W883Targeted Next-Generation Sequencing (NGS) of Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beet
Targeted Next-Generation Sequencing (NGS) of Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beet
Date: Saturday, January 14, 2017
Time: 1:33 PM
Time: 1:33 PM
Room: Towne - Meeting House
The screening of disease resistance gene analogs (RGAs) is needed to the identification of useful alleles that could be used to improve disease tolerance of cultivated beet. In this study, we applied Ion Torrent Ampliseq next-generation technology to sequence 22 RGAs genes in wild and cultivated beet.
To evaluate the Ampliseq customized panel for detection of single-nucleotide polymorphisms (SNPs) and multiple-nucleotide polymorphisms (MNPs), we selected a set of 96 individuals representing 12 genotypes (8 individuals each) from six sea beet populations and six sugar beet pollinators. The sequences were mapped against the sugar beet reference genome (RefBeet v. 1.2) and checked for known and novel mutations using Torrent Suite Software v. 4.0.2. A total of 821 mutations were detected in 91/96 (95%) samples. The number of mutations per sample ranged from 0 to 278. Individual plants showed variations in number of mutations. The plant samples with the highest number of unique mutations (n. 3) were 8, 40 and 71. Sample 8 is a susceptible line to rhizomania whereas samples 40 and 71 are resistant lines carrying Rz2. Gene 11 (Bv3_063740_usyf) showed the highest frequency of mutations (2.91% and 0.28%, respectively). As resulted from PCA analysis, only the mutations located in gene 7 (Bv8_184910_pkon) differentiated between the wild and cultivated group. This study demonstrates the feasibility of using Ion Torrent sequencing to efficiently identify mutations in wild and cultivated beet germplasm. The large number of novel mutations identified will enhance usefulness of genetic marker resources available for improvement of sugar beet.
To evaluate the Ampliseq customized panel for detection of single-nucleotide polymorphisms (SNPs) and multiple-nucleotide polymorphisms (MNPs), we selected a set of 96 individuals representing 12 genotypes (8 individuals each) from six sea beet populations and six sugar beet pollinators. The sequences were mapped against the sugar beet reference genome (RefBeet v. 1.2) and checked for known and novel mutations using Torrent Suite Software v. 4.0.2. A total of 821 mutations were detected in 91/96 (95%) samples. The number of mutations per sample ranged from 0 to 278. Individual plants showed variations in number of mutations. The plant samples with the highest number of unique mutations (n. 3) were 8, 40 and 71. Sample 8 is a susceptible line to rhizomania whereas samples 40 and 71 are resistant lines carrying Rz2. Gene 11 (Bv3_063740_usyf) showed the highest frequency of mutations (2.91% and 0.28%, respectively). As resulted from PCA analysis, only the mutations located in gene 7 (Bv8_184910_pkon) differentiated between the wild and cultivated group. This study demonstrates the feasibility of using Ion Torrent sequencing to efficiently identify mutations in wild and cultivated beet germplasm. The large number of novel mutations identified will enhance usefulness of genetic marker resources available for improvement of sugar beet.