A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

Abstract

Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 1 R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.

Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions

“…Although O. sativa and O. brachyantha separated each other for more than 15 million years and left <10% sequence conserved at the flanking regions of centromeres, our comparative analysis revealed that centromere synteny between these two Oryza genomes is still well maintained with the exception of a few subtle changes. This conservation can even extend to more distantly related grass species, such as B. distachyon, sorghum, maize, and wheat (Triticum aestivum; Qi et al, 2009Qi et al, , 2010Wang and Bennetzen, 2012). Therefore, from a genomic perspective, the location of the plant centromeres as observed here is unlikely to change substantially, supporting the view that chromosomal location may be an evolutionarily conserved primary determinant for functional centromere identity (Thakur and Sanyal, 2013).…”

Non-homologous chromosome pairing and crossover formation in haploid rice meiosis

“…Another chromosome-specific marker, OSJNBa0088I16, was located near the end of the short arm of chromosome 11. It was proved that a distinct homology of segments located at the end of the short arms of chromosomes 11 and 12 by sequence analysis (Qi et al 2009). We found OSJNBa0088I16 hybridization signals were constantly detected on the short arm of chromosome 12.…”

“…In addition, it was found that non-homologous chromosomes containing homologous fragments more easily paired in haploid rice cells during meiosis. Sequence data from the rice genome indicate a distinct homology of segments located at the end of the short arms of chromosomes 11 and 12 (Qi et al 2009), making these chromosomes, along with 11 and 12, more amenable to pairing. Besides, the normal function of meiosis-related proteins, REC8, PAIR2, and ZEP1, may promote the pairing of non-homologous chromosomes in haploid rice.…”

“…Bars 5 μm fail to form an enduring bond that will persist until metaphase I in most cells. Only non-sister chromatid exchange will occur in the short arm of chromosomes 11 and 12 because of the homologous segments (Qi et al 2009). Therefore, chromosome homology, while not essential for pairing, is apparently a prerequisite for non-sister chromatid recombination.…”

Molecular mapping of the suppressor gene Igc1 to the gametocidal gene Gc3-C1 in common wheat

“…Eventually, for the known Gc factors, we have repeated backcrossing for several decades, but we could not separate 'breaking' and 'protecting' factors by recombination. Synteny of orthologous genes between wheat and rice revealed high conservation and a one-to-one correspondence of centromeric regions between chromosome 3B of wheat and chromosome 1 of rice (Qi et al, 2009). For the centromeric region of chromosome 1 in rice, distortion of marker segregation has been found in the F 2 population of indica-japonica hybrids (Harushima et al, 2001).…”