Crop/weed gene flow:Chenopodium quinoa Willd. andC. berlandieri Moq

North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa)

Pitseed goosefoot (Chenopodium berlandieri) is a free-living North American member of an allotetraploid complex that includes the Andean pseudocereal quinoa (C. quinoa). Like quinoa, pitseed goosefoot was domesticated, possibly independently, in eastern North America (subsp. jonesianum) and Mesoamerica (subsp. nuttaliae). To test the utility of C. berlandieri as a resource for quinoa breeding, we produced the whole-genome DNA sequence of PI 433,231, a huauzontle from Puebla, México. The 1.295 Gb genome was assembled into 18 pseudomolecules and annotated using RNAseq data from multiple tissues. Alignment with the v.2.0 genome of Chilean-origin C. quinoa cv. 'QQ74' revealed several inversions and a 4A-6B reciprocal translocation. Despite these rearrangements, some quinoa x pitseed goosefoot crosses produce highly fertile hybrids with faithful recombination, as evidenced by a high-density SNP linkage map constructed from a Bolivian quinoa 'Real-1' × BYU 937 (Texas coastal pitseed goosefoot) F2 population. Recombination in that cross was comparable to a 'Real-1' × BYU 1101 (Argentine C. hircinum) F2 population. Furthermore, SNP-based phylogenetic and population structure analyses of 90 accessions supported the hypothesis of multiple independent domestications and descent from a common 4 × ancestor, with a likely North American Center of Origin.

A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa

Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.

Quinoa in Ecuador: Recent Advances under Global Expansion

Quinoa is a highly diverse crop domesticated in the Andean region of South America with broad adaptation to a wide range of marginal environments. Quinoa has garnered interest worldwide due to its nutritional and health benefits. Over the last decade, quinoa production has expanded outside of the Andean region, prompting multiple studies investigating the potential for quinoa cultivation in novel environments. Currently, quinoa is grown in countries spanning five continents, including North America, Europe, Asia, Africa, and Oceania. Here, we update the advances of quinoa research in Ecuador across different topics, including (a) current quinoa production situation with a focus on breeding progress, (b) traditional seed production, and (c) the impact of the work of the nongovernment organization “European Committee for Training and Agriculture” with quinoa farmers in Chimborazo province. Additionally, we discuss genetic diversity, primary pests and diseases, actions for adapting quinoa to tropical areas, and recent innovations in quinoa processing in Ecuador. Finally, we report a case study describing a participatory breeding project between Washington State University and the Association of Andean Seed and Nutritional Food Producers Mushuk Yuyay in the province of Cañar.

Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food?

Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.

Quinoa Abiotic Stress Responses: A Review

Quinoa (Chenopodium quinoa Willd.) is a genetically diverse Andean crop that has earned special attention worldwide due to its nutritional and health benefits and its ability to adapt to contrasting environments, including nutrient-poor and saline soils and drought stressed marginal agroecosystems. Drought and salinity are the abiotic stresses most studied in quinoa; however, studies of other important stress factors, such as heat, cold, heavy metals, and UV-B light irradiance, are severely limited. In the last few decades, the incidence of abiotic stress has been accentuated by the increase in unpredictable weather patterns. Furthermore, stresses habitually occur as combinations of two or more. The goals of this review are to: (1) provide an in-depth description of the existing knowledge of quinoa's tolerance to different abiotic stressors; (2) summarize quinoa's physiological responses to these stressors; and (3) describe novel advances in molecular tools that can aid our understanding of the mechanisms underlying quinoa's abiotic stress tolerance.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Crop-to-wild gene flow, introgression and possible fitness effects of transgenes

Crop-to-wild gene flow has received close attention over the past ten years in connection with the development and cultivation of transgenic crops. In this paper, we review key examples of crop/wild sympatry and overlapping flowering phenology, pollen and seed dispersal, the barriers to hybridisation and introgression, the evolution and fate of interspecific hybrids, their fitness, and the potential cost of transgenes. We pay particular attention to ways in which the evolution and divergence between crops and their wild relatives may interfere with these successive steps. Our review suggests that crop-to-weed gene flow is highly idiosyncratic and that crop gene dispersion will certainly be very difficult to preclude totally. Future directions for research should thus focus on the long-term establishment and effects of transgenes on natural communities.

Gene flow from cultivated to wild raspberries in Scotland: developing a basis for risk assessment for testing and deployment of transgenic cultivars

In order to help establish a basis for assessing the risk associated with the testing and large-scale deploymen of transgenic raspberries, wild and feral raspberry populations in Scotland were surveyed for evidence of the escape of genes introduced into raspberry cultivars by traditional breeding. The genes concerned were introduced into cultivars using traditional breeding techniques and were deployed at known times 20 to 30 years prior to the present survey. Escape of the semidominant L 1 gene, affecting fruit size and plant morphology, could not be detected after 30 years in test plots at the Scottish Crop Research Institute near Dundee. The recessive gene s, conferring spinelessness, was detected at very low frequencies (estimated at 0.004) in wild populations within the commercial production locales where cultivars carrying this gene had been introduced on a large scale beginning 21-years prior to this survey. This gene was not, however, found in any areas remote from the commercial production locales. The results of the survey indicate that escape does occur following large-scale deployment but that gene flow events are probably infrequent and spread is localized for genes having probable neutral selective value.

Gene flow between cultivated and wild sunflowers

With the development of transgenic crops, concern has been expressed regarding the possible escape of genetically-engineered genes via hybridization with wild relatives. This is a potential hazard for sunflowers because wild sunflowers occur as weeds in fields where cultivated sunflowers are grown and hybridization between them has been reported. In order to quantify the potential for gene escape, two experimental stands of sunflower cultivars were planted at two sites with different rainfall and altitude profiles. Populations of wild plants were planted at different distances from each cultivar stand. An allele homozygous in the cultivar (6Pgd-3-a), but absent in the wild populations, was used as a molecular marker to document the incidence and rate of gene escape from the cultivar into the wild populations of sunflowers. Three-thousand achenes were surveyed to determine the amount of gene flow from the cultivated to the wild populations. The marginal wild populations (3 m from the cultivar) showed the highest percentage (27%) of gene flow. Gene flow was found to decrease with distance; however, gene flow occurred up to distances of 1000 m from the source population. These data suggest that physical distance alone will be unlikely to prevent gene flow between cultivated and wild populations of sunflowers.