ArticleBMC genomics2019
Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 50 citations in OpenAlex.
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- Genome and GWAS analyses for soybean cyst nematode resistance in USDA world-wide common bean (Frontiers in plant science · 2025Article
- Selective Genotyping and Phenotyping for Optimization of Genomic Prediction Models for Populations with Different Diversity.Plants (Basel, Switzerland) · 2024Article
- Prediction accuracy of genomic estimated breeding values for fruit traits in cultivated tomato (Solanum lycopersicum L.).BMC plant biology · 2024Article
- Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection.The plant genome · 2024Article
- Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed.The plant genome · 2023Review
- Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection.International journal of molecular sciences · 2023Article
- Genetic dissection of maize (Zea mays L.) chlorophyll content using multi-locus genome-wide association studies.BMC genomics · 2023Article
- Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize.Genes · 2023Article
- Multi-omics assisted breeding for biotic stress resistance in soybean.Molecular biology reports · 2023Review
- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
- A genome-wide association study and genomic prediction forFrontiers in plant science · 2023Article
- Genomic prediction models for traits differing in heritability for soybean, rice, and maize.BMC plant biology · 2022Article
- A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode.Biology · 2022Review
- Identification of Candidate Genes and Genomic Selection for Seed Protein in Soybean Breeding Pipeline.Frontiers in plant science · 2022Article
- Genomic selection with fixed-effect markers improves the prediction accuracy for Capsaicinoid contents inHorticulture research · 2022Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSoybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion loss annually. With a narrow genetic background of the currently available SCN-resistant commercial cultivars, high risk of resistance breakdown can occur. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify QTL, SNP markers, and candidate genes associated with soybean leaf chlorophyll content tolerance to SCN infection, and to carry out a genomic selection (GS) study for the chlorophyll content tolerance.
resultsA total of 172 soybean genotypes were evaluated for the effect of SCN HG Type 1.2.3.5.6.7 (race 4) on soybean leaf chlorophyll. The soybean lines were genotyped using a total of 4089 filtered and high-quality SNPs. Results showed that (1) a large variation in SCN tolerance based on leaf chlorophyll content indices (CCI); (2) a total of 22, 14, and 16 SNPs associated with CCI of non-SCN-infected plants, SCN-infected plants, and reduction of CCI SCN, respectively; (3) a new locus of chlorophyll content tolerance to SCN mapped on chromosome 3; (4) candidate genes encoding for Leucine-rich repeat protein, plant hormone signaling molecules, and biomolecule transporters; and (5) an average GS accuracy ranging from 0.31 to 0.46 with all SNPs and varying from 0.55 to 0.76 when GWAS-derived SNP markers were used across five models. This study demonstrated the potential of using genome-wide selection to breed chlorophyll-content-tolerant soybean for managing SCN.
conclusionsIn this study, soybean accessions with higher CCI under SCN infestation, and molecular markers associated with chlorophyll content related to SCN were identified. In addition, a total of 15 candidate genes associated with chlorophyll content tolerance to SCN in soybean were also identified. These candidate genes will lead to a better understanding of the molecular mechanisms that control chlorophyll content tolerance to SCN in soybean. Genomic selection analysis of chlorophyll content tolerance to SCN showed that using significant SNPs obtained from GWAS could provide better GS accuracy.
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