Population genetic analysis of Xylia xylocarpa (Fabaceae—Mimosoideae) in Thailand

Wattanakulpakin, Tanat; Iamtham, Siriluck; Grubbs, Kunsiri Chaw; Volkaert, Hugo

doi:10.1007/s11295-014-0825-y

Cited by 3 publications

(5 citation statements)

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“…However, due to long and overlapping generation times and generally high levels of outcrossing and dispersal rates, trees might not respond immediately to fragmentation in terms of loss of genetic diversity (Davies et al., ; Kramer, Ison, Ashley, & Howe, ; Lowe, Boshier, Ward, Bacles, & Navarro, ). We found moderate to high levels of genetic diversity in D. cochinchinensis and D. oliveri, comparable to those of other trees species from the area (Pakkad et al., ; Senakun et al., ; Wattanakulpakin et al., ), and no evidence of inbreeding in any populations (no F IS values significantly different from zero, Table ). Further, the T 2 statistic, which detects loss of alleles not yet matched by a loss of heterozygosity, did not reveal any significant signs of a recent bottleneck.…”

Section: Discussionsupporting

confidence: 84%

“…Dalbergia oliveri seems to have a higher level of gene flow than D. cochinchinensis, which was shown by a higher and more evenly distributed level of genetic diversity and a more admixed population structure. Both species showed a markedly higher level of genetic differentiation than other Indochinese trees (Pakkad, Ueno, & Yoshimaru, ; Pakkad et al., ; Senakun et al., ; Wattanakulpakin et al., ) or Dalbergia species (Andrianoelina, Favreau, Ramamonjisoa, & Bouvet, ; Resende et al., ). The levels found for D. cochinchinensis corresponded relatively well with earlier estimations of differentiation for the species (Moritsuka et al., ; Soonhua et al., ).…”

Section: Discussionmentioning

confidence: 97%

“…The population structure of forest-associated species within central Indochina is less well studied (Blair et al, 2013;Fuchs, Ericson, & Pasquet, 2008;Morgan et al, 2011), and particularly Cambodia is underrepresented in the sampling. A few studies assess population structure of plants or trees in the region although most are limited to the local scale (Pakkad, Kanetani, & Elliot, 2014;Senakun, Changtragoon, Pramual, & Prathepha, 2011;Wattanakulpakin, Iamtham, Grubbs, & Volkaert, 2015;Zhao & Zhang, 2015;Zhao et al, 2013).…”

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confidence: 99%

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Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life‐history traits

Hartvig

Changtragoon

et al. 2017

Ecology and Evolution

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Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life‐history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had generally high levels of genetic diversity (mean H e = 0.73), but also strong genetic differentiation among populations (global GST = 0.13), while D. cochinchinensis had a moderate level of genetic diversity (mean H e = 0.55), and an even stronger level of differentiation (global GST = 0.25). These differences in genetic structure can be accounted for by a higher level of gene flow in D. oliveri due to a higher dispersal capacity, but also by the broader distribution area for D. oliveri, and the pioneer characteristics of D. cochinchinensis. This study represents the first detailed analysis of landscape genetics for tree species in Indochina, and the found patterns might be common for other species with similar ecology.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 97%

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confidence: 99%

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Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life‐history traits

Hartvig

Changtragoon

et al. 2017

Ecology and Evolution

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“…Xylia xylocarpa belongs to the genus of Xylia within the Fabaceae and distributes naturally in India, Indo-China, Myanmar, and Thailand (Wattanakulpakin et al. 2015 ). It is a fast-growing tree with a denser wood and yields a hard and durable wood used for heavy construction (Josue 2004 ).…”

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confidence: 99%

The complete chloroplast genome sequence of Xylia xylocarpa

Geng

Zhang

et al. 2020

Mitochondrial DNA Part B

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The first complete chloroplast genome (cpDNA) sequence of Xylia xylocarpa was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 161,288 bp in length, contains a large single copy region (LSC) of 89,186 bp and a small single copy region (SSC) of 19,354 bp, which were separated by a pair of inverted repeats (IR) regions of 26,370 bp. The genome contains 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.6%, and the corresponding values of the LSC, SSC, and IR regions are 34.1%, 30.8%, and 42.8%, respectively. Further phylogenomic analysis showed that X. xylocarpa clustered in a unique clade in Caesalpinioideae subfamily.

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“…Every polymorphic position that has been retained was either unambiguous on its own or confirmed by its presence in more than one genotype. Such large numbers of alleles in a species are not exceptional for natural populations of tropical plants (Wattanakulpakin et al, 2015). Even if a few polymorphic positions have been erroneously included or wrongly assigned to a haplotype by the phasing algorithm, they will not significantly impact the network structure underlying the grouping into subspecies clusters.…”

Section: Molecular Data and Networkmentioning

confidence: 99%

Genetics and diversity of Indonesian bananas

Ahmad

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Diploid fertile bananas for breedingAs cultivars are sterile, diploid fertile bananas are needed as starting genitors in breeding programs to create hybrid progenies, that later can be used for developing triploid, alloploid or parthenocarpic sterile cultivars. Genetic analysis of fertile diploids has the additional advantage of mapping desirable traits on a linkage map. Such maps can also help to reveal structural chromosome variants (Hippolyte et al., 2010) and can be combined with genomic libraries to characterize and isolate selected gene clusters (Canto-Canché et al., 2007). In breeding practices, wild bananas and related Musa species can also be useful as donor species in pre-breeding programs. This germplasm can later be crossed with diploid or triploid cultivars to create new alloploid or triploid seedless cultivars (de Oliveira et al., 2001).The most important diploid fertile accessions for banana improvement, are the ancestral M. acuminata and M. balbisiana, which occur all over Southeast Asia (Perrier et al., 2009;Volkaert 2018). Specific morphological traits that allow distinction between these two species are blotches on the pseudostem, petiole canal shape, hair on peduncle, pedicels-fruit length ratio, ovules rows configuration, bract habit and male flower color (Simmonds & Shepherd, 1955). The genetic diversity of M. acuminata is much higher than in M. balbisiana (Wong et al., 2002;Volkaert, 2011), resulting in a subdivision of M. acuminata into seven sub-species (Perrier et al., 2011;Simmonds & Shepherd, 1955), i.e. ssp. acuminata, ssp. errans (Blanco) RV Valmayor, ssp. halabanensis (Meijer) M Hotta, ssp. malaccensis (Ridl.) NW Simmonds, ssp. microcarpa (Becc.) NW Simmonds, ssp. siamea NW Simmonds and ssp. truncata (Ridl.). In addition, Nasution (1991) described fifteen additional varieties that were found in Indonesia (Figure 4). As to the smaller diversity of M. balbisiana, only four varieties were accepted in the Plant List (2013), i.e. var. brachycarpa (Backer) Häkkinen, var. liukiuensis (Matsum.) Häkkinen, var. bakeri (Hook.f.) Häkkinen and var. dechangensis (J.L.Liu & M.G.Liu) Häkkinen.Part of the overall diversity is maintained in gene banks such as the International Musa Germplasm Collection (International Transit Centre, ITC), which is hosted by the Catholic University of Leuven (KUL) in Belgium. However, the larger part of diversity is maintained in in-situ collections such as the one at the Indonesian Fruits Research Institute (ITFRI, Indonesian Centre for Horticultural Research and Development (ICHORD)) in Solok, Sumatra, Indonesia. Besides, there is a plethora of undiscovered diverse germplasm in tropical forests awaiting deployment by breeders and researchers for banana improvement. The ITC has more than 1,500 accession in tissue culture, but only a small number of accessions of wild M. acuminata (N=91) and M. balbisiana (N=32)

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Population genetic analysis of Xylia xylocarpa (Fabaceae—Mimosoideae) in Thailand

Cited by 3 publications

References 42 publications

Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life‐history traits

Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life‐history traits

The complete chloroplast genome sequence of Xylia xylocarpa

Genetics and diversity of Indonesian bananas

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