Add gene_functions files for Arachis hypogaea

Author: StevenCannon-USDA

Arachis/hypogaea/gene_functions/arahy.citations.txt

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+10.1007/s00122-025-04903-1	40358622	Tang, Zhou et al., 2025	Tang Y, Zhou X, Li X, Zhou C, Wang W, Zhou M, Hu Z, Li X, Zhang K, Wang S, Zhang Z, Chen H, Wang J, Qiao L. Genetic analysis and fine mapping reveal that AhRt3, which encodes an anthocyanin reductase, is responsible for red testa in cultivated peanuts. Theor Appl Genet. 2025 May 13;138(6):117. doi: 10.1007/s00122-025-04903-1. PMID: 40358622.

Arachis/hypogaea/gene_functions/arahy.references.txt

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+##### PUB RECORD #####
+## 10.1007/s00122-025-04903-1  40358622  Tang, Zhou et al., 2025  Tang Y, Zhou X, Li X, Zhou C, Wang W, Zhou M, Hu Z, Li X, Zhang K, Wang S, Zhang Z, Chen H, Wang J, Qiao L. Genetic analysis and fine mapping reveal that AhRt3, which encodes an anthocyanin reductase, is responsible for red testa in cultivated peanuts. Theor Appl Genet. 2025 May 13;138(6):117. doi: 10.1007/s00122-025-04903-1. PMID: 40358622. ##
+
+PMID- 40358622
+OWN - NLM
+STAT- MEDLINE
+DCOM- 20250513
+LR  - 20250615
+IS  - 1432-2242 (Electronic)
+IS  - 0040-5752 (Linking)
+VI  - 138
+IP  - 6
+DP  - 2025 May 13
+TI  - Genetic analysis and fine mapping reveal that AhRt3, which encodes an anthocyanin 
+      reductase, is responsible for red testa in cultivated peanuts.
+PG  - 117
+LID - 10.1007/s00122-025-04903-1 [doi]
+AB  - AhRt3, which governs the red testa of peanut, was narrowed down to a 125.30 kb 
+      region, and one gene encoding anthocyanin reductase was identified as the 
+      putative candidate gene. Testa color is a special characteristic of peanuts 
+      (Arachis hypogaea L.), and those with dark testa have been focused on recent 
+      years owing to their high-anthocyanin content and increased antioxidant 
+      nutritional value. However, the genetic mechanisms underlying this trait remain 
+      limited. To identify the gene responsible for the red testa color in peanuts, an 
+      F(2) population was constructed by crossing YH91 (pink testa) with JHT1 (red 
+      testa). Genetic analysis revealed that the red testa was controlled by a single 
+      dominant gene named AhRt3 (Arachis hypogaea Red Testa 3). Through bulked 
+      segregant analysis sequencing, AhRt3 was preliminarily mapped to the chromosome 
+      Arahy.03 and subsequently narrowed to a 125.30 kb genomic region containing 12 
+      potential candidate genes. RNA-seq analysis revealed that 4,880 genes were 
+      differentially expressed in the seed testa, with only the candidate gene 
+      Arahy.W8TDEC exhibiting higher expression levels in JHT1 than in YH91. 
+      Additionally, sequence variation, functional annotation, and expression profiling 
+      confirmed that Arahy.W8TDEC, which encodes an anthocyanin reductase, may be a 
+      candidate gene for AhRt3. The structural variation involving an inversion between 
+      the sixth exon and the 3'UTR of Arahy.W8TDEC resulted in altered amino acids 
+      closely associated with the red testa phenotype in peanuts. In conclusion, this 
+      study highlights the role of a novel gene in regulating red testa and contributes 
+      valuable insights into the genetic basis of seed testa in peanuts.
+CI  - (c) 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, 
+      part of Springer Nature.
+FAU - Tang, Yanyan
+AU  - Tang Y
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Zhou, Xiantao
+AU  - Zhou X
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Li, Xin
+AU  - Li X
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Zhou, Cai
+AU  - Zhou C
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Wang, Wenlin
+AU  - Wang W
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Zhou, Mo
+AU  - Zhou M
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Hu, Zhicheng
+AU  - Hu Z
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Li, Xiaobei
+AU  - Li X
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Zhang, Kaiyuan
+AU  - Zhang K
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Wang, Siming
+AU  - Wang S
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Zhang, Zhihao
+AU  - Zhang Z
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Chen, Hao
+AU  - Chen H
+AD  - Institute of Crop Sciences, Fujian Research Station of Crop Gene Resource & 
+      Germplasm Enhancement, Fujian Academy of Agricultural Sciences, Fuzhou, China.
+FAU - Wang, Jingshan
+AU  - Wang J
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China.
+FAU - Qiao, Lixian
+AU  - Qiao L
+AUID- ORCID: 0000-0002-8231-7911
+AD  - College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, 
+      China. lxqiao73@163.com.
+LA  - eng
+GR  - SDAIT-29-03/Salt-Alkali Agriculture Industry System of Shandong Province/
+GR  - 23-1-3-8-zyyd-nsh/Qingdao Science & Technology Key Projects/
+GR  - 2021LZGC026-07/Shandong Province Key Research and Development Program/
+GR  - S202410435023/Shandong Province College Students'innovation and entrepreneurship 
+      training program/
+GR  - D23014/Innovation Intellectual Program for Higher Education Disciplines/
+PT  - Journal Article
+DEP - 20250513
+PL  - Germany
+TA  - Theor Appl Genet
+JT  - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
+JID - 0145600
+RN  - 0 (Anthocyanins)
+RN  - EC 1.- (Oxidoreductases)
+RN  - 0 (Plant Proteins)
+SB  - IM
+MH  - *Arachis/genetics/enzymology
+MH  - Chromosome Mapping
+MH  - *Anthocyanins/metabolism
+MH  - *Oxidoreductases/genetics/metabolism
+MH  - *Plant Proteins/genetics/metabolism
+MH  - Phenotype
+MH  - *Pigmentation/genetics
+MH  - Genes, Plant
+MH  - Gene Expression Regulation, Plant
+MH  - Chromosomes, Plant/genetics
+COIS- Declarations. Conflict of interest: The authors declare that they have no 
+      conflict of interest.
+EDAT- 2025/05/13 13:50
+MHDA- 2025/05/13 13:51
+CRDT- 2025/05/13 11:02
+PHST- 2024/11/11 00:00 [received]
+PHST- 2025/04/09 00:00 [accepted]
+PHST- 2025/05/13 13:51 [medline]
+PHST- 2025/05/13 13:50 [pubmed]
+PHST- 2025/05/13 11:02 [entrez]
+AID - 10.1007/s00122-025-04903-1 [pii]
+AID - 10.1007/s00122-025-04903-1 [doi]
+PST - epublish
+SO  - Theor Appl Genet. 2025 May 13;138(6):117. doi: 10.1007/s00122-025-04903-1.
+
+

Arachis/hypogaea/gene_functions/arahy.traits.yml

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+---
+scientific_name: Arachis hypogaea
+gene_symbols:
+  - AhRt3
+gene_symbol_long: Red Testa 3
+gene_model_pub_name: Arahy.W8TDEC
+gene_model_full_id: arahy.Tifrunner.gnm2.ann1.W8TDEC
+confidence: 3
+curators:
+  - Scott Kalberer
+comments:
+  - Arachis hypogaea cultivar Yuhua 91 (YH91, female parent, pink testa) was
+      crossed with Jihuatian 1 (JHT1, male parent, red testa). All F1 seeds had
+      the red testa characteristic of JHT1. Among F2 plants the observed ratio
+      of red and pink seed coats fit a 3:1 distribution. Red testa trait was
+      controlled by a single completely dominant gene named AhRt3 (Arachis
+      hypogaea Red Testa 3).
+  - Intensity of red color in peanut seed coats is associated with higher
+      concentrations of flavonoids called proanthocyanidins (PAs). Testas were
+      frozen, pulverized, and soluble and then insoluble PAs were extracted.
+      Absorbance of red light (643 nm) was measured using the DMACA method to
+      estimate PA concentrations. JHT1 red testas contained greater soluble and
+      nonsoluble PA levels than pink YH91 testas.
+  - F3 population and parental lines were used for Bulked Segregant Analysis
+      sequencing (BSA-seq) to map AhRt3 candidate genes. Genomic DNAs extracted
+      from young leaves were turned into DNA libraries. High-quality filtered
+      DNA reads, mapped to genomic sequences of A. hypogaea cv. Tifrunner
+      (Tifrunner.gnm2.ann1.4K0L), were followed by called and filtered
+      single-nucleotide polymorphisms (SNPs) and insertion/deletions (InDels).
+      Genomic regions with a significant ΔSNP-index were associated with testa
+      color, suggesting a peak on chromosome Arahy.03 between 126.0–137.4 Mb.
+  - Researchers developed 35 InDels and 45 SNPs to validate BSA-seq results and
+      narrow the candidate region. Polymorphic markers were formed into a
+      genetic linkage map on chromosome Arahy.03. QTLs for testa color were
+      analyzed using inclusive composite interval mapping. Genotype
+      characterization of pink individuals within the F2 segregating population
+      revealed one QTL in the 7.68 Mb region between ZF16 to ZF28 that
+      explained 32.03% of phenotypic variance in testa color. Further SNP
+      development and identification of recombinants fine-mapped the genomic
+      location of AhRt3 to a 125.30 kb region between SNP43 and SNP44_2.
+  - Twelve annotated candidate gene sequences were predicted within the
+      identified region based on the Tifrunner cultivated peanut reference
+      genome. Genomic variations in resequencing data for 12 candidates pointed
+      to 34 effective SNPs/InDels between the parents. An inversion discovered
+      between the sixth exon and the 3’UTR for Arahy.W8TDEC
+      (126,104,725–126,104,948) resulted in a structural variation observed in
+      the JHT1 parent. The consequence was an altered amino acid sequence
+      closely associated with the red testa phenotype.
+  - Spatiotemporal transcription patterns of AhRt3 were assessed using RNA-seq
+      datasets for 22 different tissues of Tifrunner. Data were taken from the
+      PeanutBase.org gene expression atlas to study 12 candidate genes.
+      Arahy.W8TDEC showed greater expression levels than other candidates, and
+      Arahy.W8TDEC had high expression in seeds of Pattee stage 6 relative to
+      the other tissues, indicating Arahy.W8TDEC was related to seed coat
+      development and pigmentation.
+  - Transcriptome analysis involved extraction of total RNA from developing
+      peanut testa 60 days after pegging, synthesis of first-strand cDNAs, and
+      construction of an RNA-seq library. Raw reads and functional annotations
+      were aligned to the reference genome. A total of 4,880 genes in the seed
+      coat were differentially expressed, and 30 genes involved in flavonoid
+      biosynthesis were significantly upregulated in the JHT1 plants. Solely
+      candidate gene Arahy.W8TDEC displayed higher expression levels in JHT1
+      than in YH91. Arahy.W8TDEC encodes an anthocyanidin reductase involved in
+      flavonoid biosynthesis.
+  - AhRt3 (Arahy.W8TDEC) produces an anthocyanidin reductase enzyme (ANR) that
+      catalyzes the conversion of anthocyanidins into flavan-3-ols (catechins
+      and epicatechins). These flavan-3-ol precursors ultimately drive the
+      production of proanthocyanidins (condensed tannins) that control red
+      seed-coat color and provide antioxidant nutrition.
+phenotype_synopsis: Expression of Red Testa 3 (AhRt3) in Arachis hypogaea,
+  encoding anthocyanidin reductase (ANR), increases proanthocyanidin contents
+  of seed testas and consequently deeper red coloration. The candidate gene
+  model for AhRt3 is likely Arahy.W8TDEC.
+traits:
+  - entity_name: seed coat color
+    entity: TO:0000190
+  - entity_name: anthocyanin content
+    entity: TO:0000071
+  - entity_name: anthocyanidin reductase activity
+    entity: GO:0033729
+  - entity_name: proanthocyanidin biosynthetic process
+    entity: GO:0010023
+references:
+  - citation: Tang, Zhou et al., 2025
+    doi: 10.1007/s00122-025-04903-1
+    pmid: 40358622
+