TY - JOUR
T1 - Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation
AU - Ravelombola, Waltram Second
AU - Qin, Jun
AU - Shi, Ainong
AU - Nice, Liana
AU - Bao, Yong
AU - Lorenz, Aaron
AU - Orf, James H
AU - Young, Nevin D
AU - Chen, Senyu
N1 - Publisher Copyright:
© 2020 Ravelombola et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2020/7
Y1 - 2020/7
N2 - Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.
AB - Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.
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U2 - 10.1371/journal.pone.0235089
DO - 10.1371/journal.pone.0235089
M3 - Article
C2 - 32673346
AN - SCOPUS:85088155334
SN - 1932-6203
VL - 15
JO - PloS one
JF - PloS one
IS - 7 July
M1 - e0235089
ER -
