Itam Michael, Jung Sook, Zheng Ping, Lee Taein, Cheng Chun-Huai, Buble Katheryn, Main Dorrie, Gasic Ksenija
Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USA.
Department of Horticulture, Washington State University, PO Box 646414, Pullman, WA 99164-6414, USA.
Hortic Res. 2025 May 30;12(8):uhaf142. doi: 10.1093/hr/uhaf142. eCollection 2025 Aug.
The extensive accumulation of genetic, genomic, expression, and breeding data on species often results in valuable information being lost or difficult to access for breeding purposes. We report a recent effort to increase curation on data in the Genome Database for Rosaceae (GDR, rosaceae.org) and a case study that explores 25 years of curated data (from 1998 to 2023) to uncover the genetic architecture of key traits in species, provide actionable insights for breeding, and encourage the use of shared molecular data across species. The curated data includes 177 genetic maps, primarily for almond (19), apricot (21), peach (52), and sweet cherry (46). A total of 28 971 trait-associated loci were reported, with 72.4% derived from genome-wide association studies, 18.7% from quantitative trait loci (QTL), and 8.9% from Mendelian trait loci. Notably, 76.4% of these loci are associated with morphological and quality traits, reflecting breeders' focus on consumer preferences. We identified 16 potential QTL hotspots linked to key traits such as morphology, phenology, fruit quality, and disease resistance. Additionally, we identified 17 high-priority syntenic regions among peach, sweet cherry, and almond. The colocalized markers and genes within the QTL hotspots and syntenic regions offer a valuable resource for tool development for breeding, especially for complex polyploid genomes and lesser studied species with limited genetic and genomic data.
关于物种的遗传、基因组、表达和育种数据的大量积累，往往导致有价值的信息丢失或难以用于育种目的。我们报告了最近在蔷薇科基因组数据库（GDR，rosaceae.org）中加强数据整理的工作，以及一个案例研究，该研究探索了25年（从1998年到2023年）的整理数据，以揭示物种关键性状的遗传结构，为育种提供可行的见解，并鼓励跨物种使用共享的分子数据。整理的数据包括177个遗传图谱，主要针对杏仁（19个）、杏（21个）、桃（52个）和甜樱桃（46个）。总共报告了28971个与性状相关的位点，其中72.4%来自全基因组关联研究，18.7%来自数量性状位点（QTL），8.9%来自孟德尔性状位点。值得注意的是，这些位点中有76.4%与形态和品质性状相关，反映了育种者对消费者偏好的关注。我们确定了16个与形态、物候、果实品质和抗病性等关键性状相关的潜在QTL热点。此外，我们在桃、甜樱桃和杏仁中确定了17个高优先级的共线性区域。QTL热点和共线性区域内共定位的标记和基因，为育种工具开发提供了宝贵资源，特别是对于复杂的多倍体基因组和遗传及基因组数据有限的研究较少的物种。
