{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:41:22Z","timestamp":1790343682366,"version":"4.1.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>Aroma is a crucial factor influencing the flavor quality and economic value of longan fruits. This study employed a mapping population consisting of 98 F<jats:sub>1<\/jats:sub> progeny of \u2018Shixia \u00d7 Xiangcui\u2019 (exhibiting broad segregation in fruit aroma trait) and their parents. We performed the SNP genotyping through whole-genome resequencing to construct a high-density linkage map, followed by QTL mapping and candidate gene screening for aroma trait. We obtained a total of 554.9 Gbp of sequencing data, with an average depth of approximately 15\u00d7 for the parents and 12\u00d7 for the progeny. Three types of SNP markers (lm\u00d7ll, nn\u00d7np, and hk\u00d7hk) were developed, totaling 317 877. After merging with a 100 kb sliding window, 6 134 Bin markers were generated. A first high-density Bin map was constructed, comprising 15 linkage groups with 3 517 Bin markers (containing 264 385 SNPs), covering a total map length of 1 666.79 cM. The average marker interval was 0.48 cM, with 99.18% of gaps being less than 5 cM. Collinearity analysis confirmed the high quality of the map. Fifty-six QTLs were mapped for 9 aroma-related traits, including (E)-2-hexenal, ethyl acetate, ethyl butyrate, ethyl crotonate, (E)-2-hexenoate, ethanol, linalool, ocimene, and total ester content. These QTLs explained 19.8%\u201351.0% of the phenotypic variation rates and were distributed across 11 linkage groups, with two QTL-rich regions on LG7 and LG8. Seven pleiotropic QTLs were detected. By analyzing the expression patterns of 1 535 annotated genes within the mapped intervals, six candidate genes potentially regulating the synthesis of ester characteristic aroma compounds were identified: aldo-keto reductase AKRs, acetolactate synthase small subunit ALS2, ACC oxidase ACO1-1, and transcription factors bHLH122, AGL103, and bZip1. This work provides novel insights into the fruit aroma formation, and facilitates breeding efforts to improve quality in longan and potentially other fruit crops.<\/jats:p>","DOI":"10.3389\/fpls.2025.1642854","type":"journal-article","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T05:33:42Z","timestamp":1755149622000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Construction of high-density bin genetic map and QTL mapping of fruit aroma in longan (Dimocarpus longan Lour.)"],"prefix":"10.3389","volume":"16","author":[{"given":"Wenshun","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaojun","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qizhi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimou","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuping","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianguo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jisen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoquan","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,8,14]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/s11032-007-9108-8","article-title":"Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.)","volume":"21","author":"Amarawathi","year":"2008","journal-title":"Mol. Breed."},{"key":"B2","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1983","DOI":"10.13592\/j.cnki.ppj.2021.0061","article-title":"Genome-wide identification and expression analysis of FAR1\/FHY3 transcription factor family in tomato","volume":"57","author":"Chen","year":"2021","journal-title":"Plant Physiol. J."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1111\/tpj.15908","article-title":"The evolutionary patterns of barley pericentromeric chromosome regions. as shaped by linkage disequilibrium and domestication","volume":"111","author":"Chen","year":"2022","journal-title":"Plant J."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1743","DOI":"10.1111\/pbi.13857","article-title":"Ubiquitin ligase OsRINGzf1 regulates drought resistance by controlling the turnover of OsPIP2;1","volume":"20","author":"Chen","year":"2022","journal-title":"Plant Biotechnol. J."},{"key":"B6","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/j.plantsci.2004.12.018","article-title":"Apple aroma: alcohol acyltransferase.; a rate limiting step for ester biosynthesis, is regulated by ethylene","volume":"168","author":"Defilippi","year":"2004","journal-title":"Plant Sci."},{"key":"B8","doi-asserted-by":"publisher","first-page":"16057","DOI":"10.1038\/hortres.2016.57","article-title":"A high-density.; multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species","volume":"3","author":"Di Pierro","year":"2016","journal-title":"Horticult. Res."},{"key":"B9","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/s11295-012-0546-z","article-title":"Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps","volume":"9","author":"Eduardo","year":"2013","journal-title":"Tree Genet. Genomes"},{"key":"B10","doi-asserted-by":"publisher","first-page":"6840","DOI":"10.13271\/j.mpb.017.006840","article-title":"The research progress of plant chitinases","volume":"17","author":"Gong","year":"2019","journal-title":"Mol. Plant Breed."},{"key":"B11","doi-asserted-by":"publisher","first-page":"6142","DOI":"10.1021\/acs.jafc.8b01435","article-title":"Identification of two transcriptional activators MabZIP4\/5 in controlling aroma biosynthetic genes during banana ripening","volume":"66","author":"Guo","year":"2018","journal-title":"J. Agric. Food Chem."},{"key":"B12","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.scienta.2011.11.007","article-title":"Identification of stable QTLs related to trunk girth in Longan","volume":"134","author":"Guo","year":"2012","journal-title":"Sci. Horticult."},{"key":"B13","doi-asserted-by":"publisher","first-page":"2203","DOI":"10.5504\/bbeq.2011.0014","article-title":"QTLs analysis of several traits in Longan","volume":"25","author":"Guo","year":"2011","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"B14","doi-asserted-by":"publisher","first-page":"655","DOI":"10.16420\/j.issn.0513-353x.2009.05.006","article-title":"Construction of a molecular genetic map for Longan based on RAPD, ISSR, SRAP and AFLP markers","volume":"36","author":"Guo","year":"2009","journal-title":"Acta Hortic. Sin."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.16420\/j.issn.0513-353x.2015-0131","article-title":"Identification and genetic diversity of reciprocal hybrids in longan (Dimocarpus longan) by SSR","volume":"42","author":"Hu","year":"2015","journal-title":"Acta Hortic. Sin."},{"key":"B16","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1038\/s41588-020-0607-4","article-title":"Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution","volume":"52","author":"Huang","year":"2020","journal-title":"Nat. Genet."},{"key":"B17","doi-asserted-by":"publisher","first-page":"371","DOI":"10.16420\/j.issn.0513-353x.2011.02.023","article-title":"Research advance in regulation of ethylene during ripening and senescence of non-climacteric fruit","volume":"38","author":"Jiang","year":"2011","journal-title":"Acta Hortic. Sin."},{"key":"B18","doi-asserted-by":"publisher","first-page":"S1791","DOI":"10.3233\/BME-151480","article-title":"Faster single-end alignment generation utilizing multi-thread for BWA","volume":"26","author":"Jo","year":"2015","journal-title":"Bio-med. Mater. Eng."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1016\/j.scienta.2021.110086","article-title":"SNP-based high-density genetic map construction and candidate gene identification for fruit quality traits of Dimocarpus longan Lour","volume":"284","author":"Jue","year":"2021","journal-title":"Sci. Hortic."},{"key":"B20","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.jcs.2017.06.006","article-title":"Identification of SNPs, QTLs and dominant markers associated with wheat grain flavor using genotyping-by-sequencing","volume":"76","author":"Kiszonas","year":"2017","journal-title":"J. Cereal Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1186\/s12870-022-03842-z","article-title":"Genetic architecture of berry aroma compounds in a QTL (quantitative trait loci) mapping population of interspecific hybrid grapes (Vitis labruscana \u00d7 Vitis vinifera)","volume":"22","author":"Koyama","year":"2022","journal-title":"BMC Plant Biol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/genetics\/121.1.185","article-title":"Mapping Mendelian factors underlying quantitative traits using RFLP markers","volume":"121","author":"Lander","year":"1989","journal-title":"Genetics"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3390\/horticulturae9040433","article-title":"QTL mapping of leaf-related traits using a high-density bin map in Brassica rapa","volume":"9","author":"Li","year":"2023","journal-title":"Horticulturae"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.13925\/j.cnki.gsxb.20220031","article-title":"Research progress in genetic map construction and QTL mapping for disease resistance in grapevine","volume":"40","author":"Li","year":"2023","journal-title":"J. Fruit Sci."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix023","article-title":"Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics","volume":"5","author":"Lin","year":"2017","journal-title":"Gigascience"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.524","article-title":"Molecular evolution of acetohydroxyacid synthase in bacteria","volume":"6","author":"Liu","year":"2017","journal-title":"Microbiologyopen"},{"key":"B27","doi-asserted-by":"publisher","first-page":"e2322375121","DOI":"10.1073\/pnas.2322375121","article-title":"Arabidopsis protein S-acyl transferases positively mediates BR signaling through S-acylation of BSK1","volume":"121","author":"Liu","year":"2024","journal-title":"Proc. Natl. Acad. Sci. United States America"},{"key":"B28","volume-title":"Molecular mechanism of different transcription factors synergistically regulating key genes of ester biosynthesis to mediate aroma loss in cold-stored \u2018Nanguo\u2019 pears. Ph.D. Thesis","author":"Luo","year":"2022"},{"key":"B29","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1111\/pbi.13975","article-title":"Global dissection of the recombination landscape in soybean using a high-density 600K SoySNP array","volume":"21","author":"Ma","year":"2023","journal-title":"Plant Biotechnol. J."},{"key":"B30","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1186\/s12870-018-1537-5","article-title":"QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map","volume":"18","author":"Pereira","year":"2018","journal-title":"Plant Biol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"3879","DOI":"10.1007\/s00018-008-8587-z","article-title":"The MDR superfamily","volume":"65","author":"Persson","year":"2008","journal-title":"Cell. Mol. Life Sci."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Peter","year":"2008","journal-title":"BMC Bioinf."},{"key":"B33","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.hpj.2020.03.007","article-title":"Ethylene emission as a potential indicator of Fuji apple flavor quality evaluation under low temperature","volume":"6","author":"Qi","year":"2020","journal-title":"Hortic. Plant J."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhac141","article-title":"Construction of a high-density bin-map and identification of fruit quality-related quantitative trait loci and functional genes in pear","volume":"9","author":"Qin","year":"2022","journal-title":"Horticult. Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1111\/j.1365-313X.2011.04861.x","article-title":"Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening","volume":"70","author":"Qin","year":"2012","journal-title":"Plant J."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.959155","article-title":"Inheritance of esters and other volatile compounds responsible for the fruity aroma in strawberry","volume":"13","author":"Rey-Serra","year":"2022","journal-title":"Front. Plant Sci."},{"key":"B37","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41477-022-01336-2","article-title":"The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements","volume":"9","author":"Rieu","year":"2023","journal-title":"Nat. Plants"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2229-14-137","article-title":"The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population","volume":"14","author":"S\u00e1nchez","year":"2014","journal-title":"BMC Plant Biol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1104\/pp.106.093765","article-title":"A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway","volume":"144","author":"Schaffer","year":"2007","journal-title":"Plant Physiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1093\/plphys\/kiac316","article-title":"Alcohol acyl transferase genes at a high-flavor intensity locus contribute to ester biosynthesis in kiwifruit","volume":"190","author":"Souleyre","year":"2022","journal-title":"Plant Physiol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"2960","DOI":"10.1093\/hr\/uhac151","article-title":"Quantitative trait locus mapping of fruit aroma compounds in cucumber (Cucumber sativus L.) based on a recombinant inbred line population","volume":"9","author":"Sun","year":"2022","journal-title":"Horticult. Res."},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0573-1","article-title":"ALLMAPS: robust scaffold ordering based on multiple maps","volume":"16","author":"Tang","year":"2015","journal-title":"Genome Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/s0168-9452(00)00274-0","article-title":"Molecular cloning and expression of cDNAs encoding alcohol dehydrogenases from vitis vnifera L. during berry development","volume":"157","author":"Tesniere","year":"2000","journal-title":"Plant Sci."},{"key":"B45","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1111\/tpj.14795","article-title":"The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit","volume":"103","author":"Tikunov","year":"2020","journal-title":"Plant J."},{"key":"B46","volume-title":"MapQTL 6.0, software for the mapping of quantitative trait loci in experimental populations of diploid species [Z]","author":"Van Ooijen","year":"2009"},{"key":"B47","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/jhered\/93.1.77","article-title":"MapChart: software for the graphical presentation of linkage maps and QTLs","volume":"93","author":"Voorrips","year":"2002","journal-title":"J. Heredity"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1048846","article-title":"Genetic analysis and QTL mapping of aroma volatile compounds in the apple progeny \u2018Fuji\u2019\u00d7\u2019Cripps Pink\u2019","volume":"14","author":"Yang","year":"2023","journal-title":"Front. Plant Sci."},{"key":"B49","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1186\/s12864-017-4043-5","article-title":"Identification of QTLs controlling aroma volatiles using a \u2018Fortune\u2019\u00d7\u2019Murcott\u2019 (Citrus reticulata) population","volume":"18","author":"Yu","year":"2017","journal-title":"BMC Genomics"},{"key":"B50","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"B51","volume-title":"Study on apple ethylene response factor","author":"Yue","year":"2020"},{"key":"B52","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1104\/pp.20.00186","article-title":"Sensory-directed genetic and biochemical characterization of flavor-related volatile terpene production in ripe kiwifruit","volume":"183","author":"Zeng","year":"2020","journal-title":"Plant Physiol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"825","DOI":"10.3864\/j.issn.0578-1752.2022.05.001","article-title":"Mapping of QTLs for chlorophyll content in flag leaves of rice on high-density bin map","volume":"55","author":"Zhao","year":"2022","journal-title":"Sci. Agricult. Sin."},{"key":"B54","doi-asserted-by":"publisher","first-page":"1414","DOI":"10.13925\/j.cnki.gsxb.Z15","article-title":"Fruit scientific research in New China in the past 70 years: Longan","volume":"36","author":"Zheng","year":"2019","journal-title":"J. Fruit Sci."},{"key":"B55","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s12864-016-2555-z","article-title":"Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines","volume":"17","author":"Zhou","year":"2016","journal-title":"Genomics"}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2025.1642854\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T05:33:48Z","timestamp":1755149628000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2025.1642854\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,14]]},"references-count":55,"alternative-id":["10.3389\/fpls.2025.1642854"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2025.1642854","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,14]]},"article-number":"1642854"}}