TY - JOUR

T1 - Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms

AU - Kleshchev, M. A.

AU - Maltseva, A. V.

AU - Antropova, E. A.

AU - Demenkov, P. S.

AU - Ivanisenko, T. V.

AU - Orlov, Y. L.

AU - Chao, H.

AU - Chen, M.

AU - Kolchanov, N. A.

AU - Ivanisenko, V. A.

N1 - The work of MAK, AVM, EAA, PSD, TVI, YLO, NAK, and VAI was supported by the Russian-Chinese grant from the Russian Science Foundation No. 23-44-00030. The work of MCh and HCh was supported by the National Natural Science Foundation of China (No. 32261133526).

PY - 2024

Y1 - 2024

N2 - Drought is a critical factor limiting the productivity of bread wheat (Triticum aestivum L.), one of the key agricultural crops. Wheat adaptation to water deficit is ensured by complex molecular genetic mechanisms, including the coordinated work of multiple genes regulated by transcription factors and signaling non-coding RNAs, particularly microRNAs (miRNAs). miRNA-mediated regulation of gene expression is considered one of the main mechanisms of plant resistance to abiotic stresses. Studying these mechanisms necessitates computational systems biology methods. This work aims to reconstruct and analyze the gene network associated with miRNA regulation of wheat adaptation to drought. Using the ANDSystem software and the specialized Smart crop knowledge base adapted for wheat genetics and breeding, we reconstructed a wheat gene network responding to water deficit, comprising 144 genes, 1,017 proteins, and 21 wheat miRNAs. Analysis revealed that miRNAs primarily regulate genes controlling the morphogenesis of shoots and roots, crucial for morphological adaptation to drought. The key network components regulated by miRNAs are the MYBa and WRKY41 family transcription factors, heat-shock protein HSP90, and the RPM1 protein. These proteins are associated with phytohormone signaling pathways and calcium-dependent protein kinases significant in plant water deficit adaptation. Several miRNAs (MIR7757, MIR9653a, MIR9671 and MIR9672b) were identified that had not been previously discussed in wheat drought adaptation. These miRNAs regulate many network nodes and are promising candidates for experimental studies to enhance wheat resistance to water deficiency. The results obtained can find application in breeding for the development of new wheat varieties with increased resistance to water deficit, which is of substantial importance for agriculture in the context of climate change.

AB - Drought is a critical factor limiting the productivity of bread wheat (Triticum aestivum L.), one of the key agricultural crops. Wheat adaptation to water deficit is ensured by complex molecular genetic mechanisms, including the coordinated work of multiple genes regulated by transcription factors and signaling non-coding RNAs, particularly microRNAs (miRNAs). miRNA-mediated regulation of gene expression is considered one of the main mechanisms of plant resistance to abiotic stresses. Studying these mechanisms necessitates computational systems biology methods. This work aims to reconstruct and analyze the gene network associated with miRNA regulation of wheat adaptation to drought. Using the ANDSystem software and the specialized Smart crop knowledge base adapted for wheat genetics and breeding, we reconstructed a wheat gene network responding to water deficit, comprising 144 genes, 1,017 proteins, and 21 wheat miRNAs. Analysis revealed that miRNAs primarily regulate genes controlling the morphogenesis of shoots and roots, crucial for morphological adaptation to drought. The key network components regulated by miRNAs are the MYBa and WRKY41 family transcription factors, heat-shock protein HSP90, and the RPM1 protein. These proteins are associated with phytohormone signaling pathways and calcium-dependent protein kinases significant in plant water deficit adaptation. Several miRNAs (MIR7757, MIR9653a, MIR9671 and MIR9672b) were identified that had not been previously discussed in wheat drought adaptation. These miRNAs regulate many network nodes and are promising candidates for experimental studies to enhance wheat resistance to water deficiency. The results obtained can find application in breeding for the development of new wheat varieties with increased resistance to water deficit, which is of substantial importance for agriculture in the context of climate change.

KW - ANDSystem computer tool

KW - Smart crop knowledge base

KW - associative gene networks

KW - bread wheat

KW - drought

KW - genes

KW - genetic regulation

KW - microRNA

KW - plant bioinformatics

UR - https://www.mendeley.com/catalogue/a9dd4d59-8800-3f4f-957c-1589d361fdab/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85217124662&origin=inward&txGid=91236b6d1e1db1aa6c0f6256c5af2df4

U2 - 10.18699/vjgb-24-98

DO - 10.18699/vjgb-24-98

M3 - Article

C2 - 39944815

VL - 28

SP - 904

EP - 917

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 8

ER -