De novo QTL-seq identifies loci linked to blanchability in peanut (Arachis hypogaea) and refines previously identified QTL with low coverage sequence

Authors: KORANI, WALID - Hudsonalpha Institute For Biotechnology; O'CONNOR, DAN - Peanut Company Of Australia; CHU, YE - University Of Georgia; CHAVARRO, CAROLINA - University Of Georgia; BALLEN, CAROLINA - University Of Georgia; Guo, Baozhu; OZIAS-AKINS, PEGGY - University Of Georgia; WRIGHT, GRAEME - Peanut Company Of Australia; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2021
Publication Date: 10/30/2021
Citation: Korani, W., O'Connor, D., Chu, Y., Chavarro, C., Ballen, C., Guo, B., Ozias-Akins, P., Wright, G., Clevenger, J. 2021. De novo QTL-seq identifies loci linked to blanchability in peanut (Arachis hypogaea) and refines previously identified QTL with low coverage sequence. Agronomy. 11(11):2201. https://doi.org/10.3390/agronomy11112201.
DOI: https://doi.org/10.3390/agronomy11112201

Interpretive Summary: Quantitative Trait Locus Sequencing (QTL-seq) is a genetic analysis that takes advantage of the ever-decreasing cost in whole genome sequencing (WGS). Analysis of sequence data in tetraploid peanut has been difficult and relied on specialized pipelines. Accurate analysis of low coverage sequencing data for a polyploid crop such as peanut has not until now been viable. We developed a new pipeline called Khufu for the possibility of thinking about QTL-seq in a different way. The process of sequencing a bulk of 20 individuals to 20 X genome coverage is akin to computationally bulking 20 fastq files that were sequenced to 1 X genome coverage. By doing this, in a population of 300 individuals that was segregating strongly for multiple traits, each individual line was sequenced to 1 X coverage, QTL-seq could be carried out for all of the traits at once. We tested this concept using the “S” RIL population, using bulks representing 10, 20, 30, and 40% of the population. We successfully identified the TSWV QTL on chromosome A01 with high resolution. Therefore, in this study, we used the Khufu pipeline to de novo analyze a new dataset focused on blanching in peanut. We identify two QTL controlling blanching percentage in peanut. We also investigated the effect of Arachis cardenasii introgressions on blanching and these QTL. Finally, we benchmarked pipeline Khufu on previously published datasets in peanut and discuss the potential for genotyping applications in crops with complex genomes.

Technical Abstract: Blanchability is an oft overlooked, but important trait for peanut breeding. The process of blanching, removing the skin, is an important step in the processing of raw nuts for manufacturing. Under strong genetic control and requiring considerable effort to phenotype, blanchability is conducive for marker-assisted selection. We used QTL sequencing (QTL-seq) to identify two QTLs related to blanchability using previously phenotyped breeding populations. To validate the QTLs, we show that two markers can select for significantly increased blanchability in an independent Recombinant Inbred Line (RIL) population. Two wild introgressions from Arachis cardenasii conferring strong disease resistance were segregating in the population and were found to negatively impact blanchability. Finally, we show that by utilizing highly accurate sequence analysis pipelines, low coverage sequencing can be used to genotype whole populations with increased power and precision. This study highlights the potential to mine breeding data to identify and develop useful markers for genetic improvement programs and provide powerful tools for breeding for processing and quality traits.