Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms

Sailaja Bhogireddy,Paxton Payton,Manish K Pandey,Renee Arias,Vanika Garg,Rajeev K Varshney,Nancy Layland,Naveen Puppala,Abishek Xavier,Spurthi N Nayak

doi:10.1038/s41598-020-60187-z

Abstract

Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNA-seq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes.

Highlights

Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater
In order to study the phenotypic variations and its associated physiological responses for pod yield among the 10 peanut genotypes (Supplementary Table S1), field level experiments were conducted in three consecutive years from 2013–2015 by imposing deficit irrigation (DI) stress
Soil moisture content was collected, where fully irrigated soil was very moist at 48 cm for most of the growing season and at 12, 24 cm, the soil moisture had a smaller interval of dampness and dryness due to irrigation and precipitation events

Summary

Introduction

Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. Different studies have reported drought-tolerant peanut genotypes, it is essential to check the performance of these genotypes in target locations such as West Texas and eastern New Mexico regions which faces frequent problem of limited water resources. In West Texas and eastern New Mexico, the most widely cultivated Valencia-type peanut cultivar, Valencia-C (Val-C), is considered as standard reference, and an industrial standard variety that has been used as a control to compare yields and flavor of newly released varieties. In peanut, related to drought there are very limited reports regarding the identification of candidate genes/genomic regions[11,12,13] and transcriptome studies[14,15] None of these studies explored the drought tolerance mechanisms in Valencia-type peanuts; so a correct understanding of its underlying genomics will facilitate the genetic improvement of Valencia peanuts. The results obtained from this study provide a better understanding of the tolerance mechanisms and the potential candidate genes can be utilized in breeding programs

Methods

Results

Conclusion