Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice.

Apichat Suratanee,Supachitra Chadchawan,Chidchanok Chokrathok,Panita Chutimanukul,Teerapong Buaboocha,Kitiporn Plaimas,Nopphawitchayaphong Khrueasan

doi:10.3390/genes9120594

Apichat Suratanee, Supachitra Chadchawan + Show 5 more

Open Access

https://doi.org/10.3390/genes9120594

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Abstract

Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.

Highlights

Rice is one of the most important agricultural products of Thailand with the highest domestic consumption and exportation
With the ability to grow in high salinity areas, the salinity tolerance score of Khao Dawk Mali 105 (KDML105) is lower than some other rice varieties, such as IR29, KKU-LLR-039 and Niewdam Gs
The results show that, in a scale-free network, the weighted clustering coefficient was not inversely related to the connectivity, while the binary clustering coefficient was inversely related to connectivity [17]

Summary

Introduction

Rice is one of the most important agricultural products of Thailand with the highest domestic consumption and exportation. Khao Dawk Mali 105 (KDML105) rice, known as jasmine rice, is considered a high-quality rice from Thailand. It is grown mainly in the northeastern region of Thailand, where the soil contains a high salinity. This poor soil quality affects plant growth and productivity. With the ability to grow in high salinity areas, the salinity tolerance score of KDML105 is lower than some other rice varieties, such as IR29, KKU-LLR-039 and Niewdam Gs. No 88084 [1]

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