In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet

Abstract

Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) and varied in both karyotype and position of the ASGR on the ASGR-carrier chromosome among other apomictic Cenchrus/Pennisetum species. Using in silico transcript mapping and verification of physical positions of some of the transcripts via FISH, we discovered that the ASGR-carrier chromosome from P. squamulatum is collinear with chromosome 2 of foxtail millet and sorghum outside of the ASGR. The in silico ordering of the ASGR-carrier chromosome markers, previously unmapped in P. squamulatum, allowed for the identification of a backcross line with structural changes to the P. squamulatum ASGR-carrier chromosome derived from gamma irradiated pollen.

Fig 1. FISH images of BAC probes mapped to the ASGR-carrier chromosome.

Example of a mitotic chromosome spread of apomictic BC₈ (06-A-58) with the ASGR identified with a yellow arrow and the centromere of the ASGR-carrier chromosome identified by a red arrow. A-G insets are mapped ASGR-carrier chromosome BACs. The yellow arrow denotes the ASGR signal. The ASGR signal was identified either through a high copy ASGR-BAC clone (red pseudo-color) or a combination of a high (red pseudo-color) and low (green pseudo-color) ASGR-BAC clone. The red arrow denotes the centromere signal and the green arrow denotes the mapped ASGR carrier chromosome BAC signal from the following a) p285J18/PS_c2838, b) p220A02/PS_c583 and p236E19/PS_c10535 (*), c) p036L06/PS_c2448, d) p258L05/PS_c3993, e) p236E19/PS_c10535, f) p057M05/PS_c5080, and g) p142D19/PS_c5851.

Fig 2. Diagram of collinearity identified using FISH signals on the P. squamulatum ASGR-carrier chromosome and the in silico positions in sorghum and foxtail millet chromosome 2.

Chromosome lengths are not drawn to scale. Black box denotes BAC clones where linear order was confirmed. *Order of Ps26_c3993 and Ps26_c10535 BACs to each other was not verified.