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

Dingding Cao,Rebecca Njeri Damaris,Zhongyuan Lin,Longyu Huang,Pingfang Yang

doi:10.1186/s12864-021-07473-w

Dingding Cao, Rebecca Njeri Damaris + Show 3 more

Open Access

https://doi.org/10.1186/s12864-021-07473-w

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Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsIn conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome.

Highlights

The APETALA2/Ethylene Responsive Factor (AP2/ERF) family is widely present in plants and plays a crucial regulatory role in plant growth and development
We constructed a phylogenetic analysis of AP2/ERF superfamily with Nelumbo nucifera and Arabidopsis by employing the maximum likelihood (ML) method
The phylogenetic tree in lotus showed that NnAP2/ERF genes were separated into five subfamilies according to the Arabidopsis classification method, including AP2, ERF, DREB, RAV, and Soloist (Fig. 1) [5, 37]

Summary

Introduction

The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. Chinese lotus (Nelumbo nucifera) is popularly used for food and ornaments with agricultural and economic value Based on their biological characteristics and observed ecological habits, field visits, and regional experiments, the lotus was documented to exist in two natural ecotypes, namely, temperate lotus and tropical lotus. The AP2/ERF (APETALA2/Ethylene Responsive Factor) is a sizable transcription factors family in the plant kingdom. Their classification was widely studied in many model plants, including Arabidopsis and rice (Oryza sativa) [5], and many non-model plants such as the rubber tree (Hevea brasiliensis) [6], tea plant (Camellia sinensis) [7], and the Chinese cabbage Sakuma classified the AP2/ERF family into five branches, including AP2, DREB, RAV, ERF, and Soloist [9]

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