Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables

Nguyen Hoai Nguyen,Benny Jian Rong Sng,Hock Chuan Yeo,In-Cheol Jang

doi:10.1186/s12864-021-08076-1

Nguyen Hoai Nguyen, Benny Jian Rong Sng + Show 2 more

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https://doi.org/10.1186/s12864-021-08076-1

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Abstract

BackgroundPlants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored.ResultsShade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety.ConclusionsOur study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Highlights

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS)
Our study shows that two Brassicaceae species share a conserved SAS mechanism and exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms
Only B. oleracea Kai Lan exhibited a significant reduction in primary root elongation while the other B. rapa vegetables, Choy Sum and Pak Choy did not change their primary root length in response to shade (Fig. 1a)

Summary

Introduction

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). As compared to open canopies, plants growing under shade receive more far-red (FR) wavelength reflected from neighboring plants or high trees, since photosynthetic pigments in leaves of neighboring plants selectively absorb red (R) and blue (B) [1]. This reduces the total light intensity and R/FR ratio, which change plant development and exhibit a collection of phenotypes called shade avoidance syndrome or response (SAS or SAR) [2]. Under deep shade condition, activated phytochrome A (phyA) prevents degradation of auxin signaling repressors, auxin/indole3-acetic acid proteins (AUX/IAA) through the direct interaction with auxin receptor, TRANSPORT INHIBITOR RESISTANT 1 (TIR1), which leads to a reduction of SAS [15]

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