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Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers

Well-developed maize reference genomes and genotyping technology along with fast decreasing detection costs have enabled the chance of shifting essentially derived varieties (EDV) identification to high-throughput SNP genotyping technology. However, attempts of using high-throughput technologies suc...

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Autores principales: Yan, Yuanyuan, Sun, Shanqiu, Xing, Ruixia, Jiang, Haiyang, Cheng, Beijiu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9332735/
https://www.ncbi.nlm.nih.gov/pubmed/35893613
http://dx.doi.org/10.3390/plants11151909
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author Yan, Yuanyuan
Sun, Shanqiu
Xing, Ruixia
Jiang, Haiyang
Cheng, Beijiu
author_facet Yan, Yuanyuan
Sun, Shanqiu
Xing, Ruixia
Jiang, Haiyang
Cheng, Beijiu
author_sort Yan, Yuanyuan
collection PubMed
description Well-developed maize reference genomes and genotyping technology along with fast decreasing detection costs have enabled the chance of shifting essentially derived varieties (EDV) identification to high-throughput SNP genotyping technology. However, attempts of using high-throughput technologies such as SNP array on EDV identification and the essential baseline parameters such as genetic homozygosity and/or stability in EDV practices have not been characterized. Here, we selected 28 accessions of 21 classical maize inbreds, which definitely form a pedigree network from initial founders to derivatives that had made huge contribution to corn production, to demonstrate these fundamental analyses. Our data showed that average residual heterozygosity (RH) rate of these 28 accessions across genome was about 1.03%. However, the RH rate of some accessions was higher than 3%. In addition, some inbreds were found to have an overall RH rate lower than 2% but over 8% level at certain chromosomes. Genetic drift (GD) between two accessions from different years or breeding programs varied from 0.13% to 13.16%. Accessions with low GD level showed cluster distribution pattern and compared with RH distributions indicated that RH was not the only resource of GD. Both RH and GD data suggested that genetic purity analysis is an essential procedure before determining EDV. Eleven derivative lines were characterized with regard to their genome compositions and were inferred as their breeding histories. The backcross, bi-parental recycling, and mutation breeding records could be identified. The data provide insights of underlining fundamental parameters for defining EDV threshold and the results demonstrate the EDV identification process.
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spelling pubmed-93327352022-07-29 Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers Yan, Yuanyuan Sun, Shanqiu Xing, Ruixia Jiang, Haiyang Cheng, Beijiu Plants (Basel) Article Well-developed maize reference genomes and genotyping technology along with fast decreasing detection costs have enabled the chance of shifting essentially derived varieties (EDV) identification to high-throughput SNP genotyping technology. However, attempts of using high-throughput technologies such as SNP array on EDV identification and the essential baseline parameters such as genetic homozygosity and/or stability in EDV practices have not been characterized. Here, we selected 28 accessions of 21 classical maize inbreds, which definitely form a pedigree network from initial founders to derivatives that had made huge contribution to corn production, to demonstrate these fundamental analyses. Our data showed that average residual heterozygosity (RH) rate of these 28 accessions across genome was about 1.03%. However, the RH rate of some accessions was higher than 3%. In addition, some inbreds were found to have an overall RH rate lower than 2% but over 8% level at certain chromosomes. Genetic drift (GD) between two accessions from different years or breeding programs varied from 0.13% to 13.16%. Accessions with low GD level showed cluster distribution pattern and compared with RH distributions indicated that RH was not the only resource of GD. Both RH and GD data suggested that genetic purity analysis is an essential procedure before determining EDV. Eleven derivative lines were characterized with regard to their genome compositions and were inferred as their breeding histories. The backcross, bi-parental recycling, and mutation breeding records could be identified. The data provide insights of underlining fundamental parameters for defining EDV threshold and the results demonstrate the EDV identification process. MDPI 2022-07-23 /pmc/articles/PMC9332735/ /pubmed/35893613 http://dx.doi.org/10.3390/plants11151909 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yan, Yuanyuan
Sun, Shanqiu
Xing, Ruixia
Jiang, Haiyang
Cheng, Beijiu
Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title_full Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title_fullStr Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title_full_unstemmed Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title_short Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers
title_sort identifying parameters for defining “essentially derived varieties” of maize inbred lines using high-throughput genome-wide snp markers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9332735/
https://www.ncbi.nlm.nih.gov/pubmed/35893613
http://dx.doi.org/10.3390/plants11151909
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