State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
Guangchang Research School of White Lotus, Guangchang, 344900, People's Republic of China.
BMC Genomics. 2020 Feb 11;21(1):146. doi: 10.1186/s12864-019-6376-8.
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.
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.
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.
荷花（Nelumbo nucifera）是一种水生植物，具有重要的农学、园艺、艺术和宗教价值。它是基础被子植物物种，在开花植物中占据关键的进化位置。经过数千年的驯化，荷花已经分化为三种栽培类型——花莲、子莲和藕莲。尽管已经报道了基于分子标记的表型和遗传分化，但不同类型的荷花在全基因组水平上的变异仍然不清楚。
为了揭示荷花的进化和驯化特征，共选择了 69 个荷花品种，包括 45 个栽培品种、22 个野生圣莲品种和 2 个野生美洲莲品种。利用 Illumina 技术，对这些荷花品种进行了 >13×的原始数据覆盖度重测序。基于这些基因组数据，在荷花中鉴定出了 2500 万个单核苷酸多态性（SNP）。群体分析表明，藕莲和子莲是单系的，遗传上是同质的，而花莲是双系的，遗传上是异质的。利用群体 SNP 数据，我们在子莲中鉴定出了 1214 个选择区域，在藕莲中鉴定出了 95 个，在花莲中鉴定出了 37 个。这些区域的一些基因与荷花的基本驯化特征有关。子莲的选择基因主要影响莲子的重量、大小和营养品质。而花莲的选择基因则负责抗虫、抗菌免疫和抗冻耐热，以及提高藕莲的藕径大小。
从三种栽培荷花——花莲、子莲和藕莲中分别鉴定出了基因组分化和一套驯化基因。在栽培荷花中，花莲表现出最大的变异。驯化基因可能通过增强抗虫性、提高种子重量和大小或调节荷花藕径大小来显示其农业重要性。荷花的驯化历史增进了我们对多年生水生作物进化的认识，获得的数据集为未来基于基因组学的育种提供了基础。
