Table 1.
Selection of cohesin/SMC genes and cofactors with potential for inclusion in breeding initiatives in major crops.
| SMC gene and associated factors | Functional features in the literature and public databases1,2 | Locus ID as determined by TAIR, NCBI, and the Human Genome Organization (HUGO)5 | Presumed homologs of interest (rice and maize) retrieved from databases3,4,6 by the respective coding sequences (CDS) | Likely agricultural use |
|---|---|---|---|---|
| Arabidopsis HORMA-domain protein ASYNAPTIC 1 (ASY1) | Distribution of COs along meiotic chromosomes in a REC8/SYN1 dependent manner | At1g67370 | Os09g32930, GRMZM2G035996 | Knockdown alleles may reduce linkage drag in major crops |
| Human cohesin interacting factors BRG1/SMARCA4 and ARID2 (SWI/SNF subunits) | Cohesin-mediated repression of transcriptional activity, genome maintenance | HGNC:6597 and HGNC:196528 | Os05g05230, GRMZM2G102625, Os07g33860, GRMZM2G009412 | Promotion of seed longevity, intentional induction of inversions and translocations |
| Human ATP-dependent DNA helicase DEAD/H-box helicase 11 (DDX11) | Synthetically lethal with human ECO1 homolog ESCO2 (HGNC:27230) and epistatic to human WAPL (HGNC:23293). Promotes cohesion in arms and centromeres during replication, probably by promotion of SMC3 acetylation, and enhanced stability of replication forks | HGNC:1663 | Os05g13300, GRMZM2G100067 | Promotion of replication fork stability. May constitute an important layer of genome maintenance under stress across all eukaryotes |
| Arabidopsis N-acetylase ECO1/CTF7 | Acetylation of the ATP-ase domain of SMC proteins, establishment of cohesion, homology-dependent DNA repair. Its function is antagonized by WAPL | At4g31400 | Os05g31230, GRMZM2G100067; and Os04g42120, GRMZM2G075145 | Prevention of large-scale rearrangements, targeted manipulation of chromosome folding during MSUC and MSCI in meiocytes of papaya, gene expression. |
| Yeast chromatin-remodeling ATPase ISW1/YBR245C | Cohesin-dependent processes such as DNA repair and transcription in promoters | SGD:S000000449 | Os03g22900, GRMZM2G469162 | May stabilize transcription under stress across eukaryotic organisms |
| Cohesin subunit PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5A/E) | Cohesion-promoting cofactor; has a role in fork protection and stable DNA replication | At5g47690, At1g77600, At4g31880, At1g80810, and At1g15940 | For PDS5A: Os06g17840, GRMZM2G010637 | May stabilize DNA replication under stress, may be a target for the manipulation of DNA looping and chromosome folding during MSUC and MSCI in meiocytes of papaya |
| Arabidopsis SCC2 | Initial CO formation during meiosis, 3D-chromosome folding, loading of cohesin complexes, chromosome looping and DNA repair | At5g15540 | Os07g01940, GRMZM2G132504, Carica papaya evm.model.supercontig_2744.1 | Promotion of crossover resolution, targeted manipulation of chromosome folding during MSUC and MSCI in meiocytes of papaya |
| Arabidopsis SCC3 | Regulates release of α-kleisins. Regulates meiotic orientation of kinetochores in Arabidopsis, and may have a role in the prevention of large-scale rearrangements during replication, dimerization of cohesin, and chromosome looping | At2g47980 | Os05g09620, GRMZM2G131443 | May prevent chromosomal rearrangements during replication, in plants, it may provide a valuable layer of genome maintenance under stress |
| Maize SCC4/DEK15 | Mitotic chromosome segregation, endosperm and embryo formation, transcriptional regulation of kernel development in maize | GRMZM2G079796 | Os04g28010 | Promotion of embryo and endosperm development |
| Arabidopsis condensin subunit STRUCTURAL MAINTENANCE OF CHROMOSOMES 4 (SMC4) | Silencing of pericentromeric TEs, DNA methylation, transcription of genes related to translesion synthesis, male gamete development, tolerance to Boron toxicity | At5g48600 | Os05g41750, GRMZM2G416501 | May lead to enhanced tolerance to exogenous DNA damage, and improved genome maintenance in crops |
| Arabidopsis EXTRA SPINDLE POLES (AESP1), Separase | Cleavage of the REC8/SYN1 α-kleisin during anaphase I and anaphase II, allowing disjunction of homologs and sister centromeres, respectively. Proper assembly of radial microtubule system after telophase II, embryo development, cellularization of the endosperm, and vesicle trafficking | At4g22970 | Os02g53120, GRMZM2G300624 | Promotion of crossovers resolution and proper tetrad formation. May facilitate breeding of fertile cultivars in major crops |
| Arabidopsis SWITCH1/DYAD (SWI1) | Sister chromatid cohesion and meiotic chromosome organization, assembly of the chromosome axis | At5g51330 | Known as AMEIOTIC (OsAM1) in rice: Os03g44760, and AMEIOTIC (AM1) in maize (possibly GRMZM5G883855) | May facilitate the identification of new alternative meiotic α-kleisins in crops |
| Arabidopsis WINGS APART-LIKE PROTEIN 1 (WAPL1/2) | Release of meiotic α-kleisin REC8/SYN1 during prophase I. Cohesin removal by WAPL is required to complete DNA synthesis under conditions of persistent DNA replication stress. Regulates chromosome folding | At1g11060 and At1g61030 | Os10g35380, GRMZM2G034276; Os10g35380, GRMZM2G034276 | New alleles may facilitate DNA replication under persistent damage. May confer tolerance to chronic DNA damage in crops |
MSUC, meiotic silencing of unsynapsed chromatin; MSCI, meiotic sex chromosome inactivation; TE, transposable elements.
1
Database consulted was The Arabidopsis Information Resource (TAIR): https://www.arabidopsis.org/.
2
Database consulted was National Center for Biotechnology Information (NCBI): https://www.ncbi.nlm.nih.gov/.
3
Database consulted was Phytozome v12.1: https://phytozome.jgi.doe.gov/pz/portal.html.
4
Database consulted was Maize GDB: https://www.maizegdb.org/.
5
Database consulted was the Human Genome Organization (HUGO): http://www.hugo-international.org/.
6
Database consulted was the Rice Genome Annotation Project: http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/.