Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn (Hippophae salicifolia)

Seabuckthorn (Hippophae salicifolia) is a perennial, multipurpose wonder plant, popular for its immense medicinal, nutritional, and therapeutic properties. However, due to the lack of whole-genome-based studies, the molecular mechanism governing distinct sexual phenotypes is still not clear. We employed the high-throughput NGS Illumina NovaSeq paired-end technology to generate whole transcriptome profiles of male and female plants of H. salicifolia. In total, 3.2 million raw short reads were generated with an average length of 150 bp, including 50911358 reads from the male leaf tissue samples and 45850364 reads from the female leaf tissue samples. Clustering of the high-quality reads yielded de novo short read assembly of 50259 transcripts of >100 bp length. The final transcripts were assigned Gene Ontology (GO) terms. The digital expression of genes was studied using the DESeq2 of R package that identified 7180 differentially expressed genes (DEGs) between the male and female plant samples. Further, 10,850 simple sequence repeats, and 8,351 transcription factors, distributed in more than 85 transcription families, were also mined from the final assembled transcriptome. Next, COG and KEGG pathway analyses were performed to assign biological functional terms to the DEGs. The findings of the present study will provide a valuable resource for gene expression discovery and other functional genomics studies aiming towards the selection of candidate genes for the development of sex-specific markers in seabuckthorn and other closely related species.Communicated by Ramaswamy H. Sarma.

Morphometric and Microsatellite Diversity in Seabuckthorn (Hippophae rhamnoides L.) Natural Populations Originating from the Different Geographical Regions of the Indian Himalayas

Seabuckthorn (Hippophae rhamnoides L.), an upcoming superfood plant, has attracted researchers' attention worldwide for its medicinal, nutritional, and socio-economic value, along with its characteristic features to sustain extreme climatic conditions. We have studied microsatellite marker-based genetic and morphometric diversity in 93 collections of H. rhamnoides from different geographic sites representing two regions, namely Leh and Lahaul of the Indian Himalayas. Microsatellite markers were isolated using two different approaches, including screening of microsatellite-enriched genomic library, and in silico screening of in-house developed seabuckthorn EST database and whole transcriptome assembly. In Leh and Lahaul collections, 32 and 30 microsatellite markers were found polymorphic, respectively. All the markers developed for H. rhamnoides showed cross-species transferability to H. salicifolia and H. tibetana. Two to six alleles were recorded in the two sets of collections with an average of 3.71 and 3.53 alleles per locus in Leh and Lahaul collections, respectively. Mean polymorphic information content (PIC) values for microsatellite markers were 0.39 and 0.41 for Leh and Lahaul collections, respectively. The average expected heterozygosity was less than the observed heterozygosity. Wright's fixation index (F _IS) varied from (-)0.2045 to 1.0 and (-)0.1688 to 1.0 for Leh and Lahaul collections, respectively. Shannon's informative index (I) remained in the range of 0.6745 to 1.8621, and 0.6824 to 1.6308 for Leh and Lahaul collections, respectively. The UPGMA-based combined dendrogram showed clear demarcation between Leh and Lahaul collections, although a few ecotypes were regrouped with collections from the other region. No significant relationship was observed between the morphological distance matrix and molecular marker distance matrix. The findings of the present study may prove helpful in future breeding and conservation strategies aiming for seabuckthorn improvement.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11105-022-01338-6.

Diversity in sea buckthorn (Hippophae rhamnoides L.) accessions with different origins based on morphological characteristics, oil traits, and microsatellite markers

Sea buckthorn (Hippophae rhamnoides) is an ecologically and economically important species. Here, we assessed the diversity of 78 accessions cultivated in northern China using 8 agronomic characteristics, oil traits (including oil content and fatty acid composition) in seeds and fruit pulp, and SSR markers at 23 loci. The 78 accessions included 52 from ssp. mongolica, 6 from ssp. sinensis, and 20 hybrids. To assess the phenotypic diversity of these accessions, 8 agronomic fruit traits were recorded and analyzed using principal component analysis (PCA). The first two PCs accounted for approximately 78% of the variation among accessions. The oil contents were higher in pulp (3.46–38.56%) than in seeds (3.88–8.82%), especially in ssp. mongolica accessions. The polyunsaturated fatty acid (PUFA) ratio was slightly lower in the seed oil of hybrids (76.06%) than that of in ssp. mongolica (77.66%) and higher than that of in ssp. sinensis (72.22%). The monounsaturated fatty acid (MUFA) ratio in the pulp oil of ssp. sinensis (57.00%) was highest, and that in ssp. mongolica (51.00%) was equal to the ratio in the hybrids (51.20%). Using canonical correspondence analysis (CCA), we examined the correlation between agronomic traits and oil characteristics in pulp and seeds. Oil traits in pulp from different origins were correlated with morphological groupings (r = 0.8725, p = 0.0000). To assess the genotypic diversity, 23 SSR markers (including 17 loci previously reported) were used among the 78 accessions with 59 polymorphic amplified fragments obtained and an average PIC value of 0.2845. All accessions were classified into two groups based on the UPGMA method. The accessions of ssp. sinensis and ssp. mongolica were genetically distant. The hybrid accessions were close to ssp. mongolica accessions. The 8 agronomic traits, oil characteristics in seed and pulp oils, and 23 SSR markers successfully distinguished the 78 accessions. These results will be valuable for cultivar identification and genetic diversity analysis in cultivated sea buckthorn.

Characterization of the Hippophae rhamnoides WRKY gene family and functional analysis of the role of the HrWRKY21 gene in resistance to abiotic stresses

Sea buckthorn (Hippophae rhamnoides L.) is a plant with economic and ecological value. It is uniquely capable of growing well under salt and drought stress. WRKY transcription factors play important roles in the ability of plants to resist stress. In this study, 48 HrWRKY genes were identified based on RNA sequencing of H. rhamnoides. Evaluation of expression pattern of HrWRKY1, HrWRKY17, HrWRKY18, HrWRKY21, HrWRKY33-2, HrWRKY40-2, HrWRKY41, and HrWRKY71 suggested that they were involved in abiotic stress. Interestingly, HrWRKY21, one of eight HrWRKY genes, was a positive regulator of abiotic stress tolerance in H. rhamnoides. In addition, most morphological attributes of roots in transgenic Nicotiana tabacum lines (overexpressing HrWRKY21) were also markedly increased compared with the wild-type (WT), including total lengths, specific root lengths, and surface areas. Stress tolerance of transgenic lines was also correlated with higher antioxidant activity (SOD and POD), lower percentage of relative conductivity (REC), and lower activity of malondialdehyde (MDA) under stress conditions. These findings represent a foundation of knowledge about the molecular mechanisms driving resistance to adverse conditions in plants; they are a promising step towards development of tree cultivars with improved tolerance to abiotic stress.

Morphological and Genetic Diversity of Sea Buckthorn (Hippophae rhamnoides L.) in the Karakoram Mountains of Northern Pakistan

Sea buckthorn (Hippophae rhamnoides L.) is a dioecious, wind-pollinated shrub growing in Eurasia including the Karakoram Mountains of Pakistan (Gilgit-Baltistan territory). Contrary to the situation in other countries, in Pakistan this species is heavily underutilized. Moreover, a striking diversity of berry colors and shapes in Pakistan raises the question: which varieties might be more suitable for different national and international markets? Therefore, both morphological and genetic diversity of sea buckthorn were studied to characterize and evaluate the present variability, including hypothetically ongoing domestication processes. Overall, 300 sea buckthorn individuals were sampled from eight different populations and classified as wild and supposedly domesticated stands. Dendrometric, fruit and leaf morphometric traits were recorded. Twelve EST-SSRs (expressed sequence tags-simple sequence repeats) markers were used for genotyping. Significant differences in morphological traits were found across populations and between wild and village stands. A significant correlation was found between leaf area and altitude. Twenty-two color shades of berries and 20 dorsal and 15 ventral color shades of leaves were distinguished. Mean genetic diversity was comparatively high (He = 0.699). In total, three distinct genetic clusters were observed that corresponded to the populations’ geographic locations. Considering high allelic richness and genetic diversity, the Gilgit-Baltistan territory seems to be a promising source for selection of improved germplasm in sea buckthorn.

DeepSAGE based differential gene expression analysis under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.)

Seabuckthorn (Hippophae rhamnoides L.), an important plant species of Indian Himalayas, is well known for its immense medicinal and nutritional value. The plant has the ability to sustain growth in harsh environments of extreme temperatures, drought and salinity. We employed DeepSAGE, a tag based approach, to identify differentially expressed genes under cold and freeze stress in seabuckthorn. In total 36.2 million raw tags including 13.9 million distinct tags were generated using Illumina sequencing platform for three leaf tissue libraries including control (CON), cold stress (CS) and freeze stress (FS). After discarding low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In all, 11922 differentially expressed genes (DEGs) including 6539 up regulated and 5383 down regulated genes were identified in three comparative setups i.e. CON vs CS, CON vs FS and CS vs FS. Gene ontology and KEGG pathway analysis were performed to assign gene ontology term to DEGs and ascertain their biological functions. DEGs were mapped back to our existing seabuckthorn transcriptome assembly comprising of 88,297 putative unigenes leading to the identification of 428 cold and freeze stress responsive genes. Expression of randomly selected 22 DEGs was validated using qRT-PCR that further supported our DeepSAGE results. The present study provided a comprehensive view of global gene expression profile of seabuckthorn under cold and freeze stresses. The DeepSAGE data could also serve as a valuable resource for further functional genomics studies aiming selection of candidate genes for development of abiotic stress tolerant transgenic plants.