Description

An apple is a round, edible fruit produced by an apple tree (Malus spp., among them the domestic or orchard apple; Malus domestica). Apple trees are cultivated worldwide and are the most widely grown species in the genus Malus. The tree originated in Central Asia, where its wild ancestor, Malus sieversii, is still found. Apples have been grown for thousands of years in Asia and Europe and were introduced to North America by European colonists. Apples have religious and mythological significance in many cultures, including Norse, Greek, and European Christian tradition.

Apples grown from seed tend to be very different from those of their parents, and the resultant fruit frequently lacks desired characteristics. For commercial purposes, including botanical evaluation, apple cultivars are propagated by clonal grafting onto rootstocks. Apple trees grown without rootstocks tend to be larger and much slower to fruit after planting. Rootstocks are used to control the speed of growth and the size of the resulting tree, allowing for easier harvesting.

There are more than 7,500 cultivars of apples. Different cultivars are bred for various tastes and uses, including cooking, eating raw, and cider or apple juice production. Trees and fruit are prone to fungal, bacterial, and pest problems, which can be controlled by a number of organic and non-organic means. In 2010, the fruit's genome was sequenced as part of research on disease control and selective breeding in apple production.

Worldwide production of apples in 2021 was 93 million tonnes, with China accounting for nearly half of the total.

Apples are diploid (though triploid cultivars are not uncommon), have 17 chromosomes and an estimated genome size of approximately 650 Mb. Several whole genome sequences have been completed and made available. The first one in 2010 was based on the diploid cultivar 'Golden Delicious'. However, this first whole genome sequence turned out to contain several errors in part owing to the high degree of heterozygosity in diploid apples which, in combination with an ancient genome duplication, complicated the assembly. Recently, double- and trihaploid individuals have been sequenced, yielding whole genome sequences of higher quality.

The first whole genome assembly was estimated to contain around 57,000 genes, though the more recent genome sequences support estimates between 42,000 and 44,700 protein-coding genes. The availability of whole genome sequences has provided evidence that the wild ancestor of the cultivated apple most likely is Malus sieversii. Re-sequencing of multiple accessions has supported this, while also suggesting extensive introgression from Malus sylvestris following domestication.

Whole Genomes

Whole Genome Sequences & Annotations for Malus domestica

• Malus x domestica HFTH1
• Malus x domestica ASM211411v1

S genes

Malus x domestica HFTH1 S genes

Query	Chr	Size(bp)	Coordinates	Domain
MdSFBB.XVI-S9	Chr 17	33998825	29860443-29861630	F-box; F_box_assoc
MdSFBB.XVII-S9	Chr 17	33998825	29880819-29879614	F-box; F_box_assoc
MdSFBB.XIV-S9	Chr 17	33998825	29883107-29884312	F-box; F_box_assoc
MdSFBB.Ib-S9	Chr 17	33998825	29943756-29942554	F-box; F_box_assoc
MdSFBB.VI-S9	Chr 17	33998825	29999810-29998632	F-box; F_box_assoc
MdSFBB.III-S9	Chr 17	33998825	30121504-30122685	F-box; F_box_assoc
MdSFBB.II-S9	Chr 17	33998825	30224230-30225423	F-box; F_box_assoc
MdSFBB.IV-S9	Chr 17	33998825	30236989-30238173	F-box; F_box_assoc
MdSFBB.XV-S9	Chr 17	33998825	30289634-30290848	F-box; F_box_assoc
MdSFBB.Ia-S9	Chr 17	33998825	30392432-30393634	F-box; F_box_assoc
MdSFBB.X-S9	Chr 17	33998825	30477857-30476676	F-box; F_box_assoc
MdSFBB.XI-S9	Chr 17	33998825	30520884-30519700	F-box; F_box_assoc
MdSFBB.XII-S9	Chr 17	33998825	30649328-30648156	F-box; F_box_assoc
MdSFBB.XVIII-S9	Chr 17	33998825	30716312-30715128	F-box; F_box_assoc
MdSFBB.VII-S9	Chr 17	33998825	30787708-30786530	F-box; F_box_assoc
S9-RNase	Chr 17	33998825	30891703-30891452,30891307-30890873	RNase_T2
MdSFBB.V-S9	Chr 17	33998825	30933865-30935043	F-box; F_box_assoc
MdSFBB.VIII.2-S9	Chr 17	33998825	31068766-31067573	F-box; F_box_assoc
MdSFBB.VIII.1-S9	Chr 17	33998825	31116911-31115721	F-box; F_box_assoc
MdSFBB.XXI-S9	Chr 17	33998825	31827099-31828448	F-box; F_box_assoc

Downloads

The Malus x domestica S gene sequences are available in FASTA format.

CDS and Protein (FASTA file)

S-gene_Malus_x_domestica

Publications

Velasco, R., Zharkikh, A., Affourtit, J. et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42, 833–839 (2010). https://doi.org/10.1038/ng.654

Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017 Jul;49(7):1099-1106. doi: 10.1038/ng.3886.

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 GY, Cheng L, Fei Z, Chen X. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nat Commun. 2017 Aug 15;8(1):249. doi: 10.1038/s41467-017-00336-7.

Sun X, Jiao C, Schwaninger H, Chao CT, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong GY, Fei Z. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet. 2020 Dec;52(12):1423-1432. doi: 10.1038/s41588-020-00723-9.

Qin S, Xu G, He J, Li L, Ma H, Lyu D. A chromosome-scale genome assembly of Malus domestica, a multi-stress resistant apple variety. Genomics. 2023 May;115(3):110627. doi: 10.1016/j.ygeno.2023.110627.

Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H, Wang D, Tian Y, Yang C, Meng M, Yuan G, Kang G, Wu Y, Wang K, Zhang H, Wang D, Cong P. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun. 2019 Apr 2;10(1):1494. doi: 10.1038/s41467-019-09518-x.

Khan A, Carey SB, Serrano A, Zhang H, Hargarten H, Hale H, Harkess A, Honaas L. A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica). GigaByte. 2022 Sep 19;2022:gigabyte69. doi: 10.46471/gigabyte.69.