A universal chromosome identification system for maize and wildZeaspecies

Abstract

Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared to other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species. ReferencesAdawy SSM, Stupar RM, Jiang J (2004) Fluorescence in situ hybridization of knob-associated DNA elements analysis reveals multiple loci in one-knob and knobless maize lines. J (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. P Natl Acad Sci USA 116:1679-1685 Amarillo FIE, Bass HW (2007) A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion.

Extraordinarily conserved chromosomal synteny ofCitrusspecies revealed by chromosome‐specific painting

“…The nine chromosome painting probes were labeled by either digoxigenin or biotin, and detected using red and green fluorescence, respectively (Braz et al ., 2020a). A group of two or three probes (the third probe was labeled 50% digoxigenin and 50% biotin) were hybridized to metaphase chromosomes prepared from root tips of germinated seeds of C. maxima .…”

“…These oligos can then be synthesized in parallel and labeled as a FISH probe (Han et al ., 2015). Chromosomal research based on such pooled oligo probes has been reported in a rapidly increasing number of plant species (Qu et al ., 2017; Braz et al ., 2018; He et al ., 2018; Hou et al ., 2018; Meng et al ., 2018; Xin et al ., 2018; Albert et al ., 2019; Martins et al ., 2019; Simonikova et al ., 2019; Bačovský et al ., 2020; Bi et al ., 2020; Braz et al ., 2020a; Liu et al ., 2020; Song et al ., 2020; Xin et al ., 2020).…”

“…However, each painting probe allows the identification of only a single chromosome. The second class of probes contain oligos designed from multiple regions of multiple chromosomes (Braz et al ., 2018; Liu et al ., 2020; Meng et al ., 2020; Braz et al ., 2020a). Such probes generate distinct FISH signal patterns on every chromosome in the same species.…”

Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize

“…Root tips were harvested from plants and treated with N 2 O at a pressure of 160 psi ( c . 10.9 atm) for 2 h (Kato, 1999; Braz et al ., 2020a,b). The root tips were fixed in fixative solution (ethanol : acetic acid, 3 : 1) and kept at −20°C until use.…”

“…Oligo‐FISH was conducted using the previously developed maize barcode FISH probe (Braz et al ., 2020a) and two haplotype‐specific probes for maize chromosome 10 (Martins et al ., 2019). Combination of these two probes allowed identification of individual copies of chromosome 10 and their origination from either inbred B73 or H99.…”