Food authentication and traceability is one of the major concern to the food industry, strictly correlated to food fraud and food adulteration. Rice (Oryza sativa L.) is one of the most important crops, supplying food for over half of the world's population. Authenticity of rice products has become a key issue in the food industry addressed to protect the interests of quality conscious consumers, stakeholders, and importing countries. DNA markers offer a powerful tool to address the validation of food authenticity and traceability of primary products. Progress in NGS technology has provided opportunities to detect large number of DNA polymorphisms, even in the closely related cultivars. In this study, a whole-genome sequencing of Italian rice cultivar Carnaroli has been carried out from genetically pure certified seed. The sequencing yielded about 22.5 million reads. After quality trimming 21.5 million reads were mapped onto the reference sequence of Oryza sativa ssp. japonica cv. Nipponbare (IRGSP-1.0), providing about 90% coverage of the rice genome and an average coverage of 15.12x. Preliminary results, found 450,414 candidate DNA polymophisms between cultivar Nipponbare and Carnaroli. These were classified into 383,080 SNPs (85%) and 67,334 InDels (15%) by polymorphism types, 150,688 homozygous (85%) and 299,726 (15%) heterozygous by zygosity type, 371,801 intergenic (82.5%) and 78613 (17.6%) by genomic location. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. In particular, chromosome 8 and 10 showed the highest density of DNA polymorphisms (14.7% and 14.5%, respectively). This study represents the first report of whole genome sequencing of Italian rice cultivar Carnaroli and will contribute to develop targeted and un-targeted method for rice authentication and traceability This work has been supported by the European project FOODINTEGRITY (FP7-KBBE-2013-single-stage, No 613688).
AUTHENTICATION AND TRACEABILITY OF ITALIAN RICE CULTIVAR CARNAROLI BY WHOLE GENOME SEQUENCING
M FERRARA;A DE PAOLIS;
2017
Abstract
Food authentication and traceability is one of the major concern to the food industry, strictly correlated to food fraud and food adulteration. Rice (Oryza sativa L.) is one of the most important crops, supplying food for over half of the world's population. Authenticity of rice products has become a key issue in the food industry addressed to protect the interests of quality conscious consumers, stakeholders, and importing countries. DNA markers offer a powerful tool to address the validation of food authenticity and traceability of primary products. Progress in NGS technology has provided opportunities to detect large number of DNA polymorphisms, even in the closely related cultivars. In this study, a whole-genome sequencing of Italian rice cultivar Carnaroli has been carried out from genetically pure certified seed. The sequencing yielded about 22.5 million reads. After quality trimming 21.5 million reads were mapped onto the reference sequence of Oryza sativa ssp. japonica cv. Nipponbare (IRGSP-1.0), providing about 90% coverage of the rice genome and an average coverage of 15.12x. Preliminary results, found 450,414 candidate DNA polymophisms between cultivar Nipponbare and Carnaroli. These were classified into 383,080 SNPs (85%) and 67,334 InDels (15%) by polymorphism types, 150,688 homozygous (85%) and 299,726 (15%) heterozygous by zygosity type, 371,801 intergenic (82.5%) and 78613 (17.6%) by genomic location. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. In particular, chromosome 8 and 10 showed the highest density of DNA polymorphisms (14.7% and 14.5%, respectively). This study represents the first report of whole genome sequencing of Italian rice cultivar Carnaroli and will contribute to develop targeted and un-targeted method for rice authentication and traceability This work has been supported by the European project FOODINTEGRITY (FP7-KBBE-2013-single-stage, No 613688).I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
