IF 8.5

园艺研究(英文) Pub Date : 2025-08-12 eCollection Date: 2025-09-01 DOI: 10.1093/hr/uhaf159

Jun Song, Beatrice Amyotte, Leslie Campbell Palmer, Melinda Vinqvist-Tymchuk, Kyra Dougherty, Letitia Da Ros

{"title":"Untargeted metabolomic genome-wide association study reveals genetic and biochemical insights into polyphenols of apple fruit.","authors":"Jun Song, Beatrice Amyotte, Leslie Campbell Palmer, Melinda Vinqvist-Tymchuk, Kyra Dougherty, Letitia Da Ros","doi":"10.1093/hr/uhaf159","DOIUrl":"10.1093/hr/uhaf159","url":null,"abstract":"Apple (Malus × domestica) is one of the most popular fruits grown and consumed worldwide, contributing to human health with significant amounts of polyphenols and other bioactive compounds, and providing positive impacts to the economy and society. Understanding the diversity and inheritance of health-active compounds in apple can provide novel selection criteria for future breeding and cultivar development, as consumers increasingly prioritize the health benefits of their food choices. We therefore conducted an untargeted metabolomic analysis using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS) to investigate thousands of semipolar chemicals, mainly phenolic compounds, in 439 diverse apple accessions, and quantified 2066 features in positive ion mode. To identify key areas of genetic control for apple metabolite abundance, we performed a metabolomic genome-wide association study (mGWAS) on the quantified mass features using ~280 000 single nucleotide polymorphisms (SNPs). The mGWAS revealed >630 significant loci with hotspots for various groups of known and unknown phenolic compounds including flavonols on Chromosome 1, dihydrochalcones on Chromosome 5, and flavanols on Chromosomes 15 and 16. The most significant hotspot on Chromosome 16 included bHLH and C2H2 transcription factors that may play a role in controlling the abundance and complexity of phenolic compounds through regulation of the flavonoid biosynthesis pathway. Our analysis links the apple metabolome with candidate genes and biosynthetic mechanisms and establishes a foundation for marker-assisted breeding and gene editing to improve and modify phenolic compounds in apple for marketability and the benefit of human health.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 9","pages":"uhaf159"},"PeriodicalIF":8.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12377893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144980580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Discovery of bifunctional diterpene cyclases/synthases in bacteria supports a bacterial origin for the plant terpene synthase gene family. 更正：细菌中双功能二萜环化酶/合成酶的发现支持了植物萜烯合成酶基因家族的细菌起源。

IF 8.5

园艺研究(英文) Pub Date : 2025-07-28 eCollection Date: 2025-08-01 DOI: 10.1093/hr/uhaf170

引用次数: 0

Correction to: PpTCP18 is upregulated by lncRNA5 and controls branch number in peach (Prunus persica) through positive feedback regulation of strigolactone biosynthesis. 修正：PpTCP18被lncRNA5上调，并通过正反馈调节独脚金内酯生物合成来控制桃（Prunus persica）分支数。

IF 8.5

园艺研究(英文) Pub Date : 2025-05-30 eCollection Date: 2025-07-01 DOI: 10.1093/hr/uhaf139

引用次数: 0

Gapless genome assembly and population genomics highlights diversity of mango germplasms. 无间隙基因组组装和群体基因组学突出了芒果种质资源的多样性。

IF 7.6

园艺研究(英文) Pub Date : 2025-04-01 DOI: 10.1093/hr/uhaf007

Cuixian Zhang, Huaifeng Yi, Xiuxu Ye, Jingxiao Fu, Dehong Xie, Tianqi Bai, Xinyue Gong, Zhangguang Ni, Xinping Luo, Yusuf Chong Yu Lok, Qiong Luo, Peng Wang

引用次数: 0

Correction to: Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematode Meloidogyne incognita in tomato. 更正：番茄根结线虫（Meloidogyne incognita）诱导的局部和系统转录组和剪接重编程。

IF 7.6

园艺研究(英文) Pub Date : 2025-03-04 eCollection Date: 2025-03-01 DOI: 10.1093/hr/uhaf056

引用次数: 0

Correction to: Potassium stimulates fruit sugar accumulation by increasing carbon flow in Citrus sinensis. 更正：钾通过增加柑橘的碳流刺激果糖积累。

IF 7.6

园艺研究(英文) Pub Date : 2025-03-04 eCollection Date: 2025-03-01 DOI: 10.1093/hr/uhaf057

引用次数: 0

Correction to: The histone H3K27 demethylase SlJMJ4 promotes dark- and ABA-induced leaf senescence in tomato. 更正：组蛋白H3K27去甲基化酶SlJMJ4促进黑暗和aba诱导的番茄叶片衰老。

IF 7.6

园艺研究(英文) Pub Date : 2025-02-27 eCollection Date: 2025-02-01 DOI: 10.1093/hr/uhaf046

引用次数: 0

Correction to: DgbZIP3 interacts with DgbZIP2 to increase the expression of DgPOD for cold stress tolerance in chrysanthemum. 修正：DgbZIP3与DgbZIP2相互作用，增加DgPOD的表达，提高菊花抗冷胁迫能力。

IF 7.6

园艺研究(英文) Pub Date : 2025-02-24 eCollection Date: 2025-02-01 DOI: 10.1093/hr/uhaf047

引用次数: 0

Genomic data uncover complex hybridization and evolutionary history of the bunchberry species complex (Cornus L., Cornaceae). 基因组数据揭示了蔓越莓物种复合体（Cornus L., Cornaceae）的复杂杂交和进化历史。

IF 7.6

园艺研究(英文) Pub Date : 2025-01-22 eCollection Date: 2025-05-01 DOI: 10.1093/hr/uhaf026

Yanxia Sun, Winbin Zhou, Qiu-Yun Jenny Xiang

引用次数: 0

The whole-genome dissection of root system architecture provides new insights for the genetic improvement of alfalfa (Medicago sativa L.). 根系结构的全基因组剖析为紫花苜蓿（Medicago sativa L.）的遗传改良提供了新的见解。

IF 7.6

园艺研究(英文) Pub Date : 2025-01-11 eCollection Date: 2025-01-01 DOI: 10.1093/hr/uhae271

Xueqian Jiang, Xiangcui Zeng, Ming Xu, Mingna Li, Fan Zhang, Fei He, Tianhui Yang, Chuan Wang, Ting Gao, Ruicai Long, Qingchuan Yang, Junmei Kang

{"title":"The whole-genome dissection of root system architecture provides new insights for the genetic improvement of alfalfa (Medicago sativa L.).","authors":"Xueqian Jiang, Xiangcui Zeng, Ming Xu, Mingna Li, Fan Zhang, Fei He, Tianhui Yang, Chuan Wang, Ting Gao, Ruicai Long, Qingchuan Yang, Junmei Kang","doi":"10.1093/hr/uhae271","DOIUrl":"10.1093/hr/uhae271","url":null,"abstract":"Appropriate root system architecture (RSA) can improve alfalfa yield, yet its genetic basis remains largely unexplored. This study evaluated six RSA traits in 171 alfalfa genotypes grown under controlled greenhouse conditions. We also analyzed five yield-related traits in normal and drought stress environments and found a significant correlation (0.50) between root dry weight (RDW) and alfalfa dry weight under normal conditions (N_DW). A genome-wide association study (GWAS) was performed using 1 303 374 single-nucleotide polymorphisms (SNPs) to explore the relationships between RSA traits. Sixty significant SNPs (-log 10 (P) ≥ 5) were identified, with genes within the 50 kb upstream and downstream ranges primarily enriched in GO terms related to root development, hormone synthesis, and signaling, as well as morphological development. Further analysis identified 19 high-confidence candidate genes, including AUXIN RESPONSE FACTORs (ARFs), LATERAL ORGAN BOUNDARIES-DOMAIN (LBD), and WUSCHEL-RELATED HOMEOBOX (WOX). We verified that the forage dry weight under both normal and drought conditions exhibited significant differences among materials with different numbers of favorable haplotypes. Alfalfa containing more favorable haplotypes exhibited higher forage yields, whereas favorable haplotypes were not subjected to human selection during alfalfa breeding. Genomic prediction (GP) utilized SNPs from GWAS and machine learning for each RSA trait, achieving prediction accuracies ranging from 0.70 for secondary root position (SRP) to 0.80 for root length (RL), indicating robust predictive capability across the assessed traits. These findings provide new insights into the genetic underpinnings of root development in alfalfa, potentially informing future breeding strategies aimed at improving yield.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 1","pages":"uhae271"},"PeriodicalIF":7.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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