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Open AccessArticle

Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

by Fengling Wu 1,2, Jun Yang 1,2, Diqiu Yu 1,3,* and Peng Xu 1,3,4,*
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
Authors to whom correspondence should be addressed.
Agronomy 2020, 10(3), 410;
Received: 4 February 2020 / Revised: 8 March 2020 / Accepted: 16 March 2020 / Published: 19 March 2020
Saline stress severely affects rice (Oryza sativa L.) growth and development and reduces crop yield. Therefore, developing salt-tolerant and high-yielding rice using quantitative trait loci (QTLs) and linkage markers is a priority for molecular breeding. Here, the indica rice Sea Rice 86 (SR86) seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect on salinity sensitivity was demonstrated by genetic analysis. We constructed bulked segregant analysis pools using F2 populations from parents Dianjingyou 1 as the recipient and SR86 as the donor. We identified a 2.78 Mb region on chromosome 1 as the candidate region. Using simple sequence repeat markers and substitution analysis, we mapped the target region within 5.49 cM in the vicinity of markers RM8904–RM493. We speculated that this QTL, named qST1.1, might contribute significantly to the salt tolerance of SR86. The high salt tolerance of introgression lines obtained by marker assistant selection (MAS) confirmed that the qST1.1 region was associated with salinity tolerance. This newly-discovered QTL will be helpful for the analysis of the salt-tolerant mechanism of rice and breeding high-quality rice varieties using MAS. View Full-Text
Keywords: Sea Rice 86; salt tolerance; bulked segregant analysis; QTL mapping; qST1.1 Sea Rice 86; salt tolerance; bulked segregant analysis; QTL mapping; qST1.1
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    Description: Figure S1 The phenotype of SR86, T22, DJY1 and YJ26 in different salt concentrations under hydroponic conditions. NaCl dissolved and diluted in 1/4 Hoagland solution. Figure S2 SNP-index distributed on chromosomes. (a) R03 - salt tolerant pool, (b) R04 - salt sensitive pool, and (c) R03 – R04 pool. The black arrow pointed to the BSA location range. Figure S3 Linear regression graph of NaCl concentration and electrical conductivity. The blue scattered points mean different concentrations of NaCl solutions and the corresponding electrical conductivity, and the blue dotted line was the trendline. The yellow triangles represented the sample solution, the sample was diluted 5 times and determined. Figure S4 Sequence alignment of SKC1 (OsHKT1;5) protein in SR86, Nona Bokra, DJY1 and YJ26. The dark blue showed the different sites. Table S1 Grading standard of salt tolerance on the relative salt damage rate Table S2 SSR marks tested in this study Table S3 The phenotypic frequency statistics of F2 population under 1.2% NaCl treatment Table S4 Data quantity and quality of whole-genome resequencing Table S5 Sequencing depth and coverage statistics of whole-genome resequencing Table S6 SNP statistics of whole-genome resequencing Table S7 InDel statistics of whole genome and coding regions Table S8 Classification and statistics of differential genes produced by various mutations Table S9 The qST1.1 affected salt tolerance in F2 at the seedling stage Table S10 Different length homozygous overlapping segments lines screened from BC2F3
MDPI and ACS Style

Wu, F.; Yang, J.; Yu, D.; Xu, P. Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance. Agronomy 2020, 10, 410.

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