New Male Specific Markers for Hop and Application in Breeding Program

Čerenak, A.; Kolenc, Zala; Sehur, Petra; Whittock, Simon P.; Koutoulis, Anthony; Beatson, R. A.; Buck, Emily; Javornik, Branka; Škof, S.; Jakše, Jernej

doi:10.1038/s41598-019-50400-z

Cited by 16 publications

(5 citation statements)

References 55 publications

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“…In H. lupulus , sexing is reliable 1–2 years after sowing (Patzak et al ., 2002; Conway & Snyder, 2008). A few markers have been developed, but the use of Y‐specific coding sequences may increase marker quality (Patzak et al ., 2002; Cerenak et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes

et al. 2021

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We recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus, which is known also to possess XY chromosomes.Here, we used transcriptome sequencing of an F 1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETECTOR.We identified 265 sex-linked genes in H. lupulus, which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex-linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa, Y-linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation.We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21-25 Myr ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes (c. 70%), leading to a degenerated Y chromosome.

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Section: Introductionmentioning

confidence: 99%

Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes

et al. 2021

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“…PCR verification of the 32 HlMSM primers was performed on genomic DNA samples from eight hops (four females and four males). The sex confirmation was achieved using the hPb-CONT primer, a published male-specific primer (Cerenak et al 2019), while the Contig18 primer served to confirm DNA amplification and exclude false negatives (Cerenak et al 2019). Results for HlMSMs are depicted in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Molecular breeding methods, such as marker-assisted selection (MAS) (Hong et al 2022), have the potential to determine the sex of hop plants before phenotypic differences. Although a few markers have been developed, their quality could be enhanced using Y chromosome-specific sequences (Cerenak et al 2019;Patzak et al 2002). Dioecious plants exhibit genotypic differences between males and females, characterized by a non-recombining region in the heterogametic sex and a pseudo-autosomal region (Ming et al 2011;Shephard et al 2000).…”

Section: Introductionmentioning

confidence: 99%

Developing DNA Markers based on Male-Specific Chromosomal Regions for Selecting Male Plants in Hop (Humulus lupulus)

Ha,

Lyu,

et al. 2024

Plant Breed. Biotech.

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Hops are dioecious, with only female plants cultivated for resin production and primarily used in brewing. Therefore, early sex identification at the seedling stage is crucial for breeding and cultivation. Molecular marker-assisted selection facilitates rapid and reliable sex identification of hops. We developed molecular male markers by leveraging sequence information from male-specific regions in a designated public database. To assess the accuracy of sex identification using the newly generated markers, we performed PCR analysis on four cultivars of hops with known sexes. Seventy-eight percent of the tested PCR primers correlated with the male sex phenotype. Following optimization, four primer pairs were successfully converted into male-specific PCR markers.

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“…Recently, a new sex associated marker set was developed by Cerenak et al [134] by converting four male-specific DArT markers to PCR markers that can be run in a multiplex reaction. These four markers were tested on 197 plants (97 from the world collection and 100 from three segregating families) and showed 100% positive correlation with sex using the multiplex reaction.…”

Section: Plos Onementioning

confidence: 99%

Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers

et al. 2022

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Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96).

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New Male Specific Markers for Hop and Application in Breeding Program

Cited by 16 publications

References 55 publications

Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes

Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes

Developing DNA Markers based on Male-Specific Chromosomal Regions for Selecting Male Plants in Hop (Humulus lupulus)

Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers

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