Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes
Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongatio...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2023
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/163946 |
| _version_ | 1855535522331492352 |
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| author | Wang, Yamei Liu, Hongyan Meng, Yun Liu, Jindong Ye, Guoyou |
| author_browse | Liu, Hongyan Liu, Jindong Meng, Yun Wang, Yamei Ye, Guoyou |
| author_facet | Wang, Yamei Liu, Hongyan Meng, Yun Liu, Jindong Ye, Guoyou |
| author_sort | Wang, Yamei |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation. |
| format | Journal Article |
| id | CGSpace163946 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1639462025-12-08T10:29:22Z Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes Wang, Yamei Liu, Hongyan Meng, Yun Liu, Jindong Ye, Guoyou rice plant hormones haplotypes haplotype analysis Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1 and Hap2, LOC_Os04g56950-Hap1, Hap2 and Hap8, LOC_Os07g24190-Hap3, LOC_Os12g12720-Hap3 and Hap6) and six superior haplotypes (LOC_Os02g17680-Hap2, Hap5 and Hap7, LOC_Os04g56950-Hap4, LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation. 2023-05-30 2024-12-19T12:53:13Z 2024-12-19T12:53:13Z Journal Article https://hdl.handle.net/10568/163946 en Open Access Frontiers Media Wang, Yamei; Liu, Hongyan; Meng, Yun; Liu, Jindong and Ye, Guoyou. 2023. Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes. Front. Plant Sci., Volume 14 |
| spellingShingle | rice plant hormones haplotypes haplotype analysis Wang, Yamei Liu, Hongyan Meng, Yun Liu, Jindong Ye, Guoyou Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title | Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title_full | Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title_fullStr | Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title_full_unstemmed | Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title_short | Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| title_sort | validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes |
| topic | rice plant hormones haplotypes haplotype analysis |
| url | https://hdl.handle.net/10568/163946 |
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