SoySNP618K array: A high‐resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding
ABSTRACT Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for th...
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| Abstract | ABSTRACT
Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole‐genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high‐confidence genes. Identity‐by‐state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome‐wide association mapping in combination with reported quantitative trait loci enabled fine‐mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.
To accelerate breeding progress and support basic research in soybean, the customized SoySNP618K array contains 618,888 SNPs selected from > 2,000 diverse, re‐sequenced soybean genomes. SoySNP618K is a valuable genomic tool to address questions in applied breeding, germplasm management, and basic research. |
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| AbstractList | ABSTRACT
Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole‐genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high‐confidence genes. Identity‐by‐state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome‐wide association mapping in combination with reported quantitative trait loci enabled fine‐mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.
To accelerate breeding progress and support basic research in soybean, the customized SoySNP618K array contains 618,888 SNPs selected from > 2,000 diverse, re‐sequenced soybean genomes. SoySNP618K is a valuable genomic tool to address questions in applied breeding, germplasm management, and basic research. Innovations in genomics have enabled the devel-opment of low-cost, high-resolution, single nu-cleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we devel-oped and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome re-sequencing data containing 2,214 diverse soybean accessions;29.34％of the SNPs mapped to genic regions representing 86.85％ of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank man-agement. The patterns of population stratification and genomic regions enriched through domes-tication were highly consistent with previous find-ings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide asso-ciation mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research. Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research. Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole‐genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high‐confidence genes. Identity‐by‐state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome‐wide association mapping in combination with reported quantitative trait loci enabled fine‐mapping of genes known to influence flowering time, E2 and GmPRR3b , and of a new candidate gene, GmVIP5 . Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research. Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research. |
| Author | Fu, Guang‐Hui Wang, Xiao‐Bo Li, Ying‐Hui Su, Shan‐Shan Qi, Zhao‐Ming Wang, Xing Sun, Ru‐Jian Chen, Qing‐Shan Tian, Yu Reif, Jochen C. Qiu, Li‐Juan Li, Yan‐Fei Ji, Ya‐Liang Li, De‐Lin Xu, Ze‐Jun Liu, Zhang‐Xiong Liu, Ji‐Qiang |
| AuthorAffiliation | The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China%Beijing Compass Biotechnology Co.Ltd,Beijing 102206,China%Department of Breeding Research,Leibniz Institute of Plant Genetics and Crop Plant Research(IPK),Gatersleben 06466,Germany%Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China%School of Agronomy,Anhui Agricultural University,Hefei 230036,China%Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu,Xuzhou 221131,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory |
| AuthorAffiliation_xml | – name: The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China%Beijing Compass Biotechnology Co.Ltd,Beijing 102206,China%Department of Breeding Research,Leibniz Institute of Plant Genetics and Crop Plant Research(IPK),Gatersleben 06466,Germany%Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China%School of Agronomy,Anhui Agricultural University,Hefei 230036,China%Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu,Xuzhou 221131,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China;Department of Plant Genetics and Breeding,China Agricultural University,Beijing 100193,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China;Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China;Hulun Buir Institution of Agricultural Sciences,ZhalantunInner Mongolia 021000,China%Suzhou Academy of Agricultural Sciences,Suzhou 234000,China |
| Author_xml | – sequence: 1 givenname: Yan‐Fei orcidid: 0000-0001-5566-7222 surname: Li fullname: Li, Yan‐Fei organization: Chinese Academy of Agricultural Sciences – sequence: 2 givenname: Ying‐Hui orcidid: 0000-0001-7089-4263 surname: Li fullname: Li, Ying‐Hui organization: Chinese Academy of Agricultural Sciences – sequence: 3 givenname: Shan‐Shan orcidid: 0000-0003-1850-4090 surname: Su fullname: Su, Shan‐Shan organization: Beijing Compass Biotechnology Co. Ltd – sequence: 4 givenname: Jochen C. orcidid: 0000-0002-6742-265X surname: Reif fullname: Reif, Jochen C. organization: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) – sequence: 5 givenname: Zhao‐Ming orcidid: 0000-0002-0657-9127 surname: Qi fullname: Qi, Zhao‐Ming organization: Northeast Agricultural University – sequence: 6 givenname: Xiao‐Bo orcidid: 0000-0002-2810-9249 surname: Wang fullname: Wang, Xiao‐Bo organization: Anhui Agricultural University – sequence: 7 givenname: Xing orcidid: 0000-0002-9214-2385 surname: Wang fullname: Wang, Xing organization: Xuzhou Institute of Agricultural Sciences of Xu‐huai Region of Jiangsu – sequence: 8 givenname: Yu orcidid: 0000-0002-2765-0156 surname: Tian fullname: Tian, Yu organization: Chinese Academy of Agricultural Sciences – sequence: 9 givenname: De‐Lin orcidid: 0000-0002-3689-3790 surname: Li fullname: Li, De‐Lin organization: China Agricultural University – sequence: 10 givenname: Ru‐Jian orcidid: 0000-0003-0112-5713 surname: Sun fullname: Sun, Ru‐Jian organization: Hulun Buir Institution of Agricultural Sciences – sequence: 11 givenname: Zhang‐Xiong orcidid: 0000-0002-3783-2754 surname: Liu fullname: Liu, Zhang‐Xiong organization: Chinese Academy of Agricultural Sciences – sequence: 12 givenname: Ze‐Jun orcidid: 0000-0001-8379-1140 surname: Xu fullname: Xu, Ze‐Jun organization: Xuzhou Institute of Agricultural Sciences of Xu‐huai Region of Jiangsu – sequence: 13 givenname: Guang‐Hui orcidid: 0000-0002-7336-1769 surname: Fu fullname: Fu, Guang‐Hui organization: Suzhou Academy of Agricultural Sciences – sequence: 14 givenname: Ya‐Liang orcidid: 0000-0001-8772-2986 surname: Ji fullname: Ji, Ya‐Liang organization: Beijing Compass Biotechnology Co. Ltd – sequence: 15 givenname: Qing‐Shan orcidid: 0000-0002-3714-9066 surname: Chen fullname: Chen, Qing‐Shan organization: Northeast Agricultural University – sequence: 16 givenname: Ji‐Qiang orcidid: 0000-0002-7419-5379 surname: Liu fullname: Liu, Ji‐Qiang organization: Beijing Compass Biotechnology Co. Ltd – sequence: 17 givenname: Li‐Juan orcidid: 0000-0001-5777-3344 surname: Qiu fullname: Qiu, Li‐Juan email: qiulijuan@caas.cn organization: Chinese Academy of Agricultural Sciences |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34914170$$D View this record in MEDLINE/PubMed |
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| Keywords | soybean genomic selection marker-assisted selection gene discovery functional single nucleotide polymorphism array genome-wide association studies |
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| PublicationPlace | China (Republic : 1949- ) |
| PublicationPlace_xml | – name: China (Republic : 1949- ) – name: Hoboken |
| PublicationTitle | Journal of integrative plant biology |
| PublicationTitleAlternate | J Integr Plant Biol |
| PublicationTitle_FL | Journal of Integrative Plant Biology |
| PublicationYear | 2022 |
| Publisher | Wiley Subscription Services, Inc Department of Plant Genetics and Breeding,China Agricultural University,Beijing 100193,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China%Beijing Compass Biotechnology Co.Ltd,Beijing 102206,China%Department of Breeding Research,Leibniz Institute of Plant Genetics and Crop Plant Research(IPK),Gatersleben 06466,Germany%Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China%School of Agronomy,Anhui Agricultural University,Hefei 230036,China%Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu,Xuzhou 221131,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China Hulun Buir Institution of Agricultural Sciences,ZhalantunInner Mongolia 021000,China%Suzhou Academy of Agricultural Sciences,Suzhou 234000,China |
| Publisher_xml | – name: Wiley Subscription Services, Inc – name: Hulun Buir Institution of Agricultural Sciences,ZhalantunInner Mongolia 021000,China%Suzhou Academy of Agricultural Sciences,Suzhou 234000,China – name: The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China%Beijing Compass Biotechnology Co.Ltd,Beijing 102206,China%Department of Breeding Research,Leibniz Institute of Plant Genetics and Crop Plant Research(IPK),Gatersleben 06466,Germany%Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China%School of Agronomy,Anhui Agricultural University,Hefei 230036,China%Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu,Xuzhou 221131,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China – name: Department of Plant Genetics and Breeding,China Agricultural University,Beijing 100193,China%The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA),Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China – name: Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry),Northeast Agricultural University,Harbin 150030,China |
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| Snippet | ABSTRACT
Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that... Innovations in genomics have enabled the development of low‐cost, high‐resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate... Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate... Innovations in genomics have enabled the devel-opment of low-cost, high-resolution, single nu-cleotide polymorphism (SNP) genotyping arrays that accelerate... |
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| SubjectTerms | Arrays Crop science Crops Domestication Flowering functional single nucleotide polymorphism array Gene banks gene discovery Gene mapping Gene polymorphism Genes Genetics Genome, Plant - genetics Genome-Wide Association Study Genomes genome‐wide association studies genomic selection Genomics Genotype Genotyping Germplasm Glycine max - genetics Inbreeding Mapping marker‐assisted selection Nucleotides Plant Breeding Polymorphism Polymorphism, Single Nucleotide - genetics prediction Quantitative trait loci quantitative traits Single-nucleotide polymorphism soybean Soybeans |
| Title | SoySNP618K array: A high‐resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding |
| URI | https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fjipb.13202 https://www.ncbi.nlm.nih.gov/pubmed/34914170 https://www.proquest.com/docview/2639222281 https://www.proquest.com/docview/2610905798 https://www.proquest.com/docview/2648857284 https://d.wanfangdata.com.cn/periodical/zwxb202203003 |
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