Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high‐density, high‐resolution consensus genetic map

Tayeh, Nadim; Aluome, Christelle; Falque, Matthieu; Jacquin, Françoise; Klein, Anthony; Chauveau, Aurélie; Berard, Aurélie; Houtin, Hervé; Rond, Céline; Kreplak, Jonathan; Boucherot, Karen; Martin, Chantal; Baranger, Alain; Pilet‐Nayel, Marie‐Laure; Warkentin, Thomas D.; Brunel, Dominique; Marget, Pascal; Paslier, Marie‐Christine Le; Aubert, Grégoire; Burstin, Judith

doi:10.1111/tpj.13070

Cited by 94 publications

(187 citation statements)

References 76 publications

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“…1D). M. truncatula is a sequenced legume closely related to pea, and their genomes are collinear in this region (Tayeh et al, 2015). Reciprocal BLASTn searches of the M. truncatula genome (v4) and pea transcriptome databases showed that Crd is most similar to Med1g011630; they likely represent an orthologous pair.…”

Section: Resultsmentioning

confidence: 99%

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Linking Auxin with Photosynthetic Rate via Leaf Venation

McAdam

Eléouët

Best³

et al. 2017

Plant Physiol.

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Land plants lose vast quantities of water to the atmosphere during photosynthetic gas exchange. In angiosperms, a complex network of veins irrigates the leaf, and it is widely held that the density and placement of these veins determines maximum leaf hydraulic capacity and thus maximum photosynthetic rate. This theory is largely based on interspecific comparisons and has never been tested using vein mutants to examine the specific impact of leaf vein morphology on plant water relations. Here we characterize mutants at the Crispoid (Crd) locus in pea (Pisum sativum), which have altered auxin homeostasis and activity in developing leaves, as well as reduced leaf vein density and aberrant placement of free-ending veinlets. This altered vein phenotype in crd mutant plants results in a significant reduction in leaf hydraulic conductance and leaf gas exchange. We find Crispoid to be a member of the YUCCA family of auxin biosynthetic genes. Our results link auxin biosynthesis with maximum photosynthetic rate through leaf venation and substantiate the theory that an increase in the density of leaf veins coupled with their efficient placement can drive increases in leaf photosynthetic capacity.

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Section: Resultsmentioning

confidence: 99%

“…Nat Protoc 1: 2320-2325 Alves-Carvalho S, Aubert G, Carrère S, Cruaud C, Brochot A-L, Jacquin F, Klein A, Martin C, Boucherot K, Kreplak J, et al (2015) Full-length de…”

Section: Acknowledgmentsmentioning

confidence: 99%

Linking Auxin with Photosynthetic Rate via Leaf Venation

McAdam

Eléouët

Best³

et al. 2017

Plant Physiol.

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“…The advent of high-throughput next-generation sequencing (NGS) technologies with the possibility to sequence entire genomes more efficiently allowed to obtain large-scale SNP identification for crops and the onset of efficiency SNP genotyping platform (Schmid et al 2003;Dereeper et al 2011;Chagné et al 2012;Ganal et al 2012;Peace et al 2012;Verde et al 2012;Gardner et al 2014;Yu et al 2014;Tayeh et al 2015;Jiang et al 2016;Melo et al 2016). The abundance in the genome and the ability to identify polymorphism due to variation at single base level based on bi-allelic nature are the main advantages of SNP markers.…”

Section: Introductionmentioning

confidence: 99%

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Mercati

Lorenzis

Brancadoro

et al. 2016

Tree Genetics & Genomes

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The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne et du Vin (OIV) descriptors and a high-throughput single nucleotide polymorphism (SNP) genotyping array (Vitis18kSNP) were applied to assess genetic variability among cultivars and biotypes of the same cultivar. Ampelographic traits and high-throughput SNP genotyping platforms provided an accuracy estimation of genetic diversity in the Sicilian germplasm, showing the relationships among cultivars by cluster and multivariate analyses. The large SNP panel defined sub-clusters unable to discern among biotypes, previously classified by ampelographic analysis, belonging to each cultivar. These results suggested that a very large number of SNP did not cover the genome regions harboring few morphological traits. Genetic structure of the collection revealed a clear optimum number of groups for K = 3, clustering in the same group a significant portion of family-related genotypes. Parentage analysis highlighted significant relationships among Sicilian grape cultivars and Sangiovese, as already reported, but also the first evidences of the relationships between Nero d'Avola and both Inzolia and Catarratto. Finally, a small panel of highly informative markers (12 SNPs) allowed us to isolate a private profile for each Sicilian cultivar, providing a new tool for cultivar identification.

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“…Our knowledge of plant transformation, plant genome evolution and breeding has increased dramatically in the past decades. We now know that breeding and mutagenesis are more unpredictable and cause more genome disruption than genetic engineering [10][11][12][13]. For instance, the comparison of genomic variation in transgenic plants to the genomic variation observed in cultivars and mutagenized lines revealed that, on average, the number of genes affected by structural variations in transgenics was one order of magnitude lower than that of fast neutron mutants and two orders of magnitude lower than between cultivars [10].…”

Section: The Compatibility Of Innovative Breeding Technologies With Omentioning

confidence: 99%

“…We believe it is time to reconsider this issue in the light of new insights on genomic dynamics during breeding and evolution obtained from the many genome sequencing data from the past decade [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Why Organic Farming Should Embrace Co-Existence with Cisgenic Late Blight–Resistant Potato

Gheysen

Custers²

2017

Sustainability

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Abstract:The EU regulation on organic farming does not allow the use of genetically modified organisms (GMOs) which are subject to Directive 2001/18/EC. Mutagenesis using irradiation or chemicals is genetic modification, but the organisms obtained through these techniques are not subject to the provisions of the GMO directive. Such mutants can therefore be used in organic agriculture. Derived from its basic principles, organic farming can only use natural substances to control disease and crops should be resilient, which, in the case of disease resistance, means that durable (horizontal) resistance is preferred to vertical (single gene) resistance. Cisgenesis can achieve such a durable resistance by introducing multiple resistance genes in one step. These multiple-resistant plants only contain natural genes that can also be introduced by breeding. In case cisgenic plants are not subject to the provisions of the GMO legislation, they can even be legally used in organic agriculture. In case they are not exempted from the GMO regulation, the question is: why obstruct a cisgenic potato crop that can hardly be distinguished from a potato crop that is the result of conventional breeding? Among the reasons why organic agriculture does not allow the use of GMOs it is mentioned that genetic engineering is unpredictable, it causes genome disruption and it is unnatural. However, our knowledge of plant genome evolution and breeding has increased dramatically. We now know that breeding is more unpredictable and causes more genome disruption than genetic engineering. Recent field trials have shown the efficacy of cisgenic late blight-resistant potatoes carrying multiple resistance genes. Large-scale growing of such durably resistant potatoes would not only be environmentally beneficial by it would strongly reducing the need for fungicide sprays in conventional potato cultivation and it would also reduce the disease pressure in organic potato cultivation.

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Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high‐density, high‐resolution consensus genetic map

Cited by 94 publications

References 76 publications

Linking Auxin with Photosynthetic Rate via Leaf Venation

Linking Auxin with Photosynthetic Rate via Leaf Venation

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Why Organic Farming Should Embrace Co-Existence with Cisgenic Late Blight–Resistant Potato

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