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