Development and identification of three functional markers associated with starch content in lotus (Nelumbo nucifera)

Integrated mRNA and Small RNA Sequencing Reveals a microRNA Regulatory Network Associated with Starch Biosynthesis in Lotus (Nelumbo nucifera Gaertn.) Rhizomes

Internode starch biosynthesis is one of the most important traits in lotus rhizome because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to lotus internode starch biosynthesis would help develop molecular improvement strategies, but they are not yet well-investigated. To identify genes and miRNAs involved in internode starch biosynthesis, the cDNA and small RNA libraries of Z6-1, Z6-2, and Z6-3 were sequenced, and their expression were further studied. Through combined analyses of transcriptome data and small RNA sequencing data, a complex co-expression regulatory network was constructed, in which 20 miRNAs could modulate starch biosynthesis in different internodes by tuning the expression of 10 target genes. QRT-PCR analysis, transient co-expression experiment and dual luciferase assay comprehensively confirmed that NnumiR396a down-regulated the expression of NnSS2 and ultimately prevents the synthesis of amylopectin, and NnumiR396b down-regulated the expression of NnPGM2 and ultimately prevents the synthesis of total starch. Our results suggest that miRNAs play a critical role in starch biosynthesis in lotus rhizome, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing lotus rhizome.

LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus (Nelumbo nucifera) Rhizomes

Yields of edible rhizome from cultivation of the perennial hydrophyte lotus (Nelumbo nucifera) can be severely reduced by rhizome rot disease caused by Fusarium species. There is a lack of rapid field-applicable methods for detection of these pathogens on lotus plants displaying symptoms of rhizome rot. Fusarium commune (91%) and Fusarium oxysporum (9%) were identified at different frequencies from lotus samples showing symptoms of rhizome rot. Because these two species can cause different severity of disease and their morphology is similar, molecular diagnostic-based methods to detect these two species were developed. Based on the comparison of the mitochondrial genome of the two species, three specific DNA loci targets were found. The designed primer sets for conventional PCR, quantitative PCR, and loop-mediated isothermal amplification (LAMP) precisely distinguished the above two species when isolated from lotus and other plants. The LAMP detection limits were 10 pg/μl and 1 pg/μl of total DNA for F. commune and F. oxysporum, respectively. We also carried out field-mimicked experiments on lotus seedlings and rhizomes (including inoculated samples and field-diseased samples), and the results indicated that the LAMP primer sets and the supporting portable methods are suitable for rapid diagnosis of the lotus disease in the field. The LAMP-based detection method will aid in the rapid identification of whether F. oxysporum or F. commune is infecting lotus plants with symptoms of rhizome rot and can facilitate efficient pesticide use and prevent disease spread through vegetative propagation of Fusarium-infected lotus rhizomes.

Characterization, Functional Properties, and Resistant Starch of Freshwater Macrophytes

Several aquatic macrophytes such as Colocasia esculenta, Eleocharis dulcis, Nelumbo nucifera, Sagittaria sagittifolia, Trapa bispinosa, and Typha angustifolia possessed carbohydrate mainly in their storage and reproductive parts. Starch morphology, total starch, and amylose content of these six freshwater plant species were determined. Their functional properties, i.e., starch crystallinity, thermal properties, and rheological behaviour were assessed. Large starch granules were in N. nucifera rhizome (>15 μm), medium-sized was N. nucifera seed (8-18 μm), while the rest of the starches were small starch granules (<8 μm). Shapes of the starch granules varied from oval and irregular with centric hilum to elongated granules with the eccentric hilum. Eleocharis dulcis corm starch had significantly higher total starch content (90.87%), followed by corms of C. esculenta (82.35%) and S. sagittifolia (71.71%). Nelumbo nucifera seed starch had significantly higher amylose content (71.45%), followed by T. angustifolia pollen (36.47%). In comparison, the waxy starch was in N. nucifera rhizome (7.63%), T. bispinosa seed (8.83%), C. esculenta corm (10.61%), and T. angustifolia rhizome (13.51%). Higher resistant starch was observed mostly in rhizomes of N. nucifera (39.34%)>T. angustifolia (37.19%) and corm parts of E. dulcis (37.41%)>S. sagittifolia (35.09%) compared to seed and pollen starches. The XRD profiles of macrophytes starches displayed in all the corms and N. nucifera seed had A-type crystallinity. The T. bispinosa seed had C_A-type, whereas the rest of the starches exhibited C_B-type crystallinity. Waxy starches of C. esculenta corm had higher relative crystallinity (36.91%) and viscosity (46.2 mPa s) than regular starches. Based on thermal properties, high-amylose of N. nucifera seed and T. angustifolia pollen resulted in higher gelatinization enthalpy (19.93 and 18.66 J g⁻¹, respectively). Starch properties showed equally good potential as commercial starches in starch-based food production based on their starch properties and functionality.

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

Measurement(s)	reference genome data • whole genome sequencing • transcriptome
Technology Type(s)	Hi-C • PacBio Sequel System • Illumina sequencing • RNA sequencing • DNA sequencing
Sample Characteristic - Organism	Nelumbo nucifera

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13487271

Functional Markers for Precision Plant Breeding

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.