Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2013 Sep 17

PMID 24037269

Citations 10

Authors

Chao Wang

Xue Shi

Lin Liu

Haiyan Li

Jetty S S Ammiraju

David A Kudrna

Wentao Xiong

Hao Wang

Zhaozhao Dai

Yonglian Zheng

Jinsheng Lai

Weiwei Jin

Joachim Messing

Jeffrey L Bennetzen

Rod A Wing

Meizhong Luo

Affiliations

Soon will be listed here.

Abstract

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

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References

Woodhouse M, Schnable J, Pedersen B, Lyons E, Lisch D, Subramaniam S . Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 2010; 8(6):e1000409. PMC: 2893956. DOI: 10.1371/journal.pbio.1000409. View

Doebley J . The genetics of maize evolution. Annu Rev Genet. 2004; 38:37-59. DOI: 10.1146/annurev.genet.38.072902.092425. View

Janda J, Safar J, Kubalakova M, Bartos J, Kovarova P, Suchankova P . Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B. Plant J. 2006; 47(6):977-86. DOI: 10.1111/j.1365-313X.2006.02840.x. View

Liu Y, Nagaki K, Fujita M, Kawaura K, Uozumi M, Ogihara Y . Development of an efficient maintenance and screening system for large-insert genomic DNA libraries of hexaploid wheat in a transformation-competent artificial chromosome (TAC) vector. Plant J. 2000; 23(5):687-95. DOI: 10.1046/j.1365-313x.2000.00827.x. View

Shi X, Zeng H, Xue Y, Luo M . A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange. Plant Methods. 2011; 7:33. PMC: 3213141. DOI: 10.1186/1746-4811-7-33. View

Kim H, San Miguel P, Nelson W, Collura K, Wissotski M, Walling J . Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics. 2007; 176(1):379-90. PMC: 1893071. DOI: 10.1534/genetics.106.068783. View

Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L . Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet. 2011; 43(12):1266-9. DOI: 10.1038/ng.977. View

Deng Y, Pan Y, Luo M . Detection and correction of assembly errors of rice Nipponbare reference sequence. Plant Biol (Stuttg). 2013; 16(3):643-50. DOI: 10.1111/plb.12090. View

Calvino M, Messing J . Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol. 2011; 23(3):323-9. DOI: 10.1016/j.copbio.2011.12.002. View

10.

Swanson-Wagner R, Briskine R, Schaefer R, Hufford M, Ross-Ibarra J, Myers C . Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci U S A. 2012; 109(29):11878-83. PMC: 3406829. DOI: 10.1073/pnas.1201961109. View

11.

Feng J, Vick B, Lee M, Zhang H, Jan C . Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. Theor Appl Genet. 2006; 113(1):23-32. DOI: 10.1007/s00122-006-0265-7. View

12.

Wei F, Zhang J, Zhou S, He R, Schaeffer M, Collura K . The physical and genetic framework of the maize B73 genome. PLoS Genet. 2009; 5(11):e1000715. PMC: 2774505. DOI: 10.1371/journal.pgen.1000715. View

13.

Wu C, Nimmakayala P, Santos F, Springman R, Scheuring C, Meksem K . Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet. 2004; 109(5):1041-50. DOI: 10.1007/s00122-004-1712-y. View

14.

Lin H, Xia P, Wing R, Zhang Q, Luo M . Dynamic intra-japonica subspecies variation and resource application. Mol Plant. 2011; 5(1):218-30. DOI: 10.1093/mp/ssr085. View

15.

Tikhonov A, SanMiguel P, Nakajima Y, Gorenstein N, Bennetzen J, Avramova Z . Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci U S A. 1999; 96(13):7409-14. PMC: 22099. DOI: 10.1073/pnas.96.13.7409. View

16.

Lai J, Li R, Xu X, Jin W, Xu M, Zhao H . Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet. 2010; 42(11):1027-30. DOI: 10.1038/ng.684. View

17.

Schnable P, Ware D, Fulton R, Stein J, Wei F, Pasternak S . The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326(5956):1112-5. DOI: 10.1126/science.1178534. View

18.

Gore M, Chia J, Elshire R, Sun Q, Ersoz E, Hurwitz B . A first-generation haplotype map of maize. Science. 2009; 326(5956):1115-7. DOI: 10.1126/science.1177837. View

19.

Tao Q, Wang A, Zhang H . One large-insert plant-transformation-competent BIBAC library and three BAC libraries of Japonica rice for genome research in rice and other grasses. Theor Appl Genet. 2003; 105(6-7):1058-1066. DOI: 10.1007/s00122-002-1057-3. View

20.

Song R, Llaca V, Messing J . Mosaic organization of orthologous sequences in grass genomes. Genome Res. 2002; 12(10):1549-55. PMC: 187525. DOI: 10.1101/gr.268302. View