Comparative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera

Abstract

Background: Lotus (Nelumbo nucifera) is an aquatic plant with important agronomic, horticulture, art and religion values. It was the basal eudicot species occupying a critical phylogenetic position in flowering plants. After the domestication for thousands of years, lotus has differentiated into three cultivated types -flower lotus, seed lotus and rhizome lotus. Although the phenotypic and genetic differentiations based on molecular markers have been reported, the variation on whole-genome level among the different lotus types is still ambiguous.

Results: In order to reveal the evolution and domestication characteristics of lotus, a total of 69 lotus accessions were selected, including 45 cultivated accessions, 22 wild sacred lotus accessions, and 2 wild American lotus accessions. With Illumina technology, the genomes of these lotus accessions were resequenced to > 13× raw data coverage. On the basis of these genomic data, 25 million single-nucleotide polymorphisms (SNPs) were identified in lotus. Population analysis showed that the rhizome and seed lotus were monophyletic and genetically homogeneous, whereas the flower lotus was biphyletic and genetically heterogeneous. Using population SNP data, we identified 1214 selected regions in seed lotus, 95 in rhizome lotus, and 37 in flower lotus. Some of the genes in these regions contributed to the essential domestication traits of lotus. The selected genes of seed lotus mainly affected lotus seed weight, size and nutritional quality. While the selected genes were responsible for insect resistance, antibacterial immunity and freezing and heat stress resistance in flower lotus, and improved the size of rhizome in rhizome lotus, respectively.

Conclusions: The genome differentiation and a set of domestication genes were identified from three types of cultivated lotus- flower lotus, seed lotus and rhizome lotus, respectively. Among cultivated lotus, flower lotus showed the greatest variation. The domestication genes may show agronomic importance via enhancing insect resistance, improving seed weight and size, or regulating lotus rhizome size. The domestication history of lotus enhances our knowledge of perennial aquatic crop evolution, and the obtained dataset provides a basis for future genomics-enabled breeding.

Keywords: Domestication; Genome variation; Nelumbo nucifera; Whole-genome resequencing.

Fig. 1

Morphology of the four lotus groups. Flower (a), seeds (c) and rhizome (e) of lotus accession W06 (wild sacred lotus). A flower of lotus accession F10 (flower lotus), seeds of lotus accession S19 (seed lotus), and a rhizome of lotus accession R11 (rhizome lotus) are shown in figures (b), d and f respectively. Bar indicates 10 cm

Fig. 2

Population structure and LD decay in lotus. a The neighbor-joining tree of the 69 lotus accessions with bootstrap =1000 and the bootstrap values less than 100 were labelled. The accessions shown in red are wild sacred lotus, while yellow indicates American lotus, and purple, blue, and green represent flower lotus, rhizome lotus and seed lotus, respectively. b Principal component analysis (PCA) of the 69 lotus accessions. Two accessions of American lotus were from locations far from the sacred lotus accessions. The PCA of 67 accessions (Nelumbo nucifera) is shown on the left bottom side. c Population structure (k = 2–7) of the 69 lotus accessions determined by FRAPPE. Each accession is represented by a vertical bar, and the length of each colored segment in each vertical bar represents the proportion contributed by ancestral populations. d Differences in linkage disequilibrium (LD) between the wild and cultivated lotus groups. LD decay determined via squared correlations of allele frequencies (r2) against the distance between polymorphic sites in cultivated and wild lotus

Fig. 3

Distribution of log2π ratios and Z(F_ST) values, calculated in 10-kb windows sliding in 5-kb steps. The selected genes disscussed in the main text were marked in the selected rigions (blue pionts). Data points located to the right of the right vertical dashed lines (corresponding to the 5% right tails of the log_2⁡π ratio distribution, where the log2π ratio is 2.27 in (a), 0.46 in (b), 3.87 in (c)) and above the horizontal dashed line (the 5% right tail of the Z(F_ST) distribution, where Z(F_ST) is 1.21 in (a), 1.82 in (b), 2.22 in (c)) were identified as selected regions for seed lotus, flower lotus and rhizome lotus(blue points), respectively

Fig. 4

Examples of seven genes with strong signals of a selective sweep in cultivated lotus. Figure A, B, C, D, E, F and G correspond to the SUPERMAN-like gene(XM_010264184.1), legumin A-like gene(XM_010281131.1), 3-oxo-Δ 4,5-steroid 5β-reductase gene(XM_010274509.1), EFR gene(XM_010270240.1), UGT80B1 gene (XM_010262670.1), EMBRYONIC FLOWER 2-like gene (XM_010260462.1) and expansin-A13-like gene (XM_010247895.1) respectively. The abscissa of each figures are the physical distance. The left ordinate is the fstM value and the right ordinate is the pi value; pi-1, pi-2 and fstM values are presented in pink, green and blue and the red rectangles show the gene position. In the first column of the graph, the pi-1 and pi-2 stand for the pi values of the selected genes of flower lotus and wild lotus respectively; the pi-1 and pi-2 stand for the pi values of rhizome lotus and wild lotus respectively in the second column and the pi-1 and pi-2 stand for the pi values of wild lotus and seed lotus respectively in the third column