identifier: Tifrunner_x_GT-C20.map.Agarwal_Clevenger_2018

genetic_map: Tifrunner_x_GT-C20.Agarwal_Clevenger_2018
 
synopsis: "Genetic map of Tifrunner x GT-C20 for the study of early and late leaf spots (ELS and LLS) and tomato spotted wilt virus (TSWV)."

scientific_name: Arachis hypogaea

taxid: 3818

scientific_name_abbrev: arahy

genotype:
 - Tifrunner x GT-C20

genotyping_platform: Agarwal_Clevenger_2018

genotyping_method: "Filtered reads from Tifrunner, GT-C20 and the individual RILs were mapped to the genome assemblies of A. duranensis and A. ipaensis. Identified putative polymorphic haplotype SNPs were then used to genotype the population."

description: "WGRS of a RIL mapping population was used to develop a SNP-based high-density genetic linkage map for Arachis hypogaea. This 'T-population' was produced from a cross of the female-ovule parent Tifrunner and the male-pollen parent GT-C20. Whole-genome resequencing of genomic DNA extracted from leaf tissues was performed using the inbred parental lines and 91 of the RILs. The map is composed of 8,869 SNPs distributed across 20 linkage groups; however, many SNPs have identical cM positions such that the 8,869 SNPs are equivalent to 2,156 marker loci exhibiting independent recombination. The length of the map is 3,120.71 cM and the average distance between markers is 1.45 cM. There is an average of 107.8 mapped loci per linkage group with a range of 38 (B07) to 179 (A03) marker loci. The A-subgenome was composed of 1,219 marker loci spanning 1,637.8 cM at a 1.34 cM average marker distance, whereas the B-subgenome was composed of 937 marker loci spanning 1,484.91 cM at a 1.58 cM average marker distance. SNPs that were identified (called) using a chromosome belonging to either the A- or B-reference diploid genome (Arachis duranensis v. 1.0, A. ipaensis v. 1.0), yet were mapped onto a corresponding linkage group found within the other subgenome, are described as homeologous SNPs. There are 422 homeologous SNP markers identified from alignment with the A-subgenome that are mapped to B-subgenome linkage groups, and 317 such markers identified using the B-subgenome that appeared on A-subgenome linkage groups. Similarly, SNPs that were identified using a chromosome belonging to either the A- or B-reference diploid genome, yet were mapped onto another linkage group that was neither the orginal linkage group nor its homeologue in the corresponding A- or B-subgenome, are described as translocated SNPs. There are 309 and 104 translocated SNP markers that were incorporated into the A-subgenome and B-subgenome linkage groups, respectively."

publication_doi: 10.1111/pbi.12930

publication_title: "High-Density Genetic Map Using Whole-Genome Resequencing for Fine Mapping and Candidate Gene Discovery for Disease Resistance in Peanut"

contributors: "Gaurav Agarwal, Josh Clevenger, Manish K. Pandey, Hui Wang, Yaduru Shasidhar, Ye Chu, Jake C. Fountain, Divya Choudhary, Albert K. Culbreath, Xin Liu, Guodong Huang, Xingjun Wang, Rupesh Deshmukh, C. Corley Holbrook, David J. Bertioli, Peggy Ozias-Akins, Scott A. Jackson, Rajeev K. Varshney, and Baozhu Guo"

data_curators: Steven Cannon, Sam Hokin

public_access_level: public

license: Open

keywords: Arachis hypogaea, peanut, leaf spot, tomato spotted wilt virus, ELS, LLS, TSWV

citation: "Agarwal, G. et al. High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnol. J. 16, 1954–1967 (2018)"