Haplotype bias detection using pedigree-based transmission simulation: traces of selection that occurred in apple breeding

Abstract

Breeding perennial fruit trees like apple is constrained by long generation times and limited population sizes, which often lead to repeated use of a few elite cultivars and consequently narrow genetic diversity. To better understand how such selection processes have shaped the current genetic structure, we applied gene-drop simulations—a pedigree-based method using known parentage and genetic maps—to a curated set of 185 apple cultivars used in Japanese breeding programs, genotyped with 11 786 genome-wide single nucleotide polymorphism markers. This approach enabled us to quantify the expected distribution of founder haplotypes and identify genomic regions where observed founder haplotype frequencies significantly deviated from expectation, suggesting potential selection. Notably, biased regions overlapped with loci associated with key fruit traits, such as fructose content, exemplified by an increase in haplotypes from “Golden Delicious.” Furthermore, Gene Ontology analysis revealed enrichment for regions containing genes involved in stress-related and developmental functions, pointing to broader physiological traits under selection. Unlike traditional methods requiring phenotype data, our approach does not depend on trait measurements and can thus uncover cryptic selection signals, including traits that were not explicitly targeted during breeding. This method offers a framework for identifying overlooked genetic regions and underutilized founder alleles, which can be reintroduced to broaden the genetic base and improve breeding outcomes. Furthermore, the approach is adaptable to other perennial crops with available pedigree and genomic data. Our findings demonstrate the power of integrating pedigree structure with genomic information to reveal both historical and ongoing selection in structured breeding populations.

Author contributions

H.M., M.F.M., K.H., and H.I. conceived and designed the study. M. K., S. M., Y. K., and T. Y. extracted DNA, designed the SNP genotyping array, and performed SNP genotyping. S.M. performed phenotyping. M.F.M., M.K., and H.I. traced founder haplotypes. M.F.M. and K.N. performed GWAS. H.M., M.F.M., and K.H. performed gene-drop simulations. H.M. and M. F. M. checked the annotation and performed the GO enrichment analysis. M. F. M., K.H., and H.I. provided technical help for the statistical analysis. H.M., M.F.M., and H.I. drafted the manuscript. All the authors have read and approved the final manuscript.

Data availability

The genotype and phenotype data used in this study are publicly available from Minamikawa et al. (2021) [DOI: 10.1038/s41438-021-00485-3], which provides access to the DNA marker and trait datasets used for Japanese apple breeding. No new datasets were generated during the current study. Information on DNA markers is available from Supplementary Data Table.

Conflicts of interest statement

The authors declare that they have no conflict of interests.

Supplementary material

Supplementary material is available at Horticulture Research online.

References

[1] Janick J, Moore JN,eds. Fruit Breeding. Nashville, TN: John Wiley & Sons; 1996:

[2] Long S, Li M, Han Z. et al. Characterization of three new S-alleles and development of an S-allele-specific PCR system for rapidly identifying the S-genotype in apple cultivars. Tree Genet Genomes. 2010; 6:161-8

[3] Kovach MJ, Calingacion MN, Fitzgerald MA. et al. The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci USA. 2009; 106:14444-9

[4] Muranty H, Troggio M, Sadok IB. et al. Accuracy and responses of genomic selection on key traits in apple breeding. Hortic Res. 2015; 2:15060

[5] Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010; 11:31-46

[6] Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005; 6:95-108

[7] Minamikawa MF, Kunihisa M, Noshita K. et al. Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study. Hortic Res. 2021; 8:49

[8] Migicovsky Z, Gardner KM, Money D. et al. Genome to phenotype mapping in apple using historical data. Plant Genome. 2016;9:lantgenome2015.11.0113

[9] Amyotte B, Bowen AJ, Banks T. et al. Mapping the sensory perception of apple using descriptive sensory evaluation in a genome wide association study. PLoS One. 2017; 12: e0171710

[10] Iwata H, Uga Y, Yoshioka Y. et al. Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Züchter Genet Breed Res. 2007; 114:1437-49

[11] Maccaferri M, Zhang J, Bulli P. et al. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of Hexaploid Spring wheat (Triticum aestivum L.). G3 (Bethesda). 2015; 5:449-65

[12] Tian F, Bradbury PJ, Brown PJ. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet. 2011; 43:159-62

[13] Minamikawa MF, Takada N, Terakami S. et al. Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai). Sci Rep. 2018; 8:11994

[14] Lacy RC. Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biol. 1989; 8:111-23

[15] Abecasis GR, Cherny SS, Cookson WO. et al. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002; 30:97-101

[16] Yamashita J, Oki H, Hasegawa T. et al. Gene dropping analysis of ancestral contributions and allele survival in Japanese thoroughbred population. J Equine Sci. 2010; 21:39-45

[17] Shaw PD, Graham M, Kennedy J. et al. Helium: visualization of large scale plant pedigrees. BMC Bioinformatics. 2014; 15:259

[18] Kunihisa M, Moriya S, Abe K. et al. Genomic dissection of a “Fuji” apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection. Breed Sci. 2016; 66:499-515

[19] Ashburner M, Ball CA, Blake JA. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-9

[20] Grembecka M. Natural sweeteners in a human diet. Rocz Panstw Zakl Hig. 2015; 66:195-202

[21] Veberic R, Zadravec P, Stampar F. Fruit quality of ‘Fuji’ apple (Malus domestica Borkh.) strains. J Sci Food Agric. 2007; 87:593-9

[22] Aprea E, Charles M, Endrizzi I. et al. Sweet taste in apple: the role of sorbitol, individual sugars, organic acids and volatile compounds. Sci Rep. 2017; 7:44950

[23] Liao L, Zhang W, Zhang B. et al. Unraveling a genetic roadmap for improved taste in the domesticated apple. Mol Plant. 2021; 14:1454-71

[24] Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK. Why we thrive beneath a northern sky—genomic signals of selection in apple for adaptation to northern Sweden. Heredity (Edinb). 2024; 133:67-77

[25] Wang N, Liu W, Yu L. et al. HEAT SHOCK FACTOR A8a modulates flavonoid synthesis and drought tolerance. Plant Physiol. 2020; 184:1273-90

[26] Wei Y, Hu W, Xia F. et al. Heat shock transcription factors in banana: genome-wide characterization and expression profile analysis during development and stress response. Sci Rep. 2016; 6:6.

[27] Li S-Y, Zhang Q, Jin Y-H. et al. A MADS-box gene, EgMADS21, negatively regulates EgDGAT2 expression and decreases polyunsaturated fatty acid accumulation in oil palm (Elaeis guineensis Jacq.). Plant Cell Rep. 2020; 39:1505-16

[28] Koo SC, Bracko O, Park MS. et al. Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE6. Plant J. 2010; 62:807-16

[29] Zheng Y, Ren N, Wang H. et al. Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. Plant Cell. 2009; 21:2563-77

[30] Hugouvieux V, Silva CS, Jourdain A. et al. Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis. Nucleic Acids Res. 2018; 46:4966-77

[31] Lui S, Luo C, Zhu L. et al. Identification and expression analysis of WRKY transcription factor genes in response to fungal pathogen and hormone treatments in apple (Malus domestica). J Plant Biol. 2017; 60:215-30

[32] Li W, Wang H, Yu D. Arabidopsis WRKY transcription factors WRKY12 and WRKY13 oppositely regulate flowering under short-day conditions. Mol Plant. 2016; 9:1492-503

[33] Abe K, Iwanami H, Kotoda N. et al. Evaluation of apple genotypes and Malus species for resistance to Alternaria blotch caused by Alternaria alternata apple pathotype using detached-leaf method. Plant Breed. 2010; 129:208-18

[34] Badenes ML. Trends in Fruit Breeding. In: Byrne DH,ed. Fruit Breeding. Springer: Boston, MA, 2012.

[35] Moriya S, Shimizu T, Okada K. et al. DNA marker-assisted crossbreeding of Japanese apples. Hortic Res. 2024; 23: 163-78

[36] Sobiczewski P, Keller-Przybyłkowicz S, Lewandowski M. et al. Phenotypic and marker-assisted characterization of new apple genotypes with high resistance to fire blight. Eur J Plant Pathol. 2021; 161:49-61

[37] Omura M, Shimada T. Citrus breeding, genetics and genomics in Japan. Breed Sci. 2016; 66:3-17

[38] Li X-W, Meng XQ, Jia HJ. et al. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genet. 2013; 14:84

[39] Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81:1084-97

[40] Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001; 157:1819-29

[41] Iwata H, Hayashi T, Terakami S. et al. Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed Sci. 2013; 63: 125-40

[42] Daccord N, Celton JM, Linsmith G. et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017; 49:1099-106

[43] Yu G, Wang L-G, Han Y. et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16:284-7