Resequencing data indicate a modest effect of domestication on diversity in barley: A cultigen with multiple origins

Journal of Heredity

Volumn 105, Issue 2, 2014, Pages 253-264

  Morrell, Peter L ^a   Gonzales, Ana M ^a   Meyer, Kapua K T ^b   Clegg, Michael T ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

admixture; demography; DNA sequence diversity; Hordeum vulgare; recombination; resequencing

Indexed keywords

ADMIXTURE; DEMOGRAPHY; DNA SEQUENCE DIVERSITY; HORDEUM VULGARE; RECOMBINATION; RESEQUENCING;

BREEDING; DNA, PLANT; GENES, PLANT; GENETIC LOCI; HAPLOTYPES; HORDEUM; JAPAN; LINKAGE DISEQUILIBRIUM; MALI; NEPAL; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, DNA;

ARTICLE; BARLEY; CONTROLLED STUDY; CULTIVAR; DOMESTICATION; GENETIC VARIABILITY; HAPLOTYPE; HORDEUM; HORDEUM BULBOSUM; LANDRACE; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM;

HORDEUM; HORDEUM VULGARE;

EID: 84894289087     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/est083     Document Type: Conference Paper

References (73)

1. Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, et al. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics. 11:702.
2. Allaby RG, Fuller DQ, Brown TA. 2008. The genetic expectations of a protracted model for the origins of domesticated crops. Proc Natl Acad Sci USA. 105:13982-13986.
3. Azhaguvel P, Komatsuda T. 2007. A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley. Ann Bot. 100:1009-1015.
4. Badr A, Muller K, Schafer-Pregl R, El Rabey H, Effgen S, Ibrahim HH, Pozzi C, Rohde W, Salamini F. 2000. On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol. 17:499-510.
5. Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, Santilocchi R, Spagnoletti Zeuli P, Gioia T, Logozzo G, et al. 2013. Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol. 197:300-313.
6. Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, Zeuli PS, Logozzo G, Stougaard J, McClean P, Attene G, et al. 2012. Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci USA. 109:E788-E796.
7. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, et al. 2007. Genomewide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3:1745-1756.
8. Caldwell KS, Russell J, Langridge P, Powell W. 2006. Extreme populationdependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics. 172:557-567.
9. Charlesworth B. 1998. Measures of divergence between populations and the effect of forces that reduce variability. Mol Biol Evol. 15:538-543.
10. Chen H, Morrell PL, Ashworth VE, de la Cruz M, Clegg MT. 2009. Tracing the geographic origins of major avocado cultivars. J Hered. 100:56-65.
11. Chen H, Morrell PL, Toleno DM, Lundy KE, Clegg MT. 2010. Allelespecific PCR can improve the efficiency of experimental resolution of heterozygotes in resequencing studies. Mol Ecol Resour. 10:647-658.
12. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164:1567-1587.
13. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics. 155:1405-1413.
14. Fu YB. 2012. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region. Genome. 55:93-104.
15. Fu YB, Peterson GW. 2011. Genetic diversity analysis with 454 pyrosequencing and genomic reduction confirmed the eastern and western division in the cultivated barley gene pool. Plant Gen. 4:226.
16. Fuller DQ. 2007. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Ann Bot. 100:903-924.
17. Fuller DQ, Willcox G, Allaby RG. 2011. Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East. World Archaeol. 43:628-652.
18. Gattepaille LM, Jakobsson M. 2012. Combining markers into haplotypes can improve population structure inference. Genetics. 190:159-174.
19. Gepts P, Bliss FA. 1985. F1 hybrid weakness in the common bean: differential geographic origin suggests two gene pools in cultivated bean germplasm. J Hered. 76:447-450.
20. Glémin S, Bataillon T. 2009. A comparative view of the evolution of grasses under domestication. New Phytol. 183:273-290.
21. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
22. Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P. 2005. Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15:790-799.
23. Harris DR. 1998. The spread of neolithic agriculture from the Levant to western Central Asia. In: Damania AB, Valkoun J, Willcox G, Qualset CO, editors. The origins of agriculture and crop domestication. Aleppo (Syria): ICARDA. p. 345.
24. Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature. 490:497-501.
25. Hudson RR. 1990. Gene genealogies and the coalescent process. In: Futuyma DJ, Antonovics J, editors. Oxford series in evolutionary biology. Vol. 7. Oxford: Oxford University Press. p. 1-43.
26. Hudson RR. 2000. A new statistic for detecting genetic differentiation. Genetics. 155:2011-2014.
27. Hudson RR. 2001. Two-locus sampling distributions and their application. Genetics. 159:1805-1817.
28. Hudson RR, Boos DD, Kaplan NL. 1992. A statistical test for detecting geographic subdivision. Mol Biol Evol. 9:138-151.
29. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 111:147-164.
30. Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, et al. 2012. Comparative population genomics of maize domestication and improvement. Nat Genet. 44:808-811.
31. Kilian B, Ozkan H, Kohl J, von Haeseler A, Barale F, Deusch O, Brandolini A, Yucel C, Martin W, Salamini F. 2006. Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics. 276:230-241.
32. Kilian B, Özkan H, Walther A, Kohl J, Dagan T, Salamini F, Martin W. 2007. Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (einkorn) domestication: implications for the origin of agriculture. Mol Biol Evol. 24:2657-2668.
33. Kolkman JM, Berry ST, Leon AJ, Slabaugh MB, Tang S, Gao W, Shintani DK, Burke JM, Knapp SJ. 2007. Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics. 177:457-468.
34. Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, et al. 2007. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA. 104:1424-1429.
35. Lewis PO, Zaykin D. 2001. Genetic Data Analysis: Computer program for the analysis of allelic data. Free program distributed by the authors over the internet.
36. Lin JZ, Brown AH, Clegg MT. 2001. Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum). Proc Natl Acad Sci USA. 98:531-536.
37. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA. 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA. 103:9578-9583.
38. Martin JM, Blake TK, Hockett EA. 1991. Diversity among North American spring barley cultivars based on coefficients of parentage. Crop Sci. 31:1131-1137.
39. Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP, Graner A, Matsumoto T, Sato K, Schulman A, Muehlbauer GJ, et al. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.
40. Miller AJ, Gross BL. 2011. From forest to field: perennial fruit crop domestication. Am J Bot. 98:1389-1414.
41. Morrell PL, Buckler ES, Ross-Ibarra J. 2012. Crop genomics: advances and applications. Nat Rev Genet. 13:85-96.
42. Morrell PL, Clegg MT. 2007. Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci USA. 104:3289-3294.
43. Morrell PL, Clegg MT. 2011. Hordeum. In: Kole C, editor. Wild crop relatives: genomic and breeding resources: cereals. Berlin (Germany): Springer- Verlag. p. 309-319.
44. Morrell PL, Lundy KE, Clegg MT. 2003. Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proc Natl Acad Sci USA. 100:10812-10817.
45. Morrell PL, Toleno DM, Lundy KE, Clegg MT. 2005. Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA. 102:2442-2447.
46. Morrell PL, Toleno DM, Lundy KE, Clegg MT. 2006. Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics. 173:1705-1723.
47. Nei M, Maruyam T, Chakraborty R. 1975. The bottleneck effect and genetic variability in populations. Evolution. 29:1-10.
48. Nickerson DA, Tobe VO, Taylor SL. 1997. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescencebased resequencing. Nucleic Acids Res. 25:2745-2751.
49. Nielsen R, Signorovitch J. 2003. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor Popul Biol. 63:245-255.
50. Ordon F, Schiemann A, Friedt W. 1997. Assessment of the genetic relatedness of barley accessions (Hordeum vulgare sl) resistant to soil-borne mosaicinducing viruses (BaMMV, BaYMV, BaYMV-2) using RAPDs. Theor Appl Genet. 94:325-330.
51. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
52. Ross-Ibarra J, Gaut BS. 2008. Multiple domestications do not appear monophyletic. Proc Natl Acad Sci USA. 105:E105.
53. Ross-Ibarra J, Morrell PL, Gaut BS. 2007. Colloquium Papers: plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci USA. 104(Suppl 1):8641-8648.
54. Ross-Ibarra J, Tenaillon M, Gaut BS. 2009. Historical divergence and gene flow in the genus Zea. Genetics. 181:1399-1413.
55. Saisho D, Purugganan MD. 2007. Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World. Genetics. 177:1765-1776.
56. Sang T. 2009. Genes and mutations underlying domestication transitions in grasses. Plant Physiol. 149:63-70.
57. Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. 2006. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet. 38:375-381.
58. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics. 105:437-460.
59. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 3:585-595.
60. Takahashi R. 1955. The origin and evolution of cultivated barley. Adv Genet. 7:227-266.
61. Takahashi R. 1964. Linkage study of two complementary genes for brittle rachis in barley. Ber Ohara Inst Landw Biol, Okayama Univ. 38:81-90.
62. Teshima KM, Coop G, Przeworski M. 2006. How reliable are empirical genomic scans for selective sweeps? Genome Res. 16:702-712.
63. Thornton K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 19:2325-2327.
64. Toleno DM, Morrell PL, Clegg MT. 2007. Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. Bioinformatics. 23:1807-1814.
65. Vavilov NI. 1926. Studies on the origin of cultivated plants. Bulletin of Applied Botany, Genetics and Plant Breeding. 16:1-248.
66. Wall JD. 1999. Recombination and the power of statistical tests of neutrality. Genet Res. 74:65-79.
67. Walsh B. 2008. Using molecular markers for detecting domestication, improvement, and adaptation genes. Euphytica. 161:1-17.
68. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
69. Weaver JC. 1944. United States malting barley production. A Assoc Am Geog. 34:97-131.
70. Willcox G. 2005. The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres. Veg Hist Archaeobot. 14:534-541.
71. 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. 308:1310-1314.
72. Zeng K, Fu YX, Shi S, Wu CI. 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics. 174:1431-1439.
73. Zohary D. 1999. Monophyletic vs. polyphyletic origin of the crops on which agriculture was founded in the Near East. Genet Resour Crop Evol. 46:133-142.