Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7
Abstract Background Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic archi...
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3843-y |
| _version_ | 1811296031836471296 |
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| author | Xue Zhao Weili Teng Yinghui Li Dongyuan Liu Guanglu Cao Dongmei Li Lijuan Qiu Hongkun Zheng Yingpeng Han Wenbin Li |
| author_facet | Xue Zhao Weili Teng Yinghui Li Dongyuan Liu Guanglu Cao Dongmei Li Lijuan Qiu Hongkun Zheng Yingpeng Han Wenbin Li |
| author_sort | Xue Zhao |
| collection | DOAJ |
| description | Abstract Background Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans. Results A total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance. Conclusions A total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance. |
| first_indexed | 2024-04-13T05:42:25Z |
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| id | doaj.art-949e0367faa44a3a8c4014769c465758 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T05:42:25Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-949e0367faa44a3a8c4014769c4657582022-12-22T03:00:03ZengBMCBMC Genomics1471-21642017-06-0118111010.1186/s12864-017-3843-yLoci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7Xue Zhao0Weili Teng1Yinghui Li2Dongyuan Liu3Guanglu Cao4Dongmei Li5Lijuan Qiu6Hongkun Zheng7Yingpeng Han8Wenbin Li9Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityKey Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityInstitute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural SciencesBioinformatics Division, Biomarker Technologies CorporationKey Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityKey Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityInstitute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural SciencesBioinformatics Division, Biomarker Technologies CorporationKey Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityKey Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural UniversityAbstract Background Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans. Results A total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance. Conclusions A total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance.http://link.springer.com/article/10.1186/s12864-017-3843-yGenome-wide association mappingSoybean cyst nematode resistanceHG type 2.5.7Candidate genes |
| spellingShingle | Xue Zhao Weili Teng Yinghui Li Dongyuan Liu Guanglu Cao Dongmei Li Lijuan Qiu Hongkun Zheng Yingpeng Han Wenbin Li Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 BMC Genomics Genome-wide association mapping Soybean cyst nematode resistance HG type 2.5.7 Candidate genes |
| title | Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 |
| title_full | Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 |
| title_fullStr | Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 |
| title_full_unstemmed | Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 |
| title_short | Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7 |
| title_sort | loci and candidate genes conferring resistance to soybean cyst nematode hg type 2 5 7 |
| topic | Genome-wide association mapping Soybean cyst nematode resistance HG type 2.5.7 Candidate genes |
| url | http://link.springer.com/article/10.1186/s12864-017-3843-y |
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