Abstract
BACKGROUND: Soybean (Glycine max (L.) Merr.), a global agricultural staple, faces significant threats from Soybean Mosaic Virus (SMV). Effective resistance to SMV, particularly the SC3 strain, is crucial for sustainable soybean production. This study aims to explore the genetic variability and identify loci associated with SMV SC3 resistance in soybean. RESULTS: We assessed the resistance of 290 soybean accessions to the SMV SC3 strain, revealing considerable genetic variability: 19.9% exhibited high resistance, while 11.7% were highly susceptible. This diversity is a valuable asset for breeding programs targeting disease management. Deep sequencing and genome-wide association studies (GWAS) of the accession population structures identified five distinct clusters and 14 significant loci associated with resistance across chromosomes 2, 4, 7, 9, 13, 14, 17, 19, and 20. Notably, a known resistance locus on chromosome 13 and a novel locus on chromosome 4, Loci_04_7299944, were identified. The latter is linked to Glyma.04G086700, a gene encoding a leucine-rich repeat protein kinase integral to pathogen recognition and resistance, showing three distinct haplotypes correlated with varying resistance levels, governed by specific allelic variations at certain SNP sites. Our genomic prediction models demonstrated that expanding SNP feature sets generally improved prediction accuracy, especially with the Top 100 set, although adding more than 8000 SNPs introduced diminishing returns and potential noise. Fourteen effective SNP loci were identified as pivotal for accurately predicting the genetic architecture of complex traits related to SMV resistance. CONCLUSIONS: Our findings underscore the importance of selecting SNPs closely linked to phenotypic traits to refine prediction accuracy in genomic selection models. The identified loci, particularly Glyma.04G086700, provide a foundation for further exploration of genetic mechanisms underlying SMV SC3 resistance. These insights can guide future enhancements in soybean breeding strategies to combat SMV effectively.
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Claims 12
Claim · model-written summary
Among soybean accessions, 19.9% were highly resistant to SMV SC3.
- Taxon
- soybean
Glycine maxe1 - Material
- soybean accessionse1
- Interactor
- SMVe1pathogen
- Outcome
- high resistancee0
- Value
- 19.9%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“19.9% exhibited high resistance”
e1“290 soybean accessions to the SMV SC3 strain”
Claim · model-written summary
Among soybean accessions, 11.7% were highly susceptible to SMV SC3.
- Taxon
- soybeanGlycine maxe1
- Material
- soybean accessionse1
- Interactor
- SMVe1pathogen
- Outcome
- highly susceptiblee0
- Value
- 11.7%e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“11.7% were highly susceptible”
e1“290 soybean accessions to the SMV SC3 strain”
Claim · model-written summary
Population analysis identified five distinct soybean accession clusters.
- Taxon
- soybeanGlycine maxe1
- Material
- soybean accessionse1
- Outcome
- distinct clusterse0
- Value
- fivee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“accession population structures identified five distinct clusters”
e1“soybean accessions”
Claim · model-written summary
GWAS identified 14 significant loci associated with soybean SMV resistance across nine chromosomes.
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“14 significant loci associated with resistance across chromosomes 2, 4, 7, 9, 13, 14, 17, 19, and 20”
e1“SMV SC3 resistance in soybean”
Claim · model-written summary
A known resistance locus was identified on soybean chromosome 13.
- Taxon
- soybeanGlycine maxe1
- Interactor
- SMVe1pathogen
- Gene
- resistance locuse0
- Outcome
- a known resistance locus on chromosome 13e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a known resistance locus on chromosome 13”
e1“SMV SC3 resistance in soybean”
Claim · model-written summary
A novel soybean resistance locus, Loci_04_7299944, was identified on chromosome 4.
- Taxon
- soybeanGlycine maxe1
- Interactor
- SMVe1pathogen
- Gene
- Loci_04_7299944e0
- Outcome
- a novel locus on chromosome 4e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a novel locus on chromosome 4, Loci_04_7299944”
e1“SMV SC3 resistance in soybean”
Claim · model-written summary
Loci_04_7299944 was linked to Glyma.04G086700, which encodes a leucine-rich repeat protein kinase.
- Taxon
- soybeanGlycine maxe2
- Gene
- Glyma.04G086700e0
- Outcome
- linked to Glyma.04G086700e0
- Comparator
- Loci_04_7299944e1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The latter is linked to Glyma.04G086700, a gene encoding a leucine-rich repeat protein kinase”
e1“a novel locus on chromosome 4, Loci_04_7299944”
e2“resistance in soybean”
Claim · model-written summary
Three Glyma.04G086700 haplotypes correlated with differing soybean resistance levels.
- Taxon
- soybeanGlycine maxe2
- Interactor
- SMVe2pathogen
- Gene
- Glyma.04G086700e1
- Outcome
- varying resistance levelse0
- Value
- three distinct haplotypese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“showing three distinct haplotypes correlated with varying resistance levels, governed by specific allelic variations at certain SNP sites”
e1“linked to Glyma.04G086700”
e2“SMV SC3 resistance in soybean”
Claim · model-written summary
Larger SNP feature sets generally improved genomic prediction accuracy, particularly the Top 100 set.
- Taxon
- soybeanGlycine maxe1
- Interactor
- SMVe1pathogen
- Outcome
- prediction accuracye0
- Direction
- improvede0
- Comparator
- Top 100 sete0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“expanding SNP feature sets generally improved prediction accuracy, especially with the Top 100 set”
e1“SMV SC3 resistance in soybean”
Claim · model-written summary
Adding more than 8000 SNPs gave diminishing returns and potential noise in prediction.
- Taxon
- soybeanGlycine maxe2
- Interactor
- SMVe2pathogen
- Outcome
- diminishing returns and potential noisee0
- Value
- more than 8000 SNPse0
- Comparator
- prediction accuracye1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“adding more than 8000 SNPs introduced diminishing returns and potential noise”
e1“generally improved prediction accuracy”
e2“SMV SC3 resistance in soybean”
Claim · model-written summary
Fourteen SNP loci were identified as effective for predicting SMV resistance genetic architecture.
- Taxon
- soybeanGlycine maxe1
- Interactor
- SMVe0pathogen
- Gene
- SNP locie0
- Outcome
- accurately predicting the genetic architecture of complex traits related to SMV resistancee0
- Value
- Fourteene0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Fourteen effective SNP loci were identified as pivotal for accurately predicting the genetic architecture of complex traits related to SMV resistance”
e1“enhancements in soybean breeding strategies”
Claim · model-written summary
The authors advise selecting SNPs closely linked to phenotypic traits to improve genomic prediction accuracy.
- Taxon
- soybeanGlycine maxe1
- Outcome
- selecting SNPs closely linked to phenotypic traits to refine prediction accuracye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“selecting SNPs closely linked to phenotypic traits to refine prediction accuracy in genomic selection models”
e1“soybean breeding strategies”