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We describe both the terminology and use of symbols introduced by Mendel in his 1866 paper and discuss some misconceptions concerning their interpretation.

According to the revisionist interpretation of Mendel’s pea crosses, his primary aim was not to study the inheritance of traits. Instead, he was interested in the question raised by Linnaeus as to whether new species could arise from the hybridization of existing species. The genetic interpretation is therefore seen as ahistorical by the revisionists. This view goes back to the 1979 article “Mendel no Mendelian?” by the historian of science R.C. Olby. A closer analysis shows that Olby implicitly assumed Mendel adhered to the unusual strictest species definition for Pisum. However, we argue that Mendel only mentions the hypothetical application of this strict definition in his 1866 paper. Like most of his contemporaries, Mendel accepted variation within species where the differences between varieties and species were a matter of degree. After researching variable hybrids in peas (Pisum; 1854–1863), Mendel also studied constant hybrids in hawkweeds (Hieracium; 1866–1873), which he considered to be new species. There is no debate about the latter, but the matter becomes muddled because Olby lumps Pisum and Hieracium together, despite their having completely different reproduction systems. Based on newly discovered historical sources, we also dispute several other assumptions made by Olby. We do not consider Olby’s claim that Mendel conducted the Pisum experiments to investigate species multiplication to be tenable.

Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.

Grasspea is an important food security crop, especially under severely adverse environmental conditions such as prolonged drought. The crop has a long history, but its cultivation has declined probably due to the presence of β-ODAP, a neurotoxin, which can cause a severe disease in people and domestic animals when grasspea is the main source of nutrition in an unbalanced diet. Grasspea, and the people who depend on it, can therefore benefit from the removal of this specific compound. A wide range of genetic and genomic tools are now available which can facilitate this development. The purpose of this article is to describe genetic and genomic resources and their specific features in grasspea., AE, NE, PE, and AS were supported by the John Innes Centre Institute Development Grant, the Biotechnology and Biological Sciences Research Council (BBSRC) Detox Grass pea project (BB/L011719/1), the BBSRC SASSA UPGRADE project (BB/R020604/1), and the BBSRC Institute Strategic Programme (BBS/E/J/000PR9799). NE gratefully acknowledges the support of an Institute Strategic Fellowship from The John Innes Centre. These authors thank Cathie Martin for her support and many useful discussions. MCVP would like to acknowledge financial support by Fundação para a Ciência e Tecnologia (FCT), Portugal, through the research unit GREEN-IT (UID/04551/2020). DR was supported by AEI projects AGL2017-82907-R and PID2020-11468RB-100. JM and PN were financially supported by the Czech Academy of Science (RVO: 60077344). SK acknowledges support of the BBSRC SASSA UPGRADE project (BB/R020604/1) and a grant from Templeton World Charity Foundation, Inc. XH acknowledges support from the China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08-Z4).

Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.

A controversy arose over Mendel’s pea crossing experiments after the statistician R.A. Fisher proposed how these may have been performed and criticised Mendel’s interpretation of his data. Here we re-examine Mendel’s experiments and investigate Fisher’s statistical criticisms of bias. We describe pea varieties available in Mendel’s time and show that these could readily provide all the material Mendel needed for his experiments; the characters he chose to follow were clearly described in catalogues at the time. The combination of character states available in these varieties, together with Eichling’s report of crosses Mendel performed, suggest that two of his F3 progeny test experiments may have involved the same F2 population, and therefore that these data should not be treated as independent variables in statistical analysis of Mendel’s data. A comprehensive re-examination of Mendel’s segregation ratios does not support previous suggestions that they differ remarkably from expectation. The χ2values for his segregation ratios sum to a value close to the expectation and there is no deficiency of extreme segregation ratios. Overall the χ values for Mendel’s segregation ratios deviate slightly from the standard normal distribution; this is probably because of the variance associated with phenotypic rather than genotypic ratios and because Mendel excluded some data sets with small numbers of progeny, where he noted the ratios “deviate not insignificantly” from expectation.

Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes.

We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

Legumes represent the second most important family of crop plants after grasses, accounting for approximately 27% of the world's crop production. Past domestication processes resulted in a high degree of relatedness between modern varieties of crops, leading to a narrower genetic base of cultivated germplasm prone to pests and diseases. Crop wild relatives (CWRs) harbor genetic diversity tested by natural selection in a range of environments. To fully understand and exploit local adaptation in CWR, studies in geographical centers of origin combining ecology, physiology, and genetics are needed. With the advent of modern genomics and computation, combined with systematic phenotyping, it is feasible to revisit wild accessions and landraces and prioritize their use for breeding, providing sources of disease resistances; tolerances of drought, heat, frost, and salinity abiotic stresses; nutrient densities across major and minor elements; and food quality traits. Establishment of hybrid populations with CWRs gives breeders a considerable benefit of a prebreeding tool for identifying and harnessing wild alleles and provides extremely valuable long‐term resources. There is a need of further collecting and both ex situ and in situ conservation of CWR diversity of these taxa in the face of habitat loss and degradation and climate change. In this review, we focus on three legume crops domesticated in the Fertile Crescent, pea, chickpea, and lentil, and summarize the current state and potential of their respective CWR taxa for crop improvement.

In order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.

Gregor Mendel’s “Experiments on Plant Hybrids” (1865/1866), published 150 years ago, is without doubt one of the most brilliant works in biology. Curiously, Mendel’s later studies on Hieracium (hawkweed) are usually seen as a frustrating failure, because it is assumed that they were intended to confirm the segregation ratios he found in Pisum. Had this been his intention, such a confirmation would have failed, since, unknown to Mendel, Hieracium species mostly reproduce by means of clonal seeds (apomixis). Here we show that this assumption arises from a misunderstanding that could be explained by a missing page in Mendel’s first letter to Carl Nägeli. Mendel’s writings clearly indicate his interest in “constant hybrids,” hybrids which do not segregate, and which were “essentially different” from “variable hybrids” such as in Pisum. After the Pisum studies, Mendel worked mainly on Hieracium for 7 years where he found constant hybrids and some great surprises. He also continued to explore variable hybrids; both variable and constant hybrids were of interest to Mendel with respect to inheritance and to species evolution. Mendel considered that their similarities and differences might provide deep insights and that their differing behaviors were “individual manifestations of a higher more fundamental law.”

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

The seed-containing pod is the defining structure of plants in the legume family, yet pods exhibit a wide range of morphological variation. Within a species pod characters are likely to be correlated with reproductive strategy, and within cultivated forms will correspond to aspects of yield determination and/or end use. Here variation in pod size, described as pod length: pod width ratio, has been analyzed in pea germplasm represented by 597 accessions. This pod size variation is discussed with respect to population structure and to known classical pod morphology mutants. Variability of the pod length: width ratio can be explained by allelic variation at two genetic loci that may correspond to organ-specific negative regulators of growth.

Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes.

Nuclear magnetic resonance (NMR) spectroscopy profiling was used to provide an unbiased assessment of changes to the metabolite composition of seeds and to define genetic variation for a range of pea seed metabolites. Mature seeds from recombinant inbred lines, derived from three mapping populations for which there is substantial genetic marker linkage information, were grown in two environments/years and analyzed by non-targeted NMR. Adaptive binning of the NMR metabolite data, followed by analysis of quantitative variation among lines for individual bins, identified the main genomic regions determining this metabolic variability and the variability for selected compounds was investigated. Analysis by t-tests identified a set of bins with highly significant associations to genetic map regions, based on probability (p) values that were appreciably lower than those determined for randomized data. The correlation between bins showing high mean absolute deviation and those showing low p-values for marker association provided an indication of the extent to which the genetics of bin variation might be explained by one or a few loci. Variation in compounds related to aromatic amino acids, branched-chain amino acids, sucrose-derived metabolites, secondary metabolites and some unidentified compounds was associated with one or more genetic loci. The combined analysis shows that there are multiple loci throughout the genome that together impact on the abundance of many compounds through a network of interactions, where individual loci may affect more than one compound and vice versa. This work therefore provides a framework for the genetic analysis of the seed metabolome, and the use of genetic marker data in the breeding and selection of seeds for specific seed quality traits and compounds that have high commercial value.

Gregor Mendel’s crossing experiments in pea are the foundation of classical genetics, but since the importance of his 1866 paper was not understood until after long after his notebooks were burned, we know little..., Despite the fact that Gregor Mendel is generally respected as the founder of genetics, little is known about the origin of and motivation for his revolutionary work. No primary sources are known that discuss his work during the period of his pea crossing experiments. Here, we report on two previously unknown interconnected local newspaper articles about Mendel’s work that predate his famous Pisum lectures by 4 years. These articles describe Mendel as a plant breeder and a horticulturist. We argue that Mendel’s initial interests concerned crop improvement, but that with time he became more interested in fundamental questions about inheritance, fertilization, and natural hybridization.

Pea (Pisum sativum) is one of relatively few genetically amenable plant species with compound leaves. Pea leaves have a variety of specialized organs: leaflets, tendrils, pulvini and stipules, which enable the identification of mutations that transform or affect distinct parts of the leaf. Characterization of these mutations offers insights into the development and evolution of novel leaf traits. The previously characterized morphological gene Cochleata, conferring stipule identity, was known to interact with Stipules reduced (St), which conditions stipule size in pea, but the St gene remained unknown. Here we analysed Fast Neutron irradiated pea mutants by restriction site associated DNA sequencing. We identified St as a gene encoding a C2H2 zinc finger transcription factor that is regulated by Cochleata. St regulates both cell division and cell expansion in the stipule. Our approach shows how systematic genome-wide screens can be used successfully for the analysis of traits in species for which whole genome sequences are not available.

One of the traits studied by Mendel in pea (Pisum sativum L.) was the wrinkled-seeded phenotype, and the molecular basis for a mutation underlying this phenotype was discovered in the 1990s. Although the starch-branching enzyme gene mutation identified at the genetic locus r is most likely to be that in seeds available to Mendel in the mid-1800s, it has remained an open question as to whether or not additional natural mutations in this gene exist within Pisum germplasm collections. Here, we explore this question and show that all but two wrinkled-seeded variants in one such collection correspond to either the mutant allele described previously for the r locus or a mutation at a second genetic locus, rb, affecting the gene encoding the large subunit of Adenosine diphosphoglucose (ADP-glucose) pyrophosphorylase; the molecular basis for the rb mutation is described here. The genetic basis for the phenotype of one (JI 2110) of the two lines which are neither r nor rb has been studied in crosses with a round-seeded variant (JI 281); for which extensive genetic marker data were expected. In marked contrast to the trait studied by Mendel and the rb phenotype; the data suggest that the wrinkled-seeded phenotype in JI 2110 is maternally determined, controlled by two genetic loci, and the extent to which it is manifested is very sensitive to the environment. Metabolite analysis of the cotyledons of JI 2110 revealed a profile for sucrose and sucrose-derived compounds that was more similar to that of wild-type round-seeded, than that of wrinkled-seeded r, pea lines. However, the metabolite profile of the seed coat (testa) of JI 2110 was distinct from that of other round-seeded genotypes tested which, together with analysis of recombinant inbred progeny lines, suggests an explanation for the seed phenotype.