McCrory, M. A., Hamaker, B. R., Lovejoy, J. C. & Eichelsdoerfer, P. E. Pulse consumption, satiety, and weight management. Adv. Nutr. 1, 17–30 (2010).
Pandey, A. K. et al. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). Theor. Appl Genet 134, 755–776 (2021).
Yang, T. et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat. Genet. 54, 1553–1563 (2022).
Tayeh, N. et al. Genomic tools in pea breeding programs: status and perspectives. Front. Plant Sci. 6, 1037 (2015).
Liu, N. et al. Comparative transcriptomic analyses of vegetable and grain pea (Pisum sativum L.) seed development. Front. Plant Sci. 6, 1039 (2015).
Smykal, P. et al. From Mendel’s discovery on pea to today’s plant genetics and breeding: commemorating the 150th anniversary of the reading of Mendel’s discovery. Theor. Appl. Genet. 129, 2267–2280 (2016).
Zohary, D. & Hopf, M. Domestication of pulses in the old world: legumes were companions of wheat and barley when agriculture began in the Near East. Science 182, 887–894 (1973).
Smykal, P. et al. Legume crops phylogeny and genetic diversity for science and breeding. Crit. Rev. Plant Sci. 34, 43–104 (2015).
Kreplak, J. et al. A reference genome for pea provides insight into legume genome evolution. Nat. Genet. 51, 1411–1422 (2019).
Makani, J., Nkya, S., Collins, F. & Luzzatto, L. From Mendel to a Mendelian disorder: towards a cure for sickle cell disease. Nat. Rev. Genet. 23, 389–390 (2022).
Charlesworth, B. et al. From Mendel to quantitative genetics in the genome era: the scientific legacy of W. G. Hill. Nat. Genet. 54, 934–939 (2022).
Mendel, G. Versuche über Pflanzen-Hybriden. Brünn, Im Verlage des Vereines, 1822–1884. Biodiversity Heritage Library https://doi.org/10.5962/bhl.title.61004 (1866).
Van Dijk, P. J. & Ellis, T. H. The full breadth of Mendel’s genetics. Genetics 204, 1327–1336 (2016).
Bhattacharyya, M. K., Smith, A. M., Ellis, T. H. N., Hedley, C. & Martin, C. The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60, 115–122 (1990).
Ingram, T. J. et al. Internode length in Pisum: the Le gene controls the 3beta-hydroxylation of gibberellin A20 to gibberellin A 1. Planta 160, 455–463 (1984).
Lester, D. R., Ross, J. J., Davies, P. J. & Reid, J. B. Mendel’s stem length gene (Le) encodes a gibberellin 3 beta-hydroxylase. Plant Cell 9, 1435–1443 (1997).
Weston, D. E. et al. The Pea DELLA proteins LA and CRY are important regulators of gibberellin synthesis and root growth. Plant Physiol. 147, 199–205 (2008).
Lester, D. R., MacKenzie-Hose, A. K., Davies, P. J., Ross, J. J. & Reid, J. B. The influence of the null le-2 mutation on gibberellin levels in developing pea seeds. Plant Growth Regul. 27, 83–89 (1999).
Armstead, I. et al. Cross-species identification of Mendel’s I locus. Science 315, 73 (2007).
Sato, Y., Morita, R., Nishimura, M., Yamaguchi, H. & Kusaba, M. Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl Acad. Sci. USA 104, 14169–14174 (2007).
Hellens, R. P. et al. Identification of Mendel’s white flower character. PLoS ONE 5, e13230 (2010).
Sussmilch, F. C., Ross, J. J. & Reid, J. B. Mendel: from genes to genome. Plant Physiol. 190, 2103–2114 (2022).
Tayeh, N. et al. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map. Plant J. 84, 1257–1273 (2015).
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).
Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573–589 (2014).
Martin, D. N., Proebsting, W. M. & Hedden, P. Mendel’s dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl Acad. Sci. USA 94, 8907–8911 (1997).
Ellis, T. H. N. & Poyser, S. J. An integrated and comparative view of pea genetic and cytogenetic maps. New Phytol. 153, 17–25 (2002).
Lamprecht, H. The variation of linkage and the course of crossing over. Agri Hortic. Genet. 6, 10–48 (1948).
Shirasawa, K., Sasaki, K., Hirakawa, H. & Isobe, S. Genomic region associated with pod color variation in pea (Pisum sativum). G3 (Bethesda) 11, jkab081 (2021).
Li, J. A. et al. Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation. Plant Cell 23, 628–640 (2011).
Xu, J. et al. HEAT SHOCK PROTEIN 90.6 interacts with carbon and nitrogen metabolism components during seed development. Plant Physiol. 191, 2316–2333 (2023).
Yan, Y. et al. HSP90.2 promotes CO2 assimilation rate, grain weight and yield in wheat. Plant Biotechnol. J. 21, 1229–1239 (2023).
Martinez, C., Pons, E., Prats, G. & Leon, J. Salicylic acid regulates flowering time and links defence responses and reproductive development. Plant J. 37, 209–217 (2004).
Huang, W., Wang, Y., Li, X. & Zhang, Y. Biosynthesis and regulation of salicylic acid and N-hydroxypipecolic acid in plant immunity. Mol. Plant 13, 31–41 (2020).
Tayeh, N. et al. afila, the origin and nature of a major innovation in the history of pea breeding. New Phytol. 243, 1247–1261 (2024).
Bordat, A. et al. Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L. G3 (Bethesda) 1, 93–103 (2011).
Weeden, N. F. et al. A consensus linkage map for Pisum sativum. Pisum Genet. 30, 1–3 (1998).
Willoughby, A. C. & Nimchuk, Z. L. WOX going on: CLE peptides in plant development. Curr. Opin. Plant Biol. 63, 102056 (2021).
Balarynova, J. et al. The loss of polyphenol oxidase function is associated with hilum pigmentation and has been selected during pea domestication. N. Phytol. 235, 1807–1821 (2022).
Taylor-Teeples, M. et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575 (2015).
Nasmyth, K. The magic and meaning of Mendel’s miracle. Nat. Rev. Genet. 23, 447–452 (2022).
White, O. E. The present state of knowledge of heredity and variation in peas. Proc. Am. Phil. Soc. 56, 487–588 (1917).
Ahmad, I. S., Reid, J. F., Paulsen, M. R. & Sinclair, J. B. Color classifier for symptomatic soybean seeds using image processing. Plant Dis. 83, 320–327 (1999).
Doyle, J. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19, 11–15 (1987).
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Ou, S., Chen, J. & Jiang, N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126 (2018).
Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. 176, 1410–1422 (2018).
Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinf. 9, 18 (2008).
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Benson, D. A. et al. GenBank. Nucleic Acids Res. 46, D41–D47 (2018).
Gremme, G., Steinbiss, S. & Kurtz, S. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans. Comput. Biol. Bioinform. 10, 645–656 (2013).
Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).
Keilwagen, J., Hartung, F., Paulini, M., Twardziok, S. O. & Grau, J. Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinf. 19, 189 (2018).
Stanke, M., Steinkamp, R., Waack, S. & Morgenstern, B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32, W309–W312 (2004).
Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y. O. & Borodovsky, M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 18, 1979–1990 (2008).
Wu, T. D. & Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859–1875 (2005).
Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
UniProt, C. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. the gene ontology consortium. Nat. Genet. 25, 25–29 (2000).
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109–D114 (2012).
Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).
Zheng, Y. et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol. Plant 9, 1667–1670 (2016).
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).
Kalvari, I. et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 49, D192–D200 (2021).
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
Bao, W., Kojima, K. K. & Kohany, O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6, 11 (2015).
Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 4, 4.10.1–4.10.14 (2009).
Goel, M., Sun, H., Jiao, W. B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277 (2019).
Marcais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Cingolani, P. Variant annotation and functional prediction: SnpEff. Methods Mol. Biol. 2493, 289–314 (2022).
Retief, J. D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132, 243–258 (2000).
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
He, Z. et al. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 44, W236–W241 (2016).
Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Kang, H. M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348–354 (2010).
Li, M. X., Yeung, J. M., Cherny, S. S. & Sham, P. C. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum. Genet. 131, 747–756 (2012).
Lyu, X. L. et al. A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of a hull-less pumpkin accession. Hortic. Res. 9, uhac136 (2022).
Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat. Protoc. 11, 1650–1667 (2016).
Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 9, 559 (2008).
Kumar, L. & M, E. F. Mfuzz: a software package for soft clustering of microarray data. Bioinformation 2, 5–7 (2007).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25, 402–408 (2001).
Die, J. V., Roman, B., Nadal, S. & Gonzalez-Verdejo, C. I. Evaluation of candidate reference genes for expression studies in Pisum sativum under different experimental conditions. Planta 232, 145–153 (2010).
