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Journal of Integrative Agriculture  2022, Vol. 21 Issue (5): 1266-1277    DOI: 10.1016/S2095-3119(21)63649-3
Special Issue: 玉米遗传育种合辑Maize Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis
YANG Yue1, 2*, MA Yu-ting1, 2*, LIU Yang-yang2, 3*, Demar LYLE2, LI Dong-dong2, WANG Ping-xi2, XU Jia-liang2, ZHEN Si-han2, LU Jia-wen2, PENG Yun-ling4, CUI Yu2, FU Jun-jie2, DU Wan-li1, ZHANG Hong-wei2, WANG Jian-hua3
1 Agronomy College, Shenyang Agricultural University, Shenyang 110161, P.R.China
2 National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
3 Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R.China 4 Gansu Provincial Key Laboratory for Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, P.R.China
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Abstract  Deep-sowing is an important method for avoiding drought stress in crop species, including maize.  Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance.  This study evaluated four traits (mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12) related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms (SNPs).  The genome-wide association study detected that 273 SNPs were in linkage disequilibrium (LD) with the genetic basis of maize deep-sowing tolerance.  The RNA-sequencing analysis identified 1 944 and 2 098 differentially expressed genes (DEGs) in two comparisons, which shared 281 DEGs.  By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs, we identified seven candidate genes, of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein.  GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length, auxin, or light response.  Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length.  Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines.  These results suggest that GRMZM2G119769 is the most likely candidate gene.  This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes, which would be useful for further research on maize deep-sowing tolerance.
Keywords:  maize       mesocotyl length        association mapping        differentially expressed gene        SNF1 kinase interactor-like protein  
Received: 04 September 2020   Accepted: 19 February 2021
Fund: This research was supported by the National Key R&D Program of China (2018YFD0100903), the China Agriculture Research System of MOF and MARA (CARS-02-13) and the Natural Science Fund of Liaoning Province, China (20170540806).
About author:  Correspondence WANG Jian-hua, E-mail:; ZHANG Hong-wei, E-mail:; DU Wan-li, E-mail: * These authors contributed equally to this study.

Cite this article: 

YANG Yue, MA Yu-ting, LIU Yang-yang, Demar LYLE, LI Dong-dong, WANG Ping-xi, XU Jia-liang, ZHEN Si-han, LU Jia-wen, PENG Yun-ling, CUI Yu, FU Jun-jie, DU Wan-li, ZHANG Hong-wei, WANG Jian-hua. 2022. Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis. Journal of Integrative Agriculture, 21(5): 1266-1277.

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