Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.)
A chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide unique DNA markers are urgently needed for marker-a...
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MDPI AG
2025-01-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/15/1/169 |
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| author | Huijie Zhai Kunpeng Xu Meng Wang Zhenchuang Wang Ziyang Cai Ao Li Anxin He Xiaoming Xie Lingling Chai Mingjiu Liu Xingqi Ou Zhongfu Ni |
| author_facet | Huijie Zhai Kunpeng Xu Meng Wang Zhenchuang Wang Ziyang Cai Ao Li Anxin He Xiaoming Xie Lingling Chai Mingjiu Liu Xingqi Ou Zhongfu Ni |
| author_sort | Huijie Zhai |
| collection | DOAJ |
| description | A chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide unique DNA markers are urgently needed for marker-assisted selection. In this study, 11,016 primer pairs targeting 5036 indel sites were successfully designed for E6015-3S, with an average density of 0.36 indels per Mbp. These primer pairs are believed to be unique and polymorphic in the wheat genome; as gathered from the evidence, (i) 76.18 to 99.34% of the 11,016 primer pairs yielded a single hit during sequence alignment with 18 sequenced genomes, (ii) 83.59 to 90.98% of 1042 synthesized primer pairs amplified a single band in 16 wheat accessions, and (iii) 59.69 to 99.81% of the tested 1042 primer pairs were polymorphic between E6015-3S and 15 individual wheat accessions. These primer pairs are also anticipated with excellent resolvability on agarose or polyacrylamide gels, since most of them have indel sizes from 15 to 46 bp, amplicon sizes from 141 to 250 bp, and polymorphism ratios from 6.0 to 25.0%. Collectively, these primer pairs are ideal DNA markers for inter-varietal CSSL development and more broad applications, like germplasm classification, seed purity testing, genetic linkage mapping, and marker-assisted breeding in wheat, owing to their uniqueness, polymorphism, and easy-to-use characteristics. |
| format | Article |
| id | doaj-art-059e8c06a52e4dbcba8f66007b73148c |
| institution | Kabale University |
| issn | 2073-4395 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj-art-059e8c06a52e4dbcba8f66007b73148c2025-01-24T13:17:01ZengMDPI AGAgronomy2073-43952025-01-0115116910.3390/agronomy15010169Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.)Huijie Zhai0Kunpeng Xu1Meng Wang2Zhenchuang Wang3Ziyang Cai4Ao Li5Anxin He6Xiaoming Xie7Lingling Chai8Mingjiu Liu9Xingqi Ou10Zhongfu Ni11School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaSchool of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaFrontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, ChinaSchool of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaFrontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, ChinaSchool of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, ChinaFrontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, ChinaFrontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, ChinaSchool of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaSchool of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, ChinaFrontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, ChinaA chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide unique DNA markers are urgently needed for marker-assisted selection. In this study, 11,016 primer pairs targeting 5036 indel sites were successfully designed for E6015-3S, with an average density of 0.36 indels per Mbp. These primer pairs are believed to be unique and polymorphic in the wheat genome; as gathered from the evidence, (i) 76.18 to 99.34% of the 11,016 primer pairs yielded a single hit during sequence alignment with 18 sequenced genomes, (ii) 83.59 to 90.98% of 1042 synthesized primer pairs amplified a single band in 16 wheat accessions, and (iii) 59.69 to 99.81% of the tested 1042 primer pairs were polymorphic between E6015-3S and 15 individual wheat accessions. These primer pairs are also anticipated with excellent resolvability on agarose or polyacrylamide gels, since most of them have indel sizes from 15 to 46 bp, amplicon sizes from 141 to 250 bp, and polymorphism ratios from 6.0 to 25.0%. Collectively, these primer pairs are ideal DNA markers for inter-varietal CSSL development and more broad applications, like germplasm classification, seed purity testing, genetic linkage mapping, and marker-assisted breeding in wheat, owing to their uniqueness, polymorphism, and easy-to-use characteristics.https://www.mdpi.com/2073-4395/15/1/169wheatthermotoleranceinter-varietal CSSLE6015-3Sindel markergenome-wide uniqueness |
| spellingShingle | Huijie Zhai Kunpeng Xu Meng Wang Zhenchuang Wang Ziyang Cai Ao Li Anxin He Xiaoming Xie Lingling Chai Mingjiu Liu Xingqi Ou Zhongfu Ni Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) Agronomy wheat thermotolerance inter-varietal CSSL E6015-3S indel marker genome-wide uniqueness |
| title | Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) |
| title_full | Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) |
| title_fullStr | Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) |
| title_full_unstemmed | Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) |
| title_short | Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) |
| title_sort | development of genome wide unique indel markers for a heat sensitive genotype in wheat i triticum aestivum i l |
| topic | wheat thermotolerance inter-varietal CSSL E6015-3S indel marker genome-wide uniqueness |
| url | https://www.mdpi.com/2073-4395/15/1/169 |
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