Molecular markers reveal low genetic diversity in Casuarina equisetifolia clonal plantations in South China

Yu, Wei; Zhang, Yong; Xu, Xun; Chen, Zhong; Wei, Yongcheng; Meng, Jianghong; Yu, Chang Yeon; Li, Zhen; Bush, David R.

doi:10.1007/s11056-019-09752-7

Cited by 3 publications

(2 citation statements)

References 21 publications

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“…Previous studies reported multiple methods of identifying Casuarina species (Ghosh et al., 2011). The extent of genetic diversity in C. equisetifolia , C. cunninghamiana , and C. glauca has been investigated using random amplified polymorphic DNA markers (Ho et al., 2002; Ndoye et al., 2011), inter‐simple sequence repeat (ISSR) markers (Rasmi et al., 2011), ISSR‐PCR (Yasodha et al., 2004), sequence‐characterized amplified region (SCAR) markers (Ghosh et al., 2011), and expressed sequence tag (EST)‐SSRs (Li et al., 2018; Xu et al., 2018; Yu et al., 2020; Zhang et al., 2020). The transcripts expressed in the nodules of C. glauca have been identified by comparing sets of ESTs prepared from roots with or without nodules (Hocher et al., 2006).…”

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confidence: 99%

Chromosome‐scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana

et al. 2023

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Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca,

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Section: Introductionmentioning

confidence: 99%

Chromosome‐scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana

et al. 2023

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“…Almost 90% of the plantations established over the past 30 years are clonal [5]. However, the genetic base of these plantations is very narrow, with only 22 clones identified from plantations of coastal Casuarina shelterbelts of Guangdong, Hainan and Fujian provinces, many of which were themselves closely related [6]. This is of particular concern given that the shelterbelt plantings are required to remain resilient to both biotic and abiotic stressors.…”

Section: Introductionmentioning

confidence: 99%

Analyses of Genetic Diversity, Differentiation and Geographic Origin of Natural Provenances and Land Races of Casuarina equisetifolia Based on EST-SSR Markers

Zhang

Chen

et al. 2020

Forests

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Research Highlights: High variation of genetic diversity and differentiation among 27 seed sources within 14 natural provenances and 13 land race samples of Casuarina equisetifolia were found. High proportions of monoecious individuals may be present in some populations, as indicated by severe heterozytote deficiency and inbreeding found in many provenances and land races. The most probable origins of the land races were inferred according to the values of pairwise provenance differentiation and Nei’s genetic distances. Targeted introductions and testing of unrelated new accessions of C. equisetifolia from the Pacific and Philippines was proposed to identify Ralstonia-resistant genotypes. Background and Objectives: Casuarina equisetifolia was introduced to China a hundred years ago and has become a critically important tree species in coastal protection since the 1950s. Despite its importance, patterns of genetic variation, genetic relationships among natural provenances and probable origins of the land races remain unresolved. This has become a concern in China where Ralstonia solanacearum bacterial wilt has devastated plantations that are known to be from a narrow genetic base that urgently needs to be broadened. Materials and Methods: Fourteen natural provenances from Australia, Pacific islands and Southeast Asia, and 13 land race samples from parts of Asia and Africa outside the natural range were genotyped using 13 SSR (Simple Sequence Repeats) markers to characterize their allelic variation and genetic relationship. Results: Significant genetic diversity and differentiation among 27 seed sources within 14 provenances and 13 land race samples of C. equisetifolia was indicated. Significant heterozygote deficiency and inbreeding was indicated for a number of provenances, perhaps indicating a high proportion of monoecious parents in these populations. The most probable origins of the land races of the introduced countries were suggested according to the values of pairwise provenance differentiation (FST) and Nei’s genetic distances. Conclusions: We found significant genetic diversity and genetic differentiation among seed sources of C. equisetifolia. While individual land races do not appear to lack diversity, we were able to infer the origins of some, allowing targeted introductions of unrelated material to be made. In the case of the Chinese land race, targeting and testing new accessions from the Pacific and the Philippines may be a good strategy to identify Ralstonia-resistant genotypes.

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Identification of Commercial Cultivars in the Tabebuia Alliance Using Genotyping-by-Sequencing

Meng

Zhang

Wei

et al. 2023

Forests

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The Tabebuia alliance is widely planted in tropical and subtropical countries. However, the lack of accurate taxonomic information for many commercial cultivars leads to commercial disputes. We sought to clarify the background of commercial cultivars in China and to provide a robust basis for patent protection. We collected 82 Tabebuia cultivars and 12 reference individuals, then developed large-scale single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing. We obtained 73,219 SNPs from the test samples, which represented a substantial increase compared with previous studies of Tabebuia species. Based on these SNPs and a clustering analysis, we detected six species among the samples, as well as an uncertain population which may be a hybrid between Handroanthus impetiginosus (Mart. ex DC) Mattos and H. heptaphyllus (Vell.) Mattos. An analysis of genetic diversity to assess germplasm resources indicated that excessive heterozygosity of these cultivars in China, which may explain the genetic basis of “novel-preferred” selection in ornamental plants or a narrow genetic background. After rigorous selection, we identified numerous high-quality molecular markers for cultivar identification, then constructed a concise fingerprint with 54 SNPs. Our work clarifies the background information of commercial cultivars of Tabebuia in China and provides information for cultivar identification. It will serve as an important technical resource for genetic studies, and it will help to protect patents that involve Tabebuia species.

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Molecular markers reveal low genetic diversity in Casuarina equisetifolia clonal plantations in South China

Cited by 3 publications

References 21 publications

Chromosome‐scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana

Chromosome‐scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana

Analyses of Genetic Diversity, Differentiation and Geographic Origin of Natural Provenances and Land Races of Casuarina equisetifolia Based on EST-SSR Markers

Identification of Commercial Cultivars in the Tabebuia Alliance Using Genotyping-by-Sequencing

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