Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses

Shahzad Amir Naveed,Yun-Long Pang,Jian Zhang,Fan Zhang,Jian-Long Xu,Zhi-Kang Li,Li-Jun Meng,Tian-Qing Zheng

doi:10.1038/s41598-018-24946-3

Abstract

To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2–4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice.

Highlights

Most rice lines are sensitive to salt, at the germination and seedling stage, but there is rich variability for salt tolerance (ST) among different rice accessions
ANOVA results showed that differences among the genotypes explained an average 84% of the phenotypic variance for the traits at the seedling stage, ranging from 51.3% for shoot dry weight (SDW) to 96.7% for ratio of Na+ and K+ concentrations in roots (RNK) (Supplementary Table S1)
Differences among genotypes explained an average of 88.3% of the total phenotypic variance for ST traits measured at the germination stage, ranging from 82.4% for germination rate (GR) to 95.2% for seedling length (SL)

Summary

Introduction

Most rice lines are sensitive to salt, at the germination and seedling stage, but there is rich variability for ST among different rice accessions. In addition to genetic analyses of ST by QTL mapping, several QTL genes for rice ST have been cloned These included SKC1 which encodes a member of HKT-type transporters and is involved in maintaining K+ homeostasis in the ST variety under salt stress[13], OsCCC1 (cation-Cl− cotransporter) that OsCCC1 is reportedly involved in K+ and Cl− transport and plays a significant role in K+ and Cl− homeostasis and rice development[14]. Other cloned ST genes included OsMAPK33 whose over-expression under salinity increased Na+ uptake, suggesting its negative role in ST16, and OsNHX1, a Na+/H+ antiporter of rice[17] whose expression in roots and shoots increases under high NaCl and KCl. To date, large numbers of ST QTL have been mapped in rice, but most were identified by using bi-parental segregating populations involving a limited number of parents, which is unlikely to reveal the whole genetic variation for ST in rice germplasms[18]. The results provide valuable insights into the genetic basis of ST in rice that could be important for rice production and improvement

Methods

Results

Discussion

Conclusion