Genetic diversity of Aquilaria microcarpa Baill. in Kalimantan using RAPD Markers

Aquilaria microcarpa is one of the agarwood producers species included in the endangered category based on the IUCN red list. Kalimantan is one of the natural distributions of this species. The high demand for agarwood causes this species to be commonly cultivated in community plantations. This study aimed to assess the genetic diversity of A. microcarpa using the RAPD markers. Forty-four leaf samples of A.microcarpa were collected from the local community in Gumbil (South Kalimantan) and Sanggau (West Kalimantan). The results showed that 9 out of 24 RAPD primers were stable in amplification, and polymorphic totally consisted of 49 polymorphic loci. The values of unbiased expected heterozygosity (uHE) were at a low level; they ranged between 0.152 (Gumbil II) to 0.249 (Gumbil I). The average genetic distance between Gumbil and Sanggau is 0.1733, related to their geographic distance. A private allele was only found at Gumbil at locus G18/540 and Sanggau at locus G18/550, respectively. A great DA value between Gumbil I and II showed that the plantations originated from different seed sources. AMOVA also verified the differences between the two populations. This finding has important implications in managing plantations and seeds transfer.

Can DNA help trace the local trade of pangolins? A genetic assessment of white-bellied pangolins from the Dahomey Gap (West Africa)

We conducted in the Dahomey Gap (DG) a pioneer study on the genetic tracing of the African pangolin trade. We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellites loci. Tree-based assignment procedure showed the 'endemicity' of the pangolin trade, as strictly fed by the lineage endemic to the DG (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, inbreeding depression and lack of geographic structure. We identified a 92-98% decline in DGL effective population size 200-500 ya –concomitant with major political transformations along the 'Slave Coast' – leading to contemporaneous estimates inferior to minimum viable population size. Genetic tracing suggested that wildlife markets from the DG sourced through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of same individuals on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies and cross-validation with observed data that could trace five traded pangolins to their forest origin, c. 200-300 km away from the markets. Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the pangolin trade, our tracing ability was limited by the lack of population structure within DGL. Given the deleterious combination of genetic, demographic and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.

Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we construed high-density haplotype map by whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. The phylogenetic analysis, the principal component analysis, and the population structure profiling, indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China were clustered with the other three groups. The genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. The gene flow from the SCG to the FG was detected as well. We concluded that the origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided genetic variation features and population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants for improving Chinese plum varieties.

Gene Introgression among Closely Related Species in Sympatric Populations: A Case Study of Three Walnut (Juglans) Species

Gene introgression usually results from natural hybridization occurring among closely related species in sympatric populations. In this study, we discussed two rare and frequent gene flow phenomena between three species of Juglans plants and analyzed the possible causes for the difference. We collected 656 individuals from 40 populations of Persian walnut (Juglans regia L.), Chinese walnut (J. cathayensis Dode), and Iron walnut (J. sigillata Dode) that were genotyped at 17 expressed sequence tag simple sequence repeat (EST-SSR) loci to analyze the introgressions between J. regia and J. cathayensis, and J. regia and J. sigillata. Our study compared the spatial patterns of expected heterozygosity (HE), allelic richness (Rs), and private allele richness (PAR) so as to vividly infer the biogeographic history of related species of Juglans in the two regions. The results of the PCoA, UPGMA, and STRUCTURE analyses showed that all J. regia and J. sigillata populations clustered into one group, and the J. cathayensis populations clustered into the other group. The results of the historical gene flow analysis indicated that J. regia and J. sigillata have no genetic barriers, and the directional gene flow is mainly from J. regia to J. sigillata. For the three species of Juglans, all the above results indicated that gene flow was common among the same group of Juglans, and only rare and low-level gene flow appeared in distinct groups. Therefore, our study revealed multiple phenomena of gene flow and introgression among closely related species in sympatric populations, thereby providing a theoretical basis for the genetic evolution of the genus Juglans.

Genetic diversity in natural populations of (Cephalotaxus mannii Hook. F.) In Tay Nguyen, Vietnam base on SSR markers

Cephalotaxus mannii Hook.f. is one of 15 species of conifer in the Central Highlands. Cephalotaxus mannii is a scarce medicinal conifer endemic to the south central region of China and Vietnam. In Vietnam, although widely distributed species (Lao Cai, Ha Giang, Thanh Hoa, Nghe An, Thua Thien Hue, Kon Tum, Gia Lai, Lam Dong...) but is considered rare and vulnerable by the indiscriminately exploitation of people. In this study, 18 SSR markers were used to analyze the genetic diversity of 34 individuals C. mannii collected in Ta Nung and Hiep An of Lam Dong province. The results showed 12/18 polymorphic markers. Among 36 DNA amplified fragments, 24 were polymorphic (66.66%). Genetic diversity in Hiep An population (h = 0.269; I = 0.449 and PPB = 72.22%) was higher than that of Ta Nung (h = 0.433; I = 0.264 and PPB = 66.67%). The total level of molecular variance (AMOVA) among populations was 27.74% and among individuals within the populations was 72.26%. The average of gene flow value (Nm) of the species C. mannii populations was 3,310. Both Ta Nung and Hiep An populations had Wright’s inbreeding coefficient Fis <0 (- 0.244, - 0.052, respectively) and the private allele (Ap) (0.222, 0.333, respectively). A dendrogram constructed based on similarity matrix of 34 C. mannii samples divided into two main groups with their genetic similarity coefficient ranged from 65% (Cpm31 and Cpm32) to 100% (Cpm16 and Cpm17, Cpm21 and Cpm22). Molecular analysis results showed that C. mannii species should be protected at the population level.

Allozyme variation of the endemic and vulnerable Dyera lowii Hook.f. in Central Kalimantan: Implications for genetic resources conservation

Dyera lowii is an endemic and vulnerable tree species of commercial value as chewing gum found inpeat swamp forests, scatteredly distributed in Sumatra, Kalimantan, and Peninsular Malaysia. Their existenceis now under severe threat due to habitat conversion. This study is aimed to assess genetic diversity withinfour natural populations (Hampangen, Parahangan, Sebangau, Selat Nusa ) and one plantation in CentralKalimantan based on allozyme variation. Electrophoresis procedures were conducted with an isoelectricfocusing polyacrylamide slab gel system. The result showed high genetic diversity (HE=0.52) and gene fl ow(3.402) seemed to be effective. A total of 14 alleles were found among all the analysed population. Meannumber of alleles per locus (Aa) was 3.206, and the effective number of alleles per locus (Ae) was 2.21. Geneticdifferentiation between populations (FST) was signifi cant at the moderately level (0.0685). Most allozymevariation was found within population (93.2%). Special attention is essential to conserve a private allele ofGot-1-e (9%) at Selat Nusa population. Sebangau population missed the alleles of Est-2-b and Got-1-a, as foundin other populations. Selat Nusa population is expected to enhance the effective management for geneticresources conservation of this vulnerable species in the future.