Elsevier

Scientia Horticulturae

Volume 302, 25 August 2022, 111141
Scientia Horticulturae

Transcriptome analysis reveals genes associated with kernel size in apricots cultivated for kernel consumption (Prunus armeniaca × Prunus sibirica)

https://doi.org/10.1016/j.scienta.2022.111141Get rights and content

Highlights

  • The early kernel development was important factor that determine kernel size.

  • Six hub genes were identified to related to kernel size.

  • The phytohormone metabolic pathways were involves kernel size.

Abstract

Seed size is an important component of overall seed yield trait, and apricots cultivated for consumable kernels produce kernels that are large and sweet. However, the molecular mechanism of kernel development in kernel consumption apricots remains unclear. We measured kernel weight, length, width, and thickness and investigated the transcriptome profiles of kernel consumption apricots (Prunus armeniaca × Prunus sibirica) at six different developmental stages. The phenotypic analysis results showed that rapid kernel size development occurred from 15 to 45 days after flowering (DAF), and that the kernel coat size almost reached its the maximum at 45 DAF, suggesting that the early kernel development was important factor that determine overall kernel size. A total of 8,108 differentially expressed genes (DEGs) were identified, and a weighted gene co-expression network analysis revealed that turquoise module was strongly correlated with the kernel size. Six hub genes were identified as potential regulators of the kernel size. Furthermore, we analyzed the DEGs related to kernel size in the phytohormones metabolic pathways, ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase signaling, and HAIKU pathway, which were considered to be important regulators of kernel size. Our findings provide new insights into the molecular mechanisms underlying the regulation of kernel size in kernel consumption apricots.

Introduction

The apricot is a Rosaceae family member belonging to the section Armeniaca (Lam.) Koch (Rehder, 1940), and it is generally cultivated for its fruit. In recent years, apricots have been cultivated for production of consumable apricot kernels (kernel consumption apricots), predominantly grown in North China, and these apricots typically produce large and sweet kernels (Li et al., 2014). This provides ecological, economic, and nutritional benefits. Specifically, the oil and protein content of the apricot kernel are 27.7 - 66.7% and 14.1 - 45.35%, respectively (Liu et al., 2012; Alpaslan and Hayta, 2006), therefore, these apricots are a potential source of oil and plant protein. Kernel size is one of the most important factors determining apricot kernel yield. The kernel consumption apricots variety, including ‘Longwangmao’, ‘Yiwangfeng’, ‘Baiyubian’, ‘Guoren’, and ‘Fengren’, are highly productive and/or produces large kernels (Liu et al., 2012), which may be considered as main cultivars for kernel production in China.

Seed size is one of the main factors affecting the yields of seed crops (Li et al., 2019a). Seeds are important sources of human food, animal feed, and biofuel, and they account for over 70% of human food intake (Savadi, 2018). Therefore, seed size and number are important selection traits of crop plants (Fan et al., 2006). Plant seeds are comprised of the embryo, the endosperm, and the seed coat, and the seed development process involves seed growth and maturation (Locascio et al., 2014). Seed growth mainly involves cell division and expansion, while seed maturation involves accumulation of seed storage materials (Bian et al., 2019; Locascio et al., 2014). Recently, many loci, candidate genes, and signaling pathways associated with seed-related traits have been identified in model plants, such as Arabidopsis thaliana, Oryza sativa, and Zea. mays (Li et al., 2019b; Liu et al., 2020; Si et al., 2016; Song et al., 2007; Sun et al., 2021; Sundaresan, 2005). Research has provided useful information to help understand the molecular mechanisms underlying seed development.

Previous studies on apricots predominantly focused on the physiological characteristics of the kernels; however, research on the kernel size in kernel consumption apricots is lacking thus far. To better understand the mechanisms affecting kernel size, we performed the RNA-sequencing (RNA-Seq) of kernels in different development stages to identify the key genes associated with kernel size. This study provides novel insights into the molecular mechanism underlying kernel development and may thus be useful for further improving the yield of kernel consumption apricots.

Section snippets

Plant materials

Kernel consumption apricots (‘Longwangmao’) were grown located at the experimental farm of Research Institute of Non-timber Forestry in Yuanyang County, Henan Province, China. The different developmental stages of kernels were harvested at 15 days after flowering (DAF, S1), 30 DAF (S2), 45 DAF (S3), 60 DAF (S4), 75 DAF (S5), and 90 DAF (S6), respectively, which ranged from March to June 2020. The kernels were initial formation and mature (seed coat turned brown) at S1and S6 stage, respectively.

Morphological examination of apricot kernel size over fruit development

The occurrence of kernels was observed at six different developmental stages, from 15 DAF to 90 DAF (S1-S6, Fig. 1). Kernel weight, length, width, and thickness showed rapid development from S1 to S3, during which the seed coat size grew rapidly. The weight of developing kernels was approximately 9.6-fold higher at S2 than at S1 and 1.7-fold higher at S3 than at S2. From S4 to S6, almost no observable changes in kernel size occurred. In addition, kernel weight decreased slightly after

Discussion

Seed development determines seed yield and quality in seed crops, and many candidate pathways and genes involved in seed development have been identified in model plants. To understand the molecular mechanisms underlying kernel development in kernel consumption apricots, we performed a phenotypic and transcriptome analysis to identify the candidate genes which may be involved in kernel development. Seed development comprises the seed size change phase and the phase of accumulating various

Authors’ contribution

T.W., L.H., and L.W. designed the experiments. L.W. analyzed the results and wrote the manuscript. W.B., W.X., M.H., G.Z., H.Z., C.C., H.B., and J.C. performed sample collections and help analyzed the data. T.W., L.H., and L.W. revised the manuscript. All of the authors have reviewed and approved the final manuscript.

Declaration of Competing Interest

The authors declare that they have no competing interests.

Data available

Raw transcriptome sequencing reads were deposited into the Genome Sequence Archive (GSA) under BioProject accession ID PRJCA007599.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (31901342).

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