Genome-wide mining seed-specific candidate genes from peanut for promoter cloning

Cuiling Yuan,Yingzhen Kong,Quanxi Sun,Jin-Song Zhang

doi:10.1371/journal.pone.0214025

Cuiling Yuan, Yingzhen Kong + Show 2 more

Open Access

https://doi.org/10.1371/journal.pone.0214025

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Abstract

Peanut seeds are ideal bioreactors for the production of foreign recombinant proteins and/or nutrient metabolites. Seed-Specific Promoters (SSPs) are important molecular tools for bioreactor research. However, few SSPs have been characterized in peanut seeds. The mining of Seed-Specific Candidate Genes (SSCGs) is a prerequisite for promoter cloning. Here, we described an approach for the genome-wide mining of SSCGs via comparative gene expression between seed and nonseed tissues. Three hundred thirty-seven SSCGs were ultimately identified, and the top 108 SSCGs were characterized. Gene Ontology (GO) analysis revealed that some SSCGs were involved in seed development, allergens, seed storage and fatty acid metabolism. RY REPEAT and GCN4 motifs, which are commonly found in SSPs, were dispersed throughout most of the promoters of SSCGs. Expression pattern analysis revealed that all 108 SSCGs were expressed specifically or preferentially in the seed. These results indicated that the promoters of the 108 SSCGs may perform functions in a seed-specific and/or seed-preferential manner. Moreover, a novel SSP was cloned and characterized from a paralogous gene of SSCG29 from cultivated peanut. Together with the previously characterized SSP of the SSCG5 paralogous gene in cultivated peanut, these results implied that the method for SSCG identification in this study was feasible and accurate. The SSCGs identified in this work could be widely applied to SSP cloning by other researchers. Additionally, this study identified a low-cost, high-throughput approach for exploring tissue-specific genes in other crop species.

Highlights

Peanut (Arachis hypogaea L., which is referred to as groundnut) is one of the most important oil crop species worldwide and plays important roles in human nutrition [1]
All of the reconstructed genes were aligned to the reference genome of A. duranensis and A. ipaensis [1] and were subsequently annotated
Gene Ontology (GO) annotation was performed using BLAST2GO, and the 337 Seed-Specific Candidate Genes (SSCGs) were categorized with particular GO annotations (S1 Fig, Table 2)

Summary

Introduction

Peanut (Arachis hypogaea L., which is referred to as groundnut) is one of the most important oil crop species worldwide and plays important roles in human nutrition [1]. Promoters are usually used in gene functional analysis [2,3,4] and are widely used for plant quality improvement [5,6,7,8]. SSPs have been widely applied in plant molecular pharming, such as that involving golden rice [8], purple endosperm rice [9], purple embryo maize [7] and fish oil canola [10]. Repetitive use of the same promoter when expressing multiple foreign proteins simultaneously is considered inadvisable owing to the likelihood of transcriptional silencing [14,15,16]. Additional peanut SSPs are needed to overexpress or knock down specific genes, regulate seed development, and modify seed content, especially to produce foreign recombinant proteins or secondary metabolites

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Discussion

Conclusion