Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

Lei Lei,Jian Sun,Hualong Liu,Jingguo Wang,Yongcai Lai,Hongliang Zheng,Xianwei Li,Jiaming Li,Hongwei Zhao,Luomiao Yang,Detang Zou,Yanli Bi

doi:10.1186/s12284-020-00416-1

Lei Lei, Jian Sun + Show 10 more

Open Access

https://doi.org/10.1186/s12284-020-00416-1

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Abstract

BackgroundSalt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited.ResultsHere, an F2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress.ConclusionThese results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).

Highlights

Salt stress is one of the main abiotic stresses that limits rice production worldwide
The shoot length (SL), root number (RN), root length (RL), and their relative values in 983 individuals were evaluated under salt stress and control condition at the bud burst stage
Using relative shoot length (RSL) as the screening trait for the two mixed pools, 40 lines with extreme salt tolerance and 40 lines with extreme salt sensitivity were selected to prepare the tolerant pool (T-pool) and sensitive pool (S-pool), respectively, which were used for DNA sequencing

Summary

Introduction

Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. Salt stress is the main factor that restricts rice production because it reduces crop yield and limits agricultural land utilization (Hossain et al 2015). Salt tolerance at the bud burst stage is a major factor that determines growth stability in salinized soil when adopting the direct seeding cultivation model in rice (Dingkuhn et al 1992). Sensitivity of rice to salt stress at the bud burst stage leads to a decrease in seedling rate, resulting in lower yields (Zeng et al 2001). Studying the genetic mechanism of rice salt tolerance at the bud burst stage, and utilizing salt tolerance-related genes for breeding rice varieties suitable for direct seeding in salinized soil is of great importance

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