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Independent validation of molecular markers for sex determination on diverse sex chromosomes in hops (Humulus lupulus L.)
Theresa Albrecht, Bianca Büttner, Sarah B. Carey, Rebecca Seidenberger, Anton Lutz, Alex Harkess and Sebastian Gresset

Humulus lupulus L. is a perennial and dioecious crop important for the beer and food industry. Sex determination in early stages of the breeding cycle is important to secure the selection of female candidates. Phenotypic selection for sex is time consuming and greenhouse capacities are limited generating the demand for an alternative method for early sex screening. Therefore, the need to develop genotypic markers for sex determination is high. Sex-linked markers developed in biparental populations were not applicable across diverse germplasm due to incomplete linkage. Recent sequence analyses have increased the knowledge about the structure and diversity of the sex chromosomes and newly developed markers are promising for the application in breeding programs. To identify sex-linked markers for the German hop breeding program, we analysed a diversity panel comprising 190 international hop varieties, wild hops and breeding material. SNP (single nucleotide polymorphism) markers were assessed with genotyping by sequencing and a genome-wide association study was performed based on the phenotypic sex expression. Significant SNP markers from the association study were analysed in two validation sets comprising selection candidates. Furthermore, recently published sex-linked markers were analysed in the diversity panel and in both validation sets. Based on both analyses, we were able to validate two SNP markers (“Scaffold_1533_203371763” and SM1) located in the sex determining region of the X and Y chromosomes. Both markers together were able to correctly assign sex to the selection candidates in both validation sets. Furthermore, genotypic clusters derived from the assays of marker (“Scaffold_1533_203371763” separated female, monoecious and male plants enabling a more targeted allocation of breeding resources in terms of field and greenhouse space as well as phenotyping and genotyping capacities. This advancement will result in an increased selection intensity and thus progress in developing more resilient hop varieties for a sustainable brewing industry.

Descriptors: Humulus lupulus, sex chromosomes, genome-wide association study, SNP markers, hop breeding

BrewingScience, 77 (November/December 2024), pp. 172-183