning

confidence: 99%

“…Here, we report the combined analysis of a total of 380 samples (313 contemporary and 67 herbarium accessions) based on the ITS-1 region [23, 24], a sex marker [25], the ndh-rpl32 cpDNA region [26] and nine microsatellite markers [27] previously used by our group.…”

Section: Introductionmentioning

confidence: 99%

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Human mediated translocation of Pacific paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)]: Genetic evidence of dispersal routes in Remote Oceania

et al. 2019

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Paper mulberry, Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae), a dioecious species, was transported by humans from Taiwan to the islands of Remote Oceania. Its introduction and cultivation in Remote Oceania was intentional due to its cultural importance as a fiber source for barkcloth textiles. The aim of this study was to explore the genetic diversity and structure of paper mulberry populations within Remote Oceania in order to infer dispersal patterns that may reflect past human interaction among island groups. We present the integrated analysis of 380 samples (313 contemporary and 67 herbarium specimens) collected in Near and Remote Oceania. Genetic characterization was based on a set of ten microsatellites developed for B . papyrifera and complemented with the analysis of the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker and the chloroplast ndhF–rpl32 intergenic spacer. Microsatellite data identify a total of 64 genotypes, despite this being a clonally propagated crop, and show three major dispersal hubs within Remote Oceania, centered on the islands of Fiji, Tonga, and Pitcairn. Of 64 genotypes identified, 55 correspond to genotypes associated to female-sexed plants that probably descend from plants introduced by the prehistoric Austronesian-speaking voyagers. The ratio of accessions to genotypes between herbarium and contemporary samples, suggests recent loss of genetic diversity. In addition to the chloroplast haplotypes described previously, we detected two new haplotypes within Remote Oceania both originating in Taiwan. This is the first study of a commensal species to show genetic structuring within Remote Oceania. In spite of the genetic bottleneck, the presence of only one sex, a timespan of less than 5000 years, and asexual propagation of this crop in Remote Oceania, we detect genetic diversity and regional structuring. These observations suggest specific migration routes between island groups within Remote Oceania.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Human mediated translocation of Pacific paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)]: Genetic evidence of dispersal routes in Remote Oceania

et al. 2019

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“…Molecular markers are excellent tools for exploring the genetic diversity of different plants, especially for classifying species that are difficult to identify using traditional classification methods [ 11 ]. Molecular markers are also useful for analyzing the evolutionary relationships between different plant groups [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Luo

Zhang

et al. 2020

BMC Genet

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Background Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum , limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions. Results Based on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers ( h = 0.47, I = 0.66) and ISSR markers ( h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers. Conclusions Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum . Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum . The SNPs identified in this study could be used to distinguish S. secundatum accessions.

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Association study between some cultivated species and their wild relatives from Apiaceae, Asteraceae and Brassicaceae families based on molecular and DNA barcoding in Egypt

Essa

Ibrahim

Soliman

2023

Genet Resour Crop Evol

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Concerns about food security worldwide have been raised due to the adverse impacts of climate change on agricultural productivity. Utilizing wild relatives of cultivated plants in breeding schemes is a potential solution to address the abovementioned challenges. Wild relatives refer to indigenous plant species that share genetic ancestry with recently cultivated plants. The capacity of plants to withstand abiotic stresses and enhance crop yield stability in cold and arid environments renders them a valuable prospective resource for breeding programs. Molecular markers are employed to assess the genetic variability of cultivated plants and their wild relatives under investigation. This study employed a set of five primers derived from ISSR (Inter Simple Sequence Repeats) and SCoT (Start Codon Targeted) to assess comparative research between cultivated species and their wild relatives from three families: Apiaceae (Apium gravolens L., A. leptophyllum (Pers.) F.Muell., Daucus carota L.& D. litoralis Sm.), Asteraceae (Lactuca sativa L. & L. serriola L.) and Brassicaceae (B. oleracea L., Brassica tourneforttii Gouan., Raphanus sativus L. & R. raphanistrum L.). The ISSR technique yields approximately 206 bands, whereas the SCoT primers generate approximately 207 bands. The ISSR primers yielded 169 polymorphic bands, exhibiting a polymorphism rate of 82.04%, whereas the SCoT primers produced 169 polymorphic bands with a polymorphism rate of 81.64%. The Brassicaceae has been found to exhibit the highest resolving power (RP) of 48.25, as determined by ISSR. The primary objective of DNA barcoding is to create a communal database of DNA sequences that can be utilized to identify organisms and clarify their taxonomic classification. The findings indicate that the internal transcribed spacer (ITS) regions exhibit high efficacy as a DNA barcoding tool. Overall, the results obtained from two molecular markers and DNA barcoding analyses suggest a significant degree of genetic diversity and relatedness among the cultivated taxa and their wild relatives examined in this study.

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Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific

Cited by 15 publications

References 42 publications

Human mediated translocation of Pacific paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)]: Genetic evidence of dispersal routes in Remote Oceania

Human mediated translocation of Pacific paper mulberry [Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae)]: Genetic evidence of dispersal routes in Remote Oceania

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Association study between some cultivated species and their wild relatives from Apiaceae, Asteraceae and Brassicaceae families based on molecular and DNA barcoding in Egypt

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