Research Progress on Iron-Heart Cunninghamia lanceolate

Cunninghamia lanceolate (Lambert.) Hooker is one of the main fast-growing timber forest species in southern China which has a long history of cultivation and spreads across 28 provinces, cities, and regions. Recently, a variant of fir was discovered in the Xiaoxi National Nature Reserve in Hunan Province. The heartwood is hard as iron and its ratio is more than 80%, with the especial character of anti-corruption. It is a natural germplasm resource, called Iron-heart Cunninghamia lanceolate. Study on it is still in the stage of data accumulation. In this paper, we studied it from three points as follows: (1) Plus tree selection and construction of germplasm resources nursery. (2) Study on cone and seed quality. (3) Genetic structure analysis of natural population. The research of Iron-heart Cunninghamia lanceolate lays a theoretical foundation for the protection, development, and utilization of the black-heart wood germplasm resources of Iron-heart Cunninghamia lanceolate in the future.

SSR-Sequencing Reveals the Inter- and Intraspecific Genetic Variation and Phylogenetic Relationships among an Extensive Collection of Radish (Raphanus) Germplasm Resources

Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.

Effects of Temperature, Scarification, Stratification, Phytohormones, and After-Ripening on the Dormancy and Germination of Eucommia ulmoides Oliv. Seeds

Eucommia ulmoides Oliv., the only member of the family Eucommiaceae, is endemic to China and has great development and utilization prospects. The seeds of E. ulmoides show dormancy but the underlying mechanism remains unknown. The aim of this study was to determine the cause of the seed dormancy and provide fundamental knowledge for the breeding, genetic improvement, and conservation of the germplasm resources of this species. According to the seed dormancy classification system developed by Jerry M. Baskin and Carol C. Baskin, we compared the germination percentage between intact seeds and isolated embryos, constructed water absorption curves, and evaluated the germination of seeds treated with scarification, cold/warm-moist stratification, after-ripening during dry storage, and gibberellic acid (GA3). The results showed that the intact seeds germinated only at 10 °C with a low germination percentage of 13.3% whereas the isolated embryos had a high normal germination percentage among a wider range of temperatures. According to the results from the scarified seeds, half seeds, and intact seeds, the seed coat significantly restricted the embryo water absorption. The scarification, after-ripening, cold/warm-moist stratification, and GA3 treatments promoted seed germination. Among them, cold-moist stratification was the most effective method and the temperature range of seed germination increased in both directions from 10 °C with prolonged stratification. The germination percentage increased significantly at constant temperatures with the highest germination percentage of 93.7 ± 0.3% at 10 °C and a light/dark cycle after 90 days of cold-moist stratification. Therefore, the freshly harvested E. ulmoides seeds exhibited a combinational dormancy comprising physical and Type 3 non-deep physiological dormancy, causing limited embryo water absorption by the seed coat and a low embryo growth potential. Given the unique phylogenetic characteristics and utility of E. ulmoides, our findings should promote studies of seed dormancy evolution and the development and application of E. ulmoides germplasm resources.

Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers

Prunus sibirica is an economically important tree species that occurs in arid and semi-arid regions of northern China. For this species, creation of a core collection is critical for future ecological and evolutionary studies, efficient economic utilization, and development and management of the broader collection of its germplasm resources. In this study, we sampled 158 accessions of P. sibirica from Russia and China using 30 pair of simple sequence repeat molecular markers and 30 different schemes to identify candidate core collections. The 30 schemes were based on combinations of two different sampling strategies, three genetic distances, and five different sample sizes of the complete germplasm resource. We determined the optimal core collection from among the 30 results based on maximization of genetic diversity among groups according to Number of observed alleles (Na), Number of effective alleles (Ne), Shannon’s information index (I), Polymorphic information content (PIC), Nei gene diversity (H) and compared to the initial collection of 158 accessions. We found that the optimal core collection resulted from preferred sampling at 25% with Nei & Li genetic distance these ratios of Na, Ne, I, PIC and H to the complete 158 germplasm resources were 73.0%, 113%, 102%, 100% and 103%, respectively, indicating that the core collection comprised a robust representation of genetic diversity in P. sibirica. The proposed core collection will be valuable for future molecular breeding of this species and management of its germplasm resources.

Development of molecular markers based on the promoter difference of LcFT1 to discriminate easy- and difficult-flowering litchi germplasm resources and its application in crossbreeding

Background Litchi is a well-known subtropical fruit crop. However, irregular bearing attributed to unstable flowering is a major ongoing problem for the development of the litchi industry. In a previous study, our laboratory proved that litchi flowering was induced by low temperature and that a FLOWERING LOCUS T (FT) homologue gene named LcFT1 played a pivotal role in this process. The present study aimed to understand the natural variation in FT among litchi germplasm resources and designed markers to verify easy- and difficult-flowering litchi germplasms. A grafting experiment was also carried out to explore whether it could shorten the seedling stage of litchi seedlings. Results Two types of LcFT1 promoter existed in different litchi germplasm resources, and we named them the ‘easy-flowering type of LcFT1 promoter’ and ‘difficult-flowering type of LcFT1 promoter’, which resulted in three different LcFT1 genotypes of litchi germplasm resources, including the homozygous easy-flowering type of the LcFT1 genotype, homozygous difficult-flowering type of the LcFT1 genotype and heterozygous LcFT1 genotype of litchi germplasm resources. The homozygous easy-flowering type of the LcFT1 genotype and heterozygous LcFT1 genotype of the litchi germplasm resources completed their floral induction more easily than the homozygous difficult-flowering type of the LcFT1 genotype of litchi germplasm resources. Herein, we designed two kinds of efficient molecular markers based on the difference in LcFT1 promoter sequences and applied them to identify of the easy- and difficult-flowering litchi germplasm resources. These two kinds of molecular markers were capable of clearly distinguishing the easy- from difficult-flowering litchi germplasm resources at the seedling stage and provided the same results. Meanwhile, grafting the scion of seedlings to the annual branches of adult litchi trees could significantly shorten the seedling stage. Conclusions Understanding the flowering characteristics of litchi germplasm resources is essential for easy-flowering litchi breeding. In the present study, molecular markers provide a rapid and accurate approach for identifying the flowering characteristics. The application of these molecular markers not only significantly shortened the artificial crossbreeding cycle of easy-flowering litchi cultivars but also greatly saved manpower, material resources and land.

Integration of transcriptome and targeted metabolome profiling reveals hormone related genes involved in the growth of Bletilla striata

Bletilla striata (Thunb.) Reichb.f. (BS) is a traditional Chinese medicine with numerous beneficial effects. In our previous study, Aspergillus flavus was isolated from B. striata. To explore the physiological and molecular mechanisms of Aspergillus flavus elicitor (1-G4) that promoted Bletilla striata growth, in this study, we performed the determination of growth indexes and transcriptomics and metabolomics analysis under 5% and 10% 1-G4 conditions. Results showed that 1-G4 elicitor could significantly promote the growth and development of B. striata. With the increasing concentration of 1-G4 elicitor, the contents of SA, ICAld, and ME-IAA significantly increased while the IP and ACC contents decreased dramatically. A total of 1657 DEGs (763 up-regulated and 894 down-regulated) between the control (CK) and 5% elicitor (CK vs G5) and 2415 DEGs (1208 up-regulated and 1207 down-regulated) between the control and 10% elicitor (CK vs G10) were identified. Further, we found that 22, 38, and 2 unigenes were involved in ME-IAA, IP, and ACC, respectively. It was indicated that these unigenes might be involved in B. striata growth. Overall, the current study laid a theoretical foundation for the effective utilization of endophytic fungi and the optimization of germplasm resources of B. striata.

Assessment of Genetic Diversity and Identification of Core Germplasm of Pueraria in Guangxi Using SSR Markers

Pueraria is not only one of the most important commercial crops, but a health supplement for human being. There are abundant Pueraria germplasm resources and a large planting scale in Guangxi. However, the genetic diversity and core germplasm of the Pueraria species in Guangxi are rarely understood. In this study, 272 individuals of Pueraria species in Guangxi combined with 23 pairs of simple sequence repeat primers were used to evaluate the genetic diversity and construct core germplasm. Ultimately, 118 alleles were identified and 112 alleles were polymorphic; the mean expected heterozygosity per locus is 0.1841, and the mean gene flow Nm is 1.7690. 272 individuals were divided into two main clusters, which is consistent with the results based on principal coordinate analysis and STRUCTURE cluster analysis. We proposed a core collection of 20 Pueraria accessions capturing 105 alleles. There was a non-significant relationship between genetic distance and geographical distance. The results could provide theoretical support for the scientific conversation of Pueraria genetic resources, which can serve as the basis for the breeding program of Pueraria.

DNA barcode reference library construction and genetic diversity and structure analysis of Amomum villosum Lour. (Zingiberaceae) populations in Guangdong Province

Background Amomum villosum Lour. is the plant that produces the famous traditional Chinese medicine Amomi Fructus. Frequent habitat destruction seriously threatens A. villosum germplasm resources. Genetic diversity is very important to the optimization of germplasm resources and population protection, but the range of inherited traits within A. villosum is unclear. In this study, we analyzed the genetic diversity and genetic structures of A. villosum populations in Guangdong and constructed a local reference DNA barcode library as a resource for conservation efforts. Methods DNA barcoding and Inter-Simple Sequence Repeat (ISSR) markers were used to investigate the population genetics of A. villosum. Five universal DNA barcodes were amplified and used in the construction of a DNA barcode reference library. Parameters including percentage of polymorphic sites (PPB), number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity index (H), and Shannon’s polymorphism information index (I) were calculated for the assessment of genetic diversity. Genetic structure was revealed by measuring Nei’s gene differentiation coefficient (Gst), total population genetic diversity (Ht), intra-group genetic diversity (Hs), and gene flow (Nm). Analysis of molecular variance (AMOVA), Mantel tests, unweighted pair-group method with arithmetic mean (UPGMA) dendrogram, and principal co-ordinates (PCoA) analysis were used to elucidate the genetic differentiation and relationship among populations. Results A total of 531 sequences were obtained from the five DNA barcodes with no variable sites from any of the barcode sequences. A total of 66 ISSR bands were generated from A. villosum populations using the selected six ISSR primers; 56 bands, 84.85% for all the seven A. villosum populations were polymorphic. The A. villosum populations showed high genetic diversity (H = 0.3281, I = 0.4895), whereas the gene flow was weak (Nm = 0.6143). Gst (0.4487) and AMOVA analysis indicated that there is obvious genetic differentiation amongA. villosum populations and more genetic variations existed within each population. The genetic relationship of each population was relatively close as the genetic distances were between 0.0844 and 0.3347.

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.