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This article is a Commentary on Higgins et al. (2021), 229: 3281–3293. [ABSTRACT FROM AUTHOR]

Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined., Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges ( HE) on gene expression in Brassica napus, a representative allotetraploid crop., We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time., This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution. [ABSTRACT FROM AUTHOR]

Recombination is a major mechanism generating genetic diversity, but the control of the crossover rate remains a key question. In Brassica napus ( AACC, 2 n = 38), we can increase the homologous recombination between A genomes in AAC hybrids. Hypotheses for this effect include the number of C univalent chromosomes, the ratio between univalents and bivalents and, finally, which of the chromosomes are univalents., To test these hypotheses, we produced AA hybrids with zero, one, three, six or nine additional C chromosomes and four different hybrids carrying 2 n = 32 and 2 n = 35 chromosomes. The genetic map lengths for each hybrid were established to compare their recombination rates., The rates were 1.4 and 2.7 times higher in the hybrids having C6 or C9 alone than in the control (0 C). This enhancement reached 3.1 and 4.1 times in hybrids carrying six and nine C chromosomes, and it was also higher for each pair of hybrids carrying 2 n = 32 or 2 n = 35 chromosomes, with a dependence on which chromosomes remained as univalents., We have shown, for the first time, that the presence of one chromosome, C9, affects significantly the recombination rate and reduces crossover interference. This result will have fundamental implications on the regulation of crossover frequency. [ABSTRACT FROM AUTHOR]

Chromosome rearrangements are common, but their dynamics over time, mechanisms of occurrence and the genomic features that shape their distribution and rate are still poorly understood. We used allohaploid Brassica napus (AC, n = 19) as a model to analyze the effect of genomic features on the formation and diversity of meiotically driven chromosome rearrangements. We showed that allohaploid B. napus meiosis leads to extensive new structural diversity. Almost every allohaploid offspring carried a unique combination of multiple rearrangements throughout the genome, and was thus structurally differentiated from both its haploid parent and its sister plants. This large amount of genome reshuffling was remarkably well-tolerated in the heterozygous state, as neither male nor female fertility were strongly reduced, and meiosis behavior was normal in most cases. We also used a quantitative statistical model, which accounted for 75% of the observed variation in rearrangement rates, to show that the distribution of meiotically driven chromosome rearrangements was not random but was shaped by three principal genomic features. In descending order of importance, the rate of marker loss increased strongly with genetic distance from the centromere, the degree of collinearity between chromosomes, and the genome of origin (A < C). Overall, our results demonstrate that B. napus accumulates a large number of genetic changes, but these rearrangements are not randomly distributed in the genome. The structural genetic diversity produced by the allohaploid pathway and its role in the evolution of polyploid species compared to diploid meiosis are discussed. [ABSTRACT FROM AUTHOR]

In this article, the author comments on the role of polyploidy in the evolution of plants and animals. As stated, polyploid species are formed through a diversity of mechanisms in natural populations involving one progenitor species or autopolyploids or divergent parental lineages or allopolyploids. He opines that rapidly evolving sequencing technologies have enabled large-scale investigations of genomes, epigenomes, transcriptomes and natural populations of wild species of various plant lineages.

Precise chromosome segregation is vital for polyploid speciation. Here, we highlight recent findings that revitalize the old question of the genetic control of diploid-like meiosis behaviour in polyploid species. We first review new information on the genetic control of autopolyploid and allopolyploid cytological diploidization, notably in wheat and Brassica. These major advances provide new opportunities for speculating about the adaptation of meiosis during polyploid evolution. Some of these advances are discussed, and it is suggested that research on polyploidy and on meiosis should no longer be unlinked. [ABSTRACT FROM AUTHOR]

Presents information on a study that measured and compared the pattern of differentiation within and among the wild and cultivated Medicago Sativa (Leguminosae) with respect to both allozymes and quantitative traits. Role of crop-to-weed gene flow in the relationship between crops and their wild relatives; Materials and methodology; Results and discussion.

The conservation of a crop's wild relatives as genetic resources requires an understanding of the way genetic diversity is maintained in their populations, notably the effect of crop-to-wild gene flow. In this study, the amount of differentiation between natural and cultivated populations of Medicago sativa was analysed using random amplified polymorphic DNA (RAPD) markers and an extension of the AMOVA procedure adapted to autotetraploid organisms. Simulations of structured populations were performed to test whether AMOVA provides estimates of population structure in autotetraploids that can be directly compared to those obtained for allozyme data. Simulations showed that φ-statistics allow a good estimation of population differentiation when unbiased allelic frequencies are used to correct the conditional expectations of squared genetic distances. But such unbiased estimates can not be practically guaranteed, and population structure is notably overestimated when some populations are fixed for the presence of amplified fragments. However, removing fixed loci from the data set improves the statistical power of the test for population structure. The genetic variation of 15 natural and six cultivated populations of M. sativa was analysed at 25 RAPD loci and compared to estimates computed with allozymes on the same set of populations. Although RAPD markers revealed less within-population genetic diversity than allozymes, the quantitative and qualitative patterns of population structure were in full agreement with allozymes. This confirmed the conclusions drawn from the allozymic survey: crop-to-wild occurred in many locations, but some other mechanisms opposed cultivated traits to be maintained into natural populations. [ABSTRACT FROM AUTHOR]