The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers

Parijs, Frederik R. D. van; Xiao, Benze

doi:10.1007/s11032-014-0113-4

Cited by 14 publications

(8 citation statements)

References 100 publications

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“…Here, reliance was placed on an established AFLP platform, which has been used extensively for the genetic analysis of globe artichoke , Mauro et al 2012, Mauro et al 2015. While now generally superseded by other DNA-based marker systems (particularly those targeting single base variants), AFLP technology still remains a convenient and informative platform for marker assisted breeding, particularly for small-scale programs which cannot afford the capital investment needed for assaying single nucleotide polymorphisms (Zhang et al 2014), while the re-sequencing of many individuals in most situations is unnecessary and would inflate the costs.…”

Section: Discussionmentioning

confidence: 99%

An integrated model to accelerate the development of seed-propagated varieties of globe artichoke

Mauromicale

Portis

Acquadro

et al. 2018

Crop Breed. Appl. Biotechnol.

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Globe artichoke (Cynara cardunculus var. scolymus) is a cross-pollinated, highly heterozygous species, which is conventionally propagated vegetatively. A scheme is described here which combines phenotypic with genotypic selection to fast track the development of a seed-propagated variety. The scheme was tested by making three selections, on a phenotypic basis, from a Brazilian seed-propagated variety showing an high phenotypic variation. The genetic relatedness as well as the heterozygosity of the material in study, in respect to standard variety representatives, was initially assessed with a wide set of microsatellite markers. Afterwards, an AFLP-based selection demonstrated to provide a practical and cheap means of conducting marker assisted breeding, which can be easily adopted also in laboratories of small seed companies. The selection approach described here could be readily adopted also to convert current vegetatively propagated landraces into seed-propagated varieties.

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Section: Discussionmentioning

confidence: 99%

An integrated model to accelerate the development of seed-propagated varieties of globe artichoke

Mauromicale

Portis

Acquadro

et al. 2018

Crop Breed. Appl. Biotechnol.

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“…In the case of okra, several molecular markers have been used for germplasm characterization, e.g., random amplified polymorphic DNA (RAPD; Martinello, Leal, Amaral Júnior, Pereira, & Daher, 2003), inter-simple sequence repeat (ISSR; Yuan et al, 2014), amplified fragment length polymorphism (AFLP; Kyriakopoulou et al, 2014), and simple sequence repeats (SSR; Kumar et al, 2017a). The AFLP markers, in spite of being dominant, have several advantages, such as broad genome coverage, cost-effectiveness, reproducibility, and independence of sequence information (Zhang, van Parijs, & Xiao, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity among Brazilian okra landraces detected by morphoagronomic and molecular descriptors

et al. 2019

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The conservation of okra landraces [Abelmoschus esculentus (L.) Moench] in gene banks is essential for the success of their use in breeding programmes. This study evaluated the genetic diversity among okra landraces in Brazil based on morphoagronomic descriptors and AFLP markers. We studied 30 accessions of the vegetable gene bank of the Universidade Federal de Viçosa. To this end, 17 morphoagronomic descriptors and five combinations of AFLP primers were used. Genetic parameters were estimated for the quantitative traits and the accessions were grouped by Ward’s method, using the Gower’s and Jaccard’s distance measures, respectively, for the morphoagronomic and molecular data. Polymorphisms were observed for all qualitative traits, while the quantitative traits were significant by deviance analysis. The genetic parameters confirmed the existence of variability among accessions, and high accuracy and heritability indices were found for the traits related to fruit and plant height. Ward’s grouping showed no relationship between the clusters formed with the morphoagronomic and molecular data and the geographical origin of the accessions. No association between morphoagronomic descriptors and AFLP markers was observed. The lack of correlation suggests that both approaches of characterization are important to understand and differentiate the okra accessions.

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“…In our method, the key of controlling the number of DNA fragments is selective PCR amplification. Compared to the size selection strategy (using regular laboratory electrophoresis equipment), using selective PCR to control the number of baits is easier to manipulate and more repeatable (Zhang et al, ). In the selective PCR step of this study, each reaction contains a pair of selective primers with a single selective nucleotide at the 3’ end (e.g., MluI‐F‐SA/ SbfI‐R‐SC), which can theoretically amplify one‐sixteenth of the total digestion fragments.…”

Section: Discussionmentioning

confidence: 99%

“…The AFLP (amplified fragment length polymorphism) technique was established as a highly efficient genomic fingerprinting method in 1995 (Vos et al, ). Because the AFLP method is suited for fingerprinting genomic DNA of any origin and complexity, it has been widely used for applications in genetic analysis such as addressing genetic relationship, displaying population structure, and assessing genetic diversity (Mueller & Wolfenbarger, ; Vuylsteke, Peleman, & van Eijk, ; Zhang, van Parijs, & Xiao, ). The AFLP technology is based on selective PCR amplification of restriction fragments from the digested genomic DNA.…”

Section: Introductionmentioning

confidence: 99%

Sequence capture using AFLP‐generated baits: A cost‐effective method for high‐throughput phylogenetic and phylogeographic analysis

Zeng

Wang

et al. 2019

Ecology and Evolution

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Target sequence capture is an efficient technique to enrich specific genomic regions for high‐throughput sequencing in ecological and evolutionary studies. In recent years, many sequence capture approaches have been proposed, but most of them rely on commercial synthetic baits which make the experiment expensive. Here, we present a novel sequence capture approach called AFLP‐based genome sequence capture (AFLP Capture). This method uses the AFLP (amplified fragment length polymorphism) technique to generate homemade capture baits without the need for prior genome information, thus is applicable to any organisms. In this approach, biotinylated AFLP fragments representing a random fraction of the genome are used as baits to capture the homologous fragments from genomic shotgun sequencing libraries. In a trial study, by using AFLP Capture, we successfully obtained 511 orthologous loci (>700,000 bp in total length) from 11 Odorrana species and more than 100,000 single nucleotide polymorphisms (SNPs) in four analyzed individuals of an Odorrana species. This result shows that our method can be used to address questions of various evolutionary depths (from interspecies level to intraspecies level). We also discuss the flexibility in bait preparation and how the sequencing data are analyzed. In summary, AFLP Capture is a rapid and flexible tool and can significantly reduce the experimental cost for phylogenetic studies that require analyzing genome‐scale data (hundreds or thousands of loci).

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The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers

Cited by 14 publications

References 100 publications

An integrated model to accelerate the development of seed-propagated varieties of globe artichoke

An integrated model to accelerate the development of seed-propagated varieties of globe artichoke

Genetic diversity among Brazilian okra landraces detected by morphoagronomic and molecular descriptors

Sequence capture using AFLP‐generated baits: A cost‐effective method for high‐throughput phylogenetic and phylogeographic analysis

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