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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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/15/1909 |
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| author | Yuanyuan Yan Shanqiu Sun Ruixia Xing Haiyang Jiang Beijiu Cheng |
| author_facet | Yuanyuan Yan Shanqiu Sun Ruixia Xing Haiyang Jiang Beijiu Cheng |
| author_sort | Yuanyuan Yan |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T10:06:57Z |
| format | Article |
| id | doaj.art-edfbd79a9ec744a39f649b733303ae33 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T10:06:57Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-edfbd79a9ec744a39f649b733303ae332023-12-01T23:06:00ZengMDPI AGPlants2223-77472022-07-011115190910.3390/plants11151909Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP MarkersYuanyuan Yan0Shanqiu Sun1Ruixia Xing2Haiyang Jiang3Beijiu Cheng4School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaSchool of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaSchool of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaSchool of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaSchool of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaWell-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.https://www.mdpi.com/2223-7747/11/15/1909high-throughput genotypingessentially derived varietyresidual heterozygositygenetic driftSNP chip array |
| spellingShingle | Yuanyuan Yan Shanqiu Sun Ruixia Xing Haiyang Jiang Beijiu Cheng Identifying Parameters for Defining “Essentially Derived Varieties” of Maize Inbred Lines Using High-Throughput Genome-Wide SNP Markers Plants high-throughput genotyping essentially derived variety residual heterozygosity genetic drift SNP chip array |
| 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 | high-throughput genotyping essentially derived variety residual heterozygosity genetic drift SNP chip array |
| url | https://www.mdpi.com/2223-7747/11/15/1909 |
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