Abstract
Salt stress causes significant reductions in rice production worldwide; thus, improving salt tolerance is a promising approach to meet the increasing food demand. Wild rice germplasm is considered a valuable genetic resource for improving rice cultivars. However, information regarding the improvement of salt tolerance in cultivated rice using wild rice genes is limited. In this study, we identified a salt-tolerant line Dongxiang/Ningjing 15 (DJ15) under salt-stress field conditions from the population of a salt tolerant Dongxiang wild rice × a cultivated rice variety Ningjing16 (NJ16). Genomic resequencing analysis of NJ16, DJ15 and Dongxiang wild rice revealed that the introgressed genomic fragments were unevenly distributed over the 12 chromosomes (Chr.) and mainly identified on Chr. 6, 7, 10, and 11. Using quantitative trait locus (QTL) mapping, we found 9 QTL for salt tolerance (qST) at the seedling stage located on Chr. 1, 3, 4, 5, 6, 8, and 10. In addition, sequence variant analysis within the QTL regions demonstrated that SKC1/HKT8/HKT1;5 and HAK6 transporters along with numerous transcriptional factors were the candidate genes for the salt tolerant QTL. The DJ15/Koshihikari recombinant inbred lines that contained both qST1.2 and qST6, two QTL with the highest effect for salt tolerance, were more tolerant than the parental lines under salt-stress field conditions. Furthermore, the qST6 near-isogenic lines with IR29 background were more tolerant than IR29, indicating that qST1.2 and qST6 could improve salt tolerance in rice. Overall, our study indicates that wild rice genes could markedly improve the salt tolerance of cultivated rice.
Highlights
Rice is one of the most important staple crops worldwide
By comparing Single Nucleotide Polymorphism (SNP)/Insertion or Deletion (Indel) variants of Dongxiang/Ningjing 15 (DJ15), NJ16 and Dongxiang wild rice, we found 642,349 SNP/Indel variants between DJ15 and NJ16 across the 12 chromosomes, among which 265,862 variants might be obtained from Dongxiang wild rice (Table 1)
The distribution pattern of SNPs/Indels was identical between DJ15 and Dongxiang wild rice, different between NJ16 and Dongxiang, and similar between DJ15 and NJ16. These results indicated that the regions of high density in SNP/Indel variants identified in DJ15 might be large DNA fragments introgressed from Dongxiang wild rice
Summary
Rice is one of the most important staple crops worldwide. The global demand for staple crops, including rice, increases with the continuous increase of human population. The production of staple crops is threatened by abiotic stresses including salt, drought and high/low temperature (Arzani and Ashraf, 2016; Calanca, 2017). Improving the productivity of crops in salt-stressed areas is considered essential to meet the increasing food demand. Barley and cotton, rice is a more salt sensitive crop (Chinnusamy et al, 2005). Salt tolerance in rice changes with age; it is salt sensitive at the seedling stage, becomes moderately salt tolerant at the vegetative stage, and highly sensitive at reproductive stage (Lutts et al, 1995; Zeng et al, 2002). The salt tolerance is genotype-dependent; i.e., the Oryza
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