Advances in Fruit Tree Genomics and Its Application in Genetics and Breeding

doi:10.16420/j.issn.0513-353x.2025-0685

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (10): 2919-2935.doi: 10.16420/j.issn.0513-353x.2025-0685

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Advances in Fruit Tree Genomics and Its Application in Genetics and Breeding

YI Guangquan, SUN Hongwen, GUO Qigao, LIANG Guolu, WANG Shuming, XIA Yan^*(), and JING Danlong^*()

College of Horticulture and Landscape Architecture， Southwest University，Key Laboratory of Agricultural Biosafety and Green Production in the Upper Reaches of the Yangtze River of Ministry of Education，Chongqing Key Laboratory of Forest Ecological Restoration and Utilization in the Three Gorges Reservoir Area，Academy of Agricultural Sciences of Southwest University， Chongqing 400715， China

Received:2026-04-24 Revised:2026-06-02 Online:2026-10-25 Published:2026-10-26
Contact: XIA Yan, and JING Danlong

Abstract

Abstract:

High-quality genome of fruit trees provides important support for precise molecular design breeding. Through comparative analysis of high-quality genomes，whole-genome duplication events in the evolution process of fruit trees are accurately predicted and the key genomic regions associated with the domestication process are identified. Combined with comparative genomics and genome-wide association analysis（GWAS），the expansion and contraction characteristics of fruit tree gene families can be effectively revealed and the key regulatory genes of important agronomic traits are identified；this provides remarkable genetic resources for fruit tree breeding. This paper reviews the application of genome sequencing technology in fruit tree genome evolution and breeding research，focuses on the important agronomic traits and provides a prospect for the future research direction and application.

Key words: fruit trees, genome, evolution, GWAS, agronomic trait, molecular breeding

CLC Number:

S 66

YI Guangquan, SUN Hongwen, GUO Qigao, LIANG Guolu, WANG Shuming, XIA Yan, and JING Danlong. Advances in Fruit Tree Genomics and Its Application in Genetics and Breeding[J]. Acta Horticulturae Sinica, 2026, 53(10): 2919-2935.

Figures/Tables 3

References 104

[1]	Al-Dous E K, George B, Al-Mahmoud M E, Al-Jaber M Y, Wang H, Salameh Y M, Al-Azwani E K, Chaluvadi S, Pontaroli A C, DeBarry J, Arondel V, Ohlrogge J, Saie I J, Suliman-Elmeer K M, Bennetzen J L, Kruegger R R, Malek J A. 2011. De novo genome sequencing and comparative genomics of date palm(Phoenix dactylifera). Nature Biotechnology, 29 (6):521-527. doi: 10.1038/nbt.1860 pmid: 21623354
[2]	Alvarez D, Cerda-Bennasser P, Stowe E, Ramirez-Torres F, Capell T, Dhingra A, Christou P. 2021. Fruit crops in the era of genome editing: closing the regulatory gap. Plant Cell Reports, 40 (6):915-930. doi: 10.1007/s00299-021-02664-x pmid: 33515309
[3]	Argout X, Salse J, Aury J M, Guiltinan M J, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova S N, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto J F, Sabot F, Kudrna D, Ammiraju J S, Schuster S C, Carlson J E, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci A M, Guignon V, Sabau X, Axtell M J, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza J M, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie W R, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C. 2011. The genome of Theobroma cacao. Nat Genetics, 43 (2):101-108.
[4]	Bao Y, Zeng Z, Yao W, Chen X, Jiang M, Sehrish A, Wu B, Powell C A, Chen B, Xu J, Zhang X, Zhang M. 2023. A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing(HLB)tolerance. Horticulture Research, 10 (4):uhad020.
[5]	Belser C, Baurens F C, Noel B, Martin G, Cruaud C, Istace B, Yahiaoui N, Labadie K, Hřibová E, Doležel J, Lemainque A, Wincker P, D'Hont A, Aury J M. 2021. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Communications Biology, 4 (1):1047. doi: 10.1038/s42003-021-02559-3 pmid: 34493830
[6]	Belser C, Istace B, Denis E, Dubarry M, Baurens F C, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P, Aury J M. 2018. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature Plants, 4 (11):879-887. doi: 10.1038/s41477-018-0289-4 pmid: 30390080
[7]	Cai Y, Gao X, Mao J, Liu Y, Tong L, Chen X, Liu Y, Kou W, Chang C, Foster T, Yao J, Cornille A, Tahir MM, Liu Z, Yan Z, Lin S, Ma F, Ma J, Xing L, An N, Zuo X, Lv Y, Zhao Z, Li W, Li Q, Zhao C, Hu Y, Liu H, Wang C, Shi X, Ma D, Fei Z, Jiang Y, Zhang D. 2024. Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology. Nature Communications, 15 (1):10082. doi: 10.1038/s41467-024-54428-2
[8]	Cao K, Wang B, Fang W, Zhu G, Chen C, Wang X, Li Y, Wu J, Tang T, Fei Z, Luo J, Wang L. 2022. Combined nature and human selections reshaped peach fruit metabolome. Genome Biology, 23 (1):146. doi: 10.1186/s13059-022-02719-6 pmid: 35788225
[9]	Cao Y, Feng X, Ding B, Huo H, Abdullah M, Hong J, Jiang L, Wang H, Li R, Cai Y, Li X, Xia Z, Varshney R K, Hu H, Lin M, Shen F. 2025. Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit. Plant Communications, 6 (3):101238. doi: 10.1016/j.xplc.2024.101238 URL
[10]	Chao D Y, Dilkes B, Luo H, Douglas A, Yakubova E, Lahner B, Salt D E. 2013. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science, 341 (6146):658-659.
[11]	Coletta R D, Qiu Y, Ou S, Hufford M B, Hirsch C N. 2021. How the pan-genome is changing crop genomics and improvement. Genome Biology, 22 (1):3. doi: 10.1186/s13059-020-02224-8 pmid: 33397434
[12]	Cornille A, Giraud T, Smulders M J, Roldán-Ruiz I, Gladieux P. 2014. The domestication and evolutionary ecology of apples. Trends in Genetics, 30 (2):57-65. doi: 10.1016/j.tig.2013.10.002 pmid: 24290193
[13]	Daccord N, Celton J M, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro E A, Gouzy J, Rees D J G, Guérif P, Muranty H, Durel C E, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E. 2017. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, 49 (7):1099-1106. doi: 10.1038/ng.3886 pmid: 28581499
[14]	D'Hont A, Denoeud F, Aury JM, Baurens F C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci A M, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P. 2012. The banana(Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488 (7410):213-217.
[15]	Dong Y, Duan S, Xia Q, Liang Z, Dong X, Margaryan K, Musayev M, Goryslavets S, Zdunić G, Bert P F, Lacombe T, Maul E, Nick P, Bitskinashvili K, Bisztray G D, Drori E, De Lorenzis G, Cunha J, Popescu C F, Arroyo-Garcia R, Arnold C, Ergül A, Zhu Y, Ma C, Wang S, Liu S, Tang L, Wang C, Li D, Pan Y, Li J, Yang L, Li X, Xiang G, Yang Z, Chen B, Dai Z, Wang Y, Arakelyan A, Kuliyev V, Spotar G, Girollet N, Delrot S, Ollat N, This P, Marchal C, Sarah G, Laucou V, Bacilieri R, Röckel F, Guan P, Jung A, Riemann M, Ujmajuridze L, Zakalashvili T, Maghradze D, Höhn M, Jahnke G, Kiss E, Deák T, Rahimi O, Hübner S, Grassi F, Mercati F, Sunseri F, Eiras-Dias J, Dumitru AM, Carrasco D, Rodriguez-Izquierdo A, Muñoz G, Uysal T, Özer C, Kazan K, Xu M, Wang Y, Zhu S, Lu J, Zhao M, Wang L, Jiu S, Zhang Y, Sun L, Yang H, Weiss E, Wang S, Zhu Y, Li S, Sheng J, Chen W. 2023. Dual domestications and origin of traits in grapevine evolution. Science, 379 (6635):892-901. doi: 10.1126/science.add8655 pmid: 36862793
[16]	Duan N, Bai Y, Sun H, Wang N, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, Liu J, Wang D, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong G Y, Cheng L, Fei Z, Chen X. 2017. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nature Communications, 8 (1):249. doi: 10.1038/s41467-017-00336-7 pmid: 28811498
[17]	Espino-Díaz M, Sepúlveda D R, González-Aguilar G, Olivas G I. 2016. Biochemistry of apple aroma:a review. Food Technological Biotechnology, 54 (4):375-397.
[18]	Fu W, Zhao L, Qiu W, Xu X, Ding M, Lan L, Qu S, Wang S. 2024. Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple. Plant Communications, 5 (9):100973. doi: 10.1016/j.xplc.2024.100973 URL
[19]	Fuller D Q. 2007. Contrasting patterns in crop domestication and domestication rates:recent archaeobotanical insights from the Old World. Annals of Botany, 100 (5):903-924. doi: 10.1093/aob/mcm048 URL
[20]	Guo L, Wang X, Ayhan D H, Rhaman MS, Yan M, Jiang J, Wang D, Zheng W, Mei J, Ji W, Jiao J, Chen S, Sun J, Yi S, Meng D, Wang J, Bhuiyan M N, Qin G, Guo L, Yang Q, Zhang X, Sun H, Liu C, Deng X W, Ye W. 2025a. Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement. Nature Genetics, 57 (3):741-753. doi: 10.1038/s41588-025-02111-7
[21]	Guo X, Su J, Xue H, Sun Y, Lian M, Ma J, Lei T, He Y, Li Q, Chen S, Yao L. 2025b. Genome-wide identification and expression analyses of ABSCISIC ACID-INSENSITIVE 5(ABI5)genes in Citrus sinensis reveal CsABI5-5 confers dual resistance to Huanglongbing and citrus canker. International Journal of Biological Macromolecules,306 (Pt 4):141611.
[22]	Hamza H, Villa S, Torre S, Marchesini A, Benabderrahim M A, Rejili M, Sebastiani F. 2023. Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars:diversity and evolutionary relationships. BMC Genomics, 24 (1):772. doi: 10.1186/s12864-023-09872-7
[23]	Han X, Zhang Y, Zhang Q, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng X W, Li D, He H. 2023. Two haplotype-resolved,gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Molecular Plant, 16 (2):452-470. doi: 10.1016/j.molp.2022.12.022 URL
[24]	Hancock J F. 2005. Contributions of domesticated plant studies to our understanding of plant evolution. Annals of Botany, 96 (6):953-963. doi: 10.1093/aob/mci259 pmid: 16159942
[25]	Hao Chenlu, Yu Xiaofen, Qu Minghao, Lai Enhui, Guo Sumin, Gao Lei. 2022. Progress and prospect of plant pangenome research. Acta Plant Sciencea Sinica,40:124-132. (in Chinese)
	郝晨路, 於晓芬, 曲明昊, 赖恩惠, 郭素敏, 高磊. 2022. 植物泛基因组研究进展与展望. 植物科学学报,40:124-132.
[26]	Hou L, Chen W, Zhang Z, Pang X, Li Y. 2020. Genome-wide association studies of fruit quality traits in jujube germplasm collections using genotyping-by-sequencing. Plant Genome, 13 (3):e20036. doi: 10.1002/tpg2.v13.3 URL
[27]	Huang G, Wu Z, Percy R G, Bai M, Li Y, Frelichowski JE, Hu J, Wang K, Yu JZ, Zhu Y. 2020. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics, 52 (5):516-524. doi: 10.1038/s41588-020-0607-4 pmid: 32284579
[28]	Huang X, Su L, Xian B, Yu Q, Zhang M, Fan J, Zhang C, Liu Y, He H, Zhong X, Li M, Chen S, He Y, Li Q. 2024. Genome-wide identification and characterization of the sweet orange(Citrus sinensis) basic helix-loop-helix(bHLH) family reveals a role for CsbHLH085 as a regulator of citrus bacterial canker resistance. International Journal of Biological Macromolecules,267 (Pt 2):131442.
[29]	Iwata H, Hayashi T, Terakami S, Takada N, Sawamura Y, Yamamoto T. 2013. Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breeding Science, 63 (1):125-140.
[30]	Jagannadham P T K, Anbalagan T, Balyan S, Satheesh V, Kamde S A, Kuthe J U, Deshpande C P, Murkute A A. 2024. Whole genome resequencing data of four Indian mandarin genotypes:extending our understanding of citrus genomics. Data in Brief,57:110896.
[31]	Jaillon O, Aury J M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon A F, Weissenbach J, Quétier F, Wincker P. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449 (7161):463-467. doi: 10.1038/nature06148
[32]	Jiang J, Hou R, Yang N, Li L, Deng J, Qin G, Ding D. 2021. Physiological and TMT-labeled proteomic analyses reveal important roles of sugar and secondary metabolism in Citrus junos under cold stress. Journal of Proteomics,237:104145.
[33]	Jin X, Du H, Zhu C, Wan H, Liu F, Ruan J, Mower JP, Zhu A. 2023. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nature Plants, 9 (8):1252-1266. doi: 10.1038/s41477-023-01473-2 pmid: 37537397
[34]	Jing D, Liu X, He Q, Dang J, Hu R, Xia Y, Wu D, Wang S, Zhang Y, Xia Q, Zhang C, Yu Y, Guo Q, Liang G. 2022. Genome assembly of wild loquat(Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat. Horticulture Research, 10 (2):uhac265.
[35]	Khadgi A, Weber C A. 2021. Genome-wide association study(GWAS)for examining the genomics controlling prickle production in red raspberry(Rubus idaeus L.). Agronomy, 11 (1):27.
[36]	Kircher M, Kelso J. 2010. High-throughput DNA sequencing-concepts and limitations. Bioessays, 32 (6):524-536. doi: 10.1002/bies.200900181 pmid: 20486139
[37]	Li Q, Qiao X, Li L, Gu C, Yin H, Qi K, Xie Z, Yang S, Zhao Q, Wang Z, Yang Y, Pan J, Li H, Wang J, Wang C, Rieseberg L H, Zhang S, Tao S. 2024a. Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits. Plant Communications, 5 (10):101000. doi: 10.1016/j.xplc.2024.101000 URL
[38]	Li W, Chu C, Zhang T, Sun H, Wang S, Liu Z, Wang Z, Li H, Li Y, Zhang X, Geng Z, Wang Y, Li Y, Zhang H, Fan W, Wang Y, Xu X, Cheng L, Zhang D, Xiong Y, Li H, Zhou B, Guan Q, Deng CH, Han Y, Ma H, Han Z. 2025. Pan-genome analysis reveals the evolution and diversity of Malus. Nature Genetics, 57 (5):1274-1286.
[39]	Li X, Pan Q. 2020. Research progress in biosynthesis and regulation of monoterpenoids in grape berry. Molecular Plant Breeding,9:2899-2906.
[40]	Li X, Yu S, Cheng Z, Chang X, Yun Y, Jiang M, Chen X, Wen X, Li H, Zhu W, Xu S, Xu Y, Wang X, Zhang C, Wu Q, Hu J, Lin Z, Aury J M, Van de Peer Y, Wang Z, Zhou X, Wang J, Lü P, Zhang L. 2024b. Origin and evolution of the triploid cultivated banana genome. Nature Genetics, 56(1):136-142. doi: 10.1038/s41588-023-01589-3
[41]	Lin X, Kaul S, Rounsley S, Shea T P, Benito M I, Town C D, Fujii C Y, Mason T, Bowman C L, Barnstead M, Feldblyum T V, Buell C R, Ketchum K A, Lee J, Ronning C M, Koo H L, Moffat K S, Cronin L A, Shen M, Pai G, Van Aken S, Umayam L, Tallon L J, Gill J E, Adams M D, Carrera A J, Creasy T H, Goodman H M, Somerville C R, Copenhaver G P, Preuss D, Nierman W C, White O, Eisen J A, Salzberg S L, Fraser C M, Venter J C. 1999. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 402 (6763):761-768.
[42]	Liu Z, Wang N, Su Y, Long Q, Peng Y, Shangguan L, Zhang F, Cao S, Wang X, Ge M, Xue H, Ma Z, Liu W, Xu X, Li C, Cao X, Ahmad B, Su X, Liu Y, Huang G, Du M, Liu Z, Gan Y, Sun L, Fan X, Zhang C, Zhong H, Leng X, Ren Y, Dong T, Pei D, Wu X, Jin Z, Wang Y, Liu C, Chen J, Gaut B, Huang S, Fang J, Xiao H, Zhou Y. 2024. Grapevine pangenome facilitates trait genetics and genomic breeding. Nature Genetics, 56 (12):2804-2814. doi: 10.1038/s41588-024-01967-5 pmid: 39496880
[43]	Lu G, Zhang K, Que Y, Li Y. 2023. Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome. Front Plant Science,14:1132551.
[44]	Luo Sifang, Yan Xiang, Xie Lifang, Sun Jingxian, Guo Zijing, Zhang Zuming, Chen Zhaoxing. 2025. Development and application of insertion-deletion(InDel)markers in Gannan wild Fortunella hindsii based on whole genome re-sequencing data. Acta Horticulturae Sinica, 52 (2):267-278. (in Chinese) doi: 10.16420/j.issn.0513-353x.2024-0357
	罗嗣芳, 严翔, 谢丽芳, 孙静贤, 郭紫晶, 张祖铭, 陈兆星. 2025. 赣南野生山金柑全基因组InDel标记开发及应用. 园艺学报, 52 (2):267-278. doi: 10.16420/j.issn.0513-353x.2024-0357
[45]	Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian K D, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham S A, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang Y J, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream M A, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert T H, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes H W, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby I K, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR. 1999. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature, 402 (6763):769-777.
[46]	Minamikawa M F, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S, Yoshioka T, Imai A, Hamada H, Hayashi T, Matsumoto S, Katayose Y, Toyoda A, Fujiyama A, Nakamura Y, Shimizu T, Iwata H. 2017. Genome-wide association study and genomic prediction in citrus:potential of genomics-assisted breeding for fruit quality traits. Scientific Reports, 7 (1):4721. doi: 10.1038/s41598-017-05100-x pmid: 28680114
[47]	Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw J H, Senin P, Wang W, Ly B V, Lewis K L, Salzberg S L, Feng L, Jones M R, Skelton R L, Murray J E, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull R E, Michael T P, Wall K, Rice D W, Albert H, Wang M L, Zhu Y J, Schatz M, Nagarajan N, Acob R A, Guan P, Blas A, Wai C M, Ackerman C M, Ren Y, Liu C, Wang J, Wang J, Na J K, Shakirov E V, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers J E, Gschwend A R, Delcher A L, Singh R, Suzuki J Y, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres M J, Feltus F A, Porter B, Li Y, Burroughs A M, Luo M C, Liu L, Christopher D A, Mount S M, Moore P H, Sugimura T, Jiang J, Schuler M A, Friedman V, Mitchell-Olds T, Shippen D E, dePamphilis C W, Palmer J D, Freeling M, Paterson A H, Gonsalves D, Wang L, Alam M. 2008. The draft genome of the transgenic tropical fruit tree papaya(Carica papaya Linnaeus). Nature, 452 (7190):991-996. doi: 10.1038/nature06856
[48]	Morgante M, De Paoli E, Radovic S. 2007. Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology, 10 (2):149-155. doi: 10.1016/j.pbi.2007.02.001 URL
[49]	O'Connor K M, Hayes B J, Hardner C M, Alam M, Henry R J, Topp B L. 2021. Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics, 22 (1):370. doi: 10.1186/s12864-021-07694-z
[50]	Peng Z, Song L, Chen M, Liu Z, Yuan Z, Wen H, Zhang H, Huang Y, Peng Z, Yang H, Li G, Zhang H, Hu Z, Li W, Wang X, Larkin RM, Deng X, Xu Q, Chen J, Xu J. 2024. Neofunctionalization of an OMT cluster dominates polymethoxyflavone biosynthesis associated with the domestication of citrus. Proc Natl Acad Sci, 121 (14):e2321615121. doi: 10.1073/pnas.2321615121 URL
[51]	Qiao Q, Edger P P, Xue L, Qiong L, Lu J, Zhang Y, Cao Q, Yocca A E, Platts A E, Knapp S J, Van Montagu M, Van de Peer Y, Lei J, Zhang T. 2021. Evolutionary history and pan-genome dynamics of strawberry(Fragaria spp.). Proceedings of the National Academy of Sciences of the United States of America, 118 (45):e2105431118.
[52]	Qin S, Xu G, He J, Li L, Ma H, Lyu D. 2023. A chromosome-scale genome assembly of Malus domestica,a multi-stress resistant apple variety. Genomics, 115 (3):110627. doi: 10.1016/j.ygeno.2023.110627 URL
[53]	Rao M J, Zuo H, Xu Q. 2020. Genomic insights into citrus domestication and its important agronomic traits. Plant Communications, 2 (1):100138. doi: 10.1016/j.xplc.2020.100138 URL
[54]	Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard J C, Couloux A, Cottret L, Aury J M, Szécsi J, Latrasse D, Madoui M A, François L, Fu X, Yang S H, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M. 2018. The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics, 50 (6):772-777. doi: 10.1038/s41588-018-0110-3
[55]	Ren J, Li W, Guo Z, Ma Z, Wan D, Lu S, Guo L, Gou H, Chen B, Mao J. 2023. Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple(Malus domestica Borkh. cv. Red delicious). BMC Plant Biology, 23 (1):607.
[56]	Ruiz M, Quiñones A, Martínez-Cuenca MR, Aleza P, Morillon R, Navarro L, Primo-Millo E, Martínez-Alcántara B. 2016. Tetraploidy enhances the ability to exclude chloride from leaves in carrizo citrange seedlings. J. Plant Physiology,205:1-10.
[57]	Salman-Minkov A, Sabath N, Mayrose I. 2016. Whole-genome duplication as a key factor in crop domestication. Nature Plants,2:16115.
[58]	Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, Zhong H, Wang Y, Zhang K, Velt A, Avia K, Holtgräwe D, Grimplet J, Matus J T, Ware D, Wu X, Wang H, Liu C, Fang Y, Rustenholz C, Cheng Z, Xiao H, Zhou Y. 2023. The complete reference genome for grapevine(Vitis vinifera L.) genetics and breeding. Horticulture Research, 10 (5):uhad061.
[59]	Shulaev V, Sargent D J, Crowhurst R N, Mockler T C, Folkerts O, Delcher A L, Jaiswal P, Mockaitis K, Liston A, Mane S P, Burns P, Davis T M, Slovin J P, Bassil N, Hellens R P, Evans C, Harkins T, Kodira C, Desany B, Crasta O R, Jensen R V, Allan A C, Michael T P, Setubal J C, Celton J M, Rees D J, Williams K P, Holt S H, Ruiz Rojas J J, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin S A, Troggio M, Viola R, Ashman T L, Wang H, Dharmawardhana P, Elser J, Raja R, Priest H D, Bryant D W Jr, Fox S E, Givan S A, Wilhelm L J, Naithani S, Christoffels A, Salama D Y, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter R A, Schwab W, Korban S S, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen J L, Salzberg S L, Dickerman A W, Velasco R, Borodovsky M, Veilleux R E, Folta K M. 2010. The genome of woodland strawberry(Fragaria vesca). Nature Genetics, 43 (2):109-116. doi: 10.1038/ng.740
[60]	Su W, Jing Y, Lin S, Yue Z, Yang X, Xu J, Wu J, Zhang Z, Xia R, Zhu J, An N, Chen H, Hong Y, Yuan Y, Long T, Zhang L, Jiang Y, Liu Z, Zhang H, Gao Y, Liu Y, Lin H, Wang H, Yant L, Lin S, Liu Z. 2021. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. Proceedings of the National Academy of Sciences of the United States of America, 118 (20):e2101767118.
[61]	Su Y, Yang X, Wang Y, Li J, Long Q, Cao S, Wang X, Liu Z, Huang S, Chen Z, Peng Y, Zhang F, Xue H, Cao X, Zhang M, Yisilam G, Chu Z, Gao Y, Zhou Y, Liu Z, Xiao H, Tian X. 2024. Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication. Plant Physiology, 195 (4):2799-2814. doi: 10.1093/plphys/kiae258 pmid: 38743633
[62]	Sun M, Yao C, Shu Q, He Y, Chen G, Yang G, Xu S, Liu Y, Xue Z, Wu J. 2023. Telomere-to-telomere pear(Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. Horticulture Research, 10 (11):uhad201.
[63]	Sun X, Jiao C, Schwaninger H, Chao CT, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong G Y, Fei Z. 2020. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics, 52 (12):1423-1432. doi: 10.1038/s41588-020-00723-9 pmid: 33139952
[64]	Sun Y, Shang L, Zhu Q H, Fan L, Guo L. 2022. Twenty years of plant genome sequencing:achievements and challenges. Trends in Plant Science, 27 (4):391-401. doi: 10.1016/j.tplants.2021.10.006 URL
[65]	Tian Wen, Li Zichen, Wang Lin, Wang Dajiang, Wang Kun, Sun Simiao, Wang Guangyi, Liu Zhao, Lu Xiang, Feng Jianrong, Gao Yuan. 2024. Advances in genome-wide association study associated important traits in apple. Acta Horticulturae Sinica, 51 (7):1565-1579. (in Chinese) doi: 10.16420/j.issn.0513-353x.2023-0818
	田雯, 李子琛, 王霖, 王大江, 王昆, 孙思邈, 王广艺, 刘昭, 路翔, 冯建荣, 高源. 2024. 苹果重要性状全基因组关联分析研究进展. 园艺学报, 51 (7):1565-1579.
[66]	Van den Broeck S, Ngapout Y, Panis B, Vanderschuren H. 2025. An Agrobacterium-mediated base editing approach generates transgene-free edited banana. New Phytologist, 247 (4):1790-1804. doi: 10.1111/nph.70044 pmid: 40170227
[67]	Van Dijk A D J, Kootstra G, Kruijer W, de Ridder D. 2020. Machine learning in plant science and plant breeding. iScience, 24 (1):101890. doi: 10.1016/j.isci.2020.101890 URL
[68]	Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar S K, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald L M, Gutin N, Lanchbury J, Macalma T, Mitchell J T, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu V T, King S T, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater M M, Masiero S, Lasserre P, Lespinasse Y, Allan A C, Bus V, Chagné D, Crowhurst R N, Gleave A P, Lavezzo E, Fawcett J A, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens R P, Durel CE, Gutin A, Bumgarner R E, Gardiner S E, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. 2010. The genome of the domes ticated apple(Malus × domestica Borkh.). Nature Genetics, 42 (10):833-839. doi: 10.1038/ng.654
[69]	Verde I, Abbott A G, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori M T, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel L A, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein D M, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner D S, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar D S. 2013. The high-quality draft genome of peach(Prunus persica) identifies unique patterns of genetic diversity,domestication and genome evolution. Nature Genetics, 45 (5):487-494. doi: 10.1038/ng.2586
[70]	Wang G, Qi K, Gao X, Guo L, Cao P, Li Q, Qiao X, Gu C, Zhang S. 2022. Genome-wide identification and comparative analysis of the PYL gene family in eight Rosaceae species and expression analysis of seeds germination in pear. BMC Genomics, 23 (1):233. doi: 10.1186/s12864-022-08456-1 pmid: 35337257
[71]	Wang L, He F, Huang Y, He J, Yang S, Zeng J, Deng C, Jiang X, Fang Y, Wen S, Xu R, Yu H, Yang X, Zhong G, Chen C, Yan X, Zhou C, Zhang H, Xie Z, Larkin R M, Deng X, Xu Q. 2018a. Genome of wild mandarin and domestication history of mandarin. Molecular Plant, 11 (8):1024-1037. doi: 10.1016/j.molp.2018.06.001 URL
[72]	Wang P, Luo Y, Huang J, Gao S, Zhu G, Dang Z, Gai J, Yang M, Zhu M, Zhang H, Ye X, Gao A, Tan X, Wang S, Wu S, Cahoon E B, Bai B, Zhao Z, Li Q, Wei J, Chen H, Luo R, Gong D, Tang K, Zhang B, Ni Z, Huang G, Hu S, Chen Y. 2020. The genome evolution and domestication of tropical fruit mango. Genome Biology, 21 (1):60. doi: 10.1186/s13059-020-01959-8 pmid: 32143734
[73]	Wang R, Li X, Sun M, Xue C, Korban S S, Wu J. 2023a. Genomic insights into domestication and genetic improvement of fruit crops. Plant Physiologist, 192 (4):2604-2627. doi: 10.1093/plphys/kiad273 URL
[74]	Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. 2023b. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nature Communication, 14 (1):7377. doi: 10.1038/s41467-023-43270-7
[75]	Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes R R, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis K C, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat V J, Borja F N, Mendoza J R, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo M E B, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann J C, Zhang J, Li J, Hamilton R S, Wing R A, Ruan J, Zhang G, Wei C, Alexandrov N, McNally K L, Li Z, Leung H. 2018b. Genomic variation in 3 010 diverse accessions of Asian cultivated rice. Nature, 557 (7703):43-49. doi: 10.1038/s41586-018-0063-9
[76]	Wang X, Liu Z, Zhang F, Xiao H, Cao S, Xue H, Liu W, Su Y, Liu Z, Zhong H, Zhang F, Ahmad B, Long Q, Zhang Y, Liu Y, Gan Y, Hou T, Jin Z, Wu X, Liu G, Wang Y, Peng Y, Zhou Y. 2024b. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Current Biology, 34 (16):3763-3777. doi: 10.1016/j.cub.2024.07.022 URL
[77]	Wang Y, Li P, Zhu Y, Zhang F, Zhang S, He Y, Wu Y, Lin Y, Wang H, Ren W, Wang L, Yang Y, Wang R, Zheng P, Liu Y, Wang S, Yue J. 2024c. Graph-based pangenome of Actinidia chinensis reveals structural variations mediating fruit degreening. Advanced Science(Weinh), 11 (28):e2400322.
[78]	Wang Y, Paterson A H. 2021. Loquat(Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two‐staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach. The Plant Journal, 106 (4):942-952. doi: 10.1111/tpj.v106.4 URL
[79]	Wang Y, Xin H, Fan P, Zhang J, Liu Y, Dong Y, Wang Z, Yang Y, Zhang Q, Ming R, Zhong G Y, Li S, Liang Z. 2021. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine. The Plant Journal, 105 (6):1495-1506. doi: 10.1111/tpj.15127 pmid: 33300184
[80]	Wei X, Chen M, Zhang X, Wang Y, Li L, Xu L, Wang H, Jiang M, Wang C, Zeng L, Xu J. 2023. The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry). Horticulture Research, 10 (12):uhad214.
[81]	Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan M A, Tao S, Korban S S, Wang H, Chen N J, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull R E, Bennetzen J L, Wang J, Zhang S. 2012. The genome of the pear(Pyrus bretschneideri Rehd.). Genome Research, 23 (2):396-408. doi: 10.1101/gr.144311.112 URL
[82]	Xanthopoulou A, Manioudaki M, Bazakos C, Kissoudis C, Farsakoglou AM, Karagiannis E, Michailidis M, Polychroniadou C, Zambounis A, Kazantzis K, Tsaftaris A, Madesis P, Aravanopoulos F, Molassiotis A. 2020. Ganopoulos I. Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species. Horticulture Research,7:60.
[83]	Xia H, Deng H, Li M, Xie Y, Lin L, Zhang H, Luo X, Lv X, Wang J, Liang D. 2023. Chromosome-scale genome assembly of a natural diploid kiwifruit(Actinidia chinensis var. deliciosa). Scientific Data, 10 (1):92.
[84]	Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, Sun Y, Wu D, Ye C, Zhu Q H, Fan L. 2024. Technology-enabled great leap in deciphering plant genomes. Nature Plants, 10 (4):551-566. doi: 10.1038/s41477-024-01655-6 pmid: 38509222
[85]	Xie Y, Zhang T, Yang M, Lyu H, Zou Y, Sun Y, Xiao J, Lian W, Tao J, Han H, Xu C. 2025. Engineering crop flower morphology facilitates robotization of cross-pollination and speed breeding. Cell, 188 (21):5809-5830. doi: 10.1016/j.cell.2025.07.028 pmid: 40795858
[86]	Xing S, Chen K, Zhu H, Zhang R, Zhang H, Li B, Gao C. 2020. Fine-tuning sugar content in strawberry. Genome Biology, 21 (1):230. doi: 10.1186/s13059-020-02146-5 pmid: 32883370
[87]	Xiong Z, Yin H, Wang N, Han G, Gao Y. 2024. Chromosome-level genome assembly of navel orange cv. Gannanzao(Citrus sinensis Osbeck cv. Gannanzao). G3(Bethesda), 14 (2):jkad268.
[88]	Xu Q, Chen L L, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao W B, Hao B H, Lyon M P, Chen J, Gao S, Xing F, Lan H, Chang J W, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas M K, Zeng W, Guo F, Cao H, Yang X, Xu X W, Cheng Y J, Xu J, Liu J H, Luo O J, Tang Z, Guo W W, Kuang H, Zhang H Y, Roose M L, Nagarajan N, Deng X X, Ruan Y. 2012. The draft genome of sweet orange(Citrus sinensis). Nature Genetics, 45 (1):59-66. doi: 10.1038/ng.2472
[89]	Yan Bei, Lu Yongbin, Shi Yan, Wang Haifeng. 2022. Identification of DNA methyltransferase gene family and its expression during fruit development in mango. Genomics and Applied Biology,41:1495-1504. (in Chinese)
	严贝, 卢永彬, 石岩, 王海峰. 2022. 芒果DNA甲基转移酶基因家族鉴定及其在果实发育过程的表达研究. 基因组学与应用生物学,41:1495-1504.
[90]	Yan C, Liu W, Li R, Liu G, Wang Y. 2025. VqERF1B-VqERF062-VqNSTS2 transcriptional cascade enhances stilbene biosynthesis and resistance to powdery mildew in grapevine. Plant Biotechnology Journal, 23 (6):2065-2082. doi: 10.1111/pbi.v23.6 URL
[91]	Yang H, Zou Y, Li X, Zhang M, Zhu Z, Xu R, Xu J, Deng X, Cheng Y. 2022. QTL analysis reveals the effect of CER1-1 and CER1-3 to reduce fruit water loss by increasing cuticular wax alkanes in citrus fruit. Postharvest Biology and Technology,185:111771.
[92]	Yang T, Cai Y, Huang T, Yang D, Yang X, Yin X, Zhang C, Yang Y, Yang Y. 2024. A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance. Horticulture Research, 11 (7):uhae119.
[93]	Yin M, Song X, He C, Li X, Li M, Li J, Wu H, Chen C, Zhang L, Cai Z, Lu L, Xu Y, Wang X, Yi H, Wu J. 2025. The haplotype-resolved genome assembly of an ancient citrus variety provides insights into the domestication history and fruit trait formation of loose-skin mandarins. Genome Biology, 26 (1):61. doi: 10.1186/s13059-025-03535-4 pmid: 40098183
[94]	Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna R R, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey S B, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. 2024. A chromosome-scale assembly for ‘d’Anjou’ pear. G3 Genes(Bethesda),14 (3):jkae003.
[95]	Yu X N, Guo Y, Yang Q, Yu H, Lu M J, Zhao L, Jin Z S, Xu X N, Feng J Y, Wen Y Q. 2024. Chimeric mutations in grapevine ENHANCED DISEASE RESISTANCE1 improve resistance to powdery mildew without growth penalty. Plant Physiologist, 195 (3):1995-2015. doi: 10.1093/plphys/kiae169 URL
[96]	Yue Q, Xie Y, Yang X, Zhang Y, Li Z, Liu Y, Cheng P, Zhang R, Yu Y, Wang X, Liao L, Han Y, Zhao T, Li X, Zhang H, Ma F, Guan Q. 2024. An InDel variant in the promoter of the NAC transcription factor MdNAC18.1 plays a major role in apple fruit ripening. Plant Cell, 37 (1):koaf007.
[97]	Zhang H, Ko I, Eaker A, Haney S, Khuu N, Ryan K, Appleby A B, Hoffmann B, Landis H, Pierro K A Jr, Willsea N, Hargarten H, Yocca AE, Harkess A, Honaas L, Ficklin S. 2024a. A haplotype-resolved,chromosome-scale genome for Malus domestica Borkh.‘WA 38’. G3 Genes(Bethesda),14 (12):jkae222.
[98]	Zhang H, Lian X, Gao F, Song C, Feng B, Zheng X, Wang X, Hou N, Cheng J, Wang W, Zhang L, Li J, Ye X, Feng J, Tan B. 2025. A gap-free genome of pillar peach(Prunus persica L.) provides new insights into branch angle and double flower traits. Plant Biotechnology Journal, 23 (1):81-83. doi: 10.1111/pbi.v23.1 URL
[99]	Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang G F, Xu X, Ma Z, Zhou Y. 2024b. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. Journal of Integrative Plant Biology, 66 (7):1408-1426. doi: 10.1111/jipb.v66.7 URL
[100]	Zhang W, Liao L, Xu J, Han Y, Li L. 2021. Genome-wide identification,characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh). BMC Genomics, 22 (1):632. doi: 10.1186/s12864-021-07943-1
[101]	Zhang Y, Jin J, Wang N, Sun Q, Feng D, Zhu S, Wang Z, Li S, Ye J, Chai L, Xie Z, Deng X. 2024c. Cytochrome P450 CitCYP97B modulates carotenoid accumulation diversity by hydroxylating β-cryptoxanthin in Citrus. Plant Communication, 5 (6):100847.
[102]	Zhang Y, Zhao M, Tan J, Huang M, Chu X, Li Y, Han X, Fang T, Tian Y, Jarret R, Lu D, Chen Y, Xue L, Li X, Qin G, Li B, Sun Y, Deng X W, Deng Y, Zhang X, He H. 2024d. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics, 56 (8):1750-1761. doi: 10.1038/s41588-024-01823-6
[103]	Zhou T, Huang X J, Cheng Y J, Zhang X Y, Wang X J, Li Z H. 2025. Telomere-to-telomere genome and multi-omics analysis of Prunus avium cv. Tieton provides insights into its genomic evolution and flavonoid biosynthesis. International Journal of Biological Macromolecules, 306 (Pt4):141809. doi: 10.1016/j.ijbiomac.2025.141809 URL
[104]	Zhu K, Chen H, Mei X, Lu S, Xie H, Liu J, Chai L, Xu Q, Wurtzel E T, Ye J, Deng X. 2023. Transcription factor CsMADS3 coordinately regulates chlorophyll and carotenoid pools in Citrus hesperidium. Plant Physiologist, 193 (1):519-536.

物种 Species	主要研究内容 Main research content	组装级别 Assembly level	参考文献 Reference
苹果 Malus × domestica	苹果多抗品种染色体级基因组组装 Chromosome-level genome assembly of multi-resistant apple cultivar	染色体级 Chromosome-level	Qin et al.,2023
	苹果四代突变体全基因组重测序和转录组分析 Whole-genome resequencing and transcriptome analysis of four-generation apple mutants	染色体级 Chromosome-level	Ren et al.,2023
	13个苹果种质资源泛基因组分析揭示性状相关基因结构和序列变异 Pan-genome analysis of 13 apple germplasms reveals structural and sequence variations of trait-related genes	染色体级 Chromosome-level	Wang et al.,2023b
	全基因组重测序数据鉴定与苹果果酸和果糖含量相关的候选基因和等位基因变异 Identification of candidate genes and allelic variations associated with malic acid and fructose content in apple based on whole-genome resequencing data	染色体级 Chromosome-level	Fu et al.,2024
	苹果单倍型阶段染色体水平基因组“WA 38” Chromosome-level haplotype-resolved genome of apple“WA 38”	单倍型染色体级 Haplotype-resolved chromosome-level	Zhang et al.,2024a
	泛基因组分析揭示了Malus的进化和多样性 Pan-genome analysis reveals the evolution and diversity of Malus	染色体级 Chromosome-level	Li et al.,2025
莲雾 Syzygium samarangense	单倍型解析的四倍体基因组组装为莲雾的基因组进化和果实分化提供了见解 Haplotype-resolved tetraploid genome assembly provides insights into the genomic evolution and fruit differentiation of wax apple	单倍型染色体级 Haplotype-resolved chromosome-level	Wei et al.,2023
梨 Pyrus pyrifolia	端粒到端粒梨的参考基因组分析揭示了驱动基因组进化的节段和全基因组重复 Telomere-to-telomere reference genome analysis of pear reveals segmental and whole-genome duplications driving genome evolution	T2T级别Telomere-to-telomere level	Sun et al.,2023
	‘d'Anjou’ 梨的染色体级基因组组装 Chromosome-level genome assembly of 'd'Anjou' pear	染色体级 Chromosome-level	Yocca et al.,2024
	单倍型解析的 T2T 基因组组装和梨的泛基因组图揭示了性状相关基因Haplotype-resolved T2T genome assembly and pan-genome map of pear reveal trait-related genes	T2T级别Telomere-to-telomere level	Li et al.,2024
椰枣 Phoenix dactylifera	椰枣品种的全线粒体和叶绿体基因组测序：多样性和进化关系 Complete mitochondrial and chloroplast genome sequencing of date palm cultivars：diversity and evolutionary relationships	线粒体和叶绿体级Mitochondrial and chloroplast-level	Hmaza et al.,2023
猕猴桃 Actinidia chinensis	猕猴桃天然二倍体染色体级基因组组装 Chromosome-level genome assembly of natural diploid kiwifruit	染色体级Chromosome-level	Xia et al.,2023
	猕猴桃泛基因组揭示了介导果实颜色和品质的结构变异 Pan-genome of kiwifruit reveals structural variations mediating fruit color and quality	染色体级 Chromosome-level	Wang et al.,2024c
石榴 Punica granatum	石榴第1个完整线粒体基因组的组装和分析以及叶绿体基因组分析 Assembly and analysis of the first complete mitochondrial genome and chloroplast genome analysis of pomegranate	线粒体和叶绿体级Mitochondrial and chloroplast-level	Lu et al.,2023
草莓 Fragaria vesca	草莓的进化历史和泛基因组动力学 Evolutionary history and pan-genome dynamics of strawberry	染色体级Chromosome-level	Qiao et al.,2021
	野生草莓单倍型基因组分析阐明了草莓野生种到栽培种的基因组多样性 Haplotype genome analysis of wild strawberry elucidates genomic diversity from wild to cultivated strawberry species	单倍型染色体级Haplotype-resolved chromosome-level	Jin et al.,2023
柑橘 Citrus	4种印度柑橘基因型的全基因组重测序结果分析 Whole-genome resequencing analysis of four indian citrus genotypes	染色体级 Chromosome-level	Jagannadham et al.,2024
脐橙 Citrus sinensis	脐橙品种染色体水平基因组组装与分析 Chromosome-level genome assembly and analysis of navel orange cultivars	染色体级 Chromosome-level	Xiong et al.,2024
西瓜 Citrullus lanatus	首个西瓜T2T超级泛基因组组装揭示西瓜进化和驯化过程 Assembly of the first watermelon T2T super pan-genome reveals the evolution and domestication process of watermelon	T2T级别 Telomere-to-telomere level	Zhang et al.,2024d
葡萄 Vitis vinifera	葡萄超级泛基因组分析鉴定抗霜霉病相关基因 Super pan-genome analysis of grape identifies genes associated with downy mildew resistance	染色体级 Chromosome-level	Guo et al.,2025a

物种 Species	主要研究内容 Main research content	组装级别 Assembly level	参考文献 Reference
苹果 Malus × domestica	苹果多抗品种染色体级基因组组装 Chromosome-level genome assembly of multi-resistant apple cultivar	染色体级 Chromosome-level	Qin et al.,2023
	苹果四代突变体全基因组重测序和转录组分析 Whole-genome resequencing and transcriptome analysis of four-generation apple mutants	染色体级 Chromosome-level	Ren et al.,2023
	13个苹果种质资源泛基因组分析揭示性状相关基因结构和序列变异 Pan-genome analysis of 13 apple germplasms reveals structural and sequence variations of trait-related genes	染色体级 Chromosome-level	Wang et al.,2023b
	全基因组重测序数据鉴定与苹果果酸和果糖含量相关的候选基因和等位基因变异 Identification of candidate genes and allelic variations associated with malic acid and fructose content in apple based on whole-genome resequencing data	染色体级 Chromosome-level	Fu et al.,2024
	苹果单倍型阶段染色体水平基因组“WA 38” Chromosome-level haplotype-resolved genome of apple“WA 38”	单倍型染色体级 Haplotype-resolved chromosome-level	Zhang et al.,2024a
	泛基因组分析揭示了Malus的进化和多样性 Pan-genome analysis reveals the evolution and diversity of Malus	染色体级 Chromosome-level	Li et al.,2025
莲雾 Syzygium samarangense	单倍型解析的四倍体基因组组装为莲雾的基因组进化和果实分化提供了见解 Haplotype-resolved tetraploid genome assembly provides insights into the genomic evolution and fruit differentiation of wax apple	单倍型染色体级 Haplotype-resolved chromosome-level	Wei et al.,2023
梨 Pyrus pyrifolia	端粒到端粒梨的参考基因组分析揭示了驱动基因组进化的节段和全基因组重复 Telomere-to-telomere reference genome analysis of pear reveals segmental and whole-genome duplications driving genome evolution	T2T级别Telomere-to-telomere level	Sun et al.,2023
	‘d'Anjou’ 梨的染色体级基因组组装 Chromosome-level genome assembly of 'd'Anjou' pear	染色体级 Chromosome-level	Yocca et al.,2024
	单倍型解析的 T2T 基因组组装和梨的泛基因组图揭示了性状相关基因Haplotype-resolved T2T genome assembly and pan-genome map of pear reveal trait-related genes	T2T级别Telomere-to-telomere level	Li et al.,2024
椰枣 Phoenix dactylifera	椰枣品种的全线粒体和叶绿体基因组测序：多样性和进化关系 Complete mitochondrial and chloroplast genome sequencing of date palm cultivars：diversity and evolutionary relationships	线粒体和叶绿体级Mitochondrial and chloroplast-level	Hmaza et al.,2023
猕猴桃 Actinidia chinensis	猕猴桃天然二倍体染色体级基因组组装 Chromosome-level genome assembly of natural diploid kiwifruit	染色体级Chromosome-level	Xia et al.,2023
	猕猴桃泛基因组揭示了介导果实颜色和品质的结构变异 Pan-genome of kiwifruit reveals structural variations mediating fruit color and quality	染色体级 Chromosome-level	Wang et al.,2024c
石榴 Punica granatum	石榴第1个完整线粒体基因组的组装和分析以及叶绿体基因组分析 Assembly and analysis of the first complete mitochondrial genome and chloroplast genome analysis of pomegranate	线粒体和叶绿体级Mitochondrial and chloroplast-level	Lu et al.,2023
草莓 Fragaria vesca	草莓的进化历史和泛基因组动力学 Evolutionary history and pan-genome dynamics of strawberry	染色体级Chromosome-level	Qiao et al.,2021
	野生草莓单倍型基因组分析阐明了草莓野生种到栽培种的基因组多样性 Haplotype genome analysis of wild strawberry elucidates genomic diversity from wild to cultivated strawberry species	单倍型染色体级Haplotype-resolved chromosome-level	Jin et al.,2023
柑橘 Citrus	4种印度柑橘基因型的全基因组重测序结果分析 Whole-genome resequencing analysis of four indian citrus genotypes	染色体级 Chromosome-level	Jagannadham et al.,2024
脐橙 Citrus sinensis	脐橙品种染色体水平基因组组装与分析 Chromosome-level genome assembly and analysis of navel orange cultivars	染色体级 Chromosome-level	Xiong et al.,2024
西瓜 Citrullus lanatus	首个西瓜T2T超级泛基因组组装揭示西瓜进化和驯化过程 Assembly of the first watermelon T2T super pan-genome reveals the evolution and domestication process of watermelon	T2T级别 Telomere-to-telomere level	Zhang et al.,2024d
葡萄 Vitis vinifera	葡萄超级泛基因组分析鉴定抗霜霉病相关基因 Super pan-genome analysis of grape identifies genes associated with downy mildew resistance	染色体级 Chromosome-level	Guo et al.,2025a

Advances in Fruit Tree Genomics and Its Application in Genetics and Breeding

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