Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

doi:10.1016/S2095-3119(21)63649-3

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (5): 1266-1277.DOI: 10.1016/S2095-3119(21)63649-3

所属专题：玉米遗传育种合辑Maize Genetics · Breeding · Germplasm Resources

收稿日期:2020-09-04 接受日期:2021-02-19 出版日期:2022-05-01 发布日期:2021-02-19

Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

YANG Yue^{1, 2*}, MA Yu-ting^{1, 2*}, LIU Yang-yang^{2, 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 ⁴Gansu Provincial Key Laboratory for Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, P.R.China

Received:2020-09-04 Accepted:2021-02-19 Online:2022-05-01 Published:2021-02-19
About author:Correspondence WANG Jian-hua, E-mail: wangjh63@cau.edu.cn; ZHANG Hong-wei, E-mail: zhanghongwei@caas.cn; DU Wan-li, E-mail: dwl2014@syau.edu.cn * These authors contributed equally to this study.
Supported by:
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).

摘要/Abstract

摘要：

深播是包括玉米在内的作物躲避干旱的一种重要策略，候选基因的克隆是进行玉米耐深播分子机理研究的基础工作。本研究中，我们利用包含386份玉米自交系的关联分析群体对10厘米和20厘米播种深度条件下的四个性状进行鉴定。利用50万SNP标记进行关联分析发现了273个耐深播性状显著关联的SNP。对两组不同的处理进行RNA测序分析分别发现1944和2098个差异基因，其中包含281个共同的差异基因。通过比较273个SNP和281个差异基因的位置发现了7个可能与耐深播相关的候选基因，其中GRMZM2G119769编码一个SNF1激酶互作的蛋白。由于GRMZM2G119769在其他植物中的同源基因跟器官伸长、生长素和光响应有关。同时，候选基因关联分析表明GRMZM2G119769基因的自然变异与玉米的中胚轴长度有关。另外，基因表达分析表明GRMZM2G119769在耐深播材料中表达量高。这些研究结果都支持GRMZM2G119769是玉米耐深播性状的候选基因。本研究不但评价了玉米资源的耐深播特性，还鉴定出一些可能对未来玉米耐深播研究有参考价值的候选基因。

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.

Key words: maize , mesocotyl length , association mapping , differentially expressed gene , SNF1 kinase interactor-like protein

. [J]. Journal of Integrative Agriculture, 2022, 21(5): 1266-1277.

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. Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis[J]. Journal of Integrative Agriculture, 2022, 21(5): 1266-1277.

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Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

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