Map NameTT_Tifrunner_x_GT-C20_c
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Publication Map NameTifrunner_x_GT-C20 'T-population' map
Map UnitscM
Map viewcmap-js
SpeciesArachis spp.
Mapping populationTT_Tifrunner_x_GT-C20_c
Parent 1Tifrunner
Parent 2GT-C20
Population Size91
Population TypeRIL
MethodsQTL IciMapping (v. 4.1)
DescriptionWhole-genome resequencing (WGRS) of a recombinant inbred line (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. The authors then incorporated 15 of the 19 major-QTL linked microsatellite markers from the publication Pandey, Wang et al., (2017a) into the SNP-based genetic map; 13 of the 15 markers joined the same linkage groups as demonstrated earlier (A04, A05, A06, A07, B06), although the two markers originally mapped to linkage group A03 were now included in B03. Addition of the microsatellites to the SNP-based map increased the genetic map lengths of the relevant linkage groups; the overall length of the now 8,884 marker map has been expanded to 3,287.38 cM.
PublicationAgarwal, Clevenger et al., 2018a: High-Density Genetic Map Using Whole-Genome Resequencing for Fine Mapping and Candidate Gene Discovery for Disease Resistance in Peanut.
CommentThe peanut cultivar 'Tifrunner' is a late-maturing runner market type; it shows high resistance to Tomato spotted wilt virus (TSWV) and moderate resistance to Early leaf spot (ELS) and Late leaf spot (LLS). The Spanish market type cultivar GT-C20 exhibits susceptibility to TSWV, ELS, and LLS. Whole-genome shotgun sequencing of genomic DNA extracted from leaves of Tifrunner, GT-C20, and the 91 selected RILs ultimately resulted in approximately 23 billion quality-filtered reads of 93, 96, and 97 base pair average lengths, respectively. Overall, about 40% of filtered read data were mapped to the reference A-subgenome assembly (A. duranensis v. 1.0) and 60% mapped to the reference B-subgenome assembly (A. ipaensis v. 1.0); these sequence alignments were then used to identify (call) and genotype SNPs. Haplotype-based SNP calls within reads to search for potential polymorphisms between the parental lines resulted in the mining of 97,571 total SNPs of which 18,252 SNPs were of sufficient quality to retain; these SNPs were found on all 20 linkage groups although their distribution was highly uneven. Furthermore, 16,674 out of the 18,252 high-quality SNPs were polymorphic and could be used for population genotyping. The genetic linkage map was produced using a subset of 10,274 polymorphic SNPs with no segregation distortion and less than 20% missing data, of which 8,869 SNP markers were finally linked together on a map of 3,120.71 cM in length and a map density of 1.45 cM/locus.