An Affordable and Convenient Diagnostic Marker to Identify Male and Female Hop Plants

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2023 Nov 14

PMID 37963231

Authors

Shaun J Clare

Ryan M King

Anna L Tawril

Joshua S Havill

Gary J Muehlbauer

Sarah B Carey

Alex Harkess

Nahla Bassil

Kayla R Altendorf

Affiliations

Soon will be listed here.

Abstract

Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.

References

Driskill M, Pardee K, Hummer K, Zurn J, Amundsen K, Wiles A . Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PLoS One. 2022; 17(4):e0257746. PMC: 9009645. DOI: 10.1371/journal.pone.0257746. View

Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C . InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30(9):1236-40. PMC: 3998142. DOI: 10.1093/bioinformatics/btu031. View

Huang M, Liu X, Zhou Y, Summers R, Zhang Z . BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions. Gigascience. 2018; 8(2). PMC: 6365300. DOI: 10.1093/gigascience/giy154. View

Xin Z, Velten J, Oliver M, Burke J . High-throughput DNA extraction method suitable for PCR. Biotechniques. 2003; 34(4):820-4, 826. DOI: 10.2144/03344rr04. View

Jung K, Han M, Lee Y, Kim Y, Hwang I, Kim M . Rice Undeveloped Tapetum1 is a major regulator of early tapetum development. Plant Cell. 2005; 17(10):2705-22. PMC: 1242267. DOI: 10.1105/tpc.105.034090. View

Yamaoka S, Nishihama R, Yoshitake Y, Ishida S, Inoue K, Saito M . Generative Cell Specification Requires Transcription Factors Evolutionarily Conserved in Land Plants. Curr Biol. 2018; 28(3):479-486.e5. DOI: 10.1016/j.cub.2017.12.053. View

Sayers E, Bolton E, Brister J, Canese K, Chan J, Comeau D . Database resources of the national center for biotechnology information. Nucleic Acids Res. 2021; 50(D1):D20-D26. PMC: 8728269. DOI: 10.1093/nar/gkab1112. View

Liu X, Huang M, Fan B, Buckler E, Zhang Z . Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies. PLoS Genet. 2016; 12(2):e1005767. PMC: 4734661. DOI: 10.1371/journal.pgen.1005767. View

Pook T, Mayer M, Geibel J, Weigend S, Cavero D, Schoen C . Improving Imputation Quality in BEAGLE for Crop and Livestock Data. G3 (Bethesda). 2019; 10(1):177-188. PMC: 6945036. DOI: 10.1534/g3.119.400798. View

10.

Lafontaine S, Varnum S, Roland A, Delpech S, Dagan L, Vollmer D . Impact of harvest maturity on the aroma characteristics and chemistry of Cascade hops used for dry-hopping. Food Chem. 2018; 278:228-239. DOI: 10.1016/j.foodchem.2018.10.148. View

11.

Zhang R, Chang J, Li J, Lan G, Xuan C, Li H . Disruption of the bHLH transcription factor Abnormal Tapetum 1 causes male sterility in watermelon. Hortic Res. 2021; 8(1):258. PMC: 8632879. DOI: 10.1038/s41438-021-00695-9. View

12.

Yu J, Pressoir G, Briggs W, Vroh Bi I, Yamasaki M, Doebley J . A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2005; 38(2):203-8. DOI: 10.1038/ng1702. View

13.

Wang J, Zhang Z . GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction. Genomics Proteomics Bioinformatics. 2021; 19(4):629-640. PMC: 9121400. DOI: 10.1016/j.gpb.2021.08.005. View

14.

Padgitt-Cobb L, Pitra N, Matthews P, Henning J, Hendrix D . An improved assembly of the "Cascade" hop () genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. Hortic Res. 2023; 10(2):uhac281. PMC: 9930403. DOI: 10.1093/hr/uhac281. View

15.

Verma S, Negi N, Pareek S, Mudgal G, Kumar D . Auxin response factors in plant adaptation to drought and salinity stress. Physiol Plant. 2022; 174(3):e13714. DOI: 10.1111/ppl.13714. View

16.

Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney R . Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. Mol Plant. 2017; 10(8):1047-1064. DOI: 10.1016/j.molp.2017.06.008. View

17.

Carey S, Lovell J, Jenkins J, Leebens-Mack J, Schmutz J, Wilson M . Representing sex chromosomes in genome assemblies. Cell Genom. 2022; 2(5). PMC: 9205529. DOI: 10.1016/j.xgen.2022.100132. View

18.

Li N, Zhang D, Liu H, Yin C, Li X, Liang W . The rice tapetum degeneration retardation gene is required for tapetum degradation and anther development. Plant Cell. 2006; 18(11):2999-3014. PMC: 1693939. DOI: 10.1105/tpc.106.044107. View

19.

Divashuk M, Alexandrov O, Kroupin P, Karlov G . Molecular cytogenetic mapping of Humulus lupulus sex chromosomes. Cytogenet Genome Res. 2011; 134(3):213-9. DOI: 10.1159/000328831. View

20.

Yue J, Chen Q, Wang Y, Zhang L, Ye C, Wang X . Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit . Hortic Res. 2023; 10(2):uhac264. PMC: 9909506. DOI: 10.1093/hr/uhac264. View