Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.)
Water scarcity and labor shortage pose significant challenges in rice farming. Direct-seeded rice (DSR) is an efficient method that conserves water, reduces labor costs, and allows for full mechanization of cultivation. However, variable planting depth in undulated field leading to deep/shallow sowi...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1512234/full |
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| author | Vagish Mishra Vagish Mishra Shilpi Dixit Shilpi Dixit Swati Tyagi Swati Tyagi Challa Venkateswarlu Challa Venkateswarlu Pronob J. Paul Pronob J. Paul Anoop Kishor Singh Gurjar Anoop Kishor Singh Gurjar Shalabh Dixit Nitika Sandhu Smita Kurup Arvind Kumar Arvind Kumar Pallavi Sinha Pallavi Sinha Vikas Kumar Singh Vikas Kumar Singh Uma Maheshwar Singh Uma Maheshwar Singh |
| author_facet | Vagish Mishra Vagish Mishra Shilpi Dixit Shilpi Dixit Swati Tyagi Swati Tyagi Challa Venkateswarlu Challa Venkateswarlu Pronob J. Paul Pronob J. Paul Anoop Kishor Singh Gurjar Anoop Kishor Singh Gurjar Shalabh Dixit Nitika Sandhu Smita Kurup Arvind Kumar Arvind Kumar Pallavi Sinha Pallavi Sinha Vikas Kumar Singh Vikas Kumar Singh Uma Maheshwar Singh Uma Maheshwar Singh |
| author_sort | Vagish Mishra |
| collection | DOAJ |
| description | Water scarcity and labor shortage pose significant challenges in rice farming. Direct-seeded rice (DSR) is an efficient method that conserves water, reduces labor costs, and allows for full mechanization of cultivation. However, variable planting depth in undulated field leading to deep/shallow sowing of rice seeds during mechanical sowing presents a major hurdle, as existing varieties lack tolerance to deep sowing. To address this, a mapping population comprising 150 F4 lines, derived from MTU 1010 and AUS295, was developed and phenotyped for emergence from deep soil depth-related traits, including days of emergence (DE), percent germination (PG), mesocotyl length (ML), and coleoptile length (CL). The correlation revealed that DE has a significant negative correlation with PG, ML, and CL, whereas PG, ML, and CL are all positively correlated with each other. The mapping population was genotyped with mid-density SNP assay (1k-RiCA), and a linkage map was established with 414 polymorphic SNP markers. A total of 16 QTLs were identified for four traits, with phenotypic variance explained (PVE) ranging from 6.63% to 19.6% in the WS22. These included 5 QTLs for DE, 3 QTLs for PG, 4 QTLs for ML, and 4 QTLs for CL. Out of 16 QTLs identified, 12 were major effect QTLs (qDE1.2, qDE1.3, qDE1.4, qDE2.1, qDE12, qPG2.1, qPG2.2, qML2.1, qML2.2, qCL1, qCL2.2, qCL2.3) and 4 were minor effect QTLs (qPG1, qML1.2, qCL2.1). During DS23 season, QTL analysis for DE and PG traits identified seven and three QTLs, respectively. Out of the ten QTLs identified in DS23 season, eight were stable across the season. This study reported 11 novel QTLs, while 7 had been previously reported. The study pinpointed three QTL hotspot regions: one on chromosome 1 (qPG1, qCL1) and two on chromosome 2 (qPG2.1, qML2.2, qCL2.1) and (qPG2.2, qCL2.2). Candidate gene analysis in the identified QTL regions found two genes associated with hormonal pathways: OsSLR1 for gibberellin signaling and OsSAUR11 for abscisic acid signaling. Additionally, one gene (OsMT3a) associated with early seedling vigor and another (OsABA8ox1) regulates germination through coleoptile growth. The identified QTLs, genes, and breeding lines from this study provide valuable resources for developing rice varieties with enhanced tolerance to deep soil emergence, making them well-suited for mechanized DSR systems. |
| format | Article |
| id | doaj-art-97f753c86e064ee39ff6f63b127ea9ff |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-97f753c86e064ee39ff6f63b127ea9ff2025-01-29T06:46:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.15122341512234Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.)Vagish Mishra0Vagish Mishra1Shilpi Dixit2Shilpi Dixit3Swati Tyagi4Swati Tyagi5Challa Venkateswarlu6Challa Venkateswarlu7Pronob J. Paul8Pronob J. Paul9Anoop Kishor Singh Gurjar10Anoop Kishor Singh Gurjar11Shalabh Dixit12Nitika Sandhu13Smita Kurup14Arvind Kumar15Arvind Kumar16Pallavi Sinha17Pallavi Sinha18Vikas Kumar Singh19Vikas Kumar Singh20Uma Maheshwar Singh21Uma Maheshwar Singh22International Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Hub, Patancheru, Hyderabad, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Hub, Patancheru, Hyderabad, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaPlant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United KingdomInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Hub, Patancheru, Hyderabad, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaInternational Rice Research Institute, Los Baños, PhilippinesIRRI South Asia Regional Center, Varanasi, Uttar Pradesh, IndiaWater scarcity and labor shortage pose significant challenges in rice farming. Direct-seeded rice (DSR) is an efficient method that conserves water, reduces labor costs, and allows for full mechanization of cultivation. However, variable planting depth in undulated field leading to deep/shallow sowing of rice seeds during mechanical sowing presents a major hurdle, as existing varieties lack tolerance to deep sowing. To address this, a mapping population comprising 150 F4 lines, derived from MTU 1010 and AUS295, was developed and phenotyped for emergence from deep soil depth-related traits, including days of emergence (DE), percent germination (PG), mesocotyl length (ML), and coleoptile length (CL). The correlation revealed that DE has a significant negative correlation with PG, ML, and CL, whereas PG, ML, and CL are all positively correlated with each other. The mapping population was genotyped with mid-density SNP assay (1k-RiCA), and a linkage map was established with 414 polymorphic SNP markers. A total of 16 QTLs were identified for four traits, with phenotypic variance explained (PVE) ranging from 6.63% to 19.6% in the WS22. These included 5 QTLs for DE, 3 QTLs for PG, 4 QTLs for ML, and 4 QTLs for CL. Out of 16 QTLs identified, 12 were major effect QTLs (qDE1.2, qDE1.3, qDE1.4, qDE2.1, qDE12, qPG2.1, qPG2.2, qML2.1, qML2.2, qCL1, qCL2.2, qCL2.3) and 4 were minor effect QTLs (qPG1, qML1.2, qCL2.1). During DS23 season, QTL analysis for DE and PG traits identified seven and three QTLs, respectively. Out of the ten QTLs identified in DS23 season, eight were stable across the season. This study reported 11 novel QTLs, while 7 had been previously reported. The study pinpointed three QTL hotspot regions: one on chromosome 1 (qPG1, qCL1) and two on chromosome 2 (qPG2.1, qML2.2, qCL2.1) and (qPG2.2, qCL2.2). Candidate gene analysis in the identified QTL regions found two genes associated with hormonal pathways: OsSLR1 for gibberellin signaling and OsSAUR11 for abscisic acid signaling. Additionally, one gene (OsMT3a) associated with early seedling vigor and another (OsABA8ox1) regulates germination through coleoptile growth. The identified QTLs, genes, and breeding lines from this study provide valuable resources for developing rice varieties with enhanced tolerance to deep soil emergence, making them well-suited for mechanized DSR systems.https://www.frontiersin.org/articles/10.3389/fpls.2024.1512234/fulldirect-seeded rice (DSR)quantitative trait loci (QTLs)deep sowing depthseed germinationmesocotyl lengthcoleoptile length |
| spellingShingle | Vagish Mishra Vagish Mishra Shilpi Dixit Shilpi Dixit Swati Tyagi Swati Tyagi Challa Venkateswarlu Challa Venkateswarlu Pronob J. Paul Pronob J. Paul Anoop Kishor Singh Gurjar Anoop Kishor Singh Gurjar Shalabh Dixit Nitika Sandhu Smita Kurup Arvind Kumar Arvind Kumar Pallavi Sinha Pallavi Sinha Vikas Kumar Singh Vikas Kumar Singh Uma Maheshwar Singh Uma Maheshwar Singh Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) Frontiers in Plant Science direct-seeded rice (DSR) quantitative trait loci (QTLs) deep sowing depth seed germination mesocotyl length coleoptile length |
| title | Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) |
| title_full | Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) |
| title_fullStr | Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) |
| title_full_unstemmed | Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) |
| title_short | Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) |
| title_sort | unveiling genetic basis of seedling emergence from deep soil depth under dry direct seeded conditions in rice oryza sativa l |
| topic | direct-seeded rice (DSR) quantitative trait loci (QTLs) deep sowing depth seed germination mesocotyl length coleoptile length |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1512234/full |
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