Genetic mapping of the apospory-specific genomic region in Pennisetum squamulatum using retrotransposon-based molecular markers
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Pennisetum squamulatum reproduces by apomixis, a type of asexual reproduction through seeds. Apomixis in P. squamulatum is transmitted as a dominant Mendelian trait, and a genomic region, the apospory-specific genomic region (ASGR), is sufficient for inheritance of the trait. The ASGR is physically large (>50 Mb), highly heterochromatic, hemizygous, and recombinationally suppressed. These characteristics have hindered high-resolution genetic mapping and map-based cloning of apomixis genes. In this study, the long terminal repeat (LTR) regions of ASGR-abundant retrotransposons in the genome of P. squamulatum and ASGR-linked bacterial artificial chromosome clones were identified and sequenced for designing LTR-specific primers. Two hundred and ninety single-dose sequence specific amplified polymorphism (SSAP) markers were generated from 38 primer combinations. The SSAP markers combined with two previous ASGR-mapped markers were used for genetic linkage analysis and construction of a genetic map resulting in the formation of 27 linkage groups at LOD 10, one of which contained >60% of the SSAP markers. After removing identical markers (identical band scoring) on the largest linkage group, 46 markers were finally used for genetic mapping at LOD 10. The markers distributed across 10 different loci covering 19 cM; however, 45 markers were distributed within 9 cM. Six markers were recovered and sequenced. Five markers were successfully converted into sequence characterized amplified regions (SCARs). Segregation of SCAR markers was not always consistent with the SSAP markers of origin suggesting a greater level of error in the SSAP map resulting in an inflated map distance for the ASGR. One SCAR marker (Pst 56-1205-400) detected expression of an ASGR retrotransposon in root, anther, leaf and ovary of P. squamulatum, although sequencing of the RT-PCR product failed to find a functional open reading frame for the transcript.
KeywordsLong Terminal Repeat Pearl Millet Selective Amplification Sequence Characterize Amplify Region Marker Selective Nucleotide
We thank Dr. Wayne Hanna for providing plant materials and Dr. Ye Chu, Jackie Merriman, Evelyn P. Morgan and Yajuan Zeng for technical help. This work was supported by the National Science Foundation (award no. 0115911).
- Asker SE, Jerling L (1992) Apomixis in plants. CRC Press, Boca Raton, pp 5–19Google Scholar
- Bousios A, Saldana-Oyarzabal I, Valenzuela-Zapata AG, Wood C, Pearce SR (2007) Isolation and characterization of Ty1-copia retrotransposon sequences in the blue agave (Agave tequilana Weber var. azul) and their development as SSAP markers for phylogenetic analysis. Plant Sci 172:291–298CrossRefGoogle Scholar
- Boyko E, Kalendar R, Korzun V, Fellers J, Korol A, Schulman AH, Gill BS (2002) A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. Plant Mol Biol 48:767–790PubMedCrossRefGoogle Scholar
- Conner JA, Goel S, Gunawan G, Cordonnier-Pratt M, Johnson VE, Liang C, Wang H, Pratt LH, Mullet JE, DeBarry J, Yang L, Bennetzen JL, Klein PE, Ozias-Akins P (2008) Sequence analysis of BAC clones from the apospory-specific genomic region (ASGR) of Pennisetum and Cenchrus. Plant Physiol 147:1–16CrossRefGoogle Scholar
- Dujardin M, Hanna W (1989) Crossability of pearl millet with wild Pennisetum species. Crop Sci 29:77–80Google Scholar
- Goel S, Chen Z, Conner JA, Akiyama Y, Hanna WW, Ozias-Akins P (2003) Delineation by fluorescence in situ hybridization of a single hemizygous chromosomal region associated with aposporous embryo sac formation in Pennisetum squamulatum and Cenchrus ciliaris. Genetics 163:1069–1082PubMedGoogle Scholar
- Grimanelli D, Leblanc O, De Leon DG, Savidan Y (1995) Apomixis expression in maize-Tripsacum hybrid derivatives and the implications regarding its control and potential for manipulation. Apomixis Newsl 8:35–37Google Scholar
- Nogler GA (1984) Gametophytic apomixis. In: Johri BM (ed) Embryology of angiosperms. Springer, Berlin, pp 475–518Google Scholar
- Ozias-Akins P, Roche D, Hanna WW (1998) Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes. Proc Natl Acad Sci USA 95:5127–5132PubMedCrossRefGoogle Scholar
- Sambrook J, Russell DW (2001) Molecular cloning, 3rd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
- Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps, 3rd edn. Plant Research International, WageningenGoogle Scholar