In recent years, the advent of Next-Generation Sequencing (NGS) technologies has revolutionized our ability to decipher and analyze complex genomic information rapidly and cost-effectively. These cutting-edge techniques have opened new avenues in various fields of research, from genomics to personalized medicine. In this study, we harness the power of NGS by adapting the K-seq protocol (Ziarsolo et al., 2021, Plant Methods 17: 1-11) for the Zea mays genome. This protocol relies on amplifying genomic regions through two Klenow amplification steps using short oligonucleotides, designed based on k-mer sets in the genome sequence, enabling the detection of numerous genetic polymorphisms. This work was conducted within the framework of the "GER-MAIS" Project (Germplasm of Piedmontese Zea mays ecotypes), funded by the Piedmont Region (PSR 2014-2024 - Op. 10.2.1). The project is focused on developing optimal strategies for germplasm preservation and valid selection criteria to stabilize both qualitative and quantitative aspects of the production of native corn ecotypes in Piedmont. The ultimate goal is to valorize the final farmers products (polenta, gallette, bisquite) with quality labels and claims. In this initial phase of the project, we adapted the K-seq protocol to the corn genome by analyzing a subset of genotypes sampled from the seven ancient Piedmontese ecotypes, previously identified and named 'Ottofile giallo,' 'Ottofile rosso,' 'Ottofile bianco,' 'Ostenga,' 'Nostrano dell’Isola,' 'Pignoletto giallo,' and 'Pignoletto rosso'. Based on molecular data collected from the entire sample set, we will identify the most representative genotypes for each ecotype. These genotypes will be targeted for conservation in the final phase of the project. Our efforts will focus on genotypes that exhibit distinctive features and capture the majority of the genetic variability, with the goal of facilitating and optimizing their in situ ('on-farm') and ex situ conservation.
Optimization of a Klenow NGS-Based Protocol (K-seq) for Diversity Analyses in Corn (Zea mays L.) Ecotypes
Martina M.;Milani A. M;Comino C.;Portis E.
2024-01-01
Abstract
In recent years, the advent of Next-Generation Sequencing (NGS) technologies has revolutionized our ability to decipher and analyze complex genomic information rapidly and cost-effectively. These cutting-edge techniques have opened new avenues in various fields of research, from genomics to personalized medicine. In this study, we harness the power of NGS by adapting the K-seq protocol (Ziarsolo et al., 2021, Plant Methods 17: 1-11) for the Zea mays genome. This protocol relies on amplifying genomic regions through two Klenow amplification steps using short oligonucleotides, designed based on k-mer sets in the genome sequence, enabling the detection of numerous genetic polymorphisms. This work was conducted within the framework of the "GER-MAIS" Project (Germplasm of Piedmontese Zea mays ecotypes), funded by the Piedmont Region (PSR 2014-2024 - Op. 10.2.1). The project is focused on developing optimal strategies for germplasm preservation and valid selection criteria to stabilize both qualitative and quantitative aspects of the production of native corn ecotypes in Piedmont. The ultimate goal is to valorize the final farmers products (polenta, gallette, bisquite) with quality labels and claims. In this initial phase of the project, we adapted the K-seq protocol to the corn genome by analyzing a subset of genotypes sampled from the seven ancient Piedmontese ecotypes, previously identified and named 'Ottofile giallo,' 'Ottofile rosso,' 'Ottofile bianco,' 'Ostenga,' 'Nostrano dell’Isola,' 'Pignoletto giallo,' and 'Pignoletto rosso'. Based on molecular data collected from the entire sample set, we will identify the most representative genotypes for each ecotype. These genotypes will be targeted for conservation in the final phase of the project. Our efforts will focus on genotypes that exhibit distinctive features and capture the majority of the genetic variability, with the goal of facilitating and optimizing their in situ ('on-farm') and ex situ conservation.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
