Of buds and bits: a meta-QTL study identifies stable QTL for berry quality and yield traits in cranberry mapping populations(Vaccinium macrocarpon Ait.)

Authors: MAULE, ANDREW - University Of Wisconsin; LOARCA, JENYNE - University Of Wisconsin; DIAZ-GARCIA, LUIS - University Of California, Davis; LOPEZ-MORENO, HECTOR - University Of Wisconsin; JOHNSON-CICALESE, JENNIFER - Rutgers Agriculture Research & Extension Center; VORSA, NICOLI - Rutgers Agriculture Research & Extension Center; IORIZZO, MASSIMO - North Carolina State University; Neyhart, Jeffrey; Zalapa, Juan

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/31/2024
Publication Date: 9/17/2024
Citation: Maule, A., Loarca, J., Diaz-Garcia, L., Lopez-Moreno, H., Johnson-Cicalese, J., Vorsa, N., Iorizzo, M., Neyhart, J., Zalapa, J.E. 2024. Of buds and bits: a meta-QTL study identifies stable QTL for berry quality and yield traits in cranberry mapping populations(Vaccinium macrocarpon Ait.). Frontiers in Plant Science. 15:1-20. https://doi.org/10.3389/fpls.2024.1294570.
DOI: https://doi.org/10.3389/fpls.2024.1294570

Interpretive Summary: For more than a century, cranberry breeders evaluated plant performance and made selections based on reproductive branches. With the advent of high-throughput phenotyping, modern cranberry programs are moving away from traditional selection methods. This study conducts gene mapping using both cranberry traditional and modern phenotyping methods. For this research, 22 fruiting branching traits were recorded using classical screens in two breeding populations over three years. Synchronously, eight plot-sampled traits for yield, fruit rot, and chemistry were collected. For one of the two populations, 170 and 69 major genetic regions were found using one method and another 150 and 81 were found using a differ method. Of these genetic regions, 9 and 4 regions were found to be stable across multiple years. Stable genetic regions, were identified as overlapping multi-year, multi-population, cross-study, and multi-trait. Seven multi-trait genetic regions were found in one population and one in the other population, and one in the combined analysis. Twenty two stable genetic regions were found in cross-study analyses: eight in a genetic study using digital traits for berry shape and size, two in a genetic study using digital images for berry color, and twelve in a three-study cross-analysis. Together, these genetic regions anchor new phenotyping techniques to traditional screens, validating state-of-the-art methods in cranberry phenotyping.

Technical Abstract: For more than a century, cranberry (Vaccinium macrocarpon Ait.) breeders evaluated genotype performance and made selections on reproductive uprights. With the advent of high-throughput phenotyping, modern cranberry programs are moving away from traditional selection methods. This study conducts QTL mapping using both cranberry traditional and modern phenotyping methods. For this research, 22 fruiting upright traits were recorded using classical screens in two half-sib breeding populations over three years. Synchronously, eight plot-sampled traits for yield, rot, and chemistry were collected. For the CNJ02 population (n=169), 170 major QTL (R2 = 0.1) were found using interval mapping and 150 major QTL were found using model mapping. In the CNJ04 population (n=72), 69 major QTL were found using interval mapping and 81 major QTL were found using model mapping. Of these, nine QTL in CNJ02 and four QTL in CNJ04 were found to be stable across multiple years. Stable genomic regions, or metaQTL, were identified as overlapping multi-year, multi-population, cross-study, and multi-trait QTL. Seven multi-trait metaQTL were found in CN02, one in CNJ04, and one in the combined analysis of CNJ02 and CNJ04 (CNJ0x). Twenty two metaQTL were found in cross-study analyses: eight in a QTL study using digital traits for berry shape and size, two in a QTL study using digital images for berry color, and twelve in a three-study cross-analysis. Together, these metaQTL anchor high-throughput phenotyping techniques to traditional screens, validating state-of-the-art methods in cranberry phenotyping.