Biology subjects

Caraza-Harter, M. V.

Publications and source records attributed to Caraza-Harter, M. V..

3 recordsLinked to original sources

bioRxiv2024

Targeted genotyping-by-sequencing of potato and software for imputation

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics. Core IdeasO_LIA mid-density, targeted genotyping-by-sequencing (GBS) assay was developed for potato. C_LIO_LIThe GBS assay includes markers for resistance to potato virus Y, golden cyst nematode, and potato wart. C_LIO_LIThe GBS assay includes multi-allelic markers for potato maturity and tuber shape. C_LIO_LIThe polyBreedR software has functions for manipulating and imputing polyploid marker data in Variant Call Format. C_LIO_LILinkage Analysis was more accurate than the Random Forest method when imputing from 2K to 10K markers. C_LI

genomics↗

bioRxiv2022

The genetic architectures of vine and skin maturity in tetraploid potato

Potato vine and skin maturity, which refer to foliar senescence and adherence of the tuber periderm, respectively, are both important to production and therefore breeding. Our objective was to investigate the genetic architectures of these traits in a genome-wide association panel of 586 genotypes, and through joint linkage mapping in a half-diallel subset (N = 397). Skin maturity was measured by image analysis after mechanized harvest 120 days after planting. To correct for the influence of vine maturity on skin maturity under these conditions, the former was used as a covariate in the analysis. The genomic heritability based on a 10K SNP array was 0.33 for skin maturity vs. 0.46 for vine maturity. Only minor QTL were detected for skin maturity, the largest being on chromosome 9 and explaining 8% of the variation. As in many previous studies, S. tuberosum Cycling DOF Factor 1 (CDF1) had a large influence on vine maturity, explaining 33% of the variation in the panel as a bi-allelic SNP and 44% in the half-diallel as a multi-allelic QTL. From the estimated effects of the parental haplotypes in the half-diallel and prior knowledge of the allelic series for CDF1, the CDF1 allele for each haplotype was predicted and ultimately confirmed through whole-genome sequencing. The ability to connect statistical alleles from QTL models with biological alleles based on DNA sequencing represents a new milestone in genomics-assisted breeding for tetraploid species.

genetics↗

bioRxiv2019

Image-based Phenotyping and Genetic Analysis of Potato Skin Set and Color

Image-based phenotyping offers new opportunities for fast, objective, and reliable measurement for breeding and genetics research. In the current study, image analysis was used to quantify potato skin color and skin set, which are critical for the marketability of new varieties. A set of 15 red potato varieties and advanced breeding lines was evaluated over two years at a single location, with two harvest times in the second year. After mechanical harvest and grading, 7-8 representative tubers per plot were photographed, and the photos were analyzed with ImageJ to measure skinning (as % surface area) and skin color using the Hue, Chroma and Lightness (HCL) representation. The plot-based heritability was consistently high (> 0.77) across traits and environments; the genetic correlation between environments was also high, ranging from 0.81 to 0.98. Significant increases in Lightness and Chroma, as well as a decrease in skinning, were observed at the late compared to early harvest, while the opposite trends for color were observed after six weeks of storage. The three color traits were unexpectedly collinear in this study, with the first principal component explaining 86% of the variation. This result may reflect the physiology of red color in potato, but the highly selected nature of the 15 genotypes may also be a factor. Image-based phenotyping offers new opportunities to advance genetic gain and understanding for tuber appearance traits that have been difficult to precisely measure in the past.

genetics↗