Detection of Highly Differentiated Genomic Regions Between Lotus (Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture

Abstract

The lotus (Nelumbo nucifera Gaertn.) is one of the most economically and ornamentally important perennial aquatic plants. Plant architecture is an important trait for lotus classification, cultivation, breeding, and applications. In this study, traits representing plant architecture were measured in 390 lotus germplasms for 3 years. According to the phenotypic distribution, 21 large architecture (LA) and 22 small architecture (SA) germplasms exhibiting extreme phenotypes were selected as representatives of plant architecture. Microscopy analyses revealed that LA lotuses possessed far more vertical cells and longer cell lengths than SA lotuses, and there was a closer linear relationship between vertical cell number and plant architecture than cell length and plant architecture. Furthermore, based on whole genome re-sequencing data from 10 LA and 10 SA lotus germplasms, fixation index (FST) genome scan identified 11.02 Mb of genomic regions that were highly differentiated between the LA and SA lotus groups. Chi-square test revealed that 17,154 single nucleotide polymorphisms (SNPs) and 1,554 insertions and deletions (InDels) showed distinct allelic distribution between the LA and SA lotus groups within these regions. A total of 126 variants with distinct allelic distribution in the highly differentiated region were predicted to cause amino acid changes in 60 genes. Among the 41 genes with functional annotation, the expression patterns of six genes involved in cell division and cell wall construction were confirmed using quantitative reverse-transcription PCR (qRT-PCR). In addition, 34 plant architecture-associated InDel markers were developed and verified in the remaining 11 LA and 12 SA lotus plant architecture representatives. This study identified promising functional markers and candidates for molecular breeding and will facilitate further elucidation of the genetic mechanisms underlying plant architecture in the lotus.

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

“…The SNP marker has been researched in many economic traits of various species, such as maize [ 82 ], soybean [ 83 ], and longan [ 60 , 84 ]. With the genetic and molecular studies in lotus, many molecular genetic markers have been researched and developed, including insertions and deletions (InDels), simple sequence repeats (SSRs), and abundant SNPs [ 32 , 85 , 86 ]. In lotus, the genome-wide analysis of SNP on AP2 domain demonstrated that, compared with other transcription factor gene families like MYB and RING finger, AP2/ERF gene family in lotus have a lower gene mutation of a loss of function [ 32 ], which implied that AP2 domain suffered a lower selection pressure.…”

Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plantNelumbo nucifera

“…Lotus is an economically important aquatic plant that has been widely used for food, medicinal, and ornamental purposes. As a basal eudicot plant with numerous monocot characteristics, lotus has been an important subject of evolutionary and taxonomic studies (The Angiosperm Phylogeny Group, 2009; Ming et al, 2013; Zhao et al, 2018b). Meanwhile, lotus plays a vital role in cultural and religious activities and is extensively distributed throughout Asia and Northern Australia.…”

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

“…Since the first draft genome assembly of the lotus variety China Antique was released 9 , many genomic studies have been carried out on lotus, such as whole-genome resequencing 7 , 10 , 11 , transcriptomic 12 – 14 , miRNA-based 15 – 17 and gene family studies 18 , 19 . The recent chromosome-level assembly of the China Antique genome facilitates genome-wide studies of functional genes and the evolution of lotus, but a web-based public database of lotus is still unavailable 8 .…”