[1]

Zhou Y, Muyle A, Gaut BS. 2019. Evolutionary genomics and the domestication of grapes. In The Grape Genome, eds Cantu D, Walker M. Springer, Cham. pp. 39−55. https://doi.org/10.1007/978-3-030-18601-2_3

[2]

Massonnet M, Cochetel N, Minio A, Vondras AM, Lin J, et al. 2020. The genetic basis of sex determination in grapes. Nature Communications 11:2902

doi: 10.1038/s41467-020-16700-z
[3]

Minio A, Cochetel N, Vondras AM, Massonnet M, Cantu D. 2022. Assembly of complete diploid-phased chromosomes from draft genome sequences. G3 Genes|Genomes|Genetics 12:jkac143

doi: 10.1093/g3journal/jkac143
[4]

Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, et al. 2019. Iso-Seq allows genome-independent transcriptome profiling of grape berry development. G3 Genes|Genomes| Genetics 9:755−67

doi: 10.1534/g3.118.201008
[5]

Shirasawa K, Hirakawa H, Azuma A, Taniguchi F, Yamamoto T, et al. 2022. De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. DNA Research 29:dsac040

doi: 10.1093/dnares/dsac040
[6]

Girollet N, Rubio B, Lopez-Roques C, Valière S, Ollat N, et al. 2019. De novo phased assembly of the Vitis riparia grape genome. Scientific Data 6:127

doi: 10.1038/s41597-019-0133-3
[7]

Cochetel N, Minio A, Massonnet M, Vondras AM, Figueroa-Balderas R, et al. 2021. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. G3 Genes|Genomes|Genetics 11:jkab033

doi: 10.1093/g3journal/jkab033
[8]

Wang Y, Xin H, Fan P, Zhang J, Liu Y, et al. 2021. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine. The Plant Journal 105:1495−506

doi: 10.1111/tpj.15127
[9]

Cheng G, Wu D, Guo R, Li H, Wei R, et al. 2023. Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes. Frontiers in Plant Science 14:1124046

doi: 10.3389/fpls.2023.1124046
[10]

Liang Z, Duan S, Sheng J, Zhu S, Ni X, et al. 2019. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nature Communications 10:1190

doi: 10.1038/s41467-019-09135-8
[11]

Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, et al. 2019. The population genetics of structural variants in grapevine domestication. Nature Plants 5:965−79

doi: 10.1038/s41477-019-0507-8
[12]

Dong Y, Duan S, Xia Q, Liang Z, Dong X, et al. 2023. Dual domestications and origin of traits in grapevine evolution. Science 379:892−901

doi: 10.1126/science.add8655
[13]

Li J, Ma T, Bao S, Yin D, Ge Q, et al. 2023. Suitable crop loading: an effective method to improve "Shine Muscat" grape quality. Food Chemistry 424:136451

doi: 10.1016/j.foodchem.2023.136451
[14]

Wen J, Ma ZY. 2021. On the recognition of the long neglected Vitis adenoclada Hand-Mazz. (Vitaceae) from southern China. PhytoKeys 179:29−33

doi: 10.3897/phytokeys.179.65519
[15]

Wu D, Cheng G, Li H, Zhou S, Yao N, et al. 2020. The cultivation techniques and quality characteristics of a new germplasm of Vitis adenoclada hand.-Mazz grape. Agronomy 10:1851

doi: 10.3390/agronomy10121851
[16]

Fu J, Hao Y, Li H, Reif JC, Chen S, et al. 2022. Integration of genomic selection with doubled-haploid evaluation in hybrid breeding: from GS 1.0 to GS 4.0 and beyond. Molecular Plant 15:577−80

doi: 10.1016/j.molp.2022.02.005
[17]

Kim MS, Lozano R, Kim JH, Bae DN, Kim ST, et al. 2021. The patterns of deleterious mutations during the domestication of soybean. Nature Communications 12:97

doi: 10.1038/s41467-020-20337-3
[18]

Wu Y, Li D, Hu Y, Li H, Ramstein GP, et al. 2023. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186:2313−2328.e15

doi: 10.1016/j.cell.2023.04.008
[19]

Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, et al. 2023. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. Trends Plant Science 28:685−97

doi: 10.1016/j.tplants.2023.01.006
[20]

Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890

doi: 10.1093/bioinformatics/bty560
[21]

Shi X, Cao S, Wang X, Huang S, Wang Y, et al. 2023. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Horticulture Research 10:uhad061

doi: 10.1093/hr/uhad061
[22]

Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987−93

doi: 10.1093/bioinformatics/btr509
[23]

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078−79

doi: 10.1093/bioinformatics/btp352
[24]

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. 2011. The variant call format and VCFtools. Bioinformatics 27:2156−58

doi: 10.1093/bioinformatics/btr330
[25]

Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, et al. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4:s13742-015-0047-8

doi: 10.1186/s13742-015-0047-8
[26]

Price MN, Dehal PS, Arkin AP. 2010. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490

doi: 10.1371/journal.pone.0009490
[27]

Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19:1655−64

doi: 10.1101/gr.094052.109
[28]

Szpiech ZA, Hernandez RD. 2014. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution 31:2824−27

doi: 10.1093/molbev/msu211
[29]

Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12:59−60

doi: 10.1038/nmeth.3176
[30]

Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. 2016. SIFT missense predictions for genomes. Nature Protocols 11:1−9

doi: 10.1038/nprot.2015.123
[31]

Deng Y, Ning Y, Yang DL, Zhai K, Wang GL, et al. 2020. Molecular basis of disease resistance and perspectives on breeding strategies for resistance improvement in crops. Molecular Plant 13:1402−19

doi: 10.1016/j.molp.2020.09.018
[32]

Saucet SB, Ma Y, Sarris PF, Furzer OJ, Sohn KH, et al. 2015. Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4. Nature Communications 6:6338

doi: 10.1038/ncomms7338
[33]

Song WY, Wang GL, Chen LL, Kim HS, Pi LY, et al. 1995. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804−06

doi: 10.1126/science.270.5243.1804
[34]

Liu Y, Du M, Deng L, Shen J, Fang M, et al. 2019. MYC2 regulates the termination of jasmonate signaling via an autoregulatory negative feedback loop. The Plant Cell 31:106−27

doi: 10.1105/tpc.18.00405
[35]

Zhang Z, Wu Y, Gao M, Zhang J, Kong Q, et al. 2012. Disruption of PAMP-induced MAP kinase cascade by a Pseudomonas syringae effector activates plant immunity mediated by the NB-LRR protein SUMM2. Cell Host & Microbe 11:253−63

doi: 10.1016/j.chom.2012.01.015
[36]

Bittner-Eddy PD, Crute IR, Holub EB, Beynon JL. 2000. RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. The Plant Journal 21:177−88

doi: 10.1046/j.1365-313x.2000.00664.x
[37]

Zhang W, Fraiture M, Kolb D, Löffelhardt B, Desaki Y, et al. 2013. Arabidopsis RECEPTOR-LIKE PROTEIN30 and receptor-like kinase SUPPRESSOR OF BIR1-1/EVERSHED mediate innate immunity to necrotrophic fungi. The Plant Cell 25:4227−41

doi: 10.1105/tpc.113.117010
[38]

Ron M, Avni A. 2004. The receptor for the fungal elicitor ethylene-inducing xylanase is a member of a resistance-like gene family in tomato. The Plant Cell 16:1604−15

doi: 10.1105/tpc.022475
[39]

Nakabayashi R, Saito K. 2015. Integrated metabolomics for abiotic stress responses in plants. Current Opinion in Plant Biology 24:10−6

doi: 10.1016/j.pbi.2015.01.003
[40]

Tholl D. 2015. Biosynthesis and biological functions of terpenoids in plants. In Biotechnology of Isoprenoids, eds Schrader J, Bohlmann J. Springer, Cham. 148:63−106. https://doi.org/10.1007/10_2014_295

[41]

López ME, Cádiz MI, Rondeau EB, Koop BF, Yáñez JM. 2021. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Scientific Reports 11:9685

doi: 10.1038/s41598-021-86154-w
[42]

Sun S, Wang B, Li C, Xu G, Yang J, et al. 2023. Unraveling prevalence and effects of deleterious mutations in maize elite lines across decades of modern breeding. Molecular Biology and Evolution 40:msad170

doi: 10.1093/molbev/msad170
[43]

Ji F, Ma Q, Zhang W, Liu J, Feng Y, et al. 2021. A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits. Genome Biology 22:300

doi: 10.1186/s13059-021-02517-6