--- scientific_name: Pisum sativum classical_locus: Gp gene_symbols: - PsChlG gene_symbol_long: Chlorophyll synthase gene_model_pub_name: Psat03G0413700 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat3g126440 confidence: 4 curators: - Raegan Nelson comments: - 100kb deletion upstream of ChlG generates aberrant transcripts and confers the yellow pod phenotype - yellow pods are not the only feature of gp mutants, yellow tissues are seen in the petiole, rachis, tendrils and leaflet midribs of young leaves, and also in the pedicel, peduncle and sepals - even the green leaves of gp lines have disturbed development of thylakoid membranes - 100kb deletion removes three entire genes, as well as part of exon5 and the whole of exon 6 from a gene encoding a TIR-NBS-LRR protein - the deletion upstream of ChlG in the gp lines generates a fused NLR-ChlG transcript, removing the fused NLR-ChlG transcript would restore the wild-type green pod color phenotype_synopsis: ChlG is involed in the process of making chlorophyll, which turns pea pods and other plant tissues green traits: - entity_name: Chlorophyll content entity: TO:0000495 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: R gene_symbols: - PsSBE1 gene_symbol_long: Starch Branching Enzyme 1 gene_model_pub_name: Psat03G0136800 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat3g034640 confidence: 5 curators: - Raegan Nelson comments: - The insertion of Ips-r, a 1021bp non-autonomous Ac- like transposable element, within exon 22 - The single GWAS peak indicates that there is no genetic heterogeneity associated with this phenotype within the lines studied phenotype_synopsis: SBE1 is involved in seed coat texture, either round or wrinkly peas traits: - entity_name: Seed coat texture entity: TO:0000903 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: I gene_symbols: - PsSGR gene_symbol_long: Stay green gene_model_pub_name: Psat02G0529500 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat2g181040 confidence: 5 curators: - Raegan Nelson comments: - Two classes of i alleles i-1 and i-2 - SGR encodes Mg-dechelatase - i-1 is caused by a insertion of a 5,696 nt TAR element (a Ty1-Copia LTR retrotransposon) - i-2 is a novel 408 bp deletion in the promoter of the Mg-dechelatase gene phenotype_synopsis: SGR is involved in cotyledon color traits: - entity_name: Seedling cotyledon color entity: TO:0000750 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: A gene_symbols: - PsbHLH gene_model_pub_name: Psat06G0169800 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat6g060480 confidence: 5 curators: - Raegan Nelson comments: - bHLH transcription factor required for the expression of chalcone synthase in epidermal tissues which enables anthocyanin pigmentation - two most common a alleles had splice donor site variant (G to A) in Hap 5 or a additional ‘A’ nucleotide in exon 6 creating a premature stop codon in Hap 2 phenotype_synopsis: bHLH is involed in flower pigment traits: - entity_name: Flower color entity: TO:0000537 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: Le gene_symbols: - PsGA3OX1 gene_symbol_long: GA 3-oxidase 1 gene_model_pub_name: Psat05G0825300 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat5g299720 confidence: 5 curators: - Raegan Nelson comments: - reduced height le variants were exclusively found in haplotype 1, which carries the known G-A substitution at chr5:639901919 - variation at other known loci involved in plant height, or internode length does not contribute significantly to natural phenotypic variation in this trait phenotype_synopsis: GA3OX1 is involved in stem internode length traits: - entity_name: Stem internode morphology trait entity: TO:0000756 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: P gene_symbols: - PsCLE41 gene_model_pub_name: Psat01G0420500 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat1g151160 confidence: 5 curators: - Raegan Nelson comments: - p allele has a in-frame premature stop codon (R79*) upstream of the TDIF motif - the TDIF peptide interacts with a PXY-like protein to specify pea pod sclerenchyma development - the lack of a sclerenchyma layer in pea pods is conditioned by the recessive allele at either (or both) of the genes P and V phenotype_synopsis: CLE41 in involved in the development of the sclerenchyma layer, which changes pod shape traits: - entity_name: sclerenchyma entity: PO:0005427 - entity_name: plant structure growth and development trait entity: TO:0000928 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: Fa gene_symbols: - PsCIK1 gene_symbol_long: CLAVATA3 INSENSITIVE RECEPTOR KINASES 1 gene_model_pub_name: Psat04G0031700 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat0s2289g0040 confidence: 4 curators: - Raegan Nelson comments: - fa mutant lines have a 5bp deletion in exon 2, on Hap 3, creating a frameshift and premature stop codon which would render the protein non-functional - The bunched apical flowers of the mutant (fafa) are found on a wider stem with additional vascular strands derived from a broadened apical meristem phenotype_synopsis: CIK1 is involved in apical meristem development which can change fasciation traits: - entity_name: Shoot apical meristem development entity: TO:0006020 - entity_name: apical meristem entity: PO:0020144 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: V gene_symbols: - PsMYB26 gene_symbol_long: MYB 26 gene_model_pub_name: Psat05G0804500 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat5g291560 confidence: 4 curators: - Raegan Nelson comments: - PsMYB26 exhibits tissue-specific expression in the pod endocarp - A 23 kb Ogre-type LTR retrotransposon insertion, located upstream of PsMYB26 is correlated with the lack of sclerenchyma formation - The gene MYB26 is required for sclerenchyma formation in legume pods - P and V have an episatic relationship that controls the development of the sclerenchyma layer in pea pods phenotype_synopsis: PsMYB26 in involved in the development of the sclerenchyma layer, which changes pod shape traits: - entity_name: plant structure growth and development trait entity: TO:0000928 - entity_name: sclerenchyma entity: PO:0005427 references: - citation: Feng, Chen et al., 2024 doi: 10.1038/s41586-025-08891-6 pmid: 40269167 --- scientific_name: Pisum sativum classical_locus: I gene_symbols: - PsSGR gene_symbol_long: Staygreen gene_model_pub_name: AB303332 gene_model_full_id: pissa.Cameor.gnm1.ann1.Psat2g181040 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Complementation test confirms that PsSGR is the Mendelian I locus. SGR is a positive regulator of pathways involved in breakdown of chlorophyll via translational or post-translational regulation of chlorophyll degrading enzymes. The products of SGR are required to separate chlorophyll from the photosynthetic complex, allowing chlorophyll degrading enzymes access to their substrate. The sgr loss-of-function mutation is due to lower expression of the SGR gene and a small insertion that disrupts SGR protein fuction. phenotype_synopsis: The recessive phenotype sgr retains a high chlorophyll content during senescence, causing cotyledons to stay green as they mature and leaves to stay green as they die. PsSGR is a cosmetic stay-green mutant and does not retain the ability to photosynthesize. traits: - entity_name: chlorophyll catabolic process entity: GO:0015996 - entity_name: positive regulation of chlorophyll catabolic process entity: GO:1903648 - entity_name: plant embryo cotyledon color entity: TO:0000980 - entity_name: leaf senescence trait entity: TO:0000249 references: - citation: Sato, Morita et al., 2007 doi: 10.1073/pnas.0705521104 pmid: 17709752 - citation: Armstead, Donnison et al., 2007 doi: 10.1126/science.1132912 pmid: 17204643 - citation: Aubry, Mani et al., 2008 doi: 10.1007/s11103-008-9314-8 pmid: 18301989 - citation: Hortensteiner, 2009 doi: 10.1016/j.tplants.2009.01.002 pmid: 19237309