SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines
Maize production in sub-Saharan Africa (SSA) faces significant challenges due to low soil nitrogen. To enhance breeding efficiency for low nitrogen tolerance, identifying quantitative trait loci (QTLs) in tropical germplasm is crucial to facilitate marker-assisted selection (MAS). In this study, gen...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2025
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| Online Access: | https://hdl.handle.net/10568/176050 |
| _version_ | 1855543167723503616 |
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| author | Abu, P. Badu-Apraku, B. Ifie, B.E. Eleblu, J.S.Y. Ehemba, L. Tongoona, P. Offei, S. |
| author_browse | Abu, P. Badu-Apraku, B. Ehemba, L. Eleblu, J.S.Y. Ifie, B.E. Offei, S. Tongoona, P. |
| author_facet | Abu, P. Badu-Apraku, B. Ifie, B.E. Eleblu, J.S.Y. Ehemba, L. Tongoona, P. Offei, S. |
| author_sort | Abu, P. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Maize production in sub-Saharan Africa (SSA) faces significant challenges due to low soil nitrogen. To enhance breeding efficiency for low nitrogen tolerance, identifying quantitative trait loci (QTLs) in tropical germplasm is crucial to facilitate marker-assisted selection (MAS). In this study, gene targeting markers (GTM) derived from sequence-based single nucleotide polymorphisms (SeqSNP) were utilized to analyse the population structure and identify potential candidate genes associated with tolerance to low nitrogen. A total of 150 extra-early quality protein maize (QPM) inbred lines were assessed under both low (LN) and high (HN) nitrogen, followed by genotyping with 2,500 SeqSNPs targeting genes previously reported for LN tolerance-related traits. Population structure analysis revealed six sub-populations. Association mapping analysis revealed 15 significant single nucleotide polymorphisms (SNPs) linked to several key traits. Specifically, two SNPs each were associated with the low nitrogen base index (LNBI), which combines grain yield with other agronomic traits under low nitrogen, and the low nitrogen tolerance index (LNTI), a measure of grain yield performance in high nitrogen environments relative to low nitrogen environments. |
| format | Journal Article |
| id | CGSpace176050 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1760502025-12-08T10:29:22Z SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines Abu, P. Badu-Apraku, B. Ifie, B.E. Eleblu, J.S.Y. Ehemba, L. Tongoona, P. Offei, S. maize nitrogen genetic markers population genes Maize production in sub-Saharan Africa (SSA) faces significant challenges due to low soil nitrogen. To enhance breeding efficiency for low nitrogen tolerance, identifying quantitative trait loci (QTLs) in tropical germplasm is crucial to facilitate marker-assisted selection (MAS). In this study, gene targeting markers (GTM) derived from sequence-based single nucleotide polymorphisms (SeqSNP) were utilized to analyse the population structure and identify potential candidate genes associated with tolerance to low nitrogen. A total of 150 extra-early quality protein maize (QPM) inbred lines were assessed under both low (LN) and high (HN) nitrogen, followed by genotyping with 2,500 SeqSNPs targeting genes previously reported for LN tolerance-related traits. Population structure analysis revealed six sub-populations. Association mapping analysis revealed 15 significant single nucleotide polymorphisms (SNPs) linked to several key traits. Specifically, two SNPs each were associated with the low nitrogen base index (LNBI), which combines grain yield with other agronomic traits under low nitrogen, and the low nitrogen tolerance index (LNTI), a measure of grain yield performance in high nitrogen environments relative to low nitrogen environments. 2025 2025-08-08T15:26:09Z 2025-08-08T15:26:09Z Journal Article https://hdl.handle.net/10568/176050 en Open Access application/pdf Frontiers Media Abu, P., Badu-Apraku, B., Ifie, B.E., Eleblu, J.S.Y., Ehemba, G.L., Tongoona, P. B. & Offei, S.K. (2025). SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines. Frontiers in Plant Science, 16, 1558741, 1-14. |
| spellingShingle | maize nitrogen genetic markers population genes Abu, P. Badu-Apraku, B. Ifie, B.E. Eleblu, J.S.Y. Ehemba, L. Tongoona, P. Offei, S. SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title | SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title_full | SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title_fullStr | SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title_full_unstemmed | SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title_short | SeqSNP-based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| title_sort | seqsnp based genic markers reveal genetic architecture and candidate genes for low nitrogen tolerance in tropical maize inbred lines |
| topic | maize nitrogen genetic markers population genes |
| url | https://hdl.handle.net/10568/176050 |
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