Transcriptome analysis of shade-induced inhibition on leaf size in relay intercropped soybean.

Wanzhuo Gong,Junbo Du,Xiaochun Wang,Yanhong Yan,Taiwen Yong,Yushan Wu,Feng Yang,Xiaoling Wu,Xiaobo Yu,Pengfei Qi,Xin Sun,Weiguo Liu,Wenyu Yang,Chun Song,Miguel A Blazquez

doi:10.1371/journal.pone.0098465

Abstract

Multi-species intercropping is a sustainable agricultural practice worldwide used to utilize resources more efficiently. In intercropping systems, short crops often grow under vegetative shade of tall crops. Soybean, one important legume, is often planted in intercropping. However, little is known about the mechanisms of shade inhibition effect on leaf size in soybean leaves at the transcriptome level. We analyzed the transcriptome of shaded soybean leaves via RNA-Seq technology. We found that transcription 1085 genes in mature leaves and 1847 genes in young leaves were significantly affected by shade. Gene ontology analyses showed that expression of genes enriched in polysaccharide metabolism was down-regulated, but genes enriched in auxin stimulus were up-regulated in mature leaves; and genes enriched in cell cycling, DNA-replication were down-regulated in young leaves. These results suggest that the inhibition of higher auxin content and shortage of sugar supply on cell division and cell expansion contribute to smaller and thinner leaf morphology, which highlights potential research targets such as auxin and sugar regulation on leaves for crop adaptation to shade in intercropping.

Highlights

Multi-species cropping, such as intercropping and agroforestry is a sustainable agricultural practice widely distributed in many developed and developing countries to enhance food security and to use natural resources more efficiently
Shade inhibited leaf size and growth of soybean To investigate the effect of shade on leaf morphological traits, we measured leaf area, leaf mass per unit area (LMA), and leaf anatomical traits for soybean plants grown in the shade and in full sunlight. (Table 1)
The decreased leaf area, LMA, and total leaf thickness confirmed that the leaves of plants grown under long-term shade conditions became smaller and thinner as predicted [17,53]

Summary

Introduction

Multi-species cropping, such as intercropping and agroforestry is a sustainable agricultural practice widely distributed in many developed and developing countries to enhance food security and to use natural resources more efficiently. Two or more crops are grown simultaneously in the same field during a growing season [1]. Shade is ubiquitous in nature, and all plants are shaded to some degree during their lifecycle [3]. Shade conditions are characterized by low levels of photosynthetically active radiation (PAR) and a low ratio of red light to far-red light (R:FR), and both of which are important signaling factors in shade conditions [4,5]. PAR drives the light reactions of photosynthesis, and is considered to be the primary energy source for photosynthesis in shade-tolerant plants [3,6], and the R:FR ratio is considered to be a more important light signaling factor

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