PMC:4502374 / 14536-18361 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/4502374","sourcedb":"PMC","sourceid":"4502374","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4502374","text":"SNP discovery:\nArachis ipaënsis reference genome sequence (www.Peanutbase.org) was used as proxy of the B genome of A. hypogaea to discover SNPs between the rust-resistant accessions and peanut (susceptible). This was done by aligning A. magna and A. batizocoi transcripts (resistant) with the reference genome of A. ipaënsis (GenBank assembly accession GCA_000816755.1) using the NGSEP pipeline (Duitama et al. 2014) tagging the region where the main QTL for rust resistance was identified (pseudomolecule Araip.B08, peanutbase.org), in the vicinity of the microsatellite marker Ah-280 (region between 117048352 and 129519037 bp) and also for another QTL linked marker on Araip.B08, AHGS1350 (region between 346729 and 848328 bp) (Table 1). Default parameters were used, except the minimum and maximum fragment length for valid paired-end alignments, which we estimated separately for each genotype aligning their first 250,000 fragments and then plotting the distribution of estimated insert lengths (Script available at the NGSEP Web site http://sourceforge.net/projects/ngsep/files/Library/scripts/). We used the recommended parameters of NGSEP for analysis of WGS data: (1) minimum genotype quality 40; (2) minimum value allowed for a base quality score 30; and (3) Maximum number of alignments allowed to start at the same reference site 2. We also used NGSEP for filtering (the most relevant was a maximum minor allele frequency of 0.01) and conversion from VCF to other formats for primer design and visualization of SNPs with Flapjack software (Milne et al. 2010).\nTable 1 Quantitative trait loci identified for resistance to Puccinia arachidis and agronomic traits on an A. ipaënsis × A. magna F6 population\nTrait Category Trait Symbol LGa Positionb Nearest Marker(s) LODc Additive Effectd R2 (%)e\nRust resistance SI_2012 4 17.0 TC7G10 2.7 0.18 7.8\n7 38.7 AHS0598 3.0 0.16 8.2\n8 25.4 AHGS1350 / AHS2541 3.3 0.20 13.2\n8 35.9 Ah-280 6.9 0.25 21.2\nSI_2013 8 35.9 Ah-280 3.2 0.31 5.8\nTL/LA_2012 8 25.4 AHGS1350 / AHS2541 4.1 0.13 16.0\n8 35.1 Ah-280 2.9 0.09 8.9\nTL/LA_2013 8 35.9 Ah-280 3.8 0.20 12.3\nSL/LA_2012 8 35.9 Ah-280 3.8 0.07 11.1\nSL/LA_2013 8 35.9 Ah-280 3.5 0.14 11.0\nLog_IncPer_2012 8 42.9 Ah-280 / Ah-558 8.2 −0.46 59.3\nLog_IncPer_2013 8 33.1 AHS2541 / Ah-280 7.6 −0.33 33.9\n8 38.9 Ah-280 7.6 −0.33 34.8\nProductivity Log_SN 3 82.3 ML2A05 3.4 −0.11 8.6\n4 28.0 AHGS2785 2.6 −0.10 6.2\n10 35.5 AHS1488 3.1 −0.15 10.3\n10-SW 4 68.8 AHGS1279 / AHS2728 3.9 −0.32 18.4\n5 44.5 AHGS2602 2.9 0.20 8.3\nSeed Peg_Length 1 40.8 AHGS2019 / Seq12B2 3.4 −2.07 7.2\nCharacteristics 4 64.9 AHGS2155 11.2 4.18 25.8\n4 70.8 AHGS1279 / AHS2728 8.7 4.38 30.2\n5 10.4 AHS2897 3.4 2.06 6.9\n9 43.7 AHGS2018 / AHGS2235 3.0 1.91 6.3\nPod_constriction 1 37.1 AHGS2332 4.1 −0.67 9.4\n4 64.3 AHGS1917 3.4 0.59 7.4\n5 47.0 AHGS2513 3.5 −0.80 8.0\n6 25.4 AHGS2106 3.7 −0.66 9.7\n8 0.0 AHGS1383 3.5 −0.60 8.1\n9 36.3 AHGS1478_b3 / AHGS2537_b2 3.3 0.56 7.3\nPlant MSH_2009 2 37.8 RN31F06 4.8 −5.44 14.5\nArchitecture 4 64.3 AHGS1917 / AHGS2155 6.5 −5.79 17.6\n5 48.7 AHGS1228 3.2 3.61 8.1\nLog_MSH2011 4 64.9 AHGS2155 4.1 −0.10 10.7\n5 41.1 AHGS1980 4.0 1.64 10.0\n6 13.0 AHS2153 4.5 −0.11 11.4\nMSH_2012 3 23.2 TC1E06 4.0 −1.97 8.1\n4 64.3 AHGS1917 / AHGS2155 12.3 −3.56 30.4\n5 48.7 AHGS1228 3.6 2.13 7.4\na Linkage group.\nb Expressed in Kosambi cM.\nc LOD score, logarithm of the odds.\nd Positive values indicate that higher-value alleles come from A. ipaënsis K 30076, and negative values indicate that higher-value alleles come from A. magna K 30097.\ne Proportion of the phenotypic variance explained by the quantitative trait 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