Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice
Due to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constr...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.985080/full |
| _version_ | 1811182679488462848 |
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| author | Jing Yang Ji Wei Jifen Xu Yumeng Xiong Gang Deng Jing Liu Shah Fahad Shah Fahad Hongyang Wang |
| author_facet | Jing Yang Ji Wei Jifen Xu Yumeng Xiong Gang Deng Jing Liu Shah Fahad Shah Fahad Hongyang Wang |
| author_sort | Jing Yang |
| collection | DOAJ |
| description | Due to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constructed a collection of recombinant inbred lines (RIL) comprising 275 lines derived from the H335 and CHA-1 cross by the method of single seed descent. Via a genotyping-by-sequencing (GBS) strategy, a high-density genetic map containing 2498 recombination bin markers was constructed, the average physical distance between the markers was only 149.38 Kb. After anaerobic treatment, 12 phenotypes related to both the coleoptile at germination and seedling quality at budding were evaluated. There were no significant correlations between seedling and bud traits. Genetic mapping of quantitative traits was performed for these traits across two cropping seasons. A total of 20 loci were detected, named locus 1~20. Three of them were repeatedly detected across both seasons. Six loci overlapped with those in previous reports, and nine loci were associated with multiple traits at both stages. Notably, locus 3, which is located on chromosome 2 (26,713,837 to 27,333,897 bp), was detected for both the germination and bud traits. By focusing on the locus 3 interval and by combining gene annotation and expression analyses, we identified a promising candidate gene, trehalose-6-phosphate phosphatase (OsTPP1, LOC_Os02g44230). Furthermore, RILs (G289, G379, G403, G430 and G454) that have superior phenotypes and that pyramid elite alleles were recognized. The findings of present study provide new genetic resources for direct-seeding rice (DSR) varieties for molecular breeding strategies and expand our knowledge of genetic regulation of seedling establishment under anaerobic conditions. |
| first_indexed | 2024-04-11T09:34:40Z |
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| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T09:34:40Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-a45b735f4b12483abcb4391755acf2482022-12-22T04:31:44ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.985080985080Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of riceJing Yang0Ji Wei1Jifen Xu2Yumeng Xiong3Gang Deng4Jing Liu5Shah Fahad6Shah Fahad7Hongyang Wang8Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaYunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaYunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaYunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaSchool of Agriculture, Yunnan University, Kunming, ChinaYunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaDepartment of Agriculture, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, PakistanDepartment of Agronomy, The University of Haripur, Haripur, PakistanYunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, ChinaDue to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constructed a collection of recombinant inbred lines (RIL) comprising 275 lines derived from the H335 and CHA-1 cross by the method of single seed descent. Via a genotyping-by-sequencing (GBS) strategy, a high-density genetic map containing 2498 recombination bin markers was constructed, the average physical distance between the markers was only 149.38 Kb. After anaerobic treatment, 12 phenotypes related to both the coleoptile at germination and seedling quality at budding were evaluated. There were no significant correlations between seedling and bud traits. Genetic mapping of quantitative traits was performed for these traits across two cropping seasons. A total of 20 loci were detected, named locus 1~20. Three of them were repeatedly detected across both seasons. Six loci overlapped with those in previous reports, and nine loci were associated with multiple traits at both stages. Notably, locus 3, which is located on chromosome 2 (26,713,837 to 27,333,897 bp), was detected for both the germination and bud traits. By focusing on the locus 3 interval and by combining gene annotation and expression analyses, we identified a promising candidate gene, trehalose-6-phosphate phosphatase (OsTPP1, LOC_Os02g44230). Furthermore, RILs (G289, G379, G403, G430 and G454) that have superior phenotypes and that pyramid elite alleles were recognized. The findings of present study provide new genetic resources for direct-seeding rice (DSR) varieties for molecular breeding strategies and expand our knowledge of genetic regulation of seedling establishment under anaerobic conditions.https://www.frontiersin.org/articles/10.3389/fpls.2022.985080/fulldirect-seeding riceanaerobic seedling establishmentGBSRILQTL mapping |
| spellingShingle | Jing Yang Ji Wei Jifen Xu Yumeng Xiong Gang Deng Jing Liu Shah Fahad Shah Fahad Hongyang Wang Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice Frontiers in Plant Science direct-seeding rice anaerobic seedling establishment GBS RIL QTL mapping |
| title | Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| title_full | Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| title_fullStr | Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| title_full_unstemmed | Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| title_short | Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| title_sort | mapping qtls for anaerobic tolerance at germination and bud stages using new high density genetic map of rice |
| topic | direct-seeding rice anaerobic seedling establishment GBS RIL QTL mapping |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.985080/full |
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