Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil

Wei Wei, Ana Carolina Oliveira Mesquita, Adriana de A. Figueiró, Xing Wu, Shilpa Manjunatha, Daniel P. Wickland, Matthew Hudson, Fernando C. Juliatti, Steven J Clough

Research output: Contribution to journalArticle

Abstract

Background: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. A collection of 420 soybean genotypes were selected based on either reports of resistance, or from one of three different breeding programs in Brazil, two commercial, one public. Plant genotype sensitivity to SSR was evaluated by the cut stem inoculation method, and lesion lengths were measured at 4 days post inoculation. Results: Genotyping-by-sequencing was conducted to genotype the 420 soybean lines. The TASSEL 5 GBSv2 pipeline was used to call SNPs under optimized parameters, and with the extra step of trimming adapter sequences. After filtering missing data, heterozygosity, and minor allele frequency, a total of 11,811 SNPs and 275 soybean genotypes were obtained for association analyses. Using a threshold of FDR-adjusted p-values <0.1, the Compressed Mixed Linear Model (CMLM) with Genome Association and Prediction Integrated Tool (GAPIT), and the Fixed and Random Model Circulating Probability Unification (FarmCPU) methods, both approaches identified SNPs with significant association to disease response on chromosomes 1, 11, and 18. The CMLM also found significance on chromosome 19, whereas FarmCPU also identified significance on chromosomes 4, 9, and 16. Conclusions: These similar and yet different results show that the computational methods used can impact SNP associations in soybean, a plant with a high degree of linkage disequilibrium, and in SSR resistance, a trait that has a complex genetic basis. A total of 125 genes were located within linkage disequilibrium of the three loci shared between the two models. Their annotations and gene expressions in previous studies of soybean infected with S. sclerotiorum were examined to narrow down the candidates.

Original languageEnglish (US)
Article number849
JournalBMC genomics
Volume18
Issue number1
DOIs
StatePublished - Nov 7 2017

Fingerprint

Ascomycota
Soybeans
Brazil
Genotype
Genome
Single Nucleotide Polymorphism
Breeding
Linkage Disequilibrium
Linear Models
Genes
Chromosomes, Human, Pair 19
Chromosomes, Human, Pair 18
Chromosomes, Human, Pair 16
Chromosomes, Human, Pair 9
Chromosomes, Human, Pair 11
Chromosomes, Human, Pair 4
Chromosomes, Human, Pair 1
Genome-Wide Association Study
Climate
Gene Frequency

Keywords

  • CMLM
  • FarmCPU
  • GAPIT
  • GWAS
  • Genotype-by-sequencing
  • Marker
  • QTL
  • SNP
  • White mold

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil. / Wei, Wei; Mesquita, Ana Carolina Oliveira; Figueiró, Adriana de A.; Wu, Xing; Manjunatha, Shilpa; Wickland, Daniel P.; Hudson, Matthew; Juliatti, Fernando C.; Clough, Steven J.

In: BMC genomics, Vol. 18, No. 1, 849, 07.11.2017.

Research output: Contribution to journalArticle

Wei, Wei ; Mesquita, Ana Carolina Oliveira ; Figueiró, Adriana de A. ; Wu, Xing ; Manjunatha, Shilpa ; Wickland, Daniel P. ; Hudson, Matthew ; Juliatti, Fernando C. ; Clough, Steven J. / Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil. In: BMC genomics. 2017 ; Vol. 18, No. 1.
@article{4c4114b5fece46b3b434614c784c2593,
title = "Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil",
abstract = "Background: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. A collection of 420 soybean genotypes were selected based on either reports of resistance, or from one of three different breeding programs in Brazil, two commercial, one public. Plant genotype sensitivity to SSR was evaluated by the cut stem inoculation method, and lesion lengths were measured at 4 days post inoculation. Results: Genotyping-by-sequencing was conducted to genotype the 420 soybean lines. The TASSEL 5 GBSv2 pipeline was used to call SNPs under optimized parameters, and with the extra step of trimming adapter sequences. After filtering missing data, heterozygosity, and minor allele frequency, a total of 11,811 SNPs and 275 soybean genotypes were obtained for association analyses. Using a threshold of FDR-adjusted p-values <0.1, the Compressed Mixed Linear Model (CMLM) with Genome Association and Prediction Integrated Tool (GAPIT), and the Fixed and Random Model Circulating Probability Unification (FarmCPU) methods, both approaches identified SNPs with significant association to disease response on chromosomes 1, 11, and 18. The CMLM also found significance on chromosome 19, whereas FarmCPU also identified significance on chromosomes 4, 9, and 16. Conclusions: These similar and yet different results show that the computational methods used can impact SNP associations in soybean, a plant with a high degree of linkage disequilibrium, and in SSR resistance, a trait that has a complex genetic basis. A total of 125 genes were located within linkage disequilibrium of the three loci shared between the two models. Their annotations and gene expressions in previous studies of soybean infected with S. sclerotiorum were examined to narrow down the candidates.",
keywords = "CMLM, FarmCPU, GAPIT, GWAS, Genotype-by-sequencing, Marker, QTL, SNP, White mold",
author = "Wei Wei and Mesquita, {Ana Carolina Oliveira} and Figueir{\'o}, {Adriana de A.} and Xing Wu and Shilpa Manjunatha and Wickland, {Daniel P.} and Matthew Hudson and Juliatti, {Fernando C.} and Clough, {Steven J}",
year = "2017",
month = "11",
day = "7",
doi = "10.1186/s12864-017-4160-1",
language = "English (US)",
volume = "18",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil

AU - Wei, Wei

AU - Mesquita, Ana Carolina Oliveira

AU - Figueiró, Adriana de A.

AU - Wu, Xing

AU - Manjunatha, Shilpa

AU - Wickland, Daniel P.

AU - Hudson, Matthew

AU - Juliatti, Fernando C.

AU - Clough, Steven J

PY - 2017/11/7

Y1 - 2017/11/7

N2 - Background: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. A collection of 420 soybean genotypes were selected based on either reports of resistance, or from one of three different breeding programs in Brazil, two commercial, one public. Plant genotype sensitivity to SSR was evaluated by the cut stem inoculation method, and lesion lengths were measured at 4 days post inoculation. Results: Genotyping-by-sequencing was conducted to genotype the 420 soybean lines. The TASSEL 5 GBSv2 pipeline was used to call SNPs under optimized parameters, and with the extra step of trimming adapter sequences. After filtering missing data, heterozygosity, and minor allele frequency, a total of 11,811 SNPs and 275 soybean genotypes were obtained for association analyses. Using a threshold of FDR-adjusted p-values <0.1, the Compressed Mixed Linear Model (CMLM) with Genome Association and Prediction Integrated Tool (GAPIT), and the Fixed and Random Model Circulating Probability Unification (FarmCPU) methods, both approaches identified SNPs with significant association to disease response on chromosomes 1, 11, and 18. The CMLM also found significance on chromosome 19, whereas FarmCPU also identified significance on chromosomes 4, 9, and 16. Conclusions: These similar and yet different results show that the computational methods used can impact SNP associations in soybean, a plant with a high degree of linkage disequilibrium, and in SSR resistance, a trait that has a complex genetic basis. A total of 125 genes were located within linkage disequilibrium of the three loci shared between the two models. Their annotations and gene expressions in previous studies of soybean infected with S. sclerotiorum were examined to narrow down the candidates.

AB - Background: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. A collection of 420 soybean genotypes were selected based on either reports of resistance, or from one of three different breeding programs in Brazil, two commercial, one public. Plant genotype sensitivity to SSR was evaluated by the cut stem inoculation method, and lesion lengths were measured at 4 days post inoculation. Results: Genotyping-by-sequencing was conducted to genotype the 420 soybean lines. The TASSEL 5 GBSv2 pipeline was used to call SNPs under optimized parameters, and with the extra step of trimming adapter sequences. After filtering missing data, heterozygosity, and minor allele frequency, a total of 11,811 SNPs and 275 soybean genotypes were obtained for association analyses. Using a threshold of FDR-adjusted p-values <0.1, the Compressed Mixed Linear Model (CMLM) with Genome Association and Prediction Integrated Tool (GAPIT), and the Fixed and Random Model Circulating Probability Unification (FarmCPU) methods, both approaches identified SNPs with significant association to disease response on chromosomes 1, 11, and 18. The CMLM also found significance on chromosome 19, whereas FarmCPU also identified significance on chromosomes 4, 9, and 16. Conclusions: These similar and yet different results show that the computational methods used can impact SNP associations in soybean, a plant with a high degree of linkage disequilibrium, and in SSR resistance, a trait that has a complex genetic basis. A total of 125 genes were located within linkage disequilibrium of the three loci shared between the two models. Their annotations and gene expressions in previous studies of soybean infected with S. sclerotiorum were examined to narrow down the candidates.

KW - CMLM

KW - FarmCPU

KW - GAPIT

KW - GWAS

KW - Genotype-by-sequencing

KW - Marker

KW - QTL

KW - SNP

KW - White mold

UR - http://www.scopus.com/inward/record.url?scp=85033404940&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85033404940&partnerID=8YFLogxK

U2 - 10.1186/s12864-017-4160-1

DO - 10.1186/s12864-017-4160-1

M3 - Article

C2 - 29115920

AN - SCOPUS:85033404940

VL - 18

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 849

ER -