High-density linkage map construction and QTL identification in a diploid blueberry mapping population

Authors: QI, XINPENG - Non ARS Employee; Ogden, Elizabeth; BOSTON, HAMED - North Carolina State University; SARGENT, DANIEL - University Of Greenwich; WARD, JUDSON - Ohalo Genetics, Inc; GILBERT, JESSICA - Driscoll'S; ORIZZO, MASSIMO - North Carolina State University; Rowland, Lisa

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2021
Publication Date: 6/21/2021
Citation: Qi, X., Ogden, E.L., Boston, H., Sargent, D.J., Ward, J., Gilbert, J., Orizzo, M., Rowland, L.J. 2021. High-density linkage map construction and QTL identification in a diploid blueberry mapping population. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.692628.
DOI: https://doi.org/10.3389/fpls.2021.692628

Interpretive Summary: Breeding new blueberry varieties is a slow process but could be accelerated and made more efficient if breeders could quickly identify seedlings from crosses that carry the most desirable traits. A DNA-based method, called “marker assisted selection”, is available to accomplish this, but it first requires the development of a genetic map, preferably a high density map, so that DNA markers associated with important traits can be identified. In this study, scientists with the USDA-ARS, along with other collaborators, developed a high density genetic map of blueberry. The map is comprised of 17,486 markers and was successfully used to identify markers associated with several traits that are important to the blueberry industry, including chilling requirement and cold hardiness, which affect the geographical areas where plants can be grown, and fruit quality traits of firmness, color, and scar size. Scar is the opening on the back of the berry which remains when the stem is removed and can be an entry point for diseases. By aligning the map and markers to the blueberry genome sequence, the genes in the vicinity of the regions controlling these traits can be identified and tested in other studies and populations. Blueberry breeders and geneticists worldwide can use these markers to develop new cultivars with desirable traits.

Technical Abstract: Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85-20) with the parent W85-23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 116.6 Gbp raw sequenced reads. A total of 160,535 SNPs, referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers and 6,666 marker bins were obtained, spanning a total genetic distance of 1539.4 cM. Among 18 horticultural traits phenotyped in this population, QTL that were significant over at least two years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in one year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTL.