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Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.)

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Abstract

Background

Salt-tolerant breeding of maize has great significance to the development and utilization of saline–alkaline soil and the maintenance of grain security. Genome-wide association study (GWAS) has been widely used in maize genetics and breeding.

Objective

To discover new salt-tolerant genes in maize by association analysis, which can provide technical supports for the innovation and genetic improvement of salt-tolerant germplasm resources in maize.

Methods

Totally 150 maize inbred lines were genotyped with a high-density chip. GWAS was carried out to identify the significant single nucleotide polymorphisms (SNPs) which were associated with maize salt tolerance. Totally 34,972 SNPs with high quality and diversity were selected from 56,110 SNP markers, which were distributed on 10 chromosomes of maize. The GLM algorithm in TASSEL5.2 was used to analyze the five traits related to salt tolerance.

Results

Using a strict LOD threshold of 4.5, totally 7 SNP loci were identified, which were significantly correlated with plant height change rate and fresh weight change rate. The high density fingerprints of 150 inbred lines were clustered by TASSEL5.2 software to construct genetic clustering map to estimate the genetic distance and the subgroups. The 150 maize inbred lines were divided into two groups: SS group and NSS group, and the SNP loci of the salt-tolerant index showed difference in chromosome distribution. Based on previous studies, we screened 8 candidate genes for salt tolerance in maize and four of them were further validated by real-time quantitative PCR.

Conclusion

Totally 7 SNP loci and 8 candidate genes related to salt tolerance in maize were identified, which will be of special value in molecular breeding of salt-tolerant maize.

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Acknowledgements

This work was supported by the Key Research and Development Project of Jiangsu Province, China (Modern Agriculture, BE2017365), the State Key Laboratory of Crop Biology (Shandong Agricultural University) Open Fund (2016KF02), the fund from Nantong Xinhe Bio-Technology Co. Ltd. (17ZH050), and the Practice Innovation Training Program Projects for College Students.

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Author notes

  1. Yonghong Xie and Yan Feng have contributed equally to this work.

Authors and Affiliations

  1. Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, People’s Republic of China

    Yonghong Xie, Yan Feng, Qi Chen, Feike Zhao, Shuijuan Zhou, Ying Ding, Ping Li & Baohua Wang

  2. State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018, Shandong, People’s Republic of China

    Xianliang Song

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  1. Yonghong Xie
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  2. Yan Feng
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  4. Feike Zhao
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Correspondence to Xianliang Song, Ping Li or Baohua Wang.

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Xie, Y., Feng, Y., Chen, Q. et al. Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.). Genes Genom 41, 1135–1145 (2019). https://doi.org/10.1007/s13258-019-00842-6

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