QTL Mapping and Candidate Gene Analysis for Starch-Related Traits in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn)
Abstract
:1. Introduction
2. Results
2.1. Variation Analysis for Starch-Related Traits
2.2. QTL Mapping of Starch-Related Traits
2.3. QTL Cluster Analysis of Starch-Related Traits
2.4. Identification of Candidate Genes within the Major QTL Cluster qClu-4-1
2.5. Analysis of the SNP/InDel Variations of Candidate Genes for qClu-4-1
2.6. Starch Content and Expression of Candidate Genes in Two Parents
3. Discussion
4. Materials and Methods
4.1. Materials Planting and Sampling
4.2. Measurement and Analysis of the Content of Starch-Related Traits
4.3. QTL Mapping
4.4. Candidate Gene Prediction and Analyses
4.5. Verification of the SNP/InDel Variations of Candidate Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Traits | Environments | Parents | XJ-RILs Population | |||||
---|---|---|---|---|---|---|---|---|
Jinqiaomai2 | Xiaomiqiao | Mean ± SD | Range | Kurtosis | Skewness | CV (%) | ||
Amylose (%) | 2021S | 20.90 ± 0.24 b | 22.28 ± 0.91 a | 19.26 ± 1.98 | 11.19~23.45 | 0.375 | −0.528 | 10% |
2021A | 17.80 ± 0.33 b | 19.44 ± 0.61 a | 19.76 ± 1.20 | 15.70~22.50 | 0.449 | 0.031 | 6% | |
2022S | 24.97 ± 0.64 a | 26.19 ± 0.61 b | 22.39 ± 2.15 | 17.20~28.02 | −0.238 | 0.004 | 10% | |
Amylopectin (%) | 2021S | 47.03 ± 1.22 b | 50.95 ± 1.87 a | 49.83 ± 5.20 | 36.80~59.68 | −0.442 | −0.310 | 10% |
2021A | 41.65 ± 1.69 a | 43.61 ± 1.24 b | 32.09 ± 2.86 | 23.66~39.93 | 0.634 | 0.632 | 9% | |
2022S | 42.98 ± 1.62 a | 43.57 ± 1.08 a | 40.46 ± 4.32 | 30.26~51.61 | 0.013 | 0.208 | 11% | |
Total Starch (%) | 2021S | 67.92 ± 1.17 b | 73.24 ± 1.85 a | 69.08 ± 4.94 | 57.73~78.72 | −0.492 | −0.178 | 7% |
2021A | 59.45 ± 1.50 a | 63.05 ± 1.62 b | 51.84 ± 2.54 | 45.61~61.52 | 2.419 | 0.970 | 5% | |
2022S | 67.96 ± 1.49 a | 69.76 ± 1.38 b | 62.85 ± 4.46 | 53.07~74.15 | −0.201 | 0.476 | 7% |
Trait | Environment | Total Starch | Amylopectin |
---|---|---|---|
Amylose | 2021S | 0.065 | −0.315 ** |
2021A | −0.016 | −0.425 ** | |
2022S | 0.307 ** | −0.180 * | |
Amylopectin | 2021S | 0.927 ** | |
2021A | 0.912 ** | ||
2022S | 0.881 ** |
NO. | Trait | QTL | Environment | Chromosome | Position (cM) | LOD | R2 (%) | Additive Effect | Confidence Interval (cM) | Flanking Markers | Physical Interval (Mbp) |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | Amylose | qAL3-1 | 2021S | Ft3 | 37.51 | 2.68 | 5.2 | −0.51 | 35.2~39.2 | Block5303~Block5318 | 11.8~12.55 |
2 | Amylose | qAL4-1 | 2021A | Ft4 | 122.31 | 3.31 | 6.46 | 0.55 | 120.9~129.2 | Block8744~Block8836 | 39.85~42.74 |
BLUP | Ft4 | 122.31 | 5.82 | 9.52 | 0.002 | ||||||
3 | Amylose | qAL4-2 | 2021S | Ft4 | 130.41 | 4.8 | 10.12 | 0.65 | 128.4~136.5 | Block8830~Block8844 | 42.10~43.34 |
2022S | Ft4 | 131.31 | 2.58 | 5.08 | 0.49 | ||||||
BLUP | Ft4 | 131.31 | 4.42 | 7.34 | 0.002 | ||||||
4 | Amylose | qAL4-3 | 2021A | Ft4 | 153.21 | 2.7 | 6.22 | −0.34 | 152.8~155.8 | Block9021~Block9046 | 46.58~48.92 |
5 | Amylose | qAL5-1 | 2022S | Ft5 | 43.31 | 4.74 | 11.04 | −0.49 | 42.9~44.5 | Block9728~Block9753 | 8.39~9.06 |
6 | Amylopectin | qALP1-1 | BLUP | Ft1 | 36.61 | 5.31 | 8.09 | −0.17 | 35.7~38.9 | Block320~Block337 | 6.47~6.10 |
7 | Amylopectin | qALP1-2 | 2022S | Ft1 | 40.51 | 3.54 | 6.33 | −1.13 | 38.9~46.3 | Block334~Block428 | 6.45~9.15 |
8 | Amylopectin | qALP2-1 | 2021A | Ft2 | 48.21 | 4.09 | 9.04 | 2.15 | 46.9~54.2 | Block2872~Block2992 | 15.34~21.46 |
9 | Amylopectin | qALP2-2 | 2022S | Ft2 | 55.31 | 3.47 | 7.73 | 1.96 | 54.2~65.6 | Block3073~Block3468 | 12.57~31.04 |
10 | Amylopectin | qALP3-1 | 2021S | Ft3 | 62.61 | 3.37 | 7.22 | −0.79 | 54.2~65.3 | Block5579~Block5697 | 16.07~26.81 |
11 | Amylopectin | qALP4-1 | 2021S | Ft4 | 22.41 | 2.97 | 5.52 | −1.24 | 11.7~23.2 | Block7563~Block7612 | 3.01~5.65 |
12 | Amylopectin | qALP4-2 | 2021A | Ft4 | 116.61 | 3.29 | 6.76 | −1.77 | 112.4~117.7 | Block8396~Block8758 | 34.64~40.42 |
13 | Amylopectin | qALP4-3 | 2021S | Ft4 | 122.11 | 4.72 | 8.59 | −1.28 | 120.3~126.9 | Block8752~Block8836 | 39.85~42.65 |
2022S | Ft4 | 123.21 | 7.37 | 14.41 | −2.28 | ||||||
BLUP | Ft4 | 123.21 | 6.44 | 10.16 | −0.19 | ||||||
14 | Amylopectin | qALP7-1 | 2021A | Ft7 | 58.11 | 2.62 | 5.53 | 0.68 | 47.8~61.4 | Block13692~Block13766 | 12.1~15.32 |
15 | Amylopectin | qALP7-2 | 2021S | Ft7 | 120.31 | 3.61 | 6.8 | 1.37 | 116.7~121.3 | Block14329~Block14351 | 37.07~38.89 |
16 | Amylopectin | qALP7-3 | BLUP | Ft7 | 161.01 | 2.74 | 4.07 | 0.12 | 152.7~164.8 | Block14552~Block14603 | 44.53~46.04 |
17 | Total Starch | qTSC1-1 | 2022S | Ft1 | 39.81 | 2.91 | 5.76 | −1.11 | 38.9~44.6 | Block334~Block412 | 6.45~8.72 |
18 | Total Starch | qTSC1-2 | BLUP | Ft1 | 152.71 | 4.33 | 7.45 | 0.04 | 150.4~154.8 | Block709~Block714 | 44.85~45.09 |
19 | Total Starch | qTSC4-1 | 2021S | Ft4 | 194.81 | 3.01 | 5.98 | −1.12 | 193.1~195 | Block9392~Block9381 | 55.13~56.65 |
20 | Total Starch | qTSC7-1 | BLUP | Ft7 | 119.01 | 2.54 | 4.41 | 0.03 | 113.3~124.9 | Block14276~Block14405 | 35.85~40.63 |
2021A | Ft7 | 120.81 | 3.9 | 7.99 | 1.42 |
NO. | Cluster Name | Chromosome | Confidence Interval (cM) | Flanking Markers | Physical Interval (Mbp) | QTL Number | QTL |
---|---|---|---|---|---|---|---|
1 | qClu-1-1 | Ft1 | 35.7~46.3 | Block320~Block428 | 6.45~9.15 | 3 | qALP1-1, qTSC1-1, qALP1-2 |
2 | qClu-4-1 | Ft4 | 120.3~136.5 | Block8744~Block8844 | 39.85~43.34 | 3 | qALP4-3*, qAL4-1#, qAL4-2* |
3 | qClu-7-1 | Ft7 | 113.3~124.9 | Block14276~Block14405 | 35.85~40.63 | 2 | qTSC7-1#, qALP7-2 |
NO. | Name | Chr | Orientation | Times of Mutation | Mutation Type | Expression Cluster | Mutation Region | Rice Annotation |
---|---|---|---|---|---|---|---|---|
1 | FtPinG0004897000.01 | Ft4 | − | 14 | SNP/Indel | C5 | 5’ UTR/3’ UTR | LOC_Os12g05430|ribosomal protein L24, putative, expressed |
2 | FtPinG0004897100.01 | Ft4 | + | 6 | SNP/Indel | C6 | 5’ UTR/3’ UTR | LOC_Os07g39820|SHR, putative, expressed |
3 | FtPinG0004899000.01 | Ft4 | − | 1 | SNP | C6 | 5’ UTR | LOC_Os03g31690|GCN5-related N-acetyltransferase, putative, expressed |
4 | FtPinG0002636200.01 | Ft4 | + | 1 | SNP | C5 | 3’ UTR | LOC_Os02g49140|glycosyltransferase, putative, expressed |
5 | FtPinG0002635900.01 | Ft4 | − | 1 | Indel | C5 | 3’ UTR | LOC_Os03g51990|ACT domain-containing protein, expressed |
6 | FtPinG0008593800.01 | Ft4 | + | 2 | SNP | C5 | exon/3’ UTR | LOC_Os07g41570|expressed protein |
7 | FtPinG0008592400.01 | Ft4 | + | 6 | SNP/Indel | C5 | 5’ UTR/3’ UTR | LOC_Os03g07570|aminotransferase, putative, expressed |
8 | FtPinG0007101700.01 | Ft4 | + | 1 | Indel | C6 | 3’ UTR | LOC_Os08g33210|expressed protein |
9 | FtPinG0005926000.01 | Ft4 | + | 4 | SNP/Indel | C4 | 3’ UTR | LOC_Os03g60750|ribosomal RNA large subunit methyltransferase J, putative, expressed |
10 | FtPinG0005925700.01 | Ft4 | − | 2 | Indel | C5 | 3’ UTR | LOC_Os01g74146|WD repeat-containing protein, putative, expressed |
11 | FtPinG0009329200.01 | Ft4 | + | 1 | SNP | C5 | intron | LOC_Os03g17740|transporter, putative, expressed |
12 | FtPinG0006225500.01 | Ft4 | − | 1 | SNP | C6 | 3’ UTR | LOC_Os03g60720|expansin precursor, putative, expressed |
13 | FtPinG0008469200.01 | Ft4 | + | 1 | SNP | C5 | 5’ UTR | LOC_Os03g52320|GRF-interacting factor 1, putative, expressed |
14 | FtPinG0008468900.01 | Ft4 | − | 1 | SNP | C5 | intron | LOC_Os03g52320|GRF-interacting factor 1, putative, expressed |
15 | FtPinG0007371600.01 | Ft4 | + | 1 | SNP | C5 | 3’ UTR | LOC_Os03g49510|phosphatidylinositol-4-phosphate 5-kinase, putative, expressed |
16 | FtPinG0007371400.01 | Ft4 | + | 13 | SNP | C6 | 5’ UTR/3’ UTR | LOC_Os09g28110|hydroxyproline-rich glycoprotein family protein, putative, expressed |
17 | FtPinG0006002900.01 | Ft4 | + | 1 | SNP | C4 | 5’ UTR | LOC_Os12g03260|MATE efflux family protein, putative, expressed |
18 | FtPinG0005124100.01 | Ft4 | − | 1 | SNP | C5 | 5’ UTR | LOC_Os03g28940|ZIM domain-containing protein, putative, expressed |
19 | FtPinG0005109900.01 | Ft4 | − | 1 | SNP | C5 | 3’ UTR | LOC_Os02g51070|starch synthase, putative, expressed |
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Huang, J.; Liu, F.; Ren, R.; Deng, J.; Zhu, L.; Li, H.; Cai, F.; Meng, Z.; Chen, Q.; Shi, T. QTL Mapping and Candidate Gene Analysis for Starch-Related Traits in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn). Int. J. Mol. Sci. 2024, 25, 9243. https://doi.org/10.3390/ijms25179243
Huang J, Liu F, Ren R, Deng J, Zhu L, Li H, Cai F, Meng Z, Chen Q, Shi T. QTL Mapping and Candidate Gene Analysis for Starch-Related Traits in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn). International Journal of Molecular Sciences. 2024; 25(17):9243. https://doi.org/10.3390/ijms25179243
Chicago/Turabian StyleHuang, Juan, Fei Liu, Rongrong Ren, Jiao Deng, Liwei Zhu, Hongyou Li, Fang Cai, Ziye Meng, Qingfu Chen, and Taoxiong Shi. 2024. "QTL Mapping and Candidate Gene Analysis for Starch-Related Traits in Tartary Buckwheat (Fagopyrum tataricum (L.) Gaertn)" International Journal of Molecular Sciences 25, no. 17: 9243. https://doi.org/10.3390/ijms25179243