Transcriptomic Analysis Reveal the Molecular Mechanisms of Seed Coat Development in Cucurbita pepo L.

Yingyu Xue,Bingliang Xu,Zhiyan Shen,Jingjiang Zhou,Fei Tao

doi:10.3389/fpls.2022.772685

Yingyu Xue, Bingliang Xu + Show 3 more

Open Access

https://doi.org/10.3389/fpls.2022.772685

Copy DOI

Abstract

Cucurbita pepo is one of the earliest cultivated crops. It is native to Central and South America and is now widely cultivated all over the world for its rich nutrition, short growth period, and high yield, which make it suitable for intercropping. Hull-less C. pepo L. (HLCP) is a rare variant in nature that is easier to consume. Its seed has a seed kernel but lacks a seed coat. The molecular mechanism underlying the lack of seed coat development in the HLCP variety is not clear yet. The BGISEQ-500 sequencing platform was used to sequence 18 cDNA libraries of seed coats from hulled C. pepo (CP) and HLCP at three developmental stages (8, 18, and 28 days) post-pollination. We found that lignin accumulation in the seed coat of the HLCP variety was much lower than that of the CP variety. A total of 2,099 DEGs were identified in the CP variety, which were enriched mainly in the phenylpropanoid biosynthesis pathway, amino sugar, and nucleotide sugar metabolism pathways. A total of 1,831 DEGs were identified in the HLCP variety and found to be enriched mainly in the phenylpropanoid biosynthesis and metabolism pathways of starch and sucrose. Among the DEGs, hub proteins (FusA), protein kinases (IRAK4), and several transcription factors related to seed coat development (MYB, bHLH, NAC, AP2/EREBP, WRKY) were upregulated in the CP variety. The relative expression levels of 12 randomly selected DEGs were determined using quantitative real-time PCR analysis and found to be consistent with those obtained using RNA-Seq, with a correlation coefficient of 0.9474. We found that IRAK4 protein kinases, AP2/EREBP, MYB, bHLH, and NAC transcription factors may play important roles in seed coat development, leading to the formation of HLCP.

Highlights

Cucurbita belongs to the family Cucurbitaceae, which originated from the American continent (Paris, 1989; Lin, 2000; Liu et al, 2010)
At 18–35 days postpollination, the fresh weight of the C. pepo (CP) seed coats continued to increase with the maturity of the seeds, while the fresh weight of the Hull-less C. pepo L. (HLCP) seed coats showed a downward trend
The overexpression of sucrose synthase (SUS) gene of potato in cotton lead to fiber elongation and enhancement, which indicated that the importance of SUS in cell wall synthesis during cell division (Xu et al, 2012). These results indicated that the genes of starch and sucrose metabolism pathway may be closely related to the formation of seed coat

Summary

INTRODUCTION

Cucurbita belongs to the family Cucurbitaceae, which originated from the American continent (Paris, 1989; Lin, 2000; Liu et al, 2010). Studies on the seed coat formation of HLCP C. pepo were mainly focused on the phenotypic, physiological and biochemical levels in the early stage, but there was a lack of research on the molecular mechanism of seed coat development. Stuart and Loy (1983) reported that the formation of HLCP variety due to the lack of polysaccharide synthesis and accumulation, rather than a metabolic block in the process of lignin biosynthesis. Teppner (2000) believed that the seed coat traits of C. pepo are controlled by one major effect gene and 6–12 minor effect genes These studies showed that the genetic mechanism of the seed coat of C. pepo is complex and regulated by a pair of major genes and other minor genes. Revealing the formation mechanism of the seed coat of hulled and hull-less C. pepo is of great significance for clarifying the seed development of plants

MATERIALS AND METHODS

RESULTS

DISCUSSION