For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

https://biblio.ugent.be/publication/8660644/file/8672012.pdf

Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.

Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history

Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, 'Chardonnay' and 'Beibinghong', and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for 'Chardonnay' (the female parent), 48.20 for 'Beibinghong' (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.

/pdf/construction-of-a-high-density-genetic-map-for-grape-using-4jkq2su9fn.pdf

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing.

A proteomic study of resistance to Brown Ring disease in the Manila clam, Ruditapes philippinarum.

The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value. We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population. In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome.

/pdf/genome-wide-analysis-of-ap2-erf-superfamily-in-lotus-nelumbo-3pnfxw13nv.pdf

Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology

The sacred lotus (Nelumbo nucifera) is widely cultivated in China for its edible rhizomes and seeds. Traditional plant breeding methods have been used to breed cultivars with increased yields and quality of rhizomes and seeds with limited success. Currently, the available genetic maps and molecular markers in lotus are too limited to be useful for molecular genetics based breeding programs. However, the development of next-generation sequencing (NGS) technologies has enabled large-scale identification of single-nucleotide polymorphisms (SNPs) for genetic map construction. In this study, we constructed an SNP-based high-density genetic map for cultivated lotus using double digest restriction site-associated DNA sequencing (ddRADseq). An F2 population of 96 individuals was derived from a cross between the rhizome lotus cultivar ‘Juwuba’ (male parent) and the seed lotus cultivar ‘Mantianxing’ (female parent). Genomic DNAs from this population were digested with the restriction enzymes EcoRI and MspI and then sequenced. In total, 133.65 Gb of raw data containing 1,088,935,610 pair-end reads were obtained. The coverage of reads on a reference genome was 7.2 % for the female parent, 6.56 % for the male parent, and 1.46 % for F2 individuals. From these reads, 10,753 valid SNP markers were used for genetic map construction. Finally, 791 bin markers (so-segregated adjacent SNPs treated as a bin marker), consisting of 8,971 SNP markers, were sorted into 8 linkage groups (LGs) that spanned 581.3 cM, with an average marker interval of 0.74 cM. A total of 809 genome sequence scaffolds, covering about 565.9 cM of the wild sacred lotus genome, were anchored on the genetic map, accounting for 70.6 % of the genome assembly. This study reports the large-scale discovery of SNPs between cultivars of rhizome and seed lotus using a ddRADseq library combined with NGS. These SNPs have been used to construct the first high-density genetic map for cultivated lotus that can serve as a genomic reference and will facilitate genetic mapping of important traits in the parental cultivars.

/pdf/construction-of-a-high-density-high-quality-genetic-map-of-1fntz2dbeu.pdf

Construction of a high-density, high-quality genetic map of cultivated lotus ( Nelumbo nucifera ) using next-generation sequencing

The invention discloses a lotus root protected medium cultivation method and belongs to the field of lotus root protected cultivation. The lotus root protected medium cultivation method includes the following steps that (1) a greenhouse is built and a lotus root pond is built in the greenhouse; (2) a medium is added into the lotus root pond; (3) lotus roots are fixedly planted; (4) lotus root field management is performed; (5) harvesting is performed to obtain the lotus roots. According to the lotus root protected medium cultivation method, protected cultivation of the lotus roots is applied, early-ripe lotus root varieties are selected, peat, mushroom residues and vermiculite are mixed to serve as the medium, lotus root cultivation density and planting time are optimized and a proper harvesting method is applied so that finally, the lotus roots can be harvested for three times in a year, yield and qualities of the lotus roots can be remarkably improved, the planting benefits of the lotus roots are improved, and meanwhile, simple easy lotus root planting can be achieved.

Lotus root protected medium cultivation method

The invention discloses a watercress protection land substrate culture method, and belongs to the field of watercress protection land substrate culture. The watercress protection land substrate culture method comprises the following steps that (1) a greenhouse is built, and a pool is built in the greenhouse; (2) the pool is filled with substrates; (3) seeding and seedling culture are carried out, and the fixed planting of watercress is carried out in the pool; (4) growth management is carried out; (5) harvesting and obtaining are realized. The watercress protection land substrate culture method has the advantages that the protection land is adopted for culturing the watercress, peat, mushroom slag and vermiculite are mixed to be used as the substrates, the fixed planting density of the watercress is optimized, in addition, the harvesting is carried out at proper time, the three times of harvesting is achieved in one year, the watercress yield is obviously improved, the watercress quality is improved, and the planting benefits of the watercress are improved.

Watercress protection land substrate culture method

The invention discloses an artificial hybridization breeding method for water chestnuts, and relates to the technical field of agricultural breeding. The artificial hybridization breeding method for the water chestnuts includes respectively selectively cultivating male parent water chestnuts and female parent water chestnuts; bagging male parent flower buds with just cracking sepals and petals yet to be loose, selecting female parent flower buds with just cracking sepals, removing the sepals and the petals, pinching off stamens and bagging the male parent flower buds and the female parent flower buds; pollinating female parent flowers by pollen of the male parent water chestnuts in 0-4 hours after the stamens of the female parent flower buds are removed. The male parent water chestnuts flower for 0-4.5 h before the female parent flowers are pollinated by the pollen of the male parent water chestnuts. The artificial hybridization breeding method has the advantage that hybrid water chestnut seeds with strong growth vigor and stress resistance and obvious hybrid vigor can be directionally selectively bred by the aid of artificial hybridization technologies.

Artificial hybridization breeding method for water chestnuts

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Construction of a high-density, high-quality genetic map of cultivated lotus ( Nelumbo nucifera ) using next-generation sequencing

Lotus root protected medium cultivation method

Watercress protection land substrate culture method

Artificial hybridization breeding method for water chestnuts