TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.)

Knoll, J.; Ramos, María Laura; Zeng, Yajuan; Holbrook, C. Corley; Chow, Marjorie; Chen, Sixue; Maleki, Soheila J.; Bhattacharya, Anjanabha; Ozias‐Akins, Peggy

doi:10.1186/1471-2229-11-81

Cited by 87 publications

(63 citation statements)

References 43 publications

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“…These frequencies are comparable to previous studies on rice, sorghum, tomato, and Arabidopsis (2-6 mutations/Mbp) Xin et al 2008;Minoia et al 2010). These values are notably higher than the 1 mutation/Mb that was found in diploid rice and barley as well as tetraploid peanut (Caldwell et al 2004;Knoll et al 2011), but much lower than the 24-42 mutations/Mbp documented in tetraploid and hexaploid wheat (Slade et al 2005), the only species with a mutation rate .1 mutation/50 kb that has been reported so far. A higher mutation rate will, of course, reduce the population size required for effective screening, but requires tolerance of this mutational rate by the mutagenized lines.…”

Section: Mutagenized Tef Populations and Mutation Discoverysupporting

confidence: 74%

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

Zhu¹,

Smith

Ayele

et al. 2012

Genetics

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Tef (Eragrostis tef) is a major cereal crop in Ethiopia. Lodging is the primary constraint to increasing productivity in this allotetraploid species, accounting for losses of 15-45% in yield each year. As a first step toward identifying semi-dwarf varieties that might have improved lodging resistance, an 6· fosmid library was constructed and used to identify both homeologues of the dw3 semi-dwarfing gene of Sorghum bicolor. An EMS mutagenized population, consisting of 21,210 tef plants, was planted and leaf materials were collected into 23 superpools. Two dwarfing candidate genes, homeologues of dw3 of sorghum and rht1 of wheat, were sequenced directly from each superpool with 454 technology, and 120 candidate mutations were identified. Out of 10 candidates tested, six independent mutations were validated by Sanger sequencing, including two predicted detrimental mutations in both dw3 homeologues with a potential to improve lodging resistance in tef through further breeding. This study demonstrates that highthroughput sequencing can identify potentially valuable mutations in under-studied plant species like tef and has provided mutant lines that can now be combined and tested in breeding programs for improved lodging resistance.T EF [Eragrostis tef (Zucc.) Trotter] is an allotetraploid (2n = 4X = 40) species that is native to Ethiopia. Tef belongs to the grass subfamily Chloridoideae, a lineage that has received very little research attention. Tef has an estimated genome size of 713-733 Mbp (Ayele et al. 1996), which is 60% larger than the rice genome.As a staple food in Ethiopia, covering more acreage than any other crop in that nation, tef possesses several advantageous characteristics, including excellent storage properties and a very nutritious seed with excellent protein and mineral composition (Stallknecht et al. 1993). In addition, tef plants grow well under extreme environmental conditions such as drought and water-logging. However, compared to other crops, the average yield of tef is quite low, at an average of 700 kg ha 21 (Central Statistics Authority 2005). Tef has a tall and tender stem that is susceptible to lodging caused by wind and rain. As a consequence, the yield of tef is reduced 15-45% each year, depending on the weather and the variety. Furthermore, an increased incidence of lodging is associated with fertilizer application. Using QTL to improve lodging resistance indicated a positive correlation between lodging and yield, such that the most lodging-resistant progeny also had the lowest yield (Yu et al. 2007). This is probably because such traits as larger seed size and higher seed number create a heavier panicle that leads to a greater likelihood of lodging.In other cereal crops (Peng et al. 1999;Sasaki et al. 2002;Multani et al. 2003), semi-dwarf varieties have been found to provide both lodging resistance and higher yields. As shown in the earliest studies (Quinby and Karper 1954;Jennings 1964;Walcott and Laing 1976;Foster and Rutger 1978), semi-dwarf varieties have both strong s...

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Section: Mutagenized Tef Populations and Mutation Discoverysupporting

confidence: 74%

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

Zhu¹,

Smith

Ayele

et al. 2012

Genetics

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“…Some exotic, naturally occurring, peanut varieties that have clearly different allergenicity attributes have been described in literature (Krause et al, 2010;Ramos et al, 2009;Schmidt et al, 2009), but these peanut types are not commonly consumed in Western countries. Using genetic modification, attempts were made to develop new varieties of peanut that are low in certain allergens (Chandran et al, 2015;Chu et al, 2008;Knoll et al, 2011;Riascos et al, 2010). None of these peanuts are commercially available or used by the food industry in the U.S. or other Western countries.…”

Section: Consequences For Allergenicitymentioning

confidence: 99%

Allergenicity attributes of different peanut market types

Koppelman

Jayasena

Luykx

et al. 2016

Food and Chemical Toxicology

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a b s t r a c tFour different market classes of peanut (Runner, Virginia Spanish, and Valencia) are commonly consumed in Western countries, but for some consumers peanuts are a main cause of food-induced anaphylaxis. Limited information is available on the comparative allergenicity of these distinct market classes. The aim of this study was to compare allergenicity attributes of different peanut cultivars.The protein content and protein profiles were highly comparable for all tested cultivars. All cultivar samples contained the major allergens Ara h 1, Ara h 2, Ara h 3 and Ara h 6, as assessed by SDS-PAGE and RP-HPLC, although some minor differences in major allergen content were found between samples. All samples were reactive in commercial ELISAs for detection and quantification of peanut protein. IgEbinding potency differed between samples with a maximum factor of 2, indicating a highly comparable allergenicity.Based on our observations, we conclude that peanuts from the main market types consumed in Western countries are highly comparable in their allergenicity attributes, indicating that safety considerations with regard to peanut allergy are not dependent on the peanut cultivar in question.

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“…for each of the ancestral genomes of the polyploid). Allotetraploid peanut (Arachis hypogaea), on the other hand, is an exception, with about 1 mutation Mb -1 (Knoll et al, 2011). Paleopolyploids have yielded diverse mutation rates: Brassica rapa yielded a near-polyploid-like density at 16.6 mutations Mb -1 (Stephenson et al, 2010), while soybean (Glycine max) and maize (Zea mays) displayed lower mutation rates (Till et al, 2004b;Cooper et al, 2008) within the range of diploid responses.…”

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confidence: 99%

Production of a High-Efficiency TILLING Population through Polyploidization

et al. 2013

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Targeting Induced Local Lesions in Genomes (TILLING) provides a nontransgenic method for reverse genetics that is widely applicable, even in species where other functional resources are missing or expensive to build. The efficiency of TILLING, however, is greatly facilitated by high mutation density. Species vary in the number of mutations induced by comparable mutagenic treatments, suggesting that genetic background may affect the response. Allopolyploid species have often yielded higher mutation density than diploids. To examine the effect of ploidy, we autotetraploidized the Arabidopsis (Arabidopsis thaliana) ecotype Columbia, whose diploid has been used for TILLING extensively, and mutagenized it with 50 mM ethylmethane sulfonate. While the same treatment sterilized diploid Columbia, the tetraploid M1 plants produced good seed. To determine the mutation density, we searched 528 individuals for induced mutations in 15 genes for which few or no knockout alleles were previously available. We constructed tridimensional pools from the genomic DNA of M2 plants, amplified target DNA, and subjected them to Illumina sequencing. The results were analyzed with an improved version of the mutation detection software CAMBa that accepts any pooling scheme. This small population provided a rich resource with approximately 25 mutations per queried 1.5-kb fragment, including on average four severe missense and 1.3 truncation mutations. The overall mutation density of 19.4 mutations Mb -1 is 4 times that achieved in the corresponding diploid accession, indicating that genomic redundancy engenders tolerance to high mutation density. Polyploidization of diploids will allow the production of small populations, such as less than 2,000, that provide allelic series from knockout to mild loss of function for virtually all genes.

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TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.)

Cited by 87 publications

References 43 publications

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

Allergenicity attributes of different peanut market types

Production of a High-Efficiency TILLING Population through Polyploidization

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