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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #347762
Title: High-throughput SNP genotyping reveals major QTLs for domestication related traits among A-genome peanut wild species

Author
item CHOPRA, RATAN - Texas Tech University
item SIMPSON, CHARLES - Texas Agrilife
item HILLHOUSE, ANDREW - Texas A&M University
item Payton, Paxton
item SHARMA, JYOSTNA - Texas Tech University
item BUROW, MARK - Texas A&M Agrilife

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/9/2018
Publication Date: 8/1/2018
Citation: Chopra, R., Simpson, C., Hillhouse, A., Payton, P.R., Sharma, J., Burow, M. 2018. High-throughput SNP genotyping reveals major QTLs for domestication related traits among A-genome peanut wild species. Molecular Genetics and Genomics. 293. https://doi.org/10.1007/s00438-018-1472-z.
DOI: https://doi.org/10.1007/s00438-018-1472-z

Interpretive Summary: Cultivated peanut production is challenged by both biotic and abiotic stresses and limited by genetic diversity in the cultivated species. Wild relatives of the cultivated peanut possess genetic traits for tolerance to many of these stresses. However, during selection for yield, many of these traits have been lost due to their negative effect on yield. Modern techniques allow for the identification and separation of specific genetic components for stress tolerance and incorporation of these traits into elite germplasm, without the negative effects on yield. Therefore, it is important to dissect the genomic regions associated with traits like plant architecture to increase our potential to manipulate these traits. For this study, a wild diploid species of peanut which has resistance to several pests and diseases, was used to identify markers associated with the important domestication traits. These genetic markers and traits will be used for resistance and selection of good morpho-physiological traits from the populations to develop new genetic resources for the peanut community. We believe that genetic information generated in this study can be used in bridging the information between the cultivated tetraploids and existing wild species. We conclude that a high number of genetic markers could be identified between the wild species, and success of trait validation is possible if the reference used has more complete representation of genome or transcripts. Genotyping platforms with compatible chemistries provide a more flexible experimental design for breeding and genetics programs. The markers, genetic map and QTLs from this study serve as a new and valuable resources for peanut genetics and genomics.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are used routinely in many species for genetic mapping and marker-assisted breeding because SNPs can be assayed rapidly at a low cost. Polymorphic SNPs between two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references. More than 40,000 SNPs differentiated the parents, and 87.8% of the 190 SNP calls tested were confirmed and validated. SNPs were then genotyped on ninetyone F2 lines obtained from the cross between the parents using KASP chemistry on a Roche Light Cycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. This allowed for both low and high throughput analysis (96 samples x 96 SNPs) in a single experiment for developing a genetic map, and a more flexible design for marker assisted selection. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1,040 cM. Comparison of the A- genome map to the reference A. duranensis sequence revealed a high degree of similarity between the genetic and sequenced based maps. QTL analysis was also performed on the mapping population for important domestication-related architectural traits. A total of thirty-one QTLs for leaflet length, main stem height, presence of flowers on the main stem, and seed mass were identified, and could serve as information associated with domestication, useful for introgression of alleles into cultivated peanut from wild species. Many of the QTLs identified in this study explain high phenotypic variation and would allow breeders to quickly fix the alleles for these beneficial traits using a marker-assisted backcross approach.