Chinese Bulletin of Botany ›› 2023, Vol. 58 ›› Issue (3): 394-403.DOI: 10.11983/CBB22259
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Jiayi Jin1, Yiting Luo1, Huimin Yang1, Tao Lu1, Hanfei Ye1, Jiyi Xie1, Kexin Wang1, Qianyu Chen1, Yuan Fang1, Yuexing Wang2(), Yuchun Rao1()
Received:
2022-11-08
Accepted:
2023-02-09
Online:
2023-05-01
Published:
2023-05-17
Contact:
*E-mail: wangyuexing@caas.cn; ryc@zjnu.cn
Jiayi Jin, Yiting Luo, Huimin Yang, Tao Lu, Hanfei Ye, Jiyi Xie, Kexin Wang, Qianyu Chen, Yuan Fang, Yuexing Wang, Yuchun Rao. QTL Mapping and Expression Analysis on Candidate Genes Related to Chlorophyll Content in Rice[J]. Chinese Bulletin of Botany, 2023, 58(3): 394-403.
Primer name | Sequence (5′-3′) |
---|---|
LOC_Os06g11780-F-qrt | TGTTGGTCCCTGAAAACTCC |
LOC_Os06g11780-R-qrt | TCAAGCAAATTCACCCATGA |
LOC_Os06g12360-F-qrt | ATGCAAAAAGGAGAGGCTGA |
LOC_Os06g12360-R-qrt | ATGCCGATCAGGAATCTCAC |
LOC_Os06g39650-F-qrt | GTGCTCTTCAACCAGTGCAA |
LOC_Os06g39650-R-qrt | AGATTGGCACAGCATGTCAG |
LOC_Os06g39716-F-qrt | CAACCTTTTCGTAGGCATCC |
LOC_Os06g39716-R-qrt | TTGAAATTGACTGGGCTTGA |
LOC_Os08g42610-F-qrt | GCTCGCACACTGAAAACAAA |
LOC_Os08g42610-R-qrt | ATGGGATAGGCCCCAAATAG |
LOC_Os02g18500-F-qrt | AGGAGGAGGTGTTGGGAACT |
LOC_Os02g18500-R-qrt | ATGCAGTTGTTGATGGCGTA |
LOC_Os03g21240-F-qrt | TATGCCTTTGCACCAGAGTG |
LOC_Os03g21240-R-qrt | CAGCATTCGACGACTGAGAA |
LOC_Os03g21400-F-qrt | AGGAAAGCGGAGAAGAAAGG |
LOC_Os03g21400-R-qrt | TTAGACACCAGGCAGCTGTG |
LOC_Os03g21780-F-qrt | CTCCCTTCCACTCCTCCTTC |
LOC_Os03g21780-R-qrt | CTTCTCCTCCTCGACACCAG |
LOC_Os03g30950-F-qrt | TCTTCTTCTCCATGGCCTGT |
LOC_Os03g30950-R-qrt | AGCAGGGAAGGAAGTCGTG |
LOC_Os03g40550-F-qrt | CTTTGCTCCCTGCCTTGTAG |
LOC_Os03g40550-R-qrt | CACGTCTCGGAGCTCTTTTC |
Table 1 Primer sequences for qRT-PCR
Primer name | Sequence (5′-3′) |
---|---|
LOC_Os06g11780-F-qrt | TGTTGGTCCCTGAAAACTCC |
LOC_Os06g11780-R-qrt | TCAAGCAAATTCACCCATGA |
LOC_Os06g12360-F-qrt | ATGCAAAAAGGAGAGGCTGA |
LOC_Os06g12360-R-qrt | ATGCCGATCAGGAATCTCAC |
LOC_Os06g39650-F-qrt | GTGCTCTTCAACCAGTGCAA |
LOC_Os06g39650-R-qrt | AGATTGGCACAGCATGTCAG |
LOC_Os06g39716-F-qrt | CAACCTTTTCGTAGGCATCC |
LOC_Os06g39716-R-qrt | TTGAAATTGACTGGGCTTGA |
LOC_Os08g42610-F-qrt | GCTCGCACACTGAAAACAAA |
LOC_Os08g42610-R-qrt | ATGGGATAGGCCCCAAATAG |
LOC_Os02g18500-F-qrt | AGGAGGAGGTGTTGGGAACT |
LOC_Os02g18500-R-qrt | ATGCAGTTGTTGATGGCGTA |
LOC_Os03g21240-F-qrt | TATGCCTTTGCACCAGAGTG |
LOC_Os03g21240-R-qrt | CAGCATTCGACGACTGAGAA |
LOC_Os03g21400-F-qrt | AGGAAAGCGGAGAAGAAAGG |
LOC_Os03g21400-R-qrt | TTAGACACCAGGCAGCTGTG |
LOC_Os03g21780-F-qrt | CTCCCTTCCACTCCTCCTTC |
LOC_Os03g21780-R-qrt | CTTCTCCTCCTCGACACCAG |
LOC_Os03g30950-F-qrt | TCTTCTTCTCCATGGCCTGT |
LOC_Os03g30950-R-qrt | AGCAGGGAAGGAAGTCGTG |
LOC_Os03g40550-F-qrt | CTTTGCTCCCTGCCTTGTAG |
LOC_Os03g40550-R-qrt | CACGTCTCGGAGCTCTTTTC |
Figure 2 SPAD value and phenotype of the male parent HZ and the female parent Nekken2 (A) SPAD value of rice plant at tillering stage; (B) Phenotype of rice plant at tillering stage (bar=10 cm); (C) SPAD value of rice plant at maturing stage; (D) Phenotype of rice plant at maturing stage (bar=10 cm)
Trait | QTL | Chromosome | Physical distance (bp) | Position of support (cM) | Likelihood of odd (LOD) |
---|---|---|---|---|---|
Chlorophyll content at tillering stage | qFLCC6.1 | 6 | 6015262-6720585 | 25.79-28.81 | 3.13 |
qFLCC6.2 | 6 | 22337450-23745958 | 95.75-101.79 | 2.92 | |
qFLCC6.3 | 6 | 24051716-24198880 | 103.10-103.73 | 2.13 | |
qFLCC6.4 | 6 | 25991018-26126806 | 111.42-111.99 | 2.12 | |
qFLCC8.1 | 8 | 26687999-27132649 | 114.40-116.31 | 2.50 | |
qFLCC8.2 | 8 | 27513012-27730624 | 117.94-118.87 | 2.28 | |
qFLCC9.1 | 9 | 20982305-21030827 | 89.95-90.15 | 2.09 | |
Chlorophyll content at maturing stage | qFLCC1.1 | 1 | 2407127-2649258 | 10.32-11.36 | 2.63 |
qFLCC2.1 | 2 | 10729809-10871055 | 45.99-46.60 | 2.01 | |
qFLCC3.1 | 3 | 8989609-9140871 | 38.54-39.18 | 2.00 | |
qFLCC3.2 | 3 | 11602077-12505077 | 49.73-53.61 | 4.77 | |
qFLCC3.3 | 3 | 17425033-18170152 | 74.70-77.90 | 2.38 | |
qFLCC3.4 | 3 | 19142858-20859360 | 82.06-89.42 | 2.29 | |
qFLCC3.5 | 3 | 22349012-22880743 | 95.80-98.08 | 2.59 | |
qFLCC3.6 | 3 | 23094070-24507431 | 98.99-105.06 | 3.25 | |
qFLCC4.1 | 4 | 867957-1087636 | 3.72-4.66 | 2.40 | |
qFLCC4.2 | 4 | 2647701-3012559 | 11.35-12.91 | 2.30 | |
qFLCC4.3 | 4 | 6230638-6599549 | 26.71-28.29 | 2.46 | |
qFLCC7.1 | 7 | 9758981-9899583 | 41.83-42.68 | 2.45 | |
qFLCC11.1 | 11 | 3100542-3229790 | 13.29-13.85 | 2.27 |
Table 2 QTL analysis of chlorophyll content of rice recombinant inbred lines
Trait | QTL | Chromosome | Physical distance (bp) | Position of support (cM) | Likelihood of odd (LOD) |
---|---|---|---|---|---|
Chlorophyll content at tillering stage | qFLCC6.1 | 6 | 6015262-6720585 | 25.79-28.81 | 3.13 |
qFLCC6.2 | 6 | 22337450-23745958 | 95.75-101.79 | 2.92 | |
qFLCC6.3 | 6 | 24051716-24198880 | 103.10-103.73 | 2.13 | |
qFLCC6.4 | 6 | 25991018-26126806 | 111.42-111.99 | 2.12 | |
qFLCC8.1 | 8 | 26687999-27132649 | 114.40-116.31 | 2.50 | |
qFLCC8.2 | 8 | 27513012-27730624 | 117.94-118.87 | 2.28 | |
qFLCC9.1 | 9 | 20982305-21030827 | 89.95-90.15 | 2.09 | |
Chlorophyll content at maturing stage | qFLCC1.1 | 1 | 2407127-2649258 | 10.32-11.36 | 2.63 |
qFLCC2.1 | 2 | 10729809-10871055 | 45.99-46.60 | 2.01 | |
qFLCC3.1 | 3 | 8989609-9140871 | 38.54-39.18 | 2.00 | |
qFLCC3.2 | 3 | 11602077-12505077 | 49.73-53.61 | 4.77 | |
qFLCC3.3 | 3 | 17425033-18170152 | 74.70-77.90 | 2.38 | |
qFLCC3.4 | 3 | 19142858-20859360 | 82.06-89.42 | 2.29 | |
qFLCC3.5 | 3 | 22349012-22880743 | 95.80-98.08 | 2.59 | |
qFLCC3.6 | 3 | 23094070-24507431 | 98.99-105.06 | 3.25 | |
qFLCC4.1 | 4 | 867957-1087636 | 3.72-4.66 | 2.40 | |
qFLCC4.2 | 4 | 2647701-3012559 | 11.35-12.91 | 2.30 | |
qFLCC4.3 | 4 | 6230638-6599549 | 26.71-28.29 | 2.46 | |
qFLCC7.1 | 7 | 9758981-9899583 | 41.83-42.68 | 2.45 | |
qFLCC11.1 | 11 | 3100542-3229790 | 13.29-13.85 | 2.27 |
Chromosome | QTL locus | Gene ID | Functional annotation | Reference |
---|---|---|---|---|
6 | qFLCC6.1 | LOC_Os06g11780 | MYB family transcription factor, putative, expressed | |
6 | qFLCC6.1 | LOC_Os06g12360 | Pentatricopeptide, putative, expressed | |
6 | qFLCC6.2 | LOC_Os06g39650 | Pentatricopeptide repeat protein | Jiang et al., |
6 | qFLCC6.2 | LOC_Os06g39716 | Chloroplast 30S ribosomal protein S18, putative, expressed | |
8 | qFLCC8.1 | LOC_Os08g42610 | Pentatricopeptide, putative, expressed |
Table 3 The function of candidate genes related to chlorophyll content of rice at tillering stage
Chromosome | QTL locus | Gene ID | Functional annotation | Reference |
---|---|---|---|---|
6 | qFLCC6.1 | LOC_Os06g11780 | MYB family transcription factor, putative, expressed | |
6 | qFLCC6.1 | LOC_Os06g12360 | Pentatricopeptide, putative, expressed | |
6 | qFLCC6.2 | LOC_Os06g39650 | Pentatricopeptide repeat protein | Jiang et al., |
6 | qFLCC6.2 | LOC_Os06g39716 | Chloroplast 30S ribosomal protein S18, putative, expressed | |
8 | qFLCC8.1 | LOC_Os08g42610 | Pentatricopeptide, putative, expressed |
Chromosome | QTL locus | Gene ID | Functional annotation | Reference |
---|---|---|---|---|
2 | qFLCC2.1 | LOC_Os02g18500 | Chlorophyllase-2, chloroplast precursor, putative | |
3 | qFLCC3.2 | LOC_Os03g21240 | Transcription factor with a MYB domain; PHOSPHATE RESPONSE 1 | Guo et al., |
3 | qFLCC3.2 | LOC_Os03g21400 | Cytochrome P450 gene; gibberellin 13-oxidase | |
3 | qFLCC3.2 | LOC_Os03g21780 | Pentatricopeptide repeat domain containing protein, putative, expressed | |
3 | qFLCC3.3 | LOC_Os03g30950 | Acyl-desaturase, chloroplast precursor, putative, expressed | |
3 | qFLCC3.5 | LOC_Os03g40550 | pfkB-type carbohydrate kinase family protein |
Table 4 The function of candidate genes related to chlorophyll content of rice at maturing stage
Chromosome | QTL locus | Gene ID | Functional annotation | Reference |
---|---|---|---|---|
2 | qFLCC2.1 | LOC_Os02g18500 | Chlorophyllase-2, chloroplast precursor, putative | |
3 | qFLCC3.2 | LOC_Os03g21240 | Transcription factor with a MYB domain; PHOSPHATE RESPONSE 1 | Guo et al., |
3 | qFLCC3.2 | LOC_Os03g21400 | Cytochrome P450 gene; gibberellin 13-oxidase | |
3 | qFLCC3.2 | LOC_Os03g21780 | Pentatricopeptide repeat domain containing protein, putative, expressed | |
3 | qFLCC3.3 | LOC_Os03g30950 | Acyl-desaturase, chloroplast precursor, putative, expressed | |
3 | qFLCC3.5 | LOC_Os03g40550 | pfkB-type carbohydrate kinase family protein |
Figure 4 Differences in the expression level of the genes related to chlorophyll content in rice (A) Expression of genes related to chlorophyll content at tillering stage; (B) Expression of genes related to chlorophyll content at maturing stage. ** indicate significant differences at 0.01 level.
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