Genetic diversity and differentiation in Dalbergia sissoo (Fabaceae) as revealed by RAPD

De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease

Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.

Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha² in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

Genetic variability and population divergence in the rare Fritillaria tubiformis subsp. moggridgei Rix (Liliaceae) as revealed by RAPD analysis

Fritillaria tubiformis subsp. moggridgei Rix. is a rare alpine geophyte with shiny yellow flowers. This plant is sporadically distributed across the southwestern Alps where it is biogeographically close to F. tubiformis var. burnatii Planch. The latter has dark purple flowers and ranges in the majority of the Western and Central Alps. In order to develop appropriate strategies of conservation, a RAPD based analysis was conducted to study the genetic status of these taxa and the distribution of genetic variability of the subspecies by sampling seven populations distributed across the subspecies' range. Four populations of var. burnatii were chosen within this range and included in the genetic analysis. Some 264 individuals were analysed and 201 polymorphic loci were scored. Genetic diversity scored in the subspecies was in line with expectations for endemic species (H_e  = 0.194). F. tubiformis var. burnatii showed lower intraspecific diversity (H_e  = 0.173), notwithstanding a wider range than the subspecies. Most of the total phenotypic variation (about 83%) was allocated within populations, and significant lower proportions between taxa (6.45%) and between populations of the same taxon (10.64%). Moreover, PCoA analysis and Bayesian clustering separated populations into two genetically differentiated groups corresponding with the subspecific taxa. However, three populations ascribed to the subsp. moggridgei repeatedly showed genetic admixture with var. burnatii populations. Our findings suggest that: i) although the different flower colour, the two taxa are genetically very similar and share a consistent part of their gene pool, ii) the majority of genetic variability is allocated within populations rather than among them, iii) a representative amount of genetic diversity can be preserved by sampling from a restricted number of populations. The efficacy of RAPD markers in analysing genetic variation, and the contribution of the results to the preservation of biodiversity of the species, are discussed.

RAPD fingerprint construction and genetic similarity of Mesona chinensis (Lamiaceae) in China

Mesona chinensis is an economically important agricultural crop, primarily cultivated for making grass jelly. It was originally discovered in South China. We examined 18 cultivars, including cultivars from Guangdong, Fujian, and Guangxi, China, Taiwan, and Indonesia, and a hybrid (a cross between cultivars from Indonesia and Guangdong), based on RAPD markers. The genetic similarity coefficient was calculated by NTSYS 2.10 and the clustering analysis was made by UPGMA. PCR amplification with 10 primers produced 163 bands; 94% of the amplified loci were polymorphic. The primers S208, S206, and S253 could completely distinguish all 19 samples by constructing a DNA fingerprint. Cluster analysis divided the 19 cultivars into five groups, with an overall genetic similarity coefficient of 0.68. Correlations were found among regional distributions, parental sources, and RAPD markers, demonstrating the rich genetic diversity of these 19 cultivars of M. chinensis. This study provides useful information for the classification, identification, and breeding of M. chinensis.

In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm

RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000 bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.