SNP genotyping for fast and consistent clustering of maize inbred lines into heterotic groups

IF 1.5 4区农林科学 Q2 Agricultural and Biological Sciences Crop Breeding and Applied Biotechnology Pub Date : 2021-05-21 DOI:10.1590/1984-70332021V21N1A10

Lander Santos de Oliveira, I. Schuster, E. Novaes, W. A. Pereira

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Abstract

Abstract Advances in genotyping technologies have transformed the way breeding programs manage their genetic resources. The identification of single nucleotide polymorphisms (SNPs) can improve understanding of the genetic diversity of maize (Zea mays) inbred lines and their classification into heterotic groups, which is useful in determining certain crosses to obtain hybrids with higher yield performance. The genetic diversity of 293 inbred lines was investigated with 5252 SNPs with minor allele frequency (MAF)>5%. There was an average of 525 SNPs per chromosome. Polymorphism information content (PIC) averaged 0.297. The unweighted pair group method with arithmetic mean analysis (UPGMA) and principal component analysis (PCA) based on the genetic distance matrix revealed four similar clusters and high cophenetic correlation coefficients (0.953 and 0.863, respectively). The results showed consistency between genetic distance-based grouping and the heterotic groups previously established using pedigree and topcross information for the inbred lines studied.

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玉米自交系快速一致聚类的SNP基因分型

摘要基因分型技术的进步改变了育种项目管理其遗传资源的方式。单核苷酸多态性（SNPs）的鉴定可以提高对玉米自交系遗传多样性及其杂种群分类的理解，这有助于确定某些杂交组合，以获得更高产的杂交种。用5252个等位基因频率（MAF）＞5%的SNPs对293个自交系的遗传多样性进行了研究。每个染色体平均有525个SNPs。多态性信息含量（PIC）平均为0.297。基于遗传距离矩阵的算术平均分析（UPGMA）和主成分分析（PCA）的未加权对群方法显示了四个相似的聚类，并且具有很高的协方差相关系数（分别为0.953和0.863）。结果表明，对于所研究的自交系，基于遗传距离的分组与先前使用系谱和顶交信息建立的杂种群之间是一致的。

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来源期刊

Crop Breeding and Applied Biotechnology 农林科学-农艺学

CiteScore

2.40

自引率

13.30%

发文量

审稿时长

6-12 weeks

期刊介绍： The CBAB – CROP BREEDING AND APPLIED BIOTECHNOLOGY (ISSN 1984-7033) – is the official quarterly journal of the Brazilian Society of Plant Breeding, abbreviated CROP BREED APPL BIOTECHNOL. It publishes original scientific articles, which contribute to the scientific and technological development of plant breeding and agriculture. Articles should be to do with basic and applied research on improvement of perennial and annual plants, within the fields of genetics, conservation of germplasm, biotechnology, genomics, cytogenetics, experimental statistics, seeds, food quality, biotic and abiotic stress, and correlated areas. The article must be unpublished. Simultaneous submitting to another periodical is ruled out. Authors are held solely responsible for the opinions and ideas expressed, which do not necessarily reflect the view of the Editorial board. However, the Editorial board reserves the right to suggest or ask for any modifications required. The journal adopts the Ithenticate software for identification of plagiarism. Complete or partial reproduction of articles is permitted, provided the source is cited. All content of the journal, except where identified, is licensed under a Creative Commons attribution-type BY. All articles are published free of charge. This is an open access journal.