Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations
This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads re...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2018
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164847 |
| _version_ | 1855525488671326208 |
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| author | Ali, Jauhar Aslam, Umair M. Tariq, Rida Murugaiyan, Varunseelan Schnable, Patrick S. Li, Delin Marfori-Nazarea, Corinne M. Hernandez, Jose E. Arif, Muhammad Xu, Jianlong Li, Zhikang |
| author_browse | Ali, Jauhar Arif, Muhammad Aslam, Umair M. Hernandez, Jose E. Li, Delin Li, Zhikang Marfori-Nazarea, Corinne M. Murugaiyan, Varunseelan Schnable, Patrick S. Tariq, Rida Xu, Jianlong |
| author_facet | Ali, Jauhar Aslam, Umair M. Tariq, Rida Murugaiyan, Varunseelan Schnable, Patrick S. Li, Delin Marfori-Nazarea, Corinne M. Hernandez, Jose E. Arif, Muhammad Xu, Jianlong Li, Zhikang |
| author_sort | Ali, Jauhar |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1 to 4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs |
| format | Journal Article |
| id | CGSpace164847 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1648472024-12-19T14:12:37Z Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations Ali, Jauhar Aslam, Umair M. Tariq, Rida Murugaiyan, Varunseelan Schnable, Patrick S. Li, Delin Marfori-Nazarea, Corinne M. Hernandez, Jose E. Arif, Muhammad Xu, Jianlong Li, Zhikang backcrossing breeding programmes genetic variation genomics introgression introgression lines plant breeding single nucleotide polymorphism This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1 to 4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs 2018-06-22 2024-12-19T12:54:21Z 2024-12-19T12:54:21Z Journal Article https://hdl.handle.net/10568/164847 en Open Access Frontiers Media Ali, Jauhar; Aslam, Umair M.; Tariq, Rida; Murugaiyan, Varunseelan; Schnable, Patrick S.; Li, Delin; Marfori-Nazarea, Corinne M.; Hernandez, Jose E.; Arif, Muhammad; Xu, Jianlong and Li, Zhikang. 2018. Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations. Front. Plant Sci., Volume 9 |
| spellingShingle | backcrossing breeding programmes genetic variation genomics introgression introgression lines plant breeding single nucleotide polymorphism Ali, Jauhar Aslam, Umair M. Tariq, Rida Murugaiyan, Varunseelan Schnable, Patrick S. Li, Delin Marfori-Nazarea, Corinne M. Hernandez, Jose E. Arif, Muhammad Xu, Jianlong Li, Zhikang Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title | Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title_full | Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title_fullStr | Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title_full_unstemmed | Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title_short | Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression breeding populations |
| title_sort | exploiting the genomic diversity of rice oryza sativa l snp typing in 11 early backcross introgression breeding populations |
| topic | backcrossing breeding programmes genetic variation genomics introgression introgression lines plant breeding single nucleotide polymorphism |
| url | https://hdl.handle.net/10568/164847 |
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