Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops

详细信息    查看全文

• 作者：Ke Cao (1) (2)
  Zhijun Zheng (3) (4)
  Lirong Wang (1) (2)
  Xin Liu (3) (5) (6)
  Gengrui Zhu (1)
  Weichao Fang (1)
  Shifeng Cheng (3) (5) (6)
  Peng Zeng (3)
  Changwen Chen (1)
  Xinwei Wang (1)
  Min Xie (3)
  Xiao Zhong (3)
  Xiaoli Wang (1)
  Pei Zhao (1)
  Chao Bian (3)
  Yinling Zhu (3)
  Jiahui Zhang (1)
  Guosheng Ma (1)
  Chengxuan Chen (3)
  Yanjun Li (3)
  Fengge Hao (1)
  Yong Li (1)
  Guodong Huang (3)
  Yuxiang Li (3)
  Haiyan Li (1)
  Jian Guo (1)
  Xun Xu (3) (5) (6)
  Jun Wang (3)
  
  1. Zhengzhou Fruit Research Institute ; Chinese Academy of Agriculture Sciences ; Zhengzhou ; 450009 ; China
  2. The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology) ; Ministry of Agriculture ; Zhengzhou ; 450009 ; China
  3. BGI-Shenzhen ; Shenzhen ; 518083 ; China
  4. MetaGene Genomics Institute ; Hangzhou ; 310011 ; China
  5. State Key Laboratory of Agricultural Genomics ; BGI-Shenzhen ; Shenzhen ; 518083 ; China
  6. Key Laboratory of Genomics ; Ministry of Agriculture ; BGI-Shenzhen ; Shenzhen ; 518083 ; China
  
• 刊名：Genome Biology
• 出版年：2014
• 出版时间：July 2014
• 年：2014
• 卷：15
• 期：7
• 全文大小：2,500 KB
• 参考文献：1. Harlan, JR (1992) Crops and Man. Madison, Wisconsin, USA, American Society of Agronomy
  2. Zohary, D, Spiegel-Roy, P (1975) Beginnings of fruit growing in the old world. Science 187: pp. 319-327 CrossRef
  3. Hesse, CO Peaches. In: Janick, J, Moore, JN eds. (1975) Advances in Fruit Breeding. Purdue University Press, West Lafayette, IN, pp. 285-326
  4. Byrne, DH (1990) Isozyme variability in four diploid stone fruits compared with other woody perennial plants. J Hered 81: pp. 68-71
  5. Bai, Y, Lindhout, P (2007) Domestication and breeding of tomatoes: What have we gained and what can we gain in the future?. Ann Bot 100: pp. 1085-1094 CrossRef
  6. Lam, HM, Xu, X, Liu, X, Chen, W, Yang, G, Wong, F, Li, M, He, W, Qin, N, Wang, B, Li, J, Jian, M, Wang, J, Shao, G, Wang, J, Sun, SS, Zhang, G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: pp. 1053-1059 CrossRef
  7. Zheng, L, Guo, X, He, B, Sun, L, Peng, Y, Dong, S, Liu, T, Jiang, S, Ramachandran, S, Liu, C, Jing, H (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12: pp. R114 CrossRef
  8. Matthew, BH, Xu, X, Heerwaarden, JV, Pyh盲j盲rvi, T, Chia, JM, Cartwright, RA, Elshire, RJ, Glaubitz, JC, Guill, KE, Kaeppler, SM, Lai, J, Morrell, PL, Shannon, LM, Song, C, Spring, NM, Swanson-Wagner, RA, Tiffin, P, Wang, J, Zhang, G, Doebley, J, McMullen, MD, Ware, D, Buckler, ES, Yang, S, Ross-Ibarra, J (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44: pp. 808-811 CrossRef
  9. Xu, X, Liu, X, Ge, S, Jensen, JD, Hu, F, Li, X, Dong, Y, Gutenkunst, RN, Fang, L, Huang, L, Li, J, He, W, Zhang, G, Zheng, X, Zhang, F, Li, Y, Yu, C, Kristiansen, K, Zhang, X, Wang, J, Wright, M, McCouch, S, Nielsen, R, Wang, J, Wang, W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30: pp. 105-111 CrossRef
  10. Miller, AJ, Gross, BL (2011) From forest to field: Perennial fruit crop domestication. Am J Bot 98: pp. 1389-1414 CrossRef
  The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45: pp. 487-494 CrossRef
  11. Lai, J, Li, R, Xu, X, Jin, W, Xu, M, Zhao, H, Xiang, Z, Song, W, Ying, K, Zhang, M, Jiao, Y, Ni, P, Zhang, J, Li, D, Guo, X, Ye, K, Jian, M, Wang, B, Zheng, H, Liang, H, Zhang, X, Wang, S, Chen, S, Li, J, Fu, Y, Springer, NM, Yang, H, Wang, J, Dai, J, Schnable, PS (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42: pp. 1027-1030 CrossRef
  12. Vieira, FG, Fumagalli, M, Albrechtsen, A, Nielsen, R, Vieira, FG, Fumagalli, M, Albrechtsen, A, Nielsen, R (2013) Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Res 釁? pp. 釁
  13. Clark, RM, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, T, Fu, G, Hinds, DA, Chen, H, Frazer, KA, Huson, DH, Scholkopf, B, Nordborg, M, Ratsch, G, Ecker, JR, Weigel, D (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: pp. 338-342 CrossRef
  14. Watterson, GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: pp. 256-276 CrossRef
  15. Biswajit, D, Ahmed, N, Pushkar, S (2011) Prunus diversity- early and present development: a review. Int J Biodivers Conserv 3: pp. 721-734
  16. Hu, DY, Zhang, ZS, Zhang, DL, Zhang, QX, Li, JH (2005) Genetic relationship of ornamental peach determined using AFLP markers. Hortscience 40: pp. 1782-1786
  17. Tian, L (2006) The peach flower and its inter-meaning. Life World 2: pp. 86-89
  18. Wang, LR, Zhu, GR, Fang, WC (2013) Peach Genetic Resource in China. China agriculture press, Beijing
  19. Wang, Z, Zhou, J (1990) Pollen morphology of peach germplasm. Acta Horticulturae Sinica 17: pp. 161-168 CrossRef
  20. Okie, WR, Mark, R (2003) Inheritance of venation pattern in Prunus ferganensis鈥壝椻€塸ersica hybrids. Acta Hort 622: pp. 261-264
  21. Yu, DJ (1979) Stone fruits. Taxonomy of Fruit in China. China Agriculture Press, Beijing, pp. 25-81
  22. Bruce, DM, Dennis, JW, David, HB (1990) Isozyme survey of various species of Prunus in the subgenus Amygdalus. Sci Hortic 44: pp. 251-260 CrossRef
  23. Wright, SI, Bi, IV, Schroeder, SG, Yamasaki, M, Doebley, JF, McMullen, MD, Gaut, BS (2005) The effects of artificial selection on the maize genome. Science 308: pp. 1310-1314 CrossRef
  24. Jain, M, Khurana, JP (2009) Transcript profiling reveals diverse roles of auxin-responsive genes d uring reproductive development and abiotic stress in rice. FEBS J 276: pp. 3148-3162 CrossRef
  25. Illa, E, Eduardo, I, Audergon, JM, Barale, F, Dirlewanger, E, Li, X, Moing, A, Lambert, P, Dantec, LL, Gao, Z, Poessel, JL, Pozzi, C, Rossini, L, Vecchietti, A, Arus, P, Howad, W (2011) Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality. Mol Breeding 28: pp. 667-682 CrossRef
  26. Wu, J, Wang, Z, Shi, Z, Zhang, S, Ming, R, Zhu, S, Khan, MA, Tao, S, Korban, SS, Wang, H, Chen, NJ, 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 (2013) The genome of pear (Pyrus bretschneideri Rehd.). Genome Res 23: pp. 396-408 CrossRef
  27. Doebley, JF, Gaut, BS, Smith, BD (2006) The molecular genetics of crop domestication. Cell 127: pp. 1309-1321 CrossRef
  28. Disch, S, Anastasiou, E, Sharma, VK, Laux, T, Fletcher, JC, Lenhard, M (2006) The E3 ubiquitin ligase BIG BROTHER controls Arabidopsis organ size in a dosage-dependent manner. Curr Biol 16: pp. 272-279 CrossRef
  29. Song, XJ, Huang, W, Shi, M, Zhu, M, Lin, H (2007) A QTL for rice grain width and weightencodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39: pp. 623-630 CrossRef
  30. Quilot, B, Wu, B, Kervella, J, G茅nard, M, Foulongne, M, Moreau, K (2004) QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. Theor Appl Genet 109: pp. 884-897 CrossRef
  31. Remington, DL, Thornsberry, JM, Matsuoka, Y, Wilson, LM, Whitt, SR, Doebley, J, Kresovich, S, Goodman, MM, Buckler, ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 98: pp. 11479-11484 CrossRef
  32. Gupta, PK, Rustgi, S, Kulwal, PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: pp. 461-485 CrossRef
  33. Kim, S, Plagnol, V, Hu, T, Toomajian, C, Clark, RM, Ossowski, S, Ecker, JR, Weigel, D, Nordborg, M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39: pp. 1151-1155 CrossRef
  34. Xia, Q, Guo, Y, Zhang, Z, Li, D, Xuan, Z, Li, Z, Dai, F, Li, Y, Cheng, D, Li, R, Cheng, T, Jiang, T, Becquet, C, Xu, X, Liu, C, Zha, X, Fan, W, Lin, Y, Shen, Y, Jiang, L, Jensen, J, Hellmann, I, Tang, S, Zhao, P, Xu, H, Yu, C, Zhang, G, Li, J, Cao, J, Liu, S (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: pp. 433-436 CrossRef
  35. Myles, S, Boyko, AR, Owens, CL, Brown, PJ, Grassi, F, Aradhya, MK, Prins, B, Reynolds, A, Chia, JM, Ware, D, Bustamante, CD, Buckler, ES (2011) Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 108: pp. 3457-3458 CrossRef
  36. Jaillon, O, Aury, JM, 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, Bruy猫re, C, Billault, A, Segurens, B, Gouyvenoux, M, Ugarte, E, Cattonaro, F, Anthouard, V, Vico, V, Fabbro, CD, Alaux, M, Gaspero, GD, Dumas, V (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: pp. 463-467 CrossRef
  37. Cornille, A, Gladieux, P, Smulders, MJM, Rold谩n-Ruiz, I, Laurens, F, Cam, BL, Nersesyan, A, Clavel, J, Olonova, M, Feugey, L, Gabrielyan, I, Zhang, X, Tenaillon, MI, Giraud, T (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PloS Genet 8: pp. e1002703 CrossRef
  38. Mariette, S, Tavaud, M, Arunyawat, U, Capdeville, G, Millan, M, Salin, F (2010) Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. BMC Genet 11: pp. 77 CrossRef
  39. William, RR, Adam, KC (2001) Sexual recombination and the power of natural selection. Science 294: pp. 555-559 CrossRef
  40. Etienne, C, Rothan, C, Moing, A, Plomion, C, Bod茅n猫s, C, Svanella-Dumas, L, Cosson, P, Pronier, V, Monet, R, Dirlewanger, E (2002) Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105: pp. 145-159 CrossRef
  41. Fan, S, Bielenberg, DG, Zhebentyayeva, TN, Reighard, GL, Okie, WR, Holland, D, Abbott, AG (2010) Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica). New Phytol 185: pp. 917-930 CrossRef
  42. Cockram, J, White, J, Zuluaga, DL, Smith, D, Comadran, J, Macaulay, M, Luo, Z, Kearsey, MJ, Werner, P, Harrap, D, Tapsell, C, Liu, H, Hedley, PE, Stein, N, Schulte, D, Steuernagel, B, Marshall, DF, Thomas, WT, Ramsay, L, Mackay, I, Balding, DJ, Waugh, R, O'Sullivan, DM (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci U S A 107: pp. 21611-21616 CrossRef
  43. Huang, X, Wei, X, Sang, T, Zhao, Q, Feng, Q, Zhao, Y, Li, C, Zhu, C, Lu, T, Zhang, Z, Li, M, Fan, D, Guo, Y, Wang, A, Wang, L, Deng, L, Li, W, Lu, Y, Weng, Q, Liu, K, Huang, T, Zhou, T, Jing, Y, Li, W, Lin, Z, Buckler, ES, Qian, Q, Zhang, Q, Li, J, Han, B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: pp. 961-967 CrossRef
  44. Raj, KP, Sharma, R, Malosetti, M, Eeuwijk, FA, Haseneyer, G, Kilian, B, Graner, A (2012) Genome-wide association studies for agronomical traits in a worldwide spring barley collection. BMC Plant Biol 12: pp. 16 CrossRef
  45. Shulaev, V, Korban, SS, Sosinski, B, Abbott, AG, Aldwinckle, HS, Folta, KM, Iezzoni, A, Main, D, Ar煤s, P, Dandekar, AM, Lewers, K, Brown, SK, Davis, TM, Gardiner, SE, Potter, D, Veilleux, RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147: pp. 985-1003 CrossRef
  46. Peace, CP, Callahan, A, Ogundiwin, EA, Potter, D, Gradziel, TM, Bliss, FA, Crisosto, CH (2007) Endopolygalacturonase genotypic variation in Prunus. Acta Hort 738: pp. 639-646
  47. Arus, P, Verde, I, Sosinski, B, Zhebentyayeva, T, Abbott, AG (2012) The peach genome. Tree Genetics Genomes 8: pp. 531-547 CrossRef
  48. Bradbury, PJ, Zhang, Z, Kroon, DE, Casstevens, TM, Ramdoss, Y, Buckler, ES (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: pp. 2633-2635 CrossRef
  49. Miller, PJ, Parfitt, DE, Weinbaum, SA (1989) Outcrossing in peach. Hort Sci 24: pp. 359-360
  50. Scorza, R, Mehlenbacher, SA, Lightner, GW (1985) Inbreeding and coancestry of freestone peach cultivars of the eastern United States and implications for peach germplasm improvement. J Am Soc Hort Sci 110: pp. 547-552
  51. Desmond, RL, Daniele, B (2008) The Peach: Botany, Production and Uses. CABI, Oxfordshire, UK
  52. Christopher, T (1985) The History of Gardens. University of California Press, CA, US
  53. Wang, ZH, Zhuang, EJ (2001) Fruit Monograph for Peach in China. The forestry press of China, Beijing, China
  54. Murray, MG, Thompson, WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: pp. 4321-4325 CrossRef
  55. Li, R, Yu, Y, Lam, TW, Yiu, SM, Kristiansen, K, Wang, J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: pp. 1966-1967 CrossRef
  56. Li, R, Li, Y, Fang, X, Yang, H, Wang, J, Kristiansen, K, Wang, J (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: pp. 1124-1132 CrossRef
  57. 釁? SOAPindel. / 釁?/em> 釁? 釁?釁?[http://soap.genomics.org.cn/]
  58. Li, H, Durbin, R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: pp. 1754-1760 CrossRef
  59. Rausch, T, Zichner, T, Schlattl, A, Stutz, AM, Benes, V, Korbel, JO (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: pp. 333-339 CrossRef
  60. Tang, H, Peng, J, Wang, P, Risch, N (2005) Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28: pp. 289-301 CrossRef
  61. Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D, Maller, J, Sklar, P, Bakker, PI, Daly, MJ, Sham, PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: pp. 559-575 CrossRef
  62. Tajima, F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: pp. 585-595
  63. Barrett, JC, Fry, B, Maller, J, Daly, MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: pp. 263-265 CrossRef
  64. 釁? TASSEL. / 釁?/em> 釁? 釁?釁?[http://www.maizegenetics.net/]
  65. 釁? SRA. / 釁?/em> 釁? 釁?釁?[http://www.ncbi.nlm.nih.gov/sra]
  
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
• 出版者：BioMed Central
• ISSN：1465-6906

文摘

Background Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. Results We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs. Conclusions Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.