QTL identification for salt tolerance related traits at the seedling stage in indica rice using a multi-parent advanced
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ORIGINAL PAPER
QTL identification for salt tolerance related traits at the seedling stage in indica rice using a multi-parent advanced generation intercross (MAGIC) population Ya Zhang1,2 · Kimberly S. Ponce1,2 · Lijun Meng2 · Panchali Chakraborty2 · Qingyuan Zhao2 · Longbiao Guo1 · Zhenyu Gao1 · Yujia Leng2 · Guoyou Ye2,3 Received: 9 April 2020 / Accepted: 11 July 2020 © Springer Nature B.V. 2020
Abstract Salinity is one of the most important abiotic stresses, which seriously affects rice production. In this study, a multiparent advanced generation intercross population, DC1, derived from intercrossing four elite indica varieties, was used to identify QTLs conferring salt tolerance. The whole population and four parents were genotyped with a 55K rice SNP array. A total of 7 QTLs delineated from 186 significant marker-trait associations were detected on chromosomes 1, 2, 5 and 9, which accounted for 7.42–9.38% of the total phenotypic variations. Among these QTLs, one novel QTL (qRRL2) on chromosome 2 for relative root length and one multi-trait QTL (qSLST1/qRDSW1/qRB1) on chromosome 1 affecting shoot length, root dry weight and root biomass under salt treatment were detected. Gene expression analysis revealed that a transcription factor gene (LOC_Os01g66280) within the multi-trait QTL is the potential candidate gene for salt tolerance. Interestingly, we identified one significant nonsynonymous SNP in the coding region of this candidate gene. These results will facilitate fine mapping of the candidate gene and QTL pyramiding to genetically improve salt tolerance in rice. Keywords Salt tolerance · Association mapping · MAGIC population · Rice
Introduction
Ya Zhang and Kimberly S. Ponce have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10725-020-00644-x) contains supplementary material, which is available to authorized users. * Zhenyu Gao [email protected] * Yujia Leng [email protected] 1
State Key Laboratory for Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
2
CAAS‑IRRI Joint Laboratory for Genomics‑Assisted Germplasm Enhancement, Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
3
Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
Soil salinity is one of the most important abiotic stresses, which seriously affects crop production. Rice is the most sensitive among cereal crops with varying response at different growth stages. It is very sensitive at the seedling and reproductive stages, and more tolerant at the germination, tillering, and maturity stages (Singh et al. 2007). Salt stress causes photosynthetic reduction, plant growth inhibition, and partial sterility, which all translates to drastic yield reduction (Pardo 2010; Todaka et al. 2012; Quan et al. 2018). It was estimated that salt stress during reproductive stage results to 90% yield loss (Asch et
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