National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA.
Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA.
G3 (Bethesda). 2023 Dec 29;14(1). doi: 10.1093/g3journal/jkad216.
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.
啤酒花生产仅使用雌性植物，而雄性植物仅通过杂交在育种计划中产生新的变异。目前，啤酒花缺乏一种快速、准确的诊断标记来确定植物是雄性还是雌性。没有诊断标记，育种计划可能需要 1-2 年时间来确定新幼苗的性别。以前关于性连锁标记的研究仅限于特定的种群或育种计划，因此可转移性有限或可扩展性较低。一组包含 765 个已知性别表型的啤酒花基因型、测序和全基因组关联图谱的大型集合揭示了性染色体上一个非常显著的标记（LOD 分数=208.7），该标记可以在我们的种群中以 96.2%的准确率预测性别。在这项研究中，我们开发了一种用于诊断 SNP 的 PCR 等位基因竞争延伸 (PACE) 检测，测试了三种快速、高通量的 DNA 提取方法，用于快速、高通量的基因分型。此外，该标记在来自华盛顿州普罗瑟的美国农业部-农业研究局啤酒花育种计划的 15 个家族的 94 个个体的另一个群体中进行了验证，准确率为 96%。该诊断标记位于一个预测编码基本螺旋-环-螺旋转录因子蛋白的基因中，该蛋白家族以前在多种植物物种的雄性不育中被涉及，这可能表明其在决定啤酒花性别方面的作用。该标记具有诊断性、准确性、经济性和高度可扩展性，有潜力提高啤酒花育种的效率。
