Irina Baccichet1, Remo Chiozzotto1, Davide Scaglione2, Daniele Bassi1, Laura Rossini3, Marco Cirilli4. 1. Università degli Studi di Milan - DiSAA, Milano, Italy. 2. IGA Technology Services Srl, Udine, Italy. 3. Università degli Studi di Milan - DiSAA, Milano, Italy. laura.rossini@unimi.it. 4. Università degli Studi di Milan - DiSAA, Milano, Italy. marco.cirilli@unimi.it.
Abstract
BACKGROUND: Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one. RESULTS: The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies. CONCLUSIONS: Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics.
BACKGROUND: Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one. RESULTS: The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies. CONCLUSIONS: Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics.
Authors: E Dirlewanger; J Quero-García; L Le Dantec; P Lambert; D Ruiz; L Dondini; E Illa; B Quilot-Turion; J-M Audergon; S Tartarini; P Letourmy; P Arús Journal: Heredity (Edinb) Date: 2012-07-25 Impact factor: 3.821
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Authors: Ignazio Verde; Nahla Bassil; Simone Scalabrin; Barbara Gilmore; Cynthia T Lawley; Ksenija Gasic; Diego Micheletti; Umesh R Rosyara; Federica Cattonaro; Elisa Vendramin; Dorrie Main; Valeria Aramini; Andrea L Blas; Todd C Mockler; Douglas W Bryant; Larry Wilhelm; Michela Troggio; Bryon Sosinski; Maria José Aranzana; Pere Arús; Amy Iezzoni; Michele Morgante; Cameron Peace Journal: PLoS One Date: 2012-04-20 Impact factor: 3.240