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07 Aug 2023
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Genomic data suggest parallel dental vestigialization within the xenarthran radiation

What does dental gene decay tell us about the regressive evolution of teeth in South American mammals?

Recommended by based on reviews by Juan C. Opazo, Régis Debruyne and Nicolas Pollet

A group of mammals, Xenathra, evolved and diversified in South America during its long period of isolation in the early to mid Cenozoic era. More recently, as a result of the Great Faunal Interchange between South America and North America, many xenarthran species went extinct. The thirty-one extant species belong to three groups: armadillos, sloths and anteaters. They share dental degeneration. However, the level of degeneration is variable. Anteaters entirely lack teeth, sloths have intermediately regressed teeth and most armadillos have a toothless premaxilla, as well as peg-like, single-rooted teeth that lack enamel in adult animals (Vizcaíno 2009). This diversity raises a number of questions about the evolution of dentition in these mammals. Unfortunately, the fossil record is too poor to provide refined information on the different stages of regressive evolution in these clades. In such cases, the identification of loss-of-function mutations and/or relaxed selection in genes related to a character regression can be very informative (Emerling and Springer 2014; Meredith et al. 2014; Policarpo et al. 2021). Indeed, shared and unique pseudogenes/relaxed selection can tell us to what extent regression has occurred in common ancestors and whether some changes are lineage-specific. In addition, the distribution of pseudogenes/relaxed selection on the branches of a phylogenetic tree is related to the evolutionary processes involved. A much higher density of pseudogenes in the most internal branches indicates that degeneration took place early and over a short period of time, consistent with selection against the presence of the morphological character with which they are associated, while pseudogenes distributed evenly in many internal and external branches suggest a more gradual process over many millions of years, in line with relaxed selection and fixation of loss-of-function mutations by genetic drift.

In this paper (Emerling et al. 2023), the authors examined the dynamics of decay of 11 dental genes that may parallel teeth regression. The analyses of the data reported in this paper clearly point to xenarthran teeth having repeatedly regressed in parallel in the three clades. In fact, no loss-of-function mutation is shared by all species examined. However, more genes should be studied to confirm the hypothesis that the common ancestor of extant xenarthrans had normal dentition. There are distinct patterns of gene loss in different lineages that are associated with the variation in dentition observed across the clades. These patterns of gene loss suggest that regressive evolution took place both gradually and in relatively rapid, discrete phases during the diversification of xenarthrans. This study underscores the utility of using pseudogenes to reconstruct evolutionary history of morphological characters when fossils are sparse.


Emerling CA, Gibb GC, Tilak M-K, Hughes JJ, Kuch M, Duggan AT, Poinar HN, Nachman MW, Delsuc F. 2023. Genomic data suggest parallel dental vestigialization within the xenarthran radiation. bioRxiv, 2022.12.09.519446, ver 2, peer-reviewed and recommended by PCI Genomics.

Emerling CA, Springer MS. 2014. Eyes underground: Regression of visual protein networks in subterranean mammals. Molecular Phylogenetics and Evolution 78: 260-270.

Meredith RW, Zhang G, Gilbert MTP, Jarvis ED, Springer MS. 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346: 1254390.

Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff J-N, Cabau C, Klopp C, et al. 2021. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution 38: 589-605.

Vizcaíno SF. 2009. The teeth of the “toothless”: novelties and key innovations in the evolution of xenarthrans (Mammalia, Xenarthra). Paleobiology 35: 343-366.

Genomic data suggest parallel dental vestigialization within the xenarthran radiationChristopher A Emerling, Gillian C Gibb, Marie-Ka Tilak, Jonathan J Hughes, Melanie Kuch, Ana T Duggan, Hendrik N Poinar, Michael W Nachman, Frederic Delsuc<p style="text-align: justify;">The recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. As such, the analysis of gene degradati...Evolutionary genomics, VertebratesDidier Casane2022-12-12 16:01:57 View
25 Nov 2022
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Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistance

Apples and pears: two closely related species with differences in scab nonhost resistance

Recommended by based on reviews by 3 anonymous reviewers

Nonhost resistance is a common form of disease resistance exhibited by plants against microorganisms that are pathogenic to other plant species [1]. Apples and pears are two closely related species belonging to Rosaceae family, both affected by scab disease caused by fungal pathogens in the Venturia genus. These pathogens appear to be highly host-specific. While apples are nonhosts for Venturia pyrina, pears are nonhosts for Venturia inaequalis. To date, the molecular bases of scab nonhost resistance in apple and pear have not been elucidated.

This preprint by Vergne, et al (2022) [2] analyzed nonhost resistance symptoms in apple/V. pyrina and pear/V. inaequalis interactions as well as their transcriptomic responses. Interestingly, the author demonstrated that the nonhost apple/V. pyrina interaction was almost symptomless while hypersensitive reactions were observed for pear/V. inaequalis interaction. The transcriptomic analyses also revealed a number of differentially expressed genes (DEGs) that corresponded to the severity of the interactions, with very few DEGs observed during the apple/V. pyrina interaction and a much higher number of DEGs during the pear/V. inaequalis interaction.

This type of reciprocal host-pathogen interaction study is valuable in gaining new insights into how plants interact with microorganisms that are potential pathogens in related species. A few processes appeared to be involved in the pear resistance against the nonhost pathogen V. inaequalis at the transcriptomic level, such as stomata closure, modification of cell wall and production of secondary metabolites as well as phenylpropanoids. Based on the transcriptomics changes during the nonhost interaction, the author compared the responses to those of host-pathogen interactions and revealed some interesting findings. They proposed a series of cascading effects in pear induced by the presence of V. inaequalis, which I believe helps shed some light on the basic mechanism for nonhost resistance.

I am recommending this study because it provides valuable information that will strengthen our understanding of nonhost resistance in the Rosaceae family and other plant species. The knowledge gained here may be applied to genetically engineer plants for a broader resistance against a number of pathogens in the future.​


1. Senthil-Kumar M, Mysore KS (2013) Nonhost Resistance Against Bacterial Pathogens: Retrospectives and Prospects. Annual Review of Phytopathology, 51, 407–427.

2. Vergne E, Chevreau E, Ravon E, Gaillard S, Pelletier S, Bahut M, Perchepied L (2022) Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistance. bioRxiv, 2021.06.01.446506, ver. 4 peer-reviewed and recommended by Peer Community in Genomics.

Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistanceE. Vergne, E. Chevreau, E. Ravon, S. Gaillard, S. Pelletier, M. Bahut, L. Perchepied<p style="text-align: justify;"><strong>Background. </strong>Nonhost resistance is the outcome of most plant/pathogen interactions, but it has rarely been described in Rosaceous fruit species. Apple (<em>Malus x domestica</em> Borkh.) have a nonho...Functional genomics, PlantsWirulda Pootakham Jessica Soyer, Anonymous2022-05-13 15:06:08 View
22 May 2023
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Genetic bases of resistance to the rice hoja blanca disease deciphered by a QTL approach

Scoring symptoms of a plant viral disease

Recommended by based on reviews by Grégoire Aubert and Valérie Geffroy

The paper from Silva et al. (2023) provides new insights into the genetic bases of natural resistance of rice to the Rice Hoja Blanca (RHB) disease, one of its most serious diseases in tropical countries of the American continent and the Caribbean. This disease is caused by the Rice Hoja Blanca Virus, or RHBV, the vector of which is the planthopper insect Tagosodes orizicolus Müir. It is responsible for serious damage to the rice crop (Morales and Jennings 2010). The authors take a Quantitative Trait Loci (QTL) detection approach to find genomic regions statistically associated with the resistant phenotype. To this aim, they use four resistant x susceptible crosses (the susceptible parent being the same in all four crosses) to maximize the chances to find new QTLs. The F2 populations derived from the crosses are genotyped using Single Nucleotide Polymorphisms (SNPs) extracted from whole-genome sequencing (WGS) data of the resistant parents, and the F3 families derived from the F2 individuals are scored for disease symptoms. For this, they use a computer-aided image analysis protocol that they designed so they can estimate the severity of the damages in the plant. They find several new QTLs, some being apparently more associated with disease severity, others with disease incidence. They also find that a previously identified QTL of Oryza sativa ssp. japonica origin is also present in the indica cluster (Romero et al. 2014). Finally, they discuss the candidate genes that could underlie the QTLs and provide a simple model for resistance.

It has to be noted that scoring symptoms of a viral disease such as RHB is very challenging. It requires maintaining populations of viruliferous insect vectors, mastering times and conditions for infestation by nymphs, and precise symptom scoring. It also requires the preparation of segregating populations, their genotyping with enough genetic markers, and mastering QTL detection methods. All these aspects are present in this work. In particular, the phenotyping of symptom severity implemented using computer-aided image processing represents an impressive, enormous amount of work.

From the genomics side, the fine-scale genotyping is based on the WGS of the parental lines (resistant and susceptible), followed by the application of suitable bioinformatic tools for SNP extraction and primers prediction that can be used on their Fluidigm platform. It also required implementing data correction algorithms to achieve precise genetic maps in the four crosses. The QTL detection itself required careful statistical pre-processing of phenotypic data. The authors then used a combination of several QTL detection methods, including an original meta-QTL method they developed in the software MapDisto. 

The authors then perform a very complete and convincing analysis of candidate genes, which includes genes already identified for a similar disease (RSV) on chromosome 11 of rice. What remains to elucidate is whether the candidate genes are actually involved or not in the disease resistance process. The team has already started implementing gene knockout strategies to study some of them in more detail. It will be interesting to see whether those genes act against the virus itself, or against the insect vector. 

Overall the work is of high quality and represents an important advance in the knowledge of disease resistance. In addition, it has many implications for crop breeding, allowing the setup of large-scale, marker-assisted strategies, for new resistant elite varieties of rice.


Morales F and Jennings P (2010) Rice hoja blanca: a complex plant-virus-vector pathosystem. CAB Reviews.

Romero LE, Lozano I, Garavito A, et al (2014) Major QTLs control resistance to Rice hoja blanca virus and its vector Tagosodes orizicolus. G3 | Genes, Genomes, Genetics 4:133–142.

Silva A, Montoya ME, Quintero C, Cuasquer J, Tohme J, Graterol E, Cruz M, Lorieux M (2023) Genetic bases of resistance to the rice hoja blanca disease deciphered by a QTL approach. bioRxiv, 2022.11.07.515427, ver. 2 peer-reviewed and recommended by Peer Community in Genomics

Genetic bases of resistance to the rice hoja blanca disease deciphered by a QTL approachAlexander Silva, Maria Elker Montoya, Constanza Quintero, Juan Cuasquer, Joe Tohme, Eduardo Graterol, Maribel Cruz, Mathias Lorieux<p style="text-align: justify;">Rice hoja blanca (RHB) is one of the most serious diseases in rice growing areas in tropical Americas. Its causal agent is Rice hoja blanca virus (RHBV), transmitted by the planthopper <em>Tagosodes orizicolus </em>...Functional genomics, PlantsOlivier Panaud2022-11-09 09:13:30 View
15 Dec 2022
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Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs

Exploring genomic determinants of host specialization in Botrytis cinerea

Recommended by based on reviews by Cecile Lorrain and Thorsten Langner

The genomics era has pushed forward our understanding of fungal biology. Much progress has been made in unraveling new gene functions and pathways, as well as the evolution or adaptation of fungi to their hosts or environments through population studies (Hartmann et al. 2019; Gladieux et al. 2018). Closing gaps more systematically in draft genomes using the most recent long-read technologies now seems the new standard, even with fungal species presenting complex genome structures (e.g. large and highly repetitive dikaryotic genomes; Duan et al. 2022). Understanding the genomic dynamics underlying host specialization in phytopathogenic fungi is of utmost importance as it may open new avenues to combat diseases. A strong host specialization is commonly observed for biotrophic and hemi-biotrophic fungal species or for necrotrophic fungi with a narrow host range, whereas necrotrophic fungi with broad host range are considered generalists (Liang and Rollins, 2018; Newman and Derbyshire, 2020). However, some degrees of specialization towards given hosts have been reported in generalist fungi and the underlying mechanisms remain to be determined.

Botrytis cinerea is a polyphagous necrotrophic phytopathogen with a particularly wide host range and it is notably responsible for grey mould disease on many fruits, such as tomato and grapevine. Because of its importance as a plant pathogen, its relatively small genome size and its taxonomical position, it has been targeted for early genome sequencing and a first reference genome was provided in 2011 (Amselem et al. 2011). Other genomes were subsequently sequenced for other strains, and most importantly a gapless assembled version of the initial reference genome B05.10 was provided to the community (van Kan et al. 2017). This genomic resource has supported advances in various aspects of the biology of B. cinerea such as the production of specialized metabolites, which plays an important role in host-plant colonization, or more recently in the production of small RNAs which interfere with the host immune system, representing a new class of non-proteinaceous virulence effectors (Dalmais et al. 2011; Weiberg et al. 2013).

In the present study, Simon et al. (2022) use PacBio long-read sequencing for Sl3 and Vv3 strains, which represent genetic clusters in B. cinerea populations found on tomato and grapevine. The authors combined these complete and high-quality genome assemblies with the B05.10 reference genome and population sequencing data to perform a comparative genomic analysis of specialization towards the two host plants. Transposable elements generate genomic diversity due to their mobile and repetitive nature and they are of utmost importance in the evolution of fungi as they deeply reshape the genomic landscape (Lorrain et al. 2021). Accessory chromosomes are also known drivers of adaptation in fungi (Möller and Stukenbrock, 2017). Here, the authors identify several genomic features such as the presence of different sets of accessory chromosomes, the presence of differentiated repertoires of transposable elements, as well as related small RNAs in the tomato and grapevine populations, all of which may be involved in host specialization. Whereas core chromosomes are highly syntenic between strains, an accessory chromosome validated by pulse-field electrophoresis is specific of the strains isolated from grapevine. Particularly, they show that two particular retrotransposons are discriminant between the strains and that they allow the production of small RNAs that may act as effectors. The discriminant accessory chromosome of the Vv3 strain harbors one of the unraveled retrotransposons as well as new genes of yet unidentified function.

I recommend this article because it perfectly illustrates how efforts put into generating reference genomic sequences of higher quality can lead to new discoveries and allow to build strong hypotheses about biology and evolution in fungi. Also, the study combines an up-to-date genomics approach with a classical methodology such as pulse-field electrophoresis to validate the presence of accessory chromosomes. A major input of this investigation of the genomic determinants of B. cinerea is that it provides solid hints for further analysis of host-specialization at the population level in a broad-scale phytopathogenic fungus.


Amselem J, Cuomo CA, Kan JAL van, Viaud M, Benito EP, Couloux A, Coutinho PM, Vries RP de, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier J-M, Quévillon E, Sharon A, Simon A, Have A ten, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Silva CD, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun M-H, Dickman M (2011) Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLOS Genetics, 7, e1002230.

Dalmais B, Schumacher J, Moraga J, Le Pêcheur P, Tudzynski B, Collado IG, Viaud M (2011) The Botrytis cinerea phytotoxin botcinic acid requires two polyketide synthases for production and has a redundant role in virulence with botrydial. Molecular Plant Pathology, 12, 564–579.

Duan H, Jones AW, Hewitt T, Mackenzie A, Hu Y, Sharp A, Lewis D, Mago R, Upadhyaya NM, Rathjen JP, Stone EA, Schwessinger B, Figueroa M, Dodds PN, Periyannan S, Sperschneider J (2022) Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biology, 23, 84.

Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun M-H, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E (2018) Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio, 9, e01219-17.

Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annual Review of Phytopathology, 57, 431–457.

Liang X, Rollins JA (2018) Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum. Phytopathology®, 108, 1128–1140.

Lorrain C, Oggenfuss U, Croll D, Duplessis S, Stukenbrock E (2021) Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation. In: Encyclopedia of Mycology (eds Zaragoza Ó, Casadevall A), pp. 142–155. Elsevier, Oxford.

Möller M, Stukenbrock EH (2017) Evolution and genome architecture in fungal plant pathogens. Nature Reviews Microbiology, 15, 756–771.

Newman TE, Derbyshire MC (2020) The Evolutionary and Molecular Features of Broad Host-Range Necrotrophy in Plant Pathogenic Fungi. Frontiers in Plant Science, 11.

Simon A, Mercier A, Gladieux P, Poinssot B, Walker A-S, Viaud M (2022) Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs. bioRxiv, 2022.03.07.483234, ver. 4 peer-reviewed and recommended by Peer Community in Genomics.

Van Kan JAL, Stassen JHM, Mosbach A, Van Der Lee TAJ, Faino L, Farmer AD, Papasotiriou DG, Zhou S, Seidl MF, Cottam E, Edel D, Hahn M, Schwartz DC, Dietrich RA, Widdison S, Scalliet G (2017) A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18, 75–89.

Weiberg A, Wang M, Lin F-M, Zhao H, Zhang Z, Kaloshian I, Huang H-D, Jin H (2013) Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways. Science, 342, 118–123.

Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAsAdeline Simon, Alex Mercier, Pierre Gladieux, Benoit Poinssot, Anne-Sophie Walker, Muriel Viaud<p style="text-align: justify;">The fungus <em>Botrytis cinerea</em> is a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have...Fungi, Structural genomics, Viruses and transposable elementsSebastien Duplessis Cecile Lorrain, Thorsten Langner2022-03-15 11:15:48 View
10 Jul 2023
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SNP discovery by exome capture and resequencing in a pea genetic resource collection

The value of a large Pisum SNP dataset

Recommended by based on reviews by Rui Borges and 1 anonymous reviewer

One important goal of modern genetics is to establish functional associations between genotype and phenotype. Single nucleotide polymorphisms (SNPs) are numerous and widely distributed in the genome and can be obtained from nucleic acid sequencing (1). SNPs allow for the investigation of genetic diversity, which is critical for increasing crop resilience to the challenges posed by global climate change. The associations between SNPs and phenotypes can be captured in genome-wide association studies. SNPs can also be used in combination with machine learning, which is becoming more popular for predicting complex phenotypic traits like yield and biotic and abiotic stress tolerance from genotypic data (2). The availability of many SNP datasets is important in machine learning predictions because this approach requires big data to build a comprehensive model of the association between genotype and phenotype.

Aubert and colleagues have studied, as part of the PeaMUST project, the genetic diversity of 240 Pisum accessions (3). They sequenced exome-enriched genomic libraries, a technique that enables the identification of high-density, high-quality SNPs at a low cost (4). This technique involves capturing and sequencing only the exonic regions of the genome, which are the protein-coding regions. A total of 2,285,342 SNPs were obtained in this study. The analysis of these SNPs with the annotations of the genome sequence of one of the studied pea accessions (5) identified a number of SNPs that could have an impact on gene activity. Additional analyses revealed 647,220 SNPs that were unique to individual pea accessions, which might contribute to the fitness and diversity of accessions in different habitats. Phylogenetic and clustering analyses demonstrated that the SNPs could distinguish Pisum germplasms based on their agronomic and evolutionary histories. These results point out the power of selected SNPs as markers for identifying Pisum individuals.

Overall, this study found high-quality SNPs that are meaningful in a biological context. This dataset was derived from a large set of germplasm and is thus particularly useful for studying genotype-phenotype associations, as well as the diversity within Pisum species. These SNPs could also be used in breeding programs to develop new pea varieties that are resilient to abiotic and biotic stressors.  


1.         Fallah M, Jean M, Boucher St-Amour VT, O’Donoughue L, Belzile F. The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing. Genome. 2022 Aug;65(8):413–25.

2.         Gill M, Anderson R, Hu H, Bennamoun M, Petereit J, Valliyodan B, et al. Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction. BMC Plant Biology. 2022 Apr 8;22(1):180.

3.         Aubert G, Kreplak J, Leveugle M, Duborjal H, Klein A, Boucherot K, et al. SNP discovery by exome capture and resequencing in a pea genetic resource collection., biorxiv, ver. 4, peer-reviewed and recommended by Peer Community in Genomics. 

4.         Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M. Exome sequencing: current and future perspectives. G3 Genes|Genomes|Genetics. 2015 Aug 1;5(8):1543–50.

5.         Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, et al. A reference genome for pea provides insight into legume genome evolution. Nat Genet. 2019 Sep;51(9):1411–22.

SNP discovery by exome capture and resequencing in a pea genetic resource collectionG. Aubert, J. Kreplak, M. Leveugle, H. Duborjal, A. Klein, K. Boucherot, E. Vieille, M. Chabert-Martinello, C. Cruaud, V. Bourion, I. Lejeune-Hénaut, M.L. Pilet-Nayel, Y. Bouchenak-Khelladi, N. Francillonne, N. Tayeh, J.P. Pichon, N. Rivière, J. B...<p style="text-align: justify;"><strong>Background &amp; Summary</strong></p> <p style="text-align: justify;">In addition to being the model plant used by Mendel to establish genetic laws, pea (<em>Pisum sativum</em> L., 2n=14) is a major pulse c...Plants, Population genomicsWanapinun Nawae2022-11-29 09:29:06 View