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Research paper | Open Access

Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq

Jing Yanga, Zhenhua Guoa,b, Lixin Luoa, Qiaoli Gaoa, Wuming Xiaoa, Jiafeng Wanga, Hui Wanga, Zhiqiang Chena( ), Tao Guoa( )
National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, Guangdong, China
Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, Heilongjiang, China
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Abstract

Early seedling vigor (ESV) is a major breeding target in rice, especially under direct seeding. To identify quantitative trait locus (QTL) affecting ESV, a recombinant inbred line population derived from a cross between 02428 and YZX, two cultivars differing in vigor during early seedling growth, was used for QTL analysis. Nine traits associated with ESV were examined using a high-density map. Of 16 additive loci identified, three were detected in two generations and thus considered stable. Four epistatic interactions were detected, one of which was repeated in two generations. Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL. These results were combined with results from our previous QTL analysis of the germination index. The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed. These two lines showed rapid germination and strong ESV. A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents. The QTL are targets for ESV breeding and the candidate genes await functional validation. This study provides a theoretical basis and a genetic resource for the breeding of direct-seeded rice.

Keywords

Candidate genesQTL mappingDirect-seeded riceEarly seedling vigorExpression profiling

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The Crop Journal
Volume 9 Issue 2,
April 2021
Pages 360-371
DOI: 10.1016/j.cj.2020.08.010
Cite this article:
Yang J, Guo Z, Luo L, et al. Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq. The Crop Journal, 2021, 9(2): 360-371. https://doi.org/10.1016/j.cj.2020.08.010

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Received: 13 November 2019
Revised: 22 May 2020
Accepted: 10 September 2020
Published: 17 November 2020
© 2020 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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