Auxin-related genes associated with leaf petiole angle at the seedling stage are involved in adaptation to low temperature in Brassica napus

https://doi.org/10.1016/j.envexpbot.2020.104308Get rights and content

Highlights

  • GWAS identified 3525 candidate genes associated with leaf petiole angle (LPA).

  • Auxin signaling genes are involved in the changes of LPA at the seedling stage.

  • Small LPA might help the rapeseed with overwintering under low temperature.

Abstract

Rapeseed (Brassica napus L.) has winter and semi-winter ecotypes which need vernalization in the development process. Leaf development coincides with vernalization, and the leaf petiole angle (LPA) is associated with cold environmental adaptation during the overwintering period in rapeseed. In the present study, a genome-wide association study (GWAS) using a Brassica 60 K SNP array for LPA identified 45 significantly associated quantitative trait loci (QTLs) and 3525 candidate genes. Moreover, two rapeseed accessions (T193, winter type and T268, semi-winter type) with significantly different LPA degrees were used for RNA sequencing (RNA-seq). And transcriptome analysis revealed that most of the differentially expressed genes (DEGs) were involved in auxin, brassinosteroid (BR) and ethylene signaling pathways as well as the cell division pathway. Using integration of GWAS and RNA-seq analysis, several promising candidate genes, including BZR1, IAA7, IAA15, PIN3 and SPL orthologs were prioritized for further research. Quantitative real time PCR (qRT-PCR) also validated the differential expression patterns of nine candidate genes between T193 and T268. Through regulating differential cell division of the abaxial and adaxial petiole for small LPA, auxin signaling genes could be involved in the adaptation of rapeseed seedlings to low temperature conditions. These findings provide insights into the molecular mechanism of environmental adaptation at the seedling stage and provide valuable information for facilitating marker-based breeding in B. napus.

Introduction

Rapeseed (Brassica napus L.), an important oilseed crop, shows great potential for genetic changes during environmental adaptation (Nelson et al., 2016). There are three rapeseed ecotypes: winter, spring and semi-winter types (Wei et al., 2017). It has been documented that winter rapeseed requires strong vernalization and has tolerance for low-temperature conditions, while spring type rapeseed does not require vernalization (Gómez-Campo and Prakash, 1999). After its introduction to China, rapeseed was widely grown as a semi-winter crop with a biennial life cycle and moderate vernalization to adapt to the local environmental conditions (Xu et al., 2015a, Xu et al., 2015b). However, exposing to long term low temperature stress in winter, the semi-winter rapeseed will cause to plant damage and yield loss (O’neill et al., 2019). At the early leaf development stage, semi-winter rapeseed exhibits upright leaf architecture compared with the winter rapeseed. Since the leaf development coincides with vernalizaiton, the different leaf shape might associated with overwintering in rapeseed. Thus, winter oilseed rapes are grown in the mid-European regions with high latitudes where plants must survive long low temperature conditions, while semi-winter rapeseeds only undergo short overwintering period (Nelson et al., 2016).

Leaf architecture plays important roles in photosynthesis and yield as well as stress response (Tian et al., 2011; Jian et al., 2017). In plants, leaf orientation is regulated and changes with development and in response to the environment (Mullen et al., 2006). Since the main stem of rapeseed at the seedling stage does not undergo elongation, leaf petiole angle (LPA) is defined as the degree of leaf petiole deviation from the horizontal towards the ground in B. napus, which is similar to Arabidopsis (Mullen et al., 2006). In many plants, LPA determines the plant architecture and responses to environmental conditions as well as photosynthetic efficiency (Falster and Westoby, 2003; Hopkins et al., 2008). It has been reported that optimal the leaf angle at lower latitudes is more erect than that at higher latitudes (Hopkins et al., 2008). Large leaf angles can maximize photosynthesis and decrease transpiration and heat damage by avoiding direct exposure to high-intensity light (Ridao et al., 1996; Falster and Westoby, 2003). Vernalization, which refers to an extended period of cold, has been reported to affect leaf angle in Arabidopsis (Hopkins et al., 2008). LC2, a vernalization insensitive 3 (VIN3)-like protein, was identified as a repressor of cell division that regulates the leaf angle in rice (Zhao et al., 2010). However, in grass crops, leaf angle refers to the inclination between the leaf blade midrib and stem, which is closely related to crop architecture and yield (Liu et al., 2019). Erect leaves can effectively contribute to the grain yield by enhancing photosynthesis, grain filling and the leaf area index (Sakamoto et al., 2006; Li et al., 2015). Many quantitative trait loci (QTL), including ZmTAC1 and qLA4−1 (ZmCLA4), have been identified to control leaf angle in maize (Ku et al., 2011; Zhang et al., 2014).

It has been documented that plant hormones, such as brassinosteroids (BR), auxin, cytokinin, and abscisic acid (ABA), can influence leaf development and morphogenesis, including leaf angle. BRs are widely reported to influence plant height and leaf angle in plants (Sun et al., 2015; Cheng et al., 2017). In rice, the erect leaf phenotype has been associated with several BR mutants such as brd1, d61 (OsBRI1), osdwarf4 and d2 (Sakamoto et al., 2006; Yamamuro et al., 2000). Rice BRASSINOSTEROID UPREGULATED 1- LIKE1 (OsBUL1)was reported to control cell elongation and positively affect leaf angles (Jang et al., 2017). Loss the function of LAZY1 (LA1) has been reported to enhance polar auxin transport and alters the indole-3-acetic acid (IAA) distribution in shoots, affecting the leaf angle in rice (Li et al., 2007). TaSPL8 was identified to bind to the promoters of auxin response factor and BR biogenesis gene CYP90D2 to activate their expression, leading to changes of leaf angle in wheat (Liu et al., 2019). The differentially expressed target genes of ZmILI1 for regulating leaf angle were reported to be associated with auxin, cytokinin, BR and cell differentiation (Ren et al., 2020a, 2020b).

LPA in Brassiaceae and legume is the same as leaf angle in other plants. In Arabidopsis, the npq2 plants which are treated with ABA reduced the leaf inclination, suggesting that ABA is involved in the regulation of LPA (Mullen et al., 2006). In soybean, GmILPA1 has been identified to control LPA by promoting cell growth and division of the pulvinus (Gao et al., 2017). It’s well known that leaves develop from flanking regions of the shoot apical meristem (SAM), which determine the growth of the lateral organs (Kim and Cho, 2006). Leaf morphology keeps a balance between cell proliferation and polar cell division and expansion along the proximal–distal, medial–lateral and adaxial–abaxial axes (Barkoulas et al., 2007; Jang et al., 2017). In rapeseed, three LM11-like genes were characterized to control the lobed-leaf trait (Ni et al., 2017). Through integration of QTL mapping and RNA Sequencing (RNA-seq), 31 QTLs were identified for leaf morphology traits, including leaf length and width, petiole length and others (Jian et al., 2017). Lately, a genome-wide association study (GWAS) of the leaf trichome in 290 rapeseed core germplasm accessions revealed BnaA.GL1.a, BnaC.SWEET4.a and BnaC.WAT1 to be involved in leaf trichome formation (Xuan et al., 2020). However, studies on the genetics analysis of leaf petiole angle in B. napus are very limited.

In this study, we used GWAS and RNA-seq to uncover the genetic architecture of LPA and analyze the relationship of LPA with the response to low temperature in B. napus. Understanding the genetic mechanisms of LPA will not only reveal the adaptation to low temperatures during the overwintering stage but also facilitate the genetic improvement of rapeseed breeding.

Section snippets

Plant materials and field experiments

A total of 472 B. napus core germplasm collected worldwide was used in this study as previously described (Li et al., 2014). The self-pollinated seeds of each accession were preserved in the National Mid-term GeneBank for Oil Crops in Wuhan, China. Field experiments for LPA were carried out during the 2016–2017 growing season in two environments: Shijiazhuang (SJZ, 114.48 °E, 38.03 °N) and Wuhan (WH, 113.68 °E, 30.58 °N). In each environment, a randomized complete block design with three

Phenotypic variation

Winter and semi-winter types are two different ecotypes of rapeseed with specific distinguishing characteristics. During the overwintering period, winter rapeseeds are mainly creeping plants, while semi-winter rapeseeds have large LPA and are erect (Fig. 1A-B). We evaluated LPA in the association panel of 472 rapeseed accessions during 2016 and 2017 in Shijiazhuang (SJZ) and Wuhan (WH) of China, with three replications performed each year in each area. Two B. napus accessions, T193 and T268,

Discussion

Leaf morphology is an important agronomic trait that affects the photosynthesis efficiency and yield of many crops. Temperature is one important environmental regulator for plant growth and development. Warmer temperatures have been reported to result in increased auxin production and hypocotyl elongation (Galweiler et al., 1998). It has been reported that the optimal leaf petiole angle at higher latitudes is more prostrate than that at lower latitudes, indicating that the small petiole angle

Conclusions

Using association mapping, we identified 3525 candidate genes for LPA at seedling stage of rapeseed in this study. Integration of GWAS and transcriptome analysis revealed that auxin signaling genes play important roles in the regulation of LPA. During the overwintering period, the long term low temperature might induce these genes involved in auxin signaling to regulate cell proliferation and division of the abaxial and adaxial petiole, resulting in leaf creeping or smaller LPA. These results

Author Contributions

X.W and J.H. conceived and designed the experiments. J.H. and F.Z performed the experiments and data analysis. J.H. G.G., and H.L. done the phenotyping. X.W. and H.L. contributed the reagents/materials. J.H. and F.Z wrote and edited the manuscript. All authors have read and agreed to the published version of the manuscript.

Declaration of Competing Interest

The authors declare no conflict of interest.

Acknowledgements

This work was supported by the Natural Science Foundation of Hubei Province (2018CFB101), and Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2015-OCRI).

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