Project Number: 3072-21000-009-25-N
Project Type: Non-Funded Cooperative Agreement
Start Date: Dec 1, 2017
End Date: Nov 30, 2019
This proposal aims to reveal the genetic basis of bird cherry oat aphid (BCOA) resistance/tolerance in TA3516, develop genomic tools for introgression of BCOA and greenbug resistance, and select BC1F3 plants carrying the BCOA resistance QTL and Gb5 gene via marker-assisted selection.
An F6 recombinant inbred line (RIL) population derived from the cross TA3516 X Bainong418 will be used to map QTL for BCOA resistance in TA3516. A total of 248 RILs will be evaluated for BCOA resistance using a protocol we established recently. A randomized complete block design with six replicates will be used, and fifteen plants of each RIL will be evaluated in each replicate. The RIL population will be also evaluated for greenbug resistance using a standard aphid evaluation protocol. A WGR (whole genome resequencing)-based QTL mapping approach that achieves gene-level resolution will be adopted in this study. The RIL sequences will be aligned against the Chinese Spring reference genome sequence (1.0 version), and a pipeline combining Burrows–Wheeler Aligner and Sequence Alignment/Map tools (SAMtools) will be used to call SNPs in RILs. The "pileup" function of SAMtools will be used to merge the SNP dataset, and an approach based on the Hidden Markov Model will be adopted to genotype each RIL. The program R/QTL package will be used to construct a linkage map, and QTL for BCOA resistance and greenbug resistance genes will be mapped using the MQM method of the program MapQTL 5.0. SNPs significantly associated with BCOA resistance, as well as the Gb5 gene, in TA3516 will be converted to PCR-based Kompetitve Allele-Specific PCR (KASP) markers using a procedure we developed recently, and the marker-assisted selection approach will be used to identify plants carrying BCOA resistance QTL and the Gb5 gene in a breeding population.