Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm
A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conduct...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Nature Publishing Group
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/162532 |
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| author | Sehgal, Deepmala Rathan, Nagenahalli Dharmegowda Ozdemir, Fatih Keser, Mesut Akin, Beyhan Dababat, Abdelfattah A. Koc, Emrah Dreisigacker, Susanne Morgounov, Alexey |
| author_browse | Akin, Beyhan Dababat, Abdelfattah A. Dreisigacker, Susanne Keser, Mesut Koc, Emrah Morgounov, Alexey Ozdemir, Fatih Rathan, Nagenahalli Dharmegowda Sehgal, Deepmala |
| author_facet | Sehgal, Deepmala Rathan, Nagenahalli Dharmegowda Ozdemir, Fatih Keser, Mesut Akin, Beyhan Dababat, Abdelfattah A. Koc, Emrah Dreisigacker, Susanne Morgounov, Alexey |
| author_sort | Sehgal, Deepmala |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat. |
| format | Journal Article |
| id | CGSpace162532 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Nature Publishing Group |
| publisherStr | Nature Publishing Group |
| record_format | dspace |
| spelling | CGSpace1625322025-12-08T09:54:28Z Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm Sehgal, Deepmala Rathan, Nagenahalli Dharmegowda Ozdemir, Fatih Keser, Mesut Akin, Beyhan Dababat, Abdelfattah A. Koc, Emrah Dreisigacker, Susanne Morgounov, Alexey genome-wide association studies phenotypic variation yields winter wheat germplasm A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat. 2024 2024-11-21T15:40:32Z 2024-11-21T15:40:32Z Journal Article https://hdl.handle.net/10568/162532 en Open Access application/pdf Nature Publishing Group Sehgal, D., Rathan, N. D., Özdemir, F., Keser, M., Akin, B., Dababat, A. A., Koc, E., Dreisigacker, S., & Morgounov, A. (2024). Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Scientific Reports, 14(1), 8431. https://doi.org/10.1038/s41598-024-57469-1 |
| spellingShingle | genome-wide association studies phenotypic variation yields winter wheat germplasm Sehgal, Deepmala Rathan, Nagenahalli Dharmegowda Ozdemir, Fatih Keser, Mesut Akin, Beyhan Dababat, Abdelfattah A. Koc, Emrah Dreisigacker, Susanne Morgounov, Alexey Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title | Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title_full | Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title_fullStr | Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title_full_unstemmed | Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title_short | Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm |
| title_sort | genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in turkish winter wheat germplasm |
| topic | genome-wide association studies phenotypic variation yields winter wheat germplasm |
| url | https://hdl.handle.net/10568/162532 |
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