Fabio Cericola

Aarhus University | AU · Center for Quantitative Genetics and Genomics,

Genomic selection has been extensively implemented in plant breeding schemes. Genomic selection incorporates dense genome-wide markers to predict the breeding values for important traits based on information from genotype and phenotype records on traits of interest in a reference population. To date, most relevant investigations have been performed...

Making decisions on plant breeding programs require plant breeders to be able to test different breeding strategies by taking into account all the crucial factors affecting crop genetic improvement. Due to the complexity of the decisions, computer simulation serves as an important tool for researchers and plant breeders. This paper describes ADAM-p...

Perennial ryegrass is an outbreeding forage species and is one of the most widely used forage grasses in temperate regions. The aim of this study was to investigate the possibility of implementing genomic prediction in tetraploid perennial ryegrass, to study the effects of different sequencing depth when using genotyping-by-sequencing (GBS), and to...

Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction...

The aim of the this study was to identify SNP markers associated with five important wheat quality traits (grain protein content, Zeleny sedimentation, test weight, thousand-kernel weight, and falling number), and to investigate the predictive abilities of GBLUP and Bayesian Power Lasso models for genomic prediction of these traits. In total, 635 w...

Methods to handle GxE Interaction are described. Results for both GS and GWAS are presented

Wheat baking quality parameters are expensive and time-consuming to phenotype, so prediction of the phenotypes based on DNA markers is useful in breeding programs. In traditional marker-assisted selection, few DNA markers linked to QTL with large effects are used. To predict quantitative traits more accurately, genomic prediction can be used. Here,...

In plant breeding, to assess genotype by environment interactions (GEI), multi-environment trials (MET) are planned where the same genotypes are evaluated in different geographical locations and years. A widely used approach to analyze MET dataset is to consider each environment performance as a separate trait. Such a framework, called multi-traits...

In this study 672 winter wheat lines from two breeding cycles of the plant breeding company Nordic Seed were phenotyped for the baking quality parameters grain protein content, flour yield, Zeleny sedimentation, falling number, and alveograph W, P, and L. All lines were genotyped using the Illumina 15K wheat SNP chip, and the informative SNP marker...

Genome wide association studies (GWAS) reveals the markers that are causative or linked to the causative mutations related to different traits. The identification and subsequent utilization of such markers can facilitate accurate selection of superior breeding lines at an earlier stage of breeding schemes. In addition, phenotyping can be reduced wi...

Presentation showing the result of the paper: Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines.

Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phe-notyping all the material produced but only a subset of it named training population (T...

SNPs showing a significant association with the three traits under analysis. (XLSX)

Example of the GWAS based marker selection for lodging. a) top 30 markers selected; B) top 200 marker selected. (TIF)

Observed linkage disequilibrium. a) All wheat chromosomes combined; b) chromosome set A; c) chromosome set B d) chromosome set D. (TIF)

Genomic selection was recently introduced in plant breeding. The objective of this study was to develop genomic prediction for important seed quality parameters in spring barley. The aim was to predict breeding values without expensive phenotyping of large sets of lines. A total number of 309 advanced spring barley lines tested at two locations eac...

Raw genotypic data. The 309 lines were genotyped by Illumina iSelect 9K barley chip. The genotyping was outsourced to TraitGenetics [27]. (CSV)

Raw phenotypic data. (XLSX)

Genomic prediction is a novel method applied in plant breeding to identify the individuals with highest breeding values to contribute in the next generations. It uses the SNP markers spread over the whole genome. There are two main advantages in using genomic prediction: 1) it can predict individual merits on early stage of growth that can shorten...

In the last decade genomic selection (GS) has been implemented, especially for animals, as a new breeding technology. More recently, the opportunity offered by GS to speed up genetic gains in complex traits without the need of identifying markers associations with the QTLs, have attracted attention of plant breeders. However, rather inexpensive and...

Genomic selection (GS) has become a commonly used technology in animal breeding. In crops, it is expected to significantly improve the genetic gains per unit of time. So far, its implementation in plant breeding has been mainly investigated in species farmed as homogeneous varieties. Concerning crops farmed in family pools, only a few theoretical s...

An eggplant ( Solanum melongena ) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which ta...

Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute to next generation. The main goal of this study was...

We present a genomic selection study performed on 1918 rye grass families (Lolium perenne L.), which were derived from a commercial breeding program at DLF-Trifolium, Denmark. Phenotypes were recorded on standard plots, across 13 years and in 6 different countries. Variants were identified by Genotype-By-Sequencing and the allele frequency of the v...

The first high-quality genome assembly of the globe artichoke (Cynara cardunculus var. scolymus) has been recently produced at the DISAFA (Plant Genetics and Breeding) within the Compositae Genome Project (Scaglione et al. 2016, Sci. Rep. 6, 19427; doi: 10.1038/srep19427). The assembly contains 13K scaffolds (N50= 125 Kbp), which represent 725 Mb o...

Genotyping by sequencing (GBS) allows generating up to millions of molecular markers with a cost per sample which is proportional to the level of multiplexing. Increasing the sample multiplexing decreases the genotyping price but also reduces the numbers of reads per marker. In this work we investigated how this reduction of the coverage depth affe...

The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wid...

In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2...

A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data iden...