Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean
Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by compar...
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2019-10-01
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doaj-a2c6ed9776834b29aaa116be7191ee962021-04-02T15:38:05ZengKeAi Communications Co., Ltd.Crop Journal2214-51412019-10-0175677684Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybeanYu Tian0Bo Liu1Xuehui Shi2Jochen C. Reif3Rongxia Guan4Ying-hui Li5Li-juan Qiu6The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, ChinaThe National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, ChinaThe National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, ChinaDepartment of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, GermanyThe National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, ChinaThe National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China; Corresponding authors.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China; Corresponding authors.Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P < 0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18 (rhg1) and GmSHMT (Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18 (12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMT was very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3. Keywords: SCN, α-SNAP, Allelic combination, Marker-assisted selection (MAS), Haplotype analysishttp://www.sciencedirect.com/science/article/pii/S2214514119300674 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yu Tian Bo Liu Xuehui Shi Jochen C. Reif Rongxia Guan Ying-hui Li Li-juan Qiu |
spellingShingle |
Yu Tian Bo Liu Xuehui Shi Jochen C. Reif Rongxia Guan Ying-hui Li Li-juan Qiu Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean Crop Journal |
author_facet |
Yu Tian Bo Liu Xuehui Shi Jochen C. Reif Rongxia Guan Ying-hui Li Li-juan Qiu |
author_sort |
Yu Tian |
title |
Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean |
title_short |
Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean |
title_full |
Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean |
title_fullStr |
Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean |
title_full_unstemmed |
Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean |
title_sort |
deep genotyping of the gene gmsnap facilitates pyramiding resistance to cyst nematode in soybean |
publisher |
KeAi Communications Co., Ltd. |
series |
Crop Journal |
issn |
2214-5141 |
publishDate |
2019-10-01 |
description |
Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P < 0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18 (rhg1) and GmSHMT (Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18 (12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMT was very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3. Keywords: SCN, α-SNAP, Allelic combination, Marker-assisted selection (MAS), Haplotype analysis |
url |
http://www.sciencedirect.com/science/article/pii/S2214514119300674 |
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