Data Sources and their Data Sets

CATHGENE3D
CDD
GO
null
GO
HAMAP
InterMine post-processor
Gene-flanking regions created by the core InterMine post-processor
InterMine gene-flanking regions
Intergenic regions created by the InterMine core post-processor
InterMine intergenic regions
InterPro
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro data set
Mapping of GO terms to InterPro entries.
InterPro domain GO annotations
LIS Datastore
A GWAS dataset from Gangurde et al. (2020) NAM Florida-7 mapping population. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Two nested association mapping (NAM) populations, NAM_Tifrunner and NAM_Florida-07, were used in the study for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) traits in peanut. This GWAS dataset is from the Florida-7 mapping population. The study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut. (Data from Supplementary Table S5: Summary significantly associated SNPs identified for pod weight (PW) and seed weight (SW)in NAM_Florida‐07 population with details of annotation of each gene corresponding to the SNPs and their biological role.)
README.gwas.Gangurde_Wang_2020-NAMFlor7.yml
A cultivated peanut (Arachis hypogaea L.) F6 mapping population of 266 recombinant inbred lines (RILs) was advanced by single seed descent from a cross of the late leaf spot and rust disease susceptible line 'TAG 24' and the resistant variety 'GPBD 4'. The parents 'TAG 24' and 'GPBD 4' were screened with 1954 newly available markers that included 1079 A. hypogaea genomic microsatellites (AHGS), 470 A. hypogaea EST microsatellites (AHS), and 405 A. hypogaea transposable element (AhTE) AhMITE1 markers. Polymorphism between the parents was shown for 139 markers out of the 1954 tested. Data were also employed for 188 microsatellite markers used in previous studies on the 'TAG 24' x 'GPBD 4' population [Khedikar, Gowda et al., 2010a; Sujay, Gowda et al., 2012a]. The 327 total polymorphic markers were used to genotype the population of 266 RILs for linkage map construction. The final genetic map includes 289 marker loci. Four markers [GM1971, GM2724, pPGSSeq18A05, AhFAD2A.2] amplified two loci each, so that 285 unique markers appear on the map. The map contains 22 linkage groups, a total length of 1730.8 cM, and an average inter-marker distance of 6.0 cM. The sizes of linkage groups ranged from 26.7 cM to 155.9 cM. This enhanced linkage map is superior to the one published earlier by Sujay, Gowda et al. (2012a) [188 microsatellites, 1922.4 cM, 12.69 cM mean inter-locus distance].
README.map.TT_TAG24_x_GPBD4_b.yml
A cultivated peanut (Arachis hypogaea L.) F6 mapping population of 266 recombinant inbred lines (RILs) was advanced by single seed descent from a cross of the late leaf spot and rust disease susceptible line 'TAG 24' and the resistant variety 'GPBD 4'. The parents 'TAG 24' and 'GPBD 4' were screened with 1954 newly available markers that included 1079 A. hypogaea genomic microsatellites (AHGS), 470 A. hypogaea EST microsatellites (AHS), and 405 A. hypogaea transposable element (AhTE) AhMITE1 markers. Polymorphism between the parents was shown for 139 markers out of the 1954 tested. Data were also employed for 188 microsatellite markers used in previous studies on the 'TAG 24' x 'GPBD 4' population [Khedikar, Gowda et al., 2010a; Sujay, Gowda et al., 2012a]. The 327 total polymorphic markers were used to genotype the population of 266 RILs for linkage map construction. The final genetic map includes 289 marker loci. Four markers [GM1971, GM2724, pPGSSeq18A05, AhFAD2A.2] amplified two loci each, so that 285 unique markers appear on the map. The map contains 22 linkage groups, a total length of 1730.8 cM, and an average inter-marker distance of 6.0 cM. The sizes of linkage groups ranged from 26.7 cM to 155.9 cM. This enhanced linkage map is superior to the one published earlier by Sujay, Gowda et al. (2012a) [188 microsatellites, 1922.4 cM, 12.69 cM mean inter-locus distance].
README.qtl.TT_TAG24_x_GPBD4_b.yml
A mapping population of 146 F2:11 recombinant inbred lines (RILs) was produced A1:P2 a cross of the cultivated peanut (Arachis hypogaea L.) maternal inbred line 'Huayu28' and paternal inbred line 'P76'. The high-resolution genetic linkage map is composed of 2,334 markers (2,266 SNPs and 68 microsatellites) placed upon 20 linkage groups. The total length of the map is 2,586.37 cM; lengths of linkage groups range from 68.79 to 191.24 cM. The mean distance between adjacent markers is 2.25 cM for the whole map, whereas the average inter-marker distances for individual linkage groups range from 0.3 to 6.09 cM. The number of markers per linkage group ranges from 13 to 369, with the average count of markers on each linkage group being 116.7. Seven hundred of the 2,334 mapped markers across 14 linkage groups exhibited significant segregation distortion, particularly on linkage groups A04, B03, and B05. This high-density map is the first to be developed in cultivated peanut incorporating de novo polymorphic SNP markers discovered using a SLAF-seq (Specific Length Amplified Fragment Sequencing) methodology. The authors first developed 433,679 high-quality SLAFs and then discovered that 29,075 of these SNP markers were polymorphic. There were 7,949 polymorphic markers that followed an aa_x_bb segregation pattern appropriate for linkage analysis, out of which 2,266 SNPs were linked together in the final map.
README.map.TT_Huayu28_x_P76_a.yml
A mapping population of 146 F2:11 recombinant inbred lines (RILs) was produced A1:P2 a cross of the cultivated peanut (Arachis hypogaea L.) maternal inbred line 'Huayu28' and paternal inbred line 'P76'. The high-resolution genetic linkage map is composed of 2,334 markers (2,266 SNPs and 68 microsatellites) placed upon 20 linkage groups. The total length of the map is 2,586.37 cM; lengths of linkage groups range from 68.79 to 191.24 cM. The mean distance between adjacent markers is 2.25 cM for the whole map, whereas the average inter-marker distances for individual linkage groups range from 0.3 to 6.09 cM. The number of markers per linkage group ranges from 13 to 369, with the average count of markers on each linkage group being 116.7. Seven hundred of the 2,334 mapped markers across 14 linkage groups exhibited significant segregation distortion, particularly on linkage groups A04, B03, and B05. This high-density map is the first to be developed in cultivated peanut incorporating de novo polymorphic SNP markers discovered using a SLAF-seq (Specific Length Amplified Fragment Sequencing) methodology. The authors first developed 433,679 high-quality SLAFs and then discovered that 29,075 of these SNP markers were polymorphic. There were 7,949 polymorphic markers that followed an aa_x_bb segregation pattern appropriate for linkage analysis, out of which 2,266 SNPs were linked together in the final map.
README.qtl.TT_Huayu28_x_P76_a.yml
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMFlor7.obo.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMFlor7.result.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMFlor7.trait.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMTifr.obo.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMTifr.result.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Gangurde_Wang_2020-NAMTifr.trait.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Otyama_Kulkarni_2020.obo.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Otyama_Kulkarni_2020.result.tsv
Arachis hypogaea GWAS experiment.
arahy.mixed.gwas.Otyama_Kulkarni_2020.trait.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Huayu28_x_P76_a.mrk.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Huayu28_x_P76_a.obo.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Huayu28_x_P76_a.qtl.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Huayu28_x_P76_a.trait.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_SunOleic97R_x_NC94022_a.mrk.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_SunOleic97R_x_NC94022_a.obo.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_SunOleic97R_x_NC94022_a.qtl.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_SunOleic97R_x_NC94022_a.trait.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_TAG24_x_GPBD4_b.mrk.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_TAG24_x_GPBD4_b.obo.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_TAG24_x_GPBD4_b.qtl.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_TAG24_x_GPBD4_b.trait.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Tifrunner_x_GT-C20_c.mrk.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Tifrunner_x_GT-C20_c.obo.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Tifrunner_x_GT-C20_c.qtl.tsv
Arachis hypogaea QTL experiment.
arahy.mixed.qtl.TT_Tifrunner_x_GT-C20_c.trait.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_Huayu28_x_P76_a.lg.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_SunOleic97R_x_NC94022_a.lg.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_TAG24_x_GPBD4_b.lg.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_TAG24_x_GPBD4_b.mrk.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_Tifrunner_x_GT-C20_c.lg.tsv
Arachis hypogaea genetic map.
arahy.mixed.map.TT_Tifrunner_x_GT-C20_c.mrk.tsv
CDS models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.cds.fna
CDS models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.cds.fna
CDS models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.cds.fna
GWAS dataset from Gangurde, Wang, et al. (2020) NAM Tifrunner mapping population. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Two nested association mapping (NAM) populations, NAM_Tifrunner and NAM_Florida-07, were used in the publication for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) traits in peanut. This GWAS dataset is from the NAM_Tifrunner mapping population. The study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut. (Data from Supplementary Table S4: Summary significantly associated SNPs identified for pod weight (PW) and seed weight (SW) in NAM_Tifrunner population with details of annotation of each gene corresponding to the SNPs and their biological role.)
README.gwas.Gangurde_Wang_2020-NAMTifr.yml
Gene family assignments for Arachis duranensis V14167 genes and proteins.
aradu.V14167.gnm1.ann1.cxSM.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Arachis hypogaea Tifrunner gnm1 genes and proteins.
arahy.Tifrunner.gnm1.ann1.CCJH.legfed_v1_0.M65K.gfa.tsv
Gene family assignments for Arachis ipaensis K30076 genes and proteins.
araip.K30076.gnm1.ann1.J37m.legfed_v1_0.M65K.gfa.tsv
Gene model annotation for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.gene_models_main.gff3
Gene model annotation for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.gene_models_main.gff3
Gene model annotation for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.gene_models_main.gff3
LIS datastore genomic FASTA file for Arachis duranensis V14167
aradu.V14167.gnm1.SWBf.genome_main.fna
LIS datastore genomic FASTA file for Arachis hypogaea Tifrunner
arahy.Tifrunner.gnm1.KYV3.genome_main.fna
LIS datastore genomic FASTA file for Arachis ipaensis K30076
araip.K30076.gnm1.bXJ8.genome_main.fna
LIS gene families
legume.genefam.fam1.M65K.info_annot_ahrd.tsv
Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the ‘T’ population (Tifrunner x GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut.
README.qtl.TT_Tifrunner_x_GT-C20_c.yml
MRNA models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.transcript.fna
Plant Reactome pathways for aradu.V14167.gnm1
aradu.V14167.gnm1.ann1.cxSM.pathway.tsv
Plant Reactome pathways for arahy.Tifrunner.gnm1
arahy.Tifrunner.gnm1.ann1.CCJH.legfed_v1_0.M65K.pathway.tsv
Plant Reactome pathways for araip.K30076.gnm1
araip.K30076.gnm1.ann1.J37m.pathway.tsv
Protein models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.protein.faa
Protein models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.protein.faa
Protein models for the araip.K30076.gnm1 genome
araip.K30076.gnm1.ann1.J37m.protein.faa
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between aradu.V14167.gnm1 and other species.
aradu.V14167.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.aradu.V14167.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.araip.K30076.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.glyma.Wm82.gnm2.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.lupan.Tanjil.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.medtr.A17_HM341.gnm4.ann2.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.phavu.G19833.gnm1.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.phavu.G19833.gnm2.ann1.gff
Synteny between araip.K30076.gnm1 and other species.
araip.K30076.gnm1.ann1.x.vigra.VC1973A.gnm6.ann1.gff
This SSR-based genetic map was constructed using a F5:6 RIL population derived from the cross of SunOleic 97R with NC94022. The map is composed of 22 linkage groups (five of which had only 2 markers each). There are 172 mapped loci that comprise 170 SSR loci and 2 CAPS markers for ahFAD2A and adFAD2B. The map covers a total distance of 920.7 cM, exhibits an average distance between markers of 5.7 cM, and displays a range of linkage group lengths from 11.2 to 127.2 cM.
README.map.SunOleic97R_x_NC94022_a.yml
This SSR-based genetic map was constructed using a F5:6 RIL population derived from the cross of SunOleic 97R with NC94022. The map is composed of 22 linkage groups (five of which had only 2 markers each). There are 172 mapped loci that comprise 170 SSR loci and 2 CAPS markers for ahFAD2A and adFAD2B. The map covers a total distance of 920.7 cM, exhibits an average distance between markers of 5.7 cM, and displays a range of linkage group lengths from 11.2 to 127.2 cM.
README.qtl.SunOleic97R_x_NC94022_a.yml
This study reports on the identification of candidate markers associated with fatty acid composition in peanut (Arachis hypogaea). A large population of 791 accessions from the USDA peanut Core collection was genotyped using the Axiom Arachis2 SNP array. SNPs were filtered for MAF>5%, yielding 11,308 SNP markers out of 13,480 high-quality SNPs. The genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and seed fatty acid composition.
README.gwas.Otyama_Kulkarni_2020.yml
Whole-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.
README.map.TT_Tifrunner_x_GT-C20_c.yml
mRNA models for the aradu.V14167.gnm1 genome
aradu.V14167.gnm1.ann1.cxSM.transcript.fna
mRNA models for the arahy.Tifrunner.gnm1 genome
arahy.Tifrunner.gnm1.ann1.CCJH.transcript.fna
PANTHER
PFAM
PIRSF
PRINTS
PROFILE
PROSITE
Plant Ontology
null
Plant Ontology
Plant Trait Ontology
null
Plant Trait Ontology
SFLD
SMART
SSF
Sequence Ontology
null
Sequence Ontology
TIGRFAMs
null
Axiom_Arachis2_SNP genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
Tifrunner.gnm1.mrk.Axiom_Arachis2_SNP
Axiom_Arachis_58K_SNP genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
Tifrunner.gnm1.mrk.Axiom_Arachis_58K_SNP
TPop_map_Agarwai2018 genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
Tifrunner.gnm1.mrk.TPop_map_Agarwai2018
USDA
Legume Federation
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The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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