It is essential to assess environmental impact of transgene flow from genetically engineered crops to their wild or weedy relatives before commercialization. Measuring comparative trials of fitness in the transgene-flow-resulted hybrids plays the key role in the assessment, where the segregated isogenic hybrid lineages/subpopulations with or without a transgene of the same genomic background are involved. Here, we report substantial genomic differentiation between transgene-present and -absent lineages (F₂-F₃) divided by a glyphosate-resistance transgene from a crop-wild/weed hybrid population in rice. We further confirmed that such differentiation is attributed to increased frequencies of crop-parent alleles in transgenic hybrid lineages at multiple loci across the genome, as estimated by SSR (simple sequence repeat) markers. Such preferential transmission of parental alleles was also found in equally divided crop-wild/weed hybrid lineages with or without a particular neutral SSR identifier. We conclude that selecting either a transgene or neutral marker as an identifier to create hybrid lineages will result in different genomic background of the lineages due to non-random transmission of parental alleles. Non-random allele transmission may misrepresent the outcomes of fitness effects. We therefore propose seeking other means to evaluate fitness effects of transgenes for assessing environmental impact caused by crop-to-wild/weed gene flow.

As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression from japonica rice cultivars into the indica type of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples with indica and japonica components, suggesting different levels of introgression from japonica rice cultivars to the indica type of weedy rice. The principal coordinate analyses indicated indica–japonica genetic differentiation among weedy rice samples, which was positively correlated with the introgression of japonica-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop–weed introgression in agroecosystems.

Hypotheses regarding the association of increased species or genetic diversity with gradually warmer regions as a global pattern have been proposed, but no direct and solid experimental data are available to approve the association between plant genetic diversity and ambient temperatures. To test the diversity-temperature hypothesis, we studied genetic diversity and genetic differentiation of weedy rice (Oryza sativa f. spontanea) populations occurring naturally in early- and late-season rice fields that share nearly the same ecological conditions but with slightly different temperatures. Data collected from 10-year historical climatic records indicated a ~2 °C higher average air temperature in the late rice-cultivation seasons than in the early seasons. Results based on molecular fingerprints of 27 SSR (simple sequence repeat) loci showed a higher level of genetic diversity in the late-season weedy rice populations than in the early-season populations. In addition, a positive correlation was detected between the increased proportion of genetic diversity (ΔH_e) and genetic differentiation among the weedy rice populations, suggesting limited gene flow. Therefore, we conclude from this study that increased genetic diversity in the late-season weedy rice populations is probably caused by the higher ambient temperatures. This finding provides evidence for the possible association between genetic diversity and ambient temperatures.

Naked barley (Hordeum vulgare var. nudum) is a staple food crop, contributing significantly to global food security. Understanding genetic diversity will facilitate its effective conservation and utilization. To determine genetic diversity and its distribution within and among varieties, we characterized 30 naked barley varieties from Tibet, representing the traditional, modern, and germplasm-resources-bank gene pools, by analyzing SSR molecular fingerprints. The results demonstrate abundant genetic diversity in Tibetan naked barley varieties, particularly those in the traditional gene pool that holds much more private (unique) alleles. Principal coordinates and STRUCTURE analyses indicate substantial deviation of the modern varieties from the traditional and germplasm-resources-bank varieties. A considerable amount of seed mixture is detected in the modern varieties, suggesting the practices of using mixed seeds in modern-variety cultivation. Cluster analyses further indicate the narrow genetic background of the modern varieties, likely due to the limited number of traditional/germplasm-resources-bank varieties applied in breeding. Relationships between increases in genetic diversity and sample sizes within naked barley varieties highlight the importance of effective sampling strategies for field collections. The findings from this study have important implications for the sustainable utilization and effective conservation of different types of naked barley germplasm, both in Tibet and in other regions around the world.

Naked barley (Hordeum vulgare var. nudum) is a staple food crop contributing significantly to the global food security. Understanding genetic diversity will facilitate its effective conservation and utilization. To determine genetic diversity and its distribution within and among varieties, we characterized 30 naked barley varieties representing the traditional, modern, and germplasm-resources-bank gene-pools from Tibet, using the SSR molecular fingerprints. Results demonstrate abundant genetic diversity in Tibetan naked barley varieties, particularly those in the traditional gene-pool that holds much more private alleles. Principal coordinates and STRUCTURE analyses indicate substantial deviation of the modern varieties from the traditional and germplasm-resources-bank varieties. A considerable amount of seed mixture is detected in the modern varieties, suggesting the practices of using mixed seeds in modern-variety cultivation. Cluster analyses indicate the narrow genetic background of the modern varieties because of a few traditional/germplasm-resources-bank varieties used in breeding. Relationships between variation of genetic diversity and increases in sample sizes within naked barley varieties suggest effective sampling strategies for field collections. Knowledge generated from this study has important implications for the sustainable utilization and effective conservation of different types of naked barley germplasm in Tibet and in other regions of the world.