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• Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. • Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. • Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. • Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.

Background The apomictic reproductive mode of Brachiaria (syn. Urochloa ) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria , reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like ( BBML ), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis , B. brizantha , and B. decumbens . In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. Results Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F 1 mapping population ( n  = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola . High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica . The ASGR-BBML specific PCR product cosegregated with the ASGR in the F 1 mapping population, despite its location on a different carrier chromosome than B. decumbens . Conclusions The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.

Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F(1) progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid. Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.

Premise of the Study The genetic bottleneck of polyploid formation can be mitigated by multiple origins, gene flow, and recombination among different lineages. In crop plants with limited origins, efforts to increase genetic diversity have limitations. Here we used lineage recombination to increase genetic diversity in peanut, an allotetraploid likely of single origin, by crossing with a novel allopolyploid genotype and selecting improved lines. Methods Single backcross progeny from cultivated peanut × wild species‐derived allotetraploid cross were studied over successive generations. Using genetic assumptions that encompass segmental allotetraploidy, we used single nucleotide polymorphisms and whole‐genome sequence data to infer genome structures. Key Results Selected lines, despite a high proportion of wild alleles, are agronomically adapted, productive, and with improved disease resistances. Wild alleles mostly substituted homologous segments of the peanut genome. Regions of dispersed wild alleles, characteristic of gene conversion, also occurred. However, wild chromosome segments sometimes replaced cultivated peanut's homeologous subgenome; A. ipaënsis B sometimes replaced A. hypogaea A subgenome (~0.6%), and A. duranensis replaced A. hypogaea B subgenome segments (~2%). Furthermore, some subgenome regions historically lost in cultivated peanut were “recovered” by wild chromosome segments (effectively reversing the “polyploid ratchet”). These processes resulted in lines with new genome structure variations. Conclusions Genetic diversity was introduced by wild allele introgression, and by introducing new genome structure variations. These results highlight the special possibilities of segmental allotetraploidy and of using lineage recombination to increase genetic diversity in peanut, likely mirroring what occurs in natural segmental allopolyploids with multiple origins.

Evolutive studies have verified that Coffea arabica (2n = 44) is a natural segmental allopolyploid originated from a cross between two diploid (2n = 22) Coffea species. Data obtained by classical cytogenetic analyses showed that C. arabica chromosomes are small and morphologically similar, which hampers the karyogram assembly with well-identified homologue pairs. In the present study, the C. arabica complement was reanalysed using an improved cytogenetic protocol that allowed the obtention of high-quality prometaphasic and metaphasic chromosomes. The results showed that chromosomes are cytogenetically distinct (1, 2, 19, 20, 21 and 22) and identical (3-4, 5-6, 7-8, 9-10, 11-12, 13-14, 15-16 and 17-18), with regard to their total length, short and long arm sizes or chromosome classes. Our work suggests that C. arabica is a true non-segmental allotetraploid but originated from different species exhibiting similar and distinct chromosomes.

Several cytotypes (polyploids and aneuploids) have been reported in Lepisorus thunbergianus. The relationships between these cytotypes within the species remain poorly understood. We studied populations in an area where various cytotypes of L. thunbergianus as well as two diploid species, L. angustus and L. onoei, candidate parental species that may be involved in allopolyploid origins of L. thunbergianus polyploids, occur. We determined the ploidy levels of sampled materials by direct chromosome counting and flow cytometry. We elucidated the origins of L. thunbergianus polyploids by analyzing allozyme polymorphisms, and in addition, we examined the occurrence of segmental allopolyploidy by comparing allelic variation between polyploids and their parental diploids. Six cytotypes, i.e. one diploid (2n = 50), two triploid (2n = 75 and 76) and three tetraploid (2n = 100, 101, and 102) cytotypes, were observed in L. thunbergianus, and the two diploid species, L. angustus (2n =52) and L. onoei (2n =50) were confirmed to include a single cytotype each. Allozyme analyses indicated that the tetraploid (2n =100) and hypertetraploid (2n = 102) of L. thunbergianus originated by allopolyploidy between diploid L. thunbergianus (2n = 50) and diploid L. angustus (2n = 52), since the polyploids shared alleles with these two diploids that were unique to each diploid. The allozyme patterns excluded the possibility that L. thunbergianus polyploids originated from L. onoei. The unbalanced heterozygosity and homozygosity found in the tetraploid and the hypertetraploid of L. thunbergianus indicated their segmental allopolyploidy.

Teasle gourd [Momordica subangulata Blume subsp. renigera (G. Don) de Wilde, 2n = 56] exhibits morphological characters found in both M. dioica (2n = 28) and M. cochinchinensis (2n = 28). Morphological analysis of M. subangulata subsp. renigera suggests an allopolyploid origin. We present evidence elucidating the genomic relationships between M. dioica, M. cochinchinensis and M. subangulata subsp. renigera. A triploid M. dioica × M. subangulata subsp. renigera hybrid had an average of 12.76 bivalents, 13.84 univalents and 0.88 trivalents at metaphase I, while the M. cochinchinensis × M. subangulata subsp. renigera hybrid had an average of 13.08 bivalents, 12.96 univalents and 0.96 trivalents. F₁ hybrids of the two diploid species (M. dioica × M. cochinchinensis) showed an average of 9.12 bivalents and 9.76 univalents, suggesting that the genomes of these species are only partially homologous. A higher number of bivalents in the triploid hybrids suggests that M. subangulata subsp. renigera is a segmental allopolyploid of M. dioica and M. cochinchinensis and that its genomes have diverged from the parental genomes.