Domestication of Plants in the Americas: Insights from Mendelian and Molecular Genetics

PREMISE OF THE STUDY Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. KEY RESULTS We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. CONCLUSIONS Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.

From forest to field: Perennial fruit crop domestication

The technology to produce genetically engineered (GE) plants is celebrating its 30th anniversary and one of the major achievements has been the development of GE crops. The safety of GE crops is cr...

/pdf/an-overview-of-the-last-10-years-of-genetically-engineered-1a0asv43ae.pdf

An overview of the last 10 years of genetically engineered crop safety research

Summary
We have studied the nucleotide diversity of common bean, Phaseolus vulgaris, which is characterized by two independent domestications in two geographically distinct areas: Mesoamerica and the Andes. This provides an important model, as domestication can be studied as a replicate experiment.
We used nucleotide data from five gene fragments characterized by large introns to analyse 214 accessions (102 wild and 112 domesticated). The wild accessions represent a cross-section of the entire geographical distribution of P. vulgaris.
A reduction in genetic diversity in both of these gene pools was found, which was three-fold greater in Mesoamerica compared with the Andes. This appears to be a result of a bottleneck that occurred before domestication in the Andes, which strongly impoverished this wild germplasm, leading to the minor effect of the subsequent domestication bottleneck (i.e. sequential bottleneck).
These findings show the importance of considering the evolutionary history of crop species as a major factor that influences their current level and structure of genetic diversity. Furthermore, these data highlight a single domestication event within each gene pool. Although the findings should be interpreted with caution, this evidence indicates the Oaxaca valley in Mesoamerica, and southern Bolivia and northern Argentina in South America, as the origins of common bean domestication.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2012.04377.x

Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes.

To establish a successful infection plant viruses have to overcome a defense system composed of several layers. This review will overview the various strategies plants employ to combat viral infections with main emphasis on the current status of single dominant resistance (R) genes identified against plant viruses and the corresponding avirulence (Avr) genes identified so far. The most common models to explain the mode of action of dominant R genes will be presented. Finally, in brief the hypersensitive response (HR) and extreme resistance (ER), and the functional and structural similarity of R genes to sensors of innate immunity in mammalian cell systems will be described.

/pdf/dominant-resistance-against-plant-viruses-4axyua0a21.pdf

Dominant resistance against plant viruses.

Hordeum bulbosum represents the secondary gene pool of barley and constitutes a potential source of various disease resistances in barley breeding. Interspecific crosses of H. vulgare × H. bulbosum resulted in recombinant diploid-barley progeny with immunity to BaMMV after mechanical inoculation. Tests on fields contaminated with different viruses demonstrated that resistance was effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed that resistance was dominantly inherited. Marker analysis in a F5 mapping family was performed to map the introgression in the barley genome and to estimate its size after several rounds of recombination. RFLP anchor-marker alleles indicative of an H. bulbosum introgression were found to cover an interval 2.9 cM in length on chromosome 6HS. The soil-borne virus resistance locus harboured by this introgressed segment was designated Rym14
 Hb
 . For marker-assisted selection of Rym14
 Hb
 carriers, a diagnostic codominant STS marker was derived from an AFLP fragment amplified from leaf cDNA of homozygous-resistant genotypes inoculated with BaMMV.

Mapping of Rym14Hb, a gene introgressed from Hordeum bulbosum and conferring resistance to BaMMV and BaYMV in barley.

Rym16 Hb
 , a gene conferring resistance to soil-borne viruses, was introgressed from Hordeum
 bulbosum to barley chromosome 2HL. Mechanical inoculation with BaMMV and field tests on a plot contaminated with different viruses demonstrated that Rym16 Hb
 is effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed a dominant inheritance of the resistance controlled by Rym16 Hb
 . Using 2HL anchor markers, the size of the introgression was estimated to be about 30 M. In its proximal part, the introgression was characterized by a rearrangement of markers Xbcd266, ABC153 and ABC252, accompanied with pronounced linkage drag by factor 4 in segregating mapping populations. The introgression was found to be associated with a recessive lethality factor, l
 Hb
 , which was closely linked to the markers mentioned above. Recombination occurring within the introgressed H. bulbosum segment allowed us to separate l
 Hb
 from Rym16 Hb
 and to reduce the size of the introgression to 23 cM or less.

Mapping of Rym16 Hb , the second soil-borne virus-resistance gene introgressed from Hordeum bulbosum

The rice genome has proven a valuable resource for comparative approaches to address individual genomic regions in Triticeae species at the molecular level. To exploit this resource for rye genetics and breeding, an inventory was made of EST-derived markers with known genomic positions in rye, which were related with those in rice. As a first inventory set, 92 EST-SSR markers were mapped which had been drawn from a non-redundant rye EST collection representing 5,423 unigenes and 2.2 Mb of DNA. Using a BC1 mapping population which involved an exotic rye accession as donor parent, these EST-SSR markers were arranged in a linkage map together with 25 genomic SSR markers as well as 131 AFLP and four STS markers. This map comprises seven linkage groups corresponding to the seven rye chromosomes and covers 724 cM of the rye genome. For comparative studies, additional inventory sets of EST-based markers were included which originated from the rye-mapping data published by other authors. Altogether, 502 EST-based markers with known chromosomal localizations in rye were used for BlastN search and 334 of them could be in silico mapped in the rice genome. Additionally, 14 markers were included which lacked sequence information but had been genetically mapped in rice. Based on the 348 markers, each of the seven rye chromosomes could be aligned with distinct portions of the rice genome, providing improved insight into the status of the rye–rice genome relationships. Furthermore, the aligned markers provide genomic anchor points between rye and rice, enabling the identification of conserved ortholog set markers for rye. Perspectives of rice as a model for genome analysis in rye are discussed.

Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome

Restoration of male fertility is a prerequisite for hybrid rye breeding and currently the most straightforward approach to minimize ergot infection in hybrid rye varieties. Molecular markers are important tools for the efficient introgression and management of restorer genes like Rfp1 originating from unadapted genetic resources. Furthermore, closely linked markers flanking Rfp1 are indispensible for identifying and selecting individuals with haplotypes showing recombination between Rfp1 and other gene(s) that reside in close proximity and have a negative influence on yield. We identified orthologous gene sets in rice, Brachypodium, and Sorghum and used these gene models as templates to establish conserved ortholog set (COS) markers for the restorer gene Rfp1 on the long arm of rye chromosome 4R. The novel co-dominant markers delimit Rfp1 within a 0.7-cM interval and allow prediction of Rfp1 genotypes with a precision not feasible before. The COS markers enabled an alignment of the improved genetic map of rye chromosome 4R with wheat and barley maps and allowed identification of regions orthologous to Rfp1 in wheat and barley on the short arms of chromosomes 6D and 6H, respectively. Results obtained in this study revealed that micro-collinearity around the Rfp1 locus in rye is affected by rearrangements relative to other grass genomes. The impact of the novel COS markers for practical hybrid rye breeding is discussed.

Development of conserved ortholog set markers linked to the restorer gene Rfp1 in rye

One approach to ensuring coexistence of genetically modified (GM) and conventional maize (Zea mays L.) is reducing pollen-mediated gene flow. Field experiments were conducted in 2005 at four sites in Germany to compare a tall sunflower crop (Helianthus annuus L.) vs. a short clover-grass crop (Trifolium pratense L. and Lolium spp.) with regard to their ability to reduce outcrossing when grown as buffer between pollen donor and recipient maize plots. Three different maize test systems were used: (i) quantification of a donor transgene via real-time polymerase chain reaction (rt PCR), (ii) a nontransgenic test system based on a dominant kernel color trait, and (iii) a molecular marker test system based on rt PCR quantification of a cultivar-specific nontransgenic DNA sequence. We found that the three test systems yielded comparable results concerning buffer-crop effectiveness and edge effects. There was no difference in outcrossing rates when comparing the sunflower vs. clover-grass buffer crop. Outcrossing rates downwind beyond 12 m sun-flower as buffer crop within adjacent 12-m-wide recipient maize were 4.2, 11.7, and 3.8% for the GM maize, the kernel color, and the molecular marker test system compared with clover-grass with 4.3, 9.6, and 3.6%. Pronounced edge effects were detected at the edges of recipient maize fields. Based on the present study, growing sunflower as a tall crop between GM and non-GM maize cannot be recommended as an appropriate coexistence measure.

Coexistence in Maize: Do Nonmaize Buffer Zones Reduce Gene Flow between Maize Fields?

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