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SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species

Abstract

Key message

QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations.

Abstract

Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references—A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040 cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.

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Acknowledgements

The authors wish to thank Jennifer Chagoya at Texas A&M AgriLife Research, Lubbock for technical support.

Funding

This work was supported by Grants from the National Peanut Board Grant #332/TX-99/1139 to MDB and #332/TX-99/1213 to MDB and CES, Peanut Foundation award 04-858-14 to MB and CES, Ogallala Aquifer program award IPM_12.06 to MDB and PP, Peanut and Mycotoxin Innovation Lab award RC299-430/4942356 to MDB and CES, and NIFA Hatch funding project number TEX08835 to MDB.

Author information

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Authors

Contributions

RC prepared the draft of manuscripts and performed bioinformatics analysis, genotyping and genetic mapping. CS developed the mapping population and co-wrote the manuscript. AH assisted with genotyping. JS and PP helped with reviewing the manuscript. MDB conceived the idea, assisted with genotyping, genetic analysis, and with revision of the manuscript. All the authors approved this submission.

Corresponding author

Correspondence to Mark D. Burow.

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Conflict of interest

All authors declare no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

Sequences for these two accessions are deposited at NCBI under biosample runs SRR4039015 and SRR1535034. SNP variant calls using the references will be made available upon acceptance of manuscript for publication, and have already been uploaded at Figshare at https://figshare.com/account/projects/26287/articles/5568220 and https://figshare.com/account/projects/26287/articles/5568229.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Figure 1

: Differences in clustering patterns of KASP amplification on the Fluidigm Biomark HD based on amplification cycles. Panels A- 26 cycles, B- 36 cycles, and C- 46 cycles (TIF 7447 KB)

438_2018_1472_MOESM2_ESM.tif

Clustering of amplified markers which deviated from 1:2:1 ratio in F2 population. A-C plots are the SNPType assays on Fluidigm where A: two classes with a 3:1 ratio; B: three classes but fewer genotypes for parent B; and C: two classes scored by the software but could perhaps be classified as three. D-F plots are the assays on the LightCycler 480 where D- Spurious amplification and hard to classify due to high variability among accessions, could score accurately as three genotypes, E and F have one parent allele poorly amplified (TIF 5159 KB)

438_2018_1472_MOESM3_ESM.tif

Genotype data for an F2 intercross generated with 91 individuals and 144 markers. The genotypes A-Parent1, H-heterozygote, B-Parent2 are displayed in the colors red, blue, and green, respectively. In an intercross, if a 3:1 segregation ratio was observed, these are displayed in purple and orange, respectively. White pixels indicate missing data (TIF 3853 KB)

438_2018_1472_MOESM4_ESM.tif

Circos plot representing synteny between the genetic and physical maps. Chr1-Chr10 indicate the linkage groups (LG01-LG10) of the genetic map generated using SNP markers in this study and Chr11-Chr20 indicate the chromosomes of the genome sequence (AA01-AA10). Blue bar plots on Chr11-Chr20 of the physical map indicate the SNPs distribution on the genome sequence with the use of transcriptome data (TIF 14977 KB)

438_2018_1472_MOESM5_ESM.xlsx

Primer sequences for the markers used in validation of SNPs and genotyping the F2 mapping population derived from cross between A. duranensis (KSSc38901) and A. cardenasii (GKP10017) (XLSX 20 KB)

438_2018_1472_MOESM6_ESM.xlsx

Genotype and phenotype data on the mapping population obtained from allele calls of two different platforms (XLSX 96 KB)

438_2018_1472_MOESM7_ESM.xlsx

Chi-square test on segregation ratio of SNP markers and apparently dominant markers deviated in the F2 population. * - significantly departing for the expected ratio (XLSX 21 KB)

438_2018_1472_MOESM8_ESM.xlsx

Genome coordinates used from the genome assembly to evaluate the synteny between the linkage and physical map (XLSX 20 KB)

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Chopra, R., Simpson, C.E., Hillhouse, A. et al. SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species. Mol Genet Genomics 293, 1477–1491 (2018). https://doi.org/10.1007/s00438-018-1472-z

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Keywords

  • Arachis
  • Wild species
  • Domestication
  • QTLs
  • SNPs
  • Markers
  • KASP
  • Fluidigm
  • Peanut