Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

Maughan, Peter J.; Smith, Scott M.; Raney, Joshua A.

doi:10.1155/2012/405940

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…The alignment of the BAC end sequence pairs and FGS scaffolds with the amaranth assembly affirms the quality of the genome assembly and suggests the potential for using the BAC library to further consolidate the assembly. A seven‐plate, super‐pooled version of the BAC library is available and was previously shown to be amendable to high‐throughput BAC clone identification using the Fluidigm EP1 system (Maughan et al, 2012).…”

Section: Resultsmentioning

confidence: 99%

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

et al. 2016

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Amaranth (Amaranthus hypochondriacus L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2n = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N 50 of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of A. hybridus as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for A. hypochondriacus using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N 50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet (Beta vulgaris L.) and estimated, using K s analysis, the age of the most recent polyploidization event in amaranth.

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Section: Resultsmentioning

confidence: 99%

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

et al. 2016

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“…This left a panel of 43 functioning SNPs for analyses. To delimit the size of the SC5-1 introgression, the F 1 plants were genotyped first with the SNP panel by competitive allele-specific polymerase chain reaction (PCR) and KASPar chemistry (KBioscience Ltd., Hoddesdon, UK) using the Fluidigm (Fluidigm Corp., South San Francisco, CA) nanofluidic 48.48 dynamic array (Wang et al, 2009 ) according to Maughan et al ( 2012 ). Then, three of the 43 SNPs genotyped using KASPar and flanking the ends of the introgression (sca00022_3549755, located at 2,923,752 basepairs (bp) and sca00022_5424269 located at 4,891,016 bp) and another located inside the QTL interval (sca00022_4484619 located at 3,951,366 bp) (Table S2 ) were chosen for genotyping the F 2 and subsequent generations with TaqMan® chemistry (ThermoFisher Scientific, Waltham, MA) using the SNP genotyping in Universal Master Mix (Applied Biosystems, Foster City, CA).…”

Section: Methodsmentioning

confidence: 99%

QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon (Cucumis melo L.)

et al. 2017

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Sugar content is the major determinant of both fruit quality and consumer acceptance in melon (Cucumis melo L), and is a primary target for crop improvement. Near-isogenic lines (NILs) derived from the intraspecific cross between a “Piel de Sapo” (PS) type and the exotic cultivar “Songwhan Charmi” (SC), and several populations generated from the cross of PS × Ames 24294 (“Trigonus”), a wild melon, were used to identify QTL related to sugar and organic acid composition. Seventy-eight QTL were detected across several locations and different years, with three important clusters related to sugar content located on chromosomes 4, 5, and 7. Two PS × SC NILs (SC5-1 and SC5-2) sharing a common genomic interval of 1.7 Mb at the top of chromosome 5 contained QTL reducing soluble solids content (SSC) and sucrose content by an average of 29 and 68%, respectively. This cluster collocated with QTL affecting sugar content identified in other studies in lines developed from the PS × SC cross and supported the presence of a stable consensus locus involved in sugar accumulation that we named SUCQSC5.1. QTL reducing soluble solids and sucrose content identified in the “Trigonus” mapping populations, as well as QTL identified in previous studies from other ssp. agrestis sources, collocated with SUCQSC5.1, suggesting that they may be allelic and implying a role in domestication. In subNILs derived from the PS × SC5-1 cross, SUCQSC5.1 reduced SSC and sucrose content by an average of 18 and 34%, respectively, and was fine-mapped to a 56.1 kb interval containing four genes. Expression analysis of the candidate genes in mature fruit showed differences between the subNILs with PS alleles that were “high” sugar and SC alleles of “low” sugar phenotypes for MELO3C014519, encoding a putative BEL1-like homeodomain protein. Sequence differences in the gene predicted to affect protein function were restricted to SC and other ssp. agrestis cultivar groups. These results provide the basis for further investigation of genes affecting sugar accumulation in melon.

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