Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (<i>Amaranthus</i> sp.)

Maughan, Peter J.; Smith, Scott M.; Fairbanks, Daniel J.; Jellen, Eric N.

doi:10.3835/plantgenome2010.12.0027

Cited by 83 publications

(82 citation statements)

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“…This strategy is well illustrated by the weedy Amaranthus species, collectively known as pigweeds. Several Amaranthus crops are widely grown in Central and South America; however, these grain amaranths are genetically distinct from the weedy species, which are believed to have evolved from wild populations (Maughan et al, 2011). A striking example of recent weed invasion is that of waterhemp (A. tuberculatus) in corn and soybean fields (Figure 2) in the central United States over the past two decades (Steckel, 2007).…”

Section: The Origins Of Agricultural Weedsmentioning

confidence: 99%

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

2012

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Weeds are among the greatest pests of agriculture, causing billions of dollars in crop losses each year. As crop field management practices have changed over the past 12 000 years, weeds have adapted in turn to evade human removal. This evolutionary change can be startlingly rapid, making weeds an appealing system to study evolutionary processes that occur over short periods of time. An understanding of how weeds originate and adapt is needed for successful management; however, relatively little emphasis has been placed on genetically characterizing these systems. Here, we review the current literature on agricultural weed origins and their mechanisms of adaptation. Where possible, we have included examples that have been genetically well characterized. Evidence for three possible, non-mutually exclusive weed origins (from wild species, crop-wild hybrids or directly from crops) is discussed with respect to what is known about the microevolutionary signatures that result from these processes. We also discuss what is known about the genetic basis of adaptive traits in weeds and the range of genetic mechanisms that are responsible. With a better understanding of genetic mechanisms underlying adaptation in weedy species, we can address the more general process of adaptive evolution and what can be expected as we continue to apply selective pressures in agroecosystems around the world.

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Section: The Origins Of Agricultural Weedsmentioning

confidence: 99%

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

2012

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“…Так, M.A. Mallory с коллегами (2008) (Maughan et al, 2011;Park, Nishikawa, 2012;Park et al, 2014), применя емых в изучении филогении видов рода Amaranthus L.…”

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Polymorphism of RAPD and ISSR markers in grain amaranth species

et al. 2017

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Different molecular genetic markers are effectively used in agricultural genetic selection programs. Genetic markers can be used in commercial breeds certification performance, fast and reliable genotype identification, genetic maps creation, genetics, phylogeny and plant systematic studies, which can accelerate selection, provide effective study and culture genofond maintenance. Amaranth, in this regard, has not been studied well, there is not enough data to effectively perform amaranth marker selection or for the certification of new and existing varieties; there are inaccuracies in the systematization of the crop. Important are the questions about the origin of grain amaranth species and the processes of their evolutionary formation. Amaranth is a pseudo-cereal with a millennia-long history, it has been actively cultivated in many countries around the world in recent decades. A high level of alterability and the formation of a huge number of spontaneous hybrids in natural populations of amaranth significantly complicate the identification of individual genotypes and entire taxonomic units of Amaranthus L. Due to the lack of research and depending on the environmental conditions, the morphological markers of amaranth are not able to provide sufficient genomic information to the breeder; thus it is necessary to search for reliable genetic markers that allow the genetic diversity of the Amaranthus L. species to be studied and effectively maintained. This research includes grain amaranth species DNA polymorphism analysis. Using RAPD and ISSR technologies, 203 loci have been identified, of which 173 appear to be polymorphic, 30 monomorphic (found in all genotypes analyzed) and 13 unique (found only in one genotype). Unique and monomorphic DNA loci can be used as specific genetic markers, in particular, for the certification of breeds, which is especially important for the identification of plant material and plant genetic variability monitoring. A high level of DNA polymorphism was revealed (about 85 %), a genetic relationship between grain amaranth species В генетико-селекционных программах сельскохозяйственных культур для идентификации генотипов, составления генетиче-ских карт, изучения генетики, филогении и систематики растений используют различные молекулярно-генетические маркеры, это ускоряет селекцию и способствует эффективному изучению и со-хранению генофонда культуры. С помощью RAPD-и ISSR-маркеров возможно быстро идентифицировать большое количество локу-сов, что удобно при изучении генетической структуры популяций и проведении эволюционных и филогенетических исследований. С целью изучения генетического полиморфизма зерновых видов рода Amaranthus L. по молекулярно-генетическим маркерам и воз-можностей их практического использования проанализировано 18 коллекционных образцов сортов и популяций разного эколого-географического происхождения. Молекулярно-генетический ана-лиз амаранта позволил выявить высокий уровень полиморфизма ДНК-маркеров (около 85 %). Внутрипопуляционный полиморфизм, установленный с примен...

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“…We therefore evaluated all accessions used in this study with 11 PCR-based SNP markers. The markers were the most polymorphic from a set of 411 KASP markers from (Maughan et al, 2011). Each marker was polymorphic between at least two lines and each cross segregated at least for one marker (Table 2).…”

Section: Genetic Markers For Hybrid Identificationmentioning

confidence: 99%

“…Eleven KASP assays (LGC Berlin/Germany) were selected from Maughan et al (2011) to validate crosses. The assays were prepared with 5 µl DNA (10 ng/µl) and 5 µl genotyping mix and run on the LightCycler R 480 Instrument II (Roche Life Science) with standard settings as given by the KASP manual (LGC Berlin/Germany) and analyzed using the LightCycler R 480 Software.…”

Section: Evaluation Of Genetic Markersmentioning

confidence: 99%

“…For phenotypic traits to be useful, however, parents need to differ in at least one trait and the male parent needs to express the dominant allele. In contrast, molecular markers allow an efficient and early evaluation of crosses without restricting the combination of parents, and cost-efficient PCR-based marker systems are available for this purpose (Maughan et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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Supplemental Information 1: Primer Sequences

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BackgroundGrain amaranths (Amaranthus sp) have been cultivated for thousands of years in Central and South America. Their grains are of high nutritional value, but the low yield needs to be increased by selection of superior genotypes from genetically diverse breeding populations. Amaranths are adapted to harsh conditions and can be cultivated on marginal lands although little is known about their physiology. The development of controlled growing conditions and efficient crossing methods is important for research on and improvement of this ancient crop. Grain amaranth was domesticated in the Americas and is highly self-fertilizing with a large inflorescence consisting of thousands of very small flowers. We evaluated three different crossing methods (open pollination, hot water emasculation and hand emasculation) for their efficiency in amaranth and validated them with genetic markers. ResultsWe identified cultivation conditions that allow an easy control of flowering time by manipulating day length manipulation and achieved flowering times of four weeks and generation times of two months. All three different crossing methods successfully produced hybrid F 1 offspring, but with different success rates. Open pollination had the lowest (10%) and hand emasculation the highest success rate (74%). Hot water emasculation showed an intermediate success rate (26%) with a maximum of 94% success. It is simple to perform and suitable for a more large-scale production of hybrids. We further evaluated 11 single nucleotide polymorphism (SNP) markers and found that they were sufficient to validate all crosses of the genotypes used in this study for intra-and interspecific crosses. Conclusions Despite its very small flowers, crosses in amaranth can be carried out efficiently and evaluated with inexpensive SNP markers. Suitable growth conditions strongly reduce the generation time and allow the control of plant height, flowering time and seed production. In combination, this enables the rapid production of segregating populations which makes amaranth an attractive model for basic plant research but also facilitates further the improvement of this ancient crop by plant breeding.

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Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.)

Cited by 83 publications

References 51 publications

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

Polymorphism of RAPD and ISSR markers in grain amaranth species

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