SNP Calling and Validation from Transcriptome Sequences in Tall Fescue Aiming to Map QTL for Summer Dormancy

Tall fescue is an important perennial forage grass in the USA. In the Southern Great Plains, the persistence of tall fescue is significantly affected by hot and dry summer. However, tall fescue in the Mediterranean region exhibit summer dormancy for drought adaptation and persists longer period of time. Thus, understanding and utilization of summer dormancy mechanism in tall fescue would help in developing suitable cultivars for the region. RNA-seq study has been conducted using one continental (R43-64) and two summer dormant (Agrafa 103-2 and GK45115-11) tall fescue genotypes under growth chamber condition. Sample of leaves, crowns and roots were collected for RNA-Seq at six different time points of induction, optimum 1, transition, dormancy1, dormancy 2 and optimum 2 condition. De novo assembly yielded 1,031,513 contigs averaging the size of 688.43 bp. SNP calling was performed using the contigs as reference and identified total of 386,000 SNPs. Considering the discriminatory SNPs between summer dormant and continental genotypes, 53,324 SNPs were identified. The flanking region of the SNPs were aligned into Brachypodium genome and identified 17,855 SNPs regions matching with Brachypodium genome. A subset of 50 SNPs which have gene annotation in Brachypodium genome were selected and sent to KASP for validation using a bi-parental mapping population developed by crossing between R43-64 and Agrafa 103-2 along with other relevant parental genotypes. Based on validity of the SNPs, additional SNPs will be used for genotyping the population. This study will lead to identify QTL associated with summer dormancy in tall fescue thus assist the breeding efforts for integrating dormancy in tall fescue as a desired trait.