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...
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| Format: | Article |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1194119/full |
| _version_ | 1797814245270749184 |
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| author | Yamei Wang Yamei Wang Yamei Wang Hongyan Liu Yun Meng Yun Meng Jindong Liu Jindong Liu Guoyou Ye Guoyou Ye |
| author_facet | Yamei Wang Yamei Wang Yamei Wang Hongyan Liu Yun Meng Yun Meng Jindong Liu Jindong Liu Guoyou Ye Guoyou Ye |
| author_sort | Yamei Wang |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-13T08:04:46Z |
| format | Article |
| id | doaj.art-f038f43db79b40b5bad56dab637af925 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-13T08:04:46Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-f038f43db79b40b5bad56dab637af9252023-06-01T08:43:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-05-011410.3389/fpls.2023.11941191194119Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypesYamei Wang0Yamei Wang1Yamei Wang2Hongyan Liu3Yun Meng4Yun Meng5Jindong Liu6Jindong Liu7Guoyou Ye8Guoyou Ye9Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, ChinaCAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaSchool of Agriculture, Sun Yat-sen University, Shenzhen, ChinaSanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, ChinaCAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaSanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, ChinaInstitute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, ChinaCAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaCAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaStrategic Innovation Platform, International Rice Research Institute, Manila, PhilippinesMesocotyl 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1194119/fullcandidate gene association analysismesocotylhaplotypemr-MLMOryza sativa L |
| spellingShingle | Yamei Wang Yamei Wang Yamei Wang Hongyan Liu Yun Meng Yun Meng Jindong Liu Jindong Liu Guoyou Ye Guoyou Ye Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes Frontiers in Plant Science candidate gene association analysis mesocotyl haplotype mr-MLM Oryza sativa L |
| 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 | candidate gene association analysis mesocotyl haplotype mr-MLM Oryza sativa L |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1194119/full |
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