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

Abstract

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.

Genomic variation reveals demographic history and biological adaptation of the ancient relictual, lotus (Nelumbo Adans.)

“…Recently, Liu et al . [ 25 ] reported that lotuses in Northeastern China and lotuses in Southeast Asia had closer genetic relationship than those in the Yangtze River Basin, which was different from ours. We believe that our result is more reliable because of the greater sequencing depth and the higher quality of the reference genome we used, but it also depends on sample size and representativeness.…”

Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication

“…American lotus has been proposed as a subspecies of Asian lotus (Borsch & Ba Rthlott, 1994). However, several studies using molecular markers and genome resequencing analyses have reported that these two species show substantial genetic differentiation (Huang et al., 2018; Liu et al., 2020c). Thus, further comparison of the genomic diversity and variants between American and Asian lotus are necessary to resolve this issue.…”

“…The divergence among accessions of flowering lotus, seed lotus and rhizome lotus is likely to have arisen from the preferred targeting of different traits for improvement during domestication (Yang et al., 2015). Moreover, flowering lotus accessions show higher nucleotide diversity and the highest heterozygosity (Table S21), which can be explained by their complicated origin during artificial selection (Liu et al., 2020c). Notably, the wild lotus accessions showed lower genetic diversity and heterozygous ratio than the cultivated lotus accessions (Tables S20 and S21), which might be because of their isolated habitat and asexual reproduction by rhizomes as the main reproduction mode.…”

“…Wild lotus germplasm resources can be used in research on the origin and breeding of lotus. However, wild lotus accessions suffer several threats, from environmental pollution, habitat loss and the undesirable admixture of these wild populations with domesticated accessions (Liu et al., 2020c). Therefore, it is urgent to strengthen the protection of wild lotus resources.…”

Characterization of Genomic Variation from Lotus (Nelumbo Adans.) Mutants with Wide and Narrow Tepals

“…The three accessions of the NL group were the seedlings from the Okeechobee Lake population of Florida, USA, which largely differentiated and separated from the population outside Florida according to our previous work [38]. For the accessions of the WSH group, they were obtained from the seeds of the Weishan Lake population, which has always been regarded as one of the lotus populations native to China [39,40]. Additionally, high uniformity and stability were observed in the phenotypic (especially floral) characteristics of the population and the 1024 seedlings, which were irradiated with the gamma rays of cobalt-60.…”