Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the 4th selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

Cytogenetics of coffee

The genus Coffea L. has around 100 native species distributed in tropical and subtropical areas in Africa, and the most important economic species are C. arabica and C. canephora. C. arabica is exceptional in the genus since it is the only species so far analyzed which is self-compatible, and a natural polyploid with 2n=4x=44 chromosomes; it is considered to be a segmental allopolyploid because it presents a disomic inheritance and a regular meiotic behavior. All other species in the genus are self-incompatible diploids with 2n=2x=22. Cytogenetic studies in Coffea, undertaken since 1912, have followed various phases: initial studies were limited only to establishing chromosome counts. Subsequent studies characterized the karyotypes of various species using conventional cytological techniques. As the somatic metaphase chromosomes of coffee are very small (1 - 3 µm) and morphologically symmetrical, these studies resulted in uniform karyotypes that show almost no differences among species. Since genetic improvement of coffee trees has progressed mainly by means of interspecific hybridizations involving wild species, analyses of microsporogenesis in species and hybrids were needed to establish their genetic affinity and relationships. The first successful attempts to differentiate coffee chromosomes longitudinally were made by mapping pachytene chromomeric patterns and by C and NOR banding techniques. From 1998 onwards, the use of banding techniques with the fluorochromes DAPI and CMA3, and also the cytomolecular technique FISH using rDNA probes, has increased the longitudinal differentiation of coffee chromosomes. The use of the GISH technique with total genomic DNA has revealed the parental species that originated C. arabica species.

Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist?

When polyploid hybrids with closely related genomes are propagated by selfing or sib-breeding, the meiotic behaviour will turn into essentially autopolyploid behaviour as soon as the affinity between the genomes is sufficient to permit occasional homoeologous pairing. An allopolyploid will only be formed when the initial differentiation is sufficient to completely prevent homoeologous pairing (in some cases enhanced by specific genes), or when segregational dysgenesis prevents transmission of recombined chromosomes. A new polyploid hybrid may be considered a segmental allopolyploid and may show reduced multivalent formation as a result of preferential pairing between the least differentiated genomes. An established polyploid is either an autopolyploid or an allopolyploid. In exceptional cases it is thinkable that a stable segmental allopolyploid arises, in which some sets of chromosomes are well differentiated and behave as in an allopolyploid, whereas other sets are not well differentiated and behave as in an autopolyploid. No clear cases have been found in the literature so far. Key words : chromosome, pairing affinity, quadrivalent frequency, segmental allopolyploidy.

Meiotic studies of some South African cultivars of Lantana camara (Verbenaceae)

Lantana camara L. is a polyploid species with a basic chromosome number of 11 (x = l l ) . Chromosome association in 39 cultivars indicated the occurrence of univalents to heptavalents with bivalents predominating. Multivalent association analysis revealed the presence in South Africa of at least four different groups of L. camara at the diploid level. The potential for sexual reproduction must exist, at least at the diploid level, to account for differences in chromosomal behaviour that can only be attributed to hybridization. The possibility exists that the basic chromosome number may be lower than 11, or else postspeciation genomic evolution must have occurred. No cytogenetical correlation exists between the South African and Indian cultivars. The number of chiasmata per genome increases with an increase in the polyploid level. Most multivalents are of the chain type. Univalents during diakinesis are the result of asynapsis. Triploid and pentaploid plants display a markedly abnormal meiosis. L. camara is a segmental allopolyploid species.