Identification and Fine Mapping of QGR6.2, a Novel Locus Controlling Rice Seed Germination Under Salt Stress

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2021 Jan 10

PMID 33422012

Citations 20

Authors

Peng Zeng

Peiwen Zhu

Luofeng Qian

Xumei Qian

Yuxin Mi

Zefeng Lin

Shinan Dong

Henrik Aronsson

Hongsheng Zhang

Jinping Cheng

Affiliations

Soon will be listed here.

Abstract

Background: Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding.

Results: In this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BCF population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under HO and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under HO conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BCF population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2.

Conclusions: In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under HO and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS).

Citing Articles

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Identification of a key locus, qRL8.1, associated with root length traits during seed germination under salt stress via a genome-wide association study in rice.

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