Dataset Information

Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS).

ABSTRACT: The reduced acylation phenotype describes the inability of certain accessions of maize (Zea mays [L]) to produce significant amounts of acylated anthocyanins, which are typically the most abundant pigments. Acylated anthocyanins are important for their association with stability and are therefore important for the various industries using anthocyanins as natural colorants to replace synthetic dyes. Many anthocyanin acyltransferases have been characterized in other species; however, no anthocyanin acyltransferases have been characterized in maize. Therefore, a mapping population was developed from a cross between mutant stock 707G and wild-type acylation line B73 to identify the locus associated with the reduced acylation trait. High-performance liquid chromatography was used to assay the pigment content and composition of 129 F2 lines generated in the mapping population. Recessive alleles of Colorless1, Colored1, and the reduced acylation mutant all decreased anthocyanin content while Intensifier1 increased anthocyanin content in aleurone tissue. The association of increased proportions of acylation with increased anthocyanin content indicates acylation may be important for increasing the stability of anthocyanins in vivo Genotyping-by-sequencing was used to create SNP markers to map the reduced acylation locus. In the QTL analysis, a segment of Chromosome 1 containing transferase family protein GRMZM2G387394 was found to be significant. A UniformMu Mu transposon knockout of GRMZM2G387394 demonstrated this gene has anthocyanidin malonyltransferase activity and will therefore be named Anthocyanin Acyltransferase1 (AAT1). AAT1 is the first anthocyanin acyltransferase characterized in a monocot species and will increase our knowledge of all acyltransferase family members.

SUBMITTER: Paulsmeyer MN

PROVIDER: S-EPMC6222571 | biostudies-other | 2018 Nov

REPOSITORIES: biostudies-other

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Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS).

Paulsmeyer Michael N MN Brown Patrick J PJ Juvik John A JA

G3 (Bethesda, Md.) 20181106 11

The reduced acylation phenotype describes the inability of certain accessions of maize (<i>Zea mays</i> [<i>L</i>]) to produce significant amounts of acylated anthocyanins, which are typically the most abundant pigments. Acylated anthocyanins are important for their association with stability and are therefore important for the various industries using anthocyanins as natural colorants to replace synthetic dyes. Many anthocyanin acyltransferases have been characterized in other species; however, ...[more]

PMID: 30257861

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Project description:Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and one gene (GRMZM2G019183) encoding the UDP-Glycosyltransferase. The work will not only help to understand the mechanisms that control yield traits of maize, but also provide a basis for marker-assisted selection and map-based cloning in further studies.

Project description:BackgroundWith its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference.ResultsThe GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored "Mock Reference" from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available.ConclusionsBy achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.git.

Dataset Information

Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS).

Publications

Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS).

Similar Datasets

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