Patterns of genomic changes with crop domestication and breeding

Current Opinion in Plant Biology

Volumn 24, Issue , 2015, Pages 47-53

  Shi, Junpeng ^a   Lai, Jinsheng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CROP; GENETICS; PLANT BREEDING; PLANT GENOME;

CROPS, AGRICULTURAL; GENOME, PLANT; PLANT BREEDING;

EID: 84921947366     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2015.01.008     Document Type: Review

References (72)

1. Abbo S., Pinhasi Van-Oss R., Gopher A., Saranga Y., Ofner I., Peleg Z. Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends Plant Sci 2014, 19:351-360.
2. Meyer R.S., Purugganan M.D. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 2013, 14:840-852.
3. Gross B.L., Olsen K.M. Genetic perspectives on crop domestication. Trends Plant Sci 2010, 15:529-537.
4. Morrell P.L., Buckler E.S., Ross-Ibarra J. Crop genomics: advances and applications. Nat Rev Genet 2012, 13:85-96.
5. Wright S.I., Bi I.V., Schroeder S.G., Yamasaki M., Doebley J.F., McMullen M.D., Gaut B.S. The effects of artificial selection on the maize genome. Science 2005, 308:1310-1314.
6. Doebley J.F., Gaut B.S., Smith B.D. The molecular genetics of crop domestication. Cell 2006, 127:1309-1321.
7. Xu X., Liu X., Ge S., Jensen J.D., Hu F., Li X., Dong Y., Gutenkunst R.N., Fang L., Huang L., et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 2011, 30:105-111.
8. Lai J., Li R., Xu X., Jin W., Xu M., Zhao H., Xiang Z., Song W., Ying K., Zhang M., et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 2010, 42:1027-1030.
9. Nielsen R. Molecular signatures of natural selection. Annu Rev Genet 2005, 39:197.
10. Nielsen R. Genomic scans for selective sweeps using SNP data. Genome Res 2005, 15:1566-1575.
11. Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z.P., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., McDonald G.J., et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419:832-837.
12. Huang X., Kurata N., Wei X., Wang Z., Wang A., Zhao Q., Zhao Y., Liu K., Lu H., Li W., et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 2012, 490:497-501.
13. Qi J., Liu X., Shen D., Miao H., Xie B., Li X., Zeng P., Wang S., Shang Y., Gu X., et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 2013, 45:1510-1515.
14. Lin T., Zhu G., Zhang J., Xu X., Yu Q., Zheng Z., Zhang Z., Lun Y., Li S., Wang X., et al. Genomic analyses provide insights into the history of tomato breeding. Nat Genet 2014, 46:1220-1226.
15. Barreiro L.B., Laval G., Quach H., Patin E., Quintana-Murci L. Natural selection has driven population differentiation in modern humans. Nat Genet 2008, 40:340-345.
16. Chen H., Patterson N., Reich D. Population differentiation as a test for selective sweeps. Genome Res 2010, 20:393-402.
17. Ross-Ibarra J., Morrell P.L., Gaut B.S. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci U S A 2007, 104(Suppl. 1):8641-8648.
18. Hufford M.B., Xu X., van Heerwaarden J., Pyhäjärvi T., Chia J., Cartwright R.A., Elshire R.J., Glaubitz J.C., Guill K.E., Kaeppler S.M., et al. Comparative population genomics of maize domestication and improvement. Nat Genet 2012, 44:808-811.
19. Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. Curr Opin Plant Biol 2014, 18:51-59.
20. Myles S., Boyko A.R., Owens C.L., Brown P.J., Grassi F., Aradhya M.K., Prins B., Reynolds A., Chia J.M., Ware D., et al. Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 2011, 108:3530-3535.
21. Guo S., Zhang J., Sun H., Salse J., Lucas W.J., Zhang H., Zheng Y., Mao L., Ren Y., Wang Z., et al. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 2012, 45:51-58.
22. Harushima Y., Nakagahra M., Yano M., Sasaki T., Kurata N. Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 2002, 160:313-322.
23. Lam H., Xu X., Liu X., Chen W., Yang G., Wong F., Li M., He W., Qin N., Wang B., et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 2010, 42:1053-1059.
24. Jiao Y., Zhao H., Ren L., Song W., Zeng B., Guo J., Wang B., Liu Z., Chen J., Li W., et al. Genome-wide genetic changes during modern breeding of maize. Nat Genet 2012, 44:812-815.
25. Li C., Zhou A., Sang T. Rice domestication by reducing shattering. Science 2006, 311:1936-1939.
26. Wang H., Nussbaum-Wagler T., Li B., Zhao Q., Vigouroux Y., Faller M., Bomblies K., Lukens L., Doebley J.F. The origin of the naked grains of maize. Nature 2005, 436:714-719.
27. Frary A., Nesbitt T.C., Grandillo S., Knaap E., Cong B., Liu J., Meller J., Elber R., Alpert K.B., Tanksley S.D. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 2000, 289:85-88.
28. Tian Z., Wang X., Lee R., Li Y., Specht J.E., Nelson R.L., McClean P.E., Qiu L., Ma J. Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci U S A 2010, 107:8563-8568.
29. Salvi S., Sponza G., Morgante M., Tomes D., Niu X., Fengler K.A., Meeley R., Ananiev E.V., Svitashev S., Bruggemann E., et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A 2007, 104:11376-11381.
30. Studer A., Zhao Q., Ross-Ibarra J., Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 2011, 43:1160-1163.
31. Zhou L., Zhang J., Yan J., Song R. Two transposable element insertions are causative mutations for the major domestication gene teosinte branched 1 in modern maize. Cell Res 2011, 21:1267-1270.
32. Li X., Zhu C., Yeh C.T., Wu W., Takacs E.M., Petsch K.A., Tian F., Bai G., Buckler E.S., Muehlbauer G.J., et al. Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res 2012, 22:2436-2444.
33. Maurano M.T., Humbert R., Rynes E., Thurman R.E., Haugen E., Wang H., Reynolds A.P., Sandstrom R., Qu H., Brody J., et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012, 337:1190-1195.
34. Wang M., Yu Y., Haberer G., Marri P.R., Fan C., Goicoechea J.L., Zuccolo A., Song X., Kudrna D., Ammiraju J.S.S., et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014, 46:982-988.
35. Matsuoka Y., Vigouroux Y., Goodman M.M., Sanchez G.J., Buckler E., Doebley J. A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci U S A 2002, 99:6080-6084.
36. Schmutz J., McClean P.E., Mamidi S., Wu G.A., Cannon S.B., Grimwood J., Jenkins J., Shu S., Song Q., Chavarro C., et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 2014, 46:707-713.
37. Mace E.S., Tai S., Gilding E.K., Li Y., Prentis P.J., Bian L., Campbell B.C., Hu W., Innes D.J., Han X., et al. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat Commun 2013, 4:2320.
38. Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., McCarthy M.I., Ramos E.M., Cardon L.R., Chakravarti A., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
39. Springer N.M. Epigenetics and crop improvement. Trends Genet 2013, 29:241-247.
40. Zhang X. The epigenetic landscape of plants. Science 2008, 320:489-492.
41. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010, 11:204-220.
42. Schmitz R.J., Schultz M.D., Lewsey M.G., O'Malley R.C., Urich M.A., Libiger O., Schork N.J., Ecker J.R. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011, 334:369-373.
43. Ossowski S., Schneeberger K., Lucas-Lledo J.I., Warthmann N., Clark R.M., Shaw R.G., Weigel D., Lynch M. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 2009, 327:92-94.
44. Zhang L., Cheng Z., Qin R., Qiu Y., Wang J.L., Cui X., Gu L., Zhang X., Guo X., Wang D., et al. Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell 2012, 24:4407-4421.
45. Manning K., Tör M., Poole M., Hong Y., Thompson A.J., King G.J., Giovannoni J.J., Seymour G.B. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 2006, 38:948-952.
46. Becker C., Hagmann J., Müller J., Koenig D., Stegle O., Borgwardt K., Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 2011, 480:245-249.
47. Eichten S.R., Briskine R., Song J., Li Q., Swanson-Wagner R., Hermanson P.J., Waters A.J., Starr E., West P.T., Tiffin P., et al. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 2013, 25:2783-2797.
48. Schmitz R.J., Schultz M.D., Urich M.A., Nery J.R., Pelizzola M., Libiger O., Alix A., McCosh R.B., Chen H., Schork N.J., et al. Patterns of population epigenomic diversity. Nature 2013, 495:193-198.
49. Schmitz R.J., He Y., Valdes-Lopez O., Khan S.M., Joshi T., Urich M.A., Nery J.R., Diers B., Xu D., Stacey G., et al. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 2013, 23:1663-1674.
50. Chodavarapu R.K., Feng S., Ding B., Simon S.A., Lopez D., Jia Y., Wang G.L., Meyers B.C., Jacobsen S.E., Pellegrini M. Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A 2012, 109:12040-12045.
51. Shen H., He H., Li J., Chen W., Wang X., Guo L., Peng Z., He G., Zhong S., Qi Y., et al. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 2012, 24:875-892.
52. Greaves I.K., Groszmann M., Ying H., Taylor J.M., Peacock W.J., Dennis E.S. Trans chromosomal methylation in Arabidopsis hybrids. Proc Natl Acad Sci U S A 2012, 109:3570-3575.
53. Cortijo S., Wardenaar R., Colomé-Tatché M., Gilly A., Etcheverry M., Labadie K., Caillieux E., Aury J., Wincker P., Roudier F. Mapping the epigenetic basis of complex traits. Science 2014, 343:1145-1148.
54. Rakyan V.K., Down T.A., Balding D.J., Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011, 12:529-541.
55. Breitling L.P., Yang R., Korn B., Burwinkel B., Brenner H. Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am J Hum Genet 2011, 88:450-457.
56. Bell J.T., Tsai P., Yang T., Pidsley R., Nisbet J., Glass D., Mangino M., Zhai G., Zhang F., Valdes A., et al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet 2012, 8:e1002629.
57. Dick K.J., Nelson C.P., Tsaprouni L., Sandling J.K., Aïssi D., Wahl S., Meduri E., Morange P., Gagnon F., Grallert H., et al. DNA methylation and body-mass index: a genome-wide analysis. Lancet 2014, 383:1990-1998.
58. De Jager P.L., Srivastava G., Lunnon K., Burgess J., Schalkwyk L.C., Yu L., Eaton M.L., Keenan B.T., Ernst J., McCabe C., et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 2014, 17:1156-1163.
59. Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., Zhang J., Fulton L., Graves T.A., et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115.
60. Tan L., Li X., Liu F., Sun X., Li C., Zhu Z., Fu Y., Cai H., Wang X., Xie D., et al. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 2008, 40:1360-1364.
61. Jin J., Huang W., Gao J., Yang J., Shi M., Zhu M., Luo D., Lin H. Genetic control of rice plant architecture under domestication. Nat Genet 2008, 40:1365-1369.
62. Wang E., Wang J., Zhu X., Hao W., Wang L., Li Q., Zhang L., He W., Lu B., Lin H., et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 2008, 40:1370-1374.
63. Doebley J., Stec A., Gustus C. Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 1995, 141:333-346.
64. Lin Z., Li X., Shannon L.M., Yeh C., Wang M.L., Bai G., Peng Z., Li J., Trick H.N., Clemente T.E., et al. Parallel domestication of the Shattering1 genes in cereals. Nat Genet 2012, 44:720-724.
65. Fan C., Xing Y., Mao H., Lu T., Han B., Xu C., Li X., Zhang Q. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 2006, 112:1164-1171.
66. Li Y., Fan C., Xing Y., Jiang Y., Luo L., Sun L., Shao D., Xu C., Li X., Xiao J., et al. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 2011, 43:1266-1269.
67. Song X., Huang W., Shi M., Zhu M., Lin H. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 2007, 39:623-630.
68. Weng J., Gu S., Wan X., Gao H., Guo T., Su N., Lei C., Zhang X., Cheng Z., Guo X., et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 2008, 18:1199-1209.
69. Huang X., Qian Q., Liu Z., Sun H., He S., Luo D., Xia G., Chu C., Li J., Fu X. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 2009, 41:494-497.
70. Xue W., Xing Y., Weng X., Zhao Y., Tang W., Wang L., Zhou H., Yu S., Xu C., Li X., et al. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 2008, 40:761-767.
71. Li X., Qian Q., Fu Z., Wang Y., Xiong G., Zeng D., Wang X., Liu X., Teng S., Hiroshi F., et al. Control of tillering in rice. Nature 2003, 422:618-621.
72. Jiao Y., Wang Y., Xue D., Wang J., Yan M., Liu G., Dong G., Zeng D., Lu Z., Zhu X., et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 2010, 42:541-544.