Genome-Wide Association Study of Six Forage Traits in Ramie (Boehmeria nivea L. Gaud)
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Trait Analysis
2.2. GWAS Analysis for Traits RELATED to Forage
2.3. Identification of Candidate Genes
3. Discussion
3.1. Analyzing the Characteristics of Ramie and Related Indexes of Feeding Characters
3.2. Application of GWAS in Forage Ramie
3.3. Putative Candidate Genes Associated with Forage Quality
4. Materials and Methods
4.1. Plant Materials
4.2. Phenotype Evaluation
4.3. Statistical Analyses
4.4. Population Structure and LD Analysis
4.5. GWAS Analysis
4.6. Prediction of Candidate Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Traits | Years | Mean | STDEV | Skewness | Kurtosis | CV |
---|---|---|---|---|---|---|
IPH | 2019 | 80.41041 | 14.45221 | 0.08226 | −0.09009 | 0.1797 |
2020 | 66.93907 | 16.22265 | 0.0334 | −0.27588 | 0.2426 | |
FWP | 2019 | 58.87703 | 18.55376 | 0.167087 | −0.44334 | 0.3151 |
2020 | 36.75665 | 15.74601 | 0.577069 | 1.410746 | 0.4284 | |
DWP | 2019 | 8.035631 | 2.276232 | 0.011917 | −0.10541 | 0.2833 |
2020 | 5.683078 | 2.034604 | 0.670854 | 0.957744 | 0.3580 | |
LDWP | 2019 | 4.494491 | 1.159356 | −0.70925 | 1.836823 | 0.2580 |
2020 | 3.321628 | 1.009748 | 0.453133 | 0.563682 | 0.3040 | |
SDWP | 2019 | 3.510219 | 1.171264 | 0.238948 | −0.33708 | 0.3337 |
2020 | 2.36334 | 1.121519 | 1.085063 | 2.395851 | 0.4745 | |
FWPC | 2019 | 0.69955 | 0.398916 | 2.058627 | 6.861975 | 0.5702 |
2020 | 0.577711 | 0.263481 | 1.026716 | 2.199923 | 0.4561 |
2019 | IPH | FWP | DWP | LDWP | SDWP | FWPC |
---|---|---|---|---|---|---|
IPH | ||||||
FWP | 0.794 ** | |||||
DWP | 0.796 ** | 0.840 * | ||||
LDWP | 0.633 ** | 0.748 ** | 0.933 ** | |||
SDWP | 0.877 ** | 0.891 ** | 0.926 ** | 0.757 ** | ||
FWPC | 0.701 ** | 0.589 ** | 0.557 ** | 0.416 ** | 0.645 ** |
2020 | IPH | FWP | DWP | LDWP | SDWP | FWPC |
---|---|---|---|---|---|---|
IPH | ||||||
FWP | 0.825 ** | |||||
DWP | 0.850 ** | 0.915 ** | ||||
LDWP | 0.720 ** | 0.837 ** | 0.949 ** | |||
SDWP | 0.894 ** | 0.908 ** | 0.959 ** | 0.820 ** | ||
FWPC | 0.704 ** | 0.826 ** | 0.795 ** | 0.711 ** | 0.803 ** |
Chr. | SNPs | Intergenic | CDS | Intron | NS SNPs | S SNPs |
---|---|---|---|---|---|---|
Chr1 | 532,773 | 219,654 | 44,626 | 97,484 | 20,658 | 23,968 |
Chr2 | 481,607 | 191,354 | 43,443 | 93,941 | 20,173 | 23,270 |
Chr3 | 462,186 | 186,239 | 42,467 | 96,791 | 20,737 | 21,730 |
Chr4 | 493,655 | 203,277 | 43,274 | 94,759 | 20,664 | 22,610 |
Chr5 | 456,788 | 185,700 | 43,097 | 87,148 | 20,447 | 22,650 |
Chr6 | 447,197 | 150,528 | 44,799 | 88,657 | 20,438 | 24,361 |
Chr7 | 454,335 | 227,789 | 33,706 | 68,160 | 15,682 | 18,024 |
Chr8 | 391,132 | 178,009 | 31,695 | 65,775 | 14,691 | 17,004 |
Chr9 | 440,598 | 209,133 | 32,741 | 78,206 | 15,541 | 17,200 |
Chr10 | 348,653 | 130,303 | 36,950 | 68,202 | 17,607 | 19,343 |
Chr11 | 418,597 | 196,178 | 32,787 | 77,175 | 15,233 | 17,554 |
Chr12 | 337,679 | 141,539 | 29,983 | 72,029 | 14,708 | 15,275 |
Chr13 | 359,036 | 152,503 | 35,334 | 73,229 | 16,874 | 18,460 |
Chr14 | 288,534 | 133,000 | 23,759 | 48,307 | 10,490 | 13,269 |
Scaffold | 39,056 | 10,782 | 4196 | 6718 | 2008 | 2188 |
Total | 5,951,826 | 2,515,988 | 522,857 | 1,116,581 | 245,951 | 276,906 |
Chromosome Number | Gene | Associated Signal | Signal Position in Gene | Annotation | ||
---|---|---|---|---|---|---|
Trait | SNP Position | −log 10 p Values | ||||
Chr13 | Bnt13G018582 | FWPC | 7866103 | 6.3 | Intergenic region | TCP domain-containing protein |
Chr13 | Bnt13G018583 | FWPC | 7866103 | 6.3 | Intergenic region | TCP domain-containing protein |
Chr14 | Bnt14G019331 | LDWP | 1803576 | 6.0 | Upstream gene variant | Transposase-associated domain |
Chr04 | Bnt04G005762 | DWP | 9087683 | 7.0 | Intergenic region | Cation transport |
FWP | 9087683 | 6.1 | Intergenic region | |||
IPH | 9100978 | 6.5 | Downstream gene variant | |||
Chr04 | Bnt04G005636 | FWP | 7066661 | 6.2 | Intron variant | CSC1-like protein |
SDWP | 7110697 | 6.5 | Intergenic region | |||
Chr04 | Bnt04G005637 | FWP | 7110697 | 6.1 | Intergenic region | Wall-associated receptor kinase-like 9 |
SDWP | 7110697 | 6.5 | Intergenic region | |||
Chr05 | Bnt05G007759 | FWP | 11395767 | 6.3 | Upstream gene variant | MOSC, N-terminal beta barrel |
Chr04 | Bnt04G005779 | LDWP | 9261790 | 7.8 | Downstream gene variant | F-box domain-containing protein |
LDWP | 9264066 | 6.9 | Intergenic region | |||
DWP | 9264066 | 7.0 | Intergenic region | |||
DWP | 9261790 | 6.6 | Downstream gene variant | |||
Chr04 | Bnt04G005780 | LDWP | 9264066 | 6.9 | Intergenic region | F-box protein |
DWP | 9264066 | 7.0 | Intergenic region |
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Bai, X.; Wang, X.; Wang, Y.; Wei, Y.; Fu, Y.; Rao, J.; Ma, Y.; Zeng, Z.; Li, F.; Wang, M.; et al. Genome-Wide Association Study of Six Forage Traits in Ramie (Boehmeria nivea L. Gaud). Plants 2022, 11, 1443. https://doi.org/10.3390/plants11111443
Bai X, Wang X, Wang Y, Wei Y, Fu Y, Rao J, Ma Y, Zeng Z, Li F, Wang M, et al. Genome-Wide Association Study of Six Forage Traits in Ramie (Boehmeria nivea L. Gaud). Plants. 2022; 11(11):1443. https://doi.org/10.3390/plants11111443
Chicago/Turabian StyleBai, Xuehua, Xin Wang, Yanzhou Wang, Yiping Wei, Yafen Fu, Jing Rao, Yonghong Ma, Zheng Zeng, Fu Li, Mansheng Wang, and et al. 2022. "Genome-Wide Association Study of Six Forage Traits in Ramie (Boehmeria nivea L. Gaud)" Plants 11, no. 11: 1443. https://doi.org/10.3390/plants11111443