Data Sources and their Data Sets

CATHGENE3D
CDD
GO
GO
The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
HAMAP
InterMine post-processor
InterMine gene-flanking regions
Gene-flanking regions created by the core InterMine post-processor
InterMine intergenic regions
Intergenic regions created by the InterMine core post-processor
InterPro
InterPro data set
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
InterPro domain GO annotations
Mapping of GO terms to InterPro entries.
LIS Datastore
Huayu28_x_P76.gen.Hu_Zhang_2018
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. 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. QTLs associated with seed oleic and linoleic acid content were found.
ICGS44_x_ICGS76.gen.Gautami_Pandey_2012
With the aim of finding QTLs for drought tolerance, a new recombinant inbred line (RIL) mapping population, ICGS 44 x ICGS 76 (RIL-3), was created, with 83 SSR loci.
ICGS76_x_CSMG84.gen.Gautami_Pandey_2012
With the aim of finding QTLs for drought tolerance, a new RIL mapping population ICGS 76 x CSMG 84-1 (RIL-2) was created. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, a new genetic map was developed with 119 (RIL-2) SSR loci.
NAMFlor7.gwas.Gangurde_Wang_2020
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.)
NAMTifr.gwas.Gangurde_Wang_2020
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.)
PPD3
An SSR-based genetic map created from a F9:10 generation derived from the cross of A. hypogaea cultivars 'TG 26' with 'GPBD 4'
R59G
An SSR-based genetic map derived from a cross of the A. hypogaea cultivars Tifrunner and GT-C20.
SunOleic97R_x_NC94022.gen.Qin_Feng_2012
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. A derived QTL for Tomato spotted wilt virus is reported.
TAG24_x_GPBD4.gen.Kolekar_Sujay_2016
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].
TAG24_x_ICGV86031.gen.Ravi_Vadez_2011
This genetic map was developed from a population of F8:9:10 recombinant inbred lines (RILs) derived from the cross of 'TAG 24' with 'ICGV 86031'.
TG26_x_GPBD4.gen.Sujay_Gowda_2012
An SSR-based genetic map derived from an F10 recombinant inbred line (RIL) mapping population produced by a cross of 'TG 26' with 'GPBD 4'.
Tifrunner_x_GT-C20.gen.Agarwal_Clevenger_2018
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. 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.
Tifrunner_x_GT-C20.gen.Qin_Feng_2012
This SSR-based genetic map was constructed using a F5:6 RIL population derived from the cross of Tifrunner with GT-C20. The map is composed of 26 linkage groups; however, five of these linkage groups included only 2 markers each. There are 239 total mapped loci (generated using 216 primer pairs) that comprise 238 SSR loci and 1 CAPS marker for ahFAD2A. The map covers a total distance of 1213.4 cM, exhibits an average distance between markers of 5.7 cM, and displays a range of linkage group lengths from 3.1 to 136.5 cM.
USPeanutCore.gwas.Otyama_Kulkarni_2020
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.
VG9514_x_TAG24.gen.Mondal_Hadapad_2014
SSR and TE based genetic map developed from a population of F8 RILs resulting from crossing the A. hypogaea cultivars VG 9514 and TAG 24.
aradu.V14167.gnm1.SWBf
null
aradu.V14167.gnm1.ann1.cxSM
aradu.V14167.gnm1.ann1 annotation
arahy.Tifrunner.gnm1.KYV3
null
arahy.Tifrunner.gnm1.ann1.CCJH
arahy.Tifrunner.gnm1.ann1 genome annotation
araip.K30076.gnm1.ann1.J37m
araip.K30076.gnm1.ann1 annotation
araip.K30076.gnm1.bXJ8
null
legume.genefam.fam1.M65K
LIS fam1 gene families
mixed.gen.Gautami_Pandey_2012
With the aim of understanding the genetic basis and identification of QTLs for drought tolerance, two new RIL mapping populations, ICGS 76 x CSMG 84-1 (RIL-2), and ICGS 44 x ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and a previous reference map with 191 SSR loci based on TAG 24 x ICGV 86031 (RIL-1; Ravi et al. 2011), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM.
mixed.gen.Sujay_Gowda_2012
With the objective of identifying markers tightly-linked to late leaf spot and rust, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 x GPBD 4 (RIL4) and TG 26 x GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed.
PANTHER
PFAM
PIRSF
PRINTS
PROFILE
PROSITE
Plant Ontology
Plant Ontology
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies.
Plant Trait Ontology
Plant Trait Ontology
A controlled vocabulary of describe phenotypic traits in plants.
SFLD
SMART
SSF
Sequence Ontology
Sequence Ontology
The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence.
TIGRFAMs
null
arahy.Tifrunner.gnm1.mrk.Axiom_Arachis2_SNP
Axiom_Arachis2_SNP genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
arahy.Tifrunner.gnm1.mrk.Axiom_Arachis_58K_SNP
Axiom_Arachis_58K_SNP genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
arahy.Tifrunner.gnm1.mrk.TPop_map_Agarwai2018
TPop_map_Agarwai2018 genetic marker positions on the arahy.Tifrunner.gnm1 genome assembly
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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