Genetic fingerprint construction and genetic diversity analysis of sweet potato (Ipomoea batatas) germplasm resources.

BACKGROUND: China is the largest producer of sweet potato in the world, accounting for 57.0% of the global output. Germplasm resources are the basis for promoting innovations in the seed industry and ensuring food security. Individual and accurate identification of sweet potato germplasm is an important part of conservation and efficient utilization. RESULTS: In this study, nine pairs of simple sequence repeat molecular markers and 16 morphological markers were used to construct genetic fingerprints for sweet potato individual identification. Combined with basic information, typical phenotypic photographs, genotype peak graphs, and a two-dimensional code for detection and identification were generated. Finally, a genetic fingerprint database containing 1021 sweet potato germplasm resources in the "National Germplasm Guangzhou Sweet Potato Nursery Genebank in China" was constructed. Genetic diversity analysis of the 1021 sweet potato genotypes using the nine pairs of simple sequence repeat markers revealed a narrow genetic variation range of Chinese native sweet potato germplasm resources, and Chinese germplasm was close to that from Japan and the United States, far from that from the Philippines and Thailand, and the furthest from that from Peru. Sweet potato germplasm resources from Peru had the richest genetic diversity, supporting the view that Peru is the center of origin and domestication of sweet potato varieties. CONCLUSIONS: Overall, this study provides scientific guidance for the conservation, identification, and utilization of sweet potato germplasm resources and offers a reference to facilitate the discovery of important genes to boost sweet potato breeding.

Exploration of molecular mechanism of intraspecific cross-incompatibility in sweetpotato by transcriptome and metabolome analysis.

Cross-incompatibility, frequently happening in intraspecific varieties, has seriously restricted sweetpotato breeding. However, the mechanism of sweetpotato intraspecific cross-incompatibility (ICI) remains largely unexplored, especially for molecular mechanism. Treatment by inducible reagent developed by our lab provides a method to generate material for mechanism study, which could promote incompatible pollen germination and tube growth in the ICI group. Based on the differential phenotypes between treated and untreated samples, transcriptome and metabolome were employed to explore the molecular mechanism of sweetpotato ICI in this study, taking varieties 'Guangshu 146' and 'Shangshu 19', a typical incompatible combination, as materials. The results from transcriptome analysis showed oxidation-reduction, cell wall metabolism, plant-pathogen interaction, and plant hormone signal transduction were the essential pathways for sweetpotato ICI regulation. The differentially expressed genes (DEGs) enriched in these pathways were the important candidate genes to response ICI. Metabolome analysis showed that multiple differential metabolites (DMs) involved oxidation-reduction were identified. The most significant DM identified in comparison between compatible and incompatible samples was vitexin-2-O-glucoside, a flavonoid metabolite. Corresponding to it, cytochrome P450s were the most DEGs identified in oxidation-reduction, which were implicated in flavonoid biosynthesis. It further suggested oxidation-reduction play an important role in sweetpotato ICI regulation. To validate function of oxidation-reduction, reactive oxygen species (ROS) was detected in compatible and incompatible samples. The green fluorescence was observed in incompatible but not in compatible samples. It indicated ROS regulated by oxidation-reduction is important pathway to response sweetpotato ICI. The results in this study would provide valuable insights into molecular mechanisms for sweetpotato ICI.

Genome Resource for Elsinoë batatas, the Causal Agent of Stem and Foliage Scab Disease of Sweet Potato.

Elsinoë batatas is a phytopathogenic fungus causing stem and foliage scab disease of sweet potato. At present, there is no reference genome available for E. batatas, limiting basic research for the pathogen. The present study applied the Nanopore single-molecule sequencing technology to sequence the E. batatas genome. This study reports the first high-quality genome sequence of E. batatas, with a total contig size of 26.49 Mb, 50.8% GC content, and an N50 of 2,546,814 bp. The sequences obtained serve as a reference for analysis of E. batatas isolates and provide a resource to better understand the biology of stem and foliage scab disease of sweet potato.

First Report of White Rust on Sweetpotato Caused by Albugo ipomoeae-panduratae in Guangdong, China.

Sweetpotato (Ipomoea batatas) is the eighth major food crop cultivated worldwide with annual production of 89.5 million tons (FAO 2020). China is the world's biggest producer of sweetpotato, and Guangdong Province has the fourth-largest sweetpotato growing area and the biggest sweetpotato market in China (Huang et al. 2020a). Sweetpotato leaves are a key organ providing nutrients for humans and animals, and are popular with customers in Guangdong. On October 14, 2021, a white rust affecting sweetpotato leaves was observed in the fields of Yunfu, Guangdong (22°54'55''N, 112°02'40''E) when conditions were humid, rainy and relatively mild. The adaxial surface of the infected leaves initially exhibited irregular light-yellow or yellow spots, which gradually turned to brown and necrotic. Meanwhile, tiny, powdery, chalky-white pustules, typical of white rust, dispersed individually or in clusters were observed on the corresponding underside of lesions, resulting in wrinkled leaves or abscission. For further analysis in the laboratory, affected leaf pieces (5 mm × 5 mm) containing raised pustules were examined using a scanning electron microscope (S-3400N-Ⅱ, Hitachi, Japan) at 5kv. The micrographs revealed numerous cylindrical-shaped sporangia released from broken pustules. The surfaces of globose oospores were covered with tiny papillae in a reticular pattern. Based on the morphological analyses, the pathogen was preliminarily identified as an Albugo sp. Crude genomic DNA of a few pustules from the diseased leaves were extracted and subjected to PCR amplification using a 2×T5 Direct PCR kit (TSE011, Tsingke, China) with the primers, ITS1/ITS4 (White et al. 1990). PCR products were detected using agarose gel electrophoresis and sequenced by Tsingke company (Guangzhou, China). The sequences were compared against the NCBI database using the BLASTn search tool. The two best-matched alignments with over 90% query coverage showed that ITS sequence amplified from the sample, which was deposited in GenBank (OM182104), was ≥97% identical to those from two isolates of A. ipomoeae-panduratae from China (AY742741) and Korea (DQ643920). A. ipomoeae-panduratae primarily causes white rust on sweetpotato (Moyer and Clark 2013) and is an obligate parasite not culturable in vitro. To demonstrate pathogenicity, spores collected from symptomatic sweetpotato leaves were mixed with sterile water and sprayed onto leaves of three healthy sweetpotato plants. Inoculated plants were then placed at 21℃ and 93% relative humidity. Three other healthy plants treated with sterile water without spores served as the control group. After 12 days, chlorosis and necrosis were observed on the upper leaf surface; and raised white pustules appeared on the lower leaf surface. No symptoms were observed in the noninoculated control plants. To the best of our knowledge, this is the first report of white rust, caused by A. ipomoeae-panduratae, affecting sweetpotato in Guangdong, China. White rust on sweetpotato has also been reported in other provinces in China (Huang et al. 2020b), and the detrimental effects and control measures of this disease should be studied further.

Draft Genome Sequence of Diaporthe batatatis Causing Dry Rot Disease in Sweetpotato.

Dry rot caused by Diaporthe batatatis leads to the serious decay of sweetpotato storage roots during postharvest storage, which can result in considerable economic loss. Genomic research of the pathogen could provide a basis for study and prevention of sweetpotato dry rot. Herein, we report a high-quality draft genome sequence of D. batatatis CRI 302-4 isolated from infected sweetpotato storage roots in Taizhou City, Zhejiang Province, China. The size of the genome was 54.38 Mb and consisted of 36 scaffolds with a G+C content of 50.56% and an N50 of 2,950,914 bp. The information provided in this genome sequence will be an invaluable resource for molecular genetic research and disease control in sweetpotato production.

High-Quality Genome Resource of Diaporthe destruens Causing Foot Rot Disease of Sweet Potato.

Foot rot of sweet potato caused by Diaporthe destruens severely affects yield and quality worldwide. Research on this pathogen is limited due to nonavailability of genome resources. Here, we report a high-quality genome sequence of D. destruens isolate CRI 305-2, which was originally isolated from infected stem of sweet potato in Taizhou City, Zhejiang Province, China. The genome comprised a total length of 56,108,228 bp, consisted of 47 scaffolds with an overall G+C content of 48.7% and an N50 of 2,479,481 bp. This resource can be used as a reference for evolution mechanisms and comparative genomic research.

Isolation and Identification of Trichoderma asperellum, the Novel Causal Agent of Green Mold Disease in Sweetpotato.

Postharvest disease is an important limiting factor for sweetpotato production. Recently, a new green mold disease was found in sweetpotato storage roots. To investigate the mechanism underlying the pathogenesis of the disease, the pathogen was isolated and identified based on morphological and molecular features, and its characteristics were further analyzed by pathogenic and antagonistic evaluations. The results showed that the isolated pathogen (CRI-Ta1) was identified as Trichoderma asperellum based on the similar growth and morphological features with Trichoderma spp., 99% homology of internal transcribed spacer (ITS) sequence, and membership to the same phylogenetic group with the model strain of T. asperellum (CBS 433.97). The pathogenic analysis revealed that CRI-Ta1 could cause green mold disease through wound infection on the storage roots and the strains reisolated from infected storage roots could cause disease in different sweetpotato varieties, which was fulfilled in Koch's postulate. Moreover, CRI-Ta1 could also infect other common crop species, including chestnut, carrot, apple, pear, and others. It indicated that CRI-Ta1 was the pathogen to the storage roots of sweetpotato and had a wide host range. Additionally, in vitro antagonistic evaluation showed that CRI-Ta1 effectively inhibited the growth of common sweetpotato pathogens, including Fusarium solani and Rhizopus nigricans. However, further research is needed on the potential of CRI-Ta1 to control sweetpotato diseases in vivo. Collectively, our findings provided valuable insights into the characteristics of the T. asperellum CRI-Ta1 in sweetpotato and would be helpful to the prevention and control of sweetpotato green mold disease.

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development.

BACKGROUND: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars.

BACKGROUND: Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication. METHODS: A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR. RESULTS: Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication. CONCLUSIONS: The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication.

The complete mitochondrial genome of the jumping plant bug Halticus minutus Reuter, 1885 (Hemiptera: Miridae).

The complete mitochondrial genome of Halticus minutus was sequenced and analyzed in this study. The mitochondrial genome is 15,403 bp in size and comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (D-loop). The nucleotide composition of the mitogenome is 41.81% A, 32.50% T, 10.43% G, and 15.26% C. Despite only a few references available on the complete mitochondrial genome of Miridae, phylogenetic analysis suggested that H. minutus is most closely related to Nesidiocoris tenuis.

Complete chloroplast genome of a novel chlorophyll-deficient mutant (clm) in sweetpotato (Ipomoea batatas L.).

The complete chloroplast genome of a novel chlorophyll-deficient mutant (clm) and its wild type (WT) in sweetpotato (Ipomoea batatas L.) was sequenced. The complete chloroplast genome of clm and WT was 161,393 bp and 161,429 bp in length, containing a large single copy (LSC) region of 87,561 bp and 87,597 bp, respectively, a small single copy (SSC) region with the same length of 30,890 bp and a pair of inverted repeat regions (IRs) with the same length of 12,052 bp. Both of them contained 132 genes including 87 protein-coding sequences, 37 tRNA, and eight rRNA. Comparing to the WT, four SNPs and three INDELs were detected and only one INDEL in the exon affecting the translation of rpoA gene. Phylogenetic analysis showed that clm and WT were closely related to Ipomoea tabascana. The complete chloroplast genome of clm and its WT will play a role in understanding the molecular mechanism of chlorophyll deficiency and developing molecular markers in sweetpotato.

[Clone and construction of plant expression vector of AeSS gene in Aralia elata].

OBJECTIVE: To clone Aralia elata squalene synthase gene (designated as AeSS) and construct plant expression vector for transgenic research. METHODS: Isolated squalene synthase from Aralia elata with specific primers by RT-PCR and inserted AeSS gene into the plant expression vector pBI121. RESULTS: The full-length cDNA of AeSS (Genebank accession Number: GU354313) was 1 261 bp and contained a 1 245 bp open reading frame (ORF) encoding a polypeptide of 414 amino acids. The plant expression vector pAeSS was constructed by inserted AeSS gene into the downstream of 35 S promoter of plant expression vector pBI121. CONCLUSION: AeSS gene was cloned and plant expression vector was constructed for future research.