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Identification of Polymorphic Markers by High-Resolution Melting (HRM) Assay for High-Throughput SNP Genotyping in Maize

Zhigang Shang1,2, Yongzhe Zhu3, Xinmei Guo1,2, Meiai Zhao1,4,*
1 College of Agronomy, Qingdao Agricultural University, Qingdao, China
2 Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
3 College of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, China
4 Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
* Corresponding Author: Meiai Zhao. Email:
(This article belongs to this Special Issue: Plant Physiology for Crop Production and Sustainable Agriculture)

Phyton-International Journal of Experimental Botany 2021, 90(6), 1711-1725. https://doi.org/10.32604/phyton.2021.015048

Received 18 November 2020; Accepted 15 March 2021; Issue published 28 June 2021

Abstract

The development of next generation sequencing (NGS) and high throughput genotyping are important techniques for the QTL mapping and genetic analysis of different crops. High-resolution melting (HRM) is an emerging technology used for detecting single-nucleotide polymorphisms (SNPs) in various species. However, its use is still limited in maize. The HRM analysis was integrated with SNPs to identify three types of populations (NIL population, RIL population and natural population), and the useful tags were screened. The patterns of temperature-shifted melting curves were investigated from the HRM analysis, and compared these with the kit. Among all 48 pairs of primers, 10 pairs of them were selected: six pairs of primers for the NIL population, three pairs of primers for the RIL population, and one pair of primer for the natural population. The marker for the natural population was developed with a matching rate of 80% for the plant height trait, based on the data of the phenotypic characteristics measured in the field. This study provides an effective method for maize genotyping in the classification of maize germplasm resources, which can be applied to other plants for high-throughput SNP genotyping or further mapping.

Keywords

Maize; high-throughput genotyping; HRM; SNP

Cite This Article

Shang, Z., Zhu, Y., Guo, X., Zhao, M. (2021). Identification of Polymorphic Markers by High-Resolution Melting (HRM) Assay for High-Throughput SNP Genotyping in Maize. Phyton-International Journal of Experimental Botany, 90(6), 1711–1725.



This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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