Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank
Abstract
1. Introduction
2. Results
2.1. Distribution and Classification of SNPs in the Germplasm Collection
2.2. Genetic Diversity and Population Structure Analysis
2.3. Linkage Disequilibrium (LD) Analysis
2.4. Genome-Wide Association Study (GWAS) of the Hulled/Naked Trait
2.5. Associated-SNP Validation by KASP Assay across the Whole Barley Collection
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Genotyping-by-Sequencing (GBS) and SNP Calling
4.3. Genetic Diversity and Population Structure Analysis
4.4. Linkage Disequilibrium (LD) Analysis and Genome-Wide Association Studies (GWAS)
4.5. Marker Development and Genotyping
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Observed | KASP | GBS | |
---|---|---|---|
Hulled barley | 138 | 143 | 143 |
Naked barley | 45 | 39 | 40 |
0.9812 | 0.7367 |
Code | Name | Row Type | Adherence of Hulls | Code | Name | Row Type | Adherence of Hulls | Code | Name | Row Type | Adherence of Hulls |
---|---|---|---|---|---|---|---|---|---|---|---|
B113 | Laotuoxu3 | six | hulled | B137 | Humaishisihao | two | hulled | B161 | Xiaojiangdamai2 | two | hulled |
B114 | Chiadamai | six | hulled | B138 | Humaishiliuhao | two | hulled | B162 | Humai4Hai2 | two | hulled |
B115 | Mimai114 | two | naked | B139 | 97-117 | two | hulled | B163 | 77-130 | two | hulled |
B116 | Ciguqing | six | naked | B140 | Fengaierleng1 | two | hulled | B164 | 76-25 | two | hulled |
B117 | Heiliuzhu | six | naked | B141 | 81-18 | two | hulled | B165 | Jingdayihao2 | two | hulled |
B118 | ailiuzhuyuanmai | six | naked | B142 | Aizaosan | two | hulled | B166 | aomaierhao | two | hulled |
B119 | 757 | six | naked | B143 | Pu4 | two | hulled | B167 | Humaiahao2 | two | hulled |
B120 | Aiganqi | six | naked | B144 | Zhepiyihao | two | hulled | B168 | Humaishihao2 | two | hulled |
B121 | Jiadinghongjinliuzhutou2 | six | naked | B145 | Fuyinyihao | two | hulled | B170 | Hu84-165 | two | hulled |
B122 | Lizinyihao | six | naked | B146 | Kunlunliuhao | six | naked | B171 | Hu84-167 | two | hulled |
B123 | Xiaojiangdamai1 | six | hulled | B147 | Mengkeer | six | hulled | B172 | Hu905002 | two | hulled |
B124 | Jingdayihao1 | two | hulled | B148 | 78-132 | two | hulled | B173 | Hu905003 | two | hulled |
B125 | Shenmaiyihao1 | two | hulled | B149 | Yan75-21 | two | hulled | B174 | Hu905004 | two | hulled |
B126 | aoshanerleng2 | two | hulled | B150 | Zhou6121 | two | hulled | B175 | Hu905005 | two | hulled |
B127 | Qingpuerlengdamai | two | hulled | B151 | Xizhixingyeshengdamai | six | naked | B176 | Hu905006 | two | hulled |
B128 | Zhenongguangmangerleng | two | hulled | B152 | 85-2fu | two | hulled | B177 | Hu905007 | two | hulled |
B129 | Zaoshusanhao | two | hulled | B153 | S-112 | two | hulled | B180 | Hu916259 | two | hulled |
B130 | Aiaiyang | two | hulled | B154 | Guangdonghuanjingua | two | hulled | B181 | Hu916269 | two | hulled |
B131 | Humaiyihao2 | two | hulled | B155 | Ertiaodamai | two | hulled | B182 | Rudongzaosan3xuanyanxuan3 | two | hulled |
B132 | Humaisihao1 | two | hulled | B156 | Zaoshuwuhao | two | hulled | B183 | Shenmaiyihao2 | two | hulled |
B133 | Humailiuhao | two | hulled | B157 | Fuxuan48 | two | hulled | hua30 | Hua30 | two | hulled |
B134 | Humaiahao1 | two | hulled | B158 | N.grinuelam | two | naked | hua22 | Hua22 | two | hulled |
B135 | Humaishihao1 | two | hulled | B159 | Eryuanzhufushewendingcailiaoerhao | six | hulled | hua11 | Hua11 | two | hulled |
B136 | Humaishierhao | two | hulled | B160 | Fengaierleng2 | two | hulled |
Primer Name | Primer Sequence | |
---|---|---|
For PCR | PCR-F | ACGCTGACGAGATGAA |
PCR-R | TCTGACTTTGGACTTGC | |
For KASP | KASP-F | GAAGGTGACCAAGTTCATGCTTCTGGAGCTAAGTAACCTGGCG |
KASP-V | GAAGGTCGGAGTCAACGGATTACTCTGGAGCTAAGTAACCTGGCA | |
KASP-R | CACTGCTAAGGTATCTGACTTTGGACT |
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Chen, Z.; Guo, Z.; Li, L.; Halford, N.G.; Guo, G.; Zhang, S.; Zong, Y.; Liu, S.; Liu, C.; Zhou, L. Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank. Int. J. Mol. Sci. 2024, 25, 5217. https://doi.org/10.3390/ijms25105217
Chen Z, Guo Z, Li L, Halford NG, Guo G, Zhang S, Zong Y, Liu S, Liu C, Zhou L. Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank. International Journal of Molecular Sciences. 2024; 25(10):5217. https://doi.org/10.3390/ijms25105217
Chicago/Turabian StyleChen, Zhiwei, Zhenzhu Guo, Luli Li, Nigel G. Halford, Guimei Guo, Shuwei Zhang, Yingjie Zong, Shiseng Liu, Chenghong Liu, and Longhua Zhou. 2024. "Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank" International Journal of Molecular Sciences 25, no. 10: 5217. https://doi.org/10.3390/ijms25105217
APA StyleChen, Z., Guo, Z., Li, L., Halford, N. G., Guo, G., Zhang, S., Zong, Y., Liu, S., Liu, C., & Zhou, L. (2024). Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank. International Journal of Molecular Sciences, 25(10), 5217. https://doi.org/10.3390/ijms25105217