The evolutionary significance of introgression has been discussed for decades. Questions about potential impacts of transgene flow into wild and weedy populations brought renewed attention to the introgression of crop alleles into those populations. In the past two decades, the field has advanced with considerable descriptive, experimental, and theoretical activity on the dynamics of crop gene introgression and its consequences. As illustrated by five case studies employing an array of different approaches, introgression of crop alleles has occurred for a wide array of species, sometimes without significant consequence, but on occasion leading to the evolution of increased weediness. A new theoretical context has emerged for analyzing empirical data, identifying factors that influence introgression, and predicting introgression's progress. With emerging molecular techniques and analyses, research on crop allele introgression into wild and weedy populations is positioned to make contributions to both transgene risk assessment and reticulate evolution.

• Background and Aims Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. • Methods Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). • Key Results The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H_e = 0·313, I = 0·572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. • Conclusions Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.

Summary: Genetically modified (GM) rice with enhanced agronomic traits and pharmaceutical uses are ready for widespread adoption. Little is known about isolation requirements for achieving stringent transgene confinement in rice. To investigate the extent of pollen‐mediated crop‐to‐crop transgene flow, we conducted a field experiment with four plot‐size treatments of adjacent GM and nonGM rice (Oryza sativa) in China. Three insect‐resistant GM rice (Bt/CpTI) and nonGM isogenic lines were used in the study. The hygromycin‐resistance transgene (hpt) marker was used to screen seeds from the nonGM rice rows at different distance intervals from GM rice plots. Based on the examination of > 2.1 million germinated seeds, we found a dramatic reduction in transgene frequencies with increasing distance from the GM crop, ranging from c. 0.28% at 0.2 m to < 0.01% at 6.2 m. In addition, different plot size did not significantly affect the frequencies of gene flow. In conclusion, pollen‐mediated crop‐to‐crop transgene flow in rice can be maintained at negligible levels with short spatial isolation. The model can also be applied to other crops with self‐ and wind‐pollination.

Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.

Summary: Crop‐to‐crop transgene flow will affect seed purity of non‐GM rice varieties, leading to unwanted consequences. To assess the maximum probability of transgene outflow in rice ( Oryza sativa ), gene flow experiments were conducted with three cultivation patterns with different mixed‐planting proportions of adjacent GM and non‐GM rice at two sites in Fujian and Hainan Provinces of China. Three GM rice lines containing two insect‐resistance genes ( Bt / CpTI ) and their non‐GM counterparts were used in the experiments to allow natural hybridization to occur. A hygromycin resistance gene was used as a selective marker for identifying hybrids. Based on the examination of > 645 700 geminated seeds, the result showed low frequencies (0.05–0.79%) of transgene flow from GM to non‐GM rice at close spacing, although with significant variation among mixed‐planting proportions. It is concluded that rice transgene flow will occur at a very low frequency (< 1.0%), even if the GM rice is planted at close spacing with non‐GM rice, and high densities of GM rice cultivated in the neighborhood of non‐GM rice will increase the probability of outcrossing with the non‐GM rice.

Doubly uniparental inheritance (DUI) is an exception to the typical maternal inheritance of mitochondrial (mt) DNA in Metazoa, and found only in some bivalves. In species with DUI, there are two highly divergent gender-associated mt genomes: maternal (F) and paternal (M), which transmit independently and show different tissue localization. Solenaia carinatus is an endangered freshwater mussel species exclusive to Poyang Lake basin, China. Anthropogenic events in the watershed greatly threaten the survival of this species. Nevertheless, the taxonomy of S. carinatus based on shell morphology is confusing, and the subfamilial placement of the genus Solenaia remains unclear. In order to clarify the taxonomic status and discuss the phylogenetic implications of family Unionidae, the entire F and M mt genomes of S. carinatus were sequenced and compared with the mt genomes of diverse freshwater mussel species. The complete F and M mt genomes of S. carinatus are 16716 bp and 17102 bp in size, respectively. The F and M mt genomes of S. carinatus diverge by about 40% in nucleotide sequence and 48% in amino acid sequence. Compared to F counterparts, the M genome shows a more compact structure. Different gene arrangements are found in these two gender-associated mt genomes. Among these, the F genome cox2-rrnS gene order is considered to be a genome-level synapomorphy for female lineage of the subfamily Gonideinae. From maternal and paternal mtDNA perspectives, the phylogenetic analyses of Unionoida indicate that S. carinatus belongs to Gonideinae. The F and M clades in freshwater mussels are reciprocal monophyly. The phylogenetic trees advocate the classification of sampled Unionidae species into four subfamilies: Gonideinae, Ambleminae, Anodontinae, and Unioninae, which is supported by the morphological characteristics of glochidia.