Harnessing landrace diversity empowers wheat breeding

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium (LD) based haplotypes and association genetics analyses link Watkins genomes to the thousands of high-resolution quantitative trait loci (QTL), and significant marker-trait associations identified. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.</p

Origin and evolution of the bread wheat D genome

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement

Harnessing landrace diversity empowers wheat breeding

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker–trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security

Evolutionary, genetic, environmental and hormonal-induced plasticity in the fate of organs arising from axillary meristems in Passiflora spp.

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Tendrils can be found in different plant species. In legumes such as pea, tendrils are modified leaves produced by the vegetative meristem but in the grape vine, a same meristem is used to either form a tendril or an inflorescence. Passiflora species originated in ecosystems in which there is dense vegetation and competition for light. Thus climbing on other plants in order to reach regions with higher light using tendrils is an adaptive advantage. In Passiflora species, after a juvenile phase, every leaf has a subtending vegetative meristem, and a separate meristem that forms both flowers and a tendril. Thus, flowers are formed once a tendril is formed yet whether or not this flower will reach bloom depends on the environment. For example, in Passiflora edulis flowers do not develop under shaded conditions, so that tendrils are needed to bring the plant to positions were flowers can develop. This separate meristem generally forms a single tendril in different Passiflora species yet the number and position of flowers formed from the same meristem diverges among species. Here we display the variation among species as well as variation within a single species, P. edulis. We also show that the number of flowers within a specific genotype can be modulated by applying Cytokinins. Finally, this separate meristem is capable of transforming into a leaf-producing meristem under specific environmental conditions. Thus, behind what appears to be a species-specific rigid program regarding the fate of this meristem, our study helps to reveal a plasticity normally restrained by genetic, hormonal and environmental constraints. (c) 2012 Elsevier Ireland Ltd. All rights reserved.13016169Israeli Ministry of AgricultureIsrael Science FoundationGerman Israeli Project CooperationFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Evolutionary, Genetic, Environmental And Hormonal-induced Plasticity In The Fate Of Organs Arising From Axillary Meristems In Passiflora Spp.

Tendrils can be found in different plant species. In legumes such as pea, tendrils are modified leaves produced by the vegetative meristem but in the grape vine, a same meristem is used to either form a tendril or an inflorescence. Passiflora species originated in ecosystems in which there is dense vegetation and competition for light. Thus climbing on other plants in order to reach regions with higher light using tendrils is an adaptive advantage. In Passiflora species, after a juvenile phase, every leaf has a subtending vegetative meristem, and a separate meristem that forms both flowers and a tendril. Thus, flowers are formed once a tendril is formed yet whether or not this flower will reach bloom depends on the environment. For example, in Passiflora edulis flowers do not develop under shaded conditions, so that tendrils are needed to bring the plant to positions were flowers can develop. This separate meristem generally forms a single tendril in different Passiflora species yet the number and position of flowers formed from the same meristem diverges among species. Here we display the variation among species as well as variation within a single species, P. edulis. We also show that the number of flowers within a specific genotype can be modulated by applying Cytokinins. Finally, this separate meristem is capable of transforming into a leaf-producing meristem under specific environmental conditions. Thus, behind what appears to be a species-specific rigid program regarding the fate of this meristem, our study helps to reveal a plasticity normally restrained by genetic, hormonal and environmental constraints. © 2012 Elsevier Ireland Ltd.13016169Aizza, L.C., Dornelas, M.C., A genomic approach to study anthocyanin synthesis and flower pigmentation in passionflowers (2011) J. Nucleic Acids, 2011, p. 371517Akamine, E.K., Girolami, G., Pollination and fruit set in the yellow passion fruit (1959) Hawaii Agr. Expt. Sta. Bul., 39, pp. 1-44Barton, M.K., Twenty years on: the inner workings of the shoot apical meristem, a developmental dynamo (2010) Dev Biol., 341, pp. 95-113Benlloch, R., Berbel, A., Serrano-Mislata, A., Madueño, F., Floral initiation and inflorescence architecture: a comparative view (2007) Ann. Bot., 100, pp. 659-676Calonje, M., Cubas, P., Martínez-Zapater, J.M., Carmona, M.J., Floral meristem identity genes are expressed during tendril development in grapevine (2004) Plant Physiol., 135, pp. 1491-1501Cervi, A.C., Rodrigues, W.A., Nomenclatural and taxonomic review of Passifloraceae species illustrated and described by Vellozo in Flora Fluminensis (2010) Acta Bot. Bras., 24, pp. 1109-1111Cusset, G., Les vrilles des Passifloracées (1968) Bull. Soc. Bot. France, 115, pp. 45-61Gourlay, C.W., Hofer, J.M., Ellis, T.H., Pea compound leaf architecture is regulated by interactions among the genes UNIFOLIATA, cochleata, afila, and tendril-less (2000) Plant Cell, 12, pp. 1279-1294Hansen, A.K., Gilbert, L.E., Simpson, B.B., Downie, S.R., Cervi, A.C., Jansen, R.K., Phylogenetic relationships and chromosome number evolution in Passiflora (2006) Syst. Bot., 31, pp. 138-150Krosnick, S.E., Freudenstein, J.V., Monophyly and floral character homology of Old World Passiflora (subgenus Decaloba: Supersection Disemma) (2005) Syst. Bot., 30, pp. 139-152Mader, G., Zamberlan, P.M., FAgundes, N.J., Magnus, T., Salzano, F.M., Bonatto, S.L., Freitas, L.B., (2010), pp. 99-108. , The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae). Gen. Mol. Biol. 33Menzel, C.M., Simpson, D.R., (1994), 2, pp. 225-242. , Passionfruit. In Schaffer, B., Andersen, P.C. (Eds.), Handbook of Environmental Physiology of Fruit Crops vol. , CRC Press, Boca Raton, ppMoncur, M.W., (1988), Floral Development of Tropical and Subtropical Fruit and Nut Species. An Atlas of Scanning Electron Micrographs. CSIRO, CanberraMuschner, V.C., Lorenz, A.P., Cervi, A.C., Bonatto, S.L., Souza-Chies, T.T., Salzano, F.M., Freitas, L.B., A first molecular phylogenetic analysis of Passiflora (Passifloraceae) (2003) Am. J. Bot., 90, pp. 1229-1238Nave, N., Katz, E., Chayut, N., Gazit, S., Samach, A., Flower development in the passion fruit Passiflora edulis requires a photoperiod-induced systemic graft-transmissible signal (2010) Plant Cell. Environ., 33, pp. 2065-2083Okada, K., Ueda, J., Komaki, M.K., Bell, C.J., Shimura, Y., Requirement of the auxin polar transport system in early stages of Arabidopsis floral bud formation (1991) Plant Cell, 3, pp. 677-684Pope, W.T., The edible passionfruit in Hawaii (1935) Hawaii Agr. Expt. Sta. Bul., 74, pp. 1-22São-José, A.R., (1991), A cultura do maracujá no Brasil, UNESP-FUNEP, JaboticabalUlmer, T., MacDougal, J.M., (2004) Passiflora: Passionflowers of the World, , Timber Press, PortlandWang, Y., Li, J., Molecular basis of plant architecture (2008) Ann. Rev. Plant Biol., 59, pp. 253-279Whipple, C.J., Hall, D.H., DeBlasio, S., Taguchi-Shiobara, F., Schmidt, R.J., Jackson, D.P., A conserved mechanism of bract suppression in the grass family (2010) Plant Cell, 22, pp. 565-578Yotoko, K.S., Dornelas, M.C., Togni, P.D., Fonseca, T.C., Salzano, F.M., Bonatto, S.L., Freitas, L.B., Does variation in genome sizes reflect adaptive or neutral processes? New clues from Passiflora (2011) PLoS One, 6, pp. e1821

MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat

Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.Laura E. Dixon, Marianna Pasquariello, Roshani Badgami, Kara A. Levin, Gernot Poschet, Pei Qin Ng, Simon Orford, Noam Chayut, Nikolai M. Adamski, Jemima Brinton, James Simmonds, Burkhard Steuernagel, Iain R. Searle, Cristobal Uauy, Scott A. Bode

MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat

Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain

Recombinant inbred lines derived from wide crosses in Pisum

International audienceGenomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits. Recombinant inbred lines (RILs) were first developed for mouse genetics 1 but are widely used in plant genetics where self-fertilization makes their development relatively straightforward. RILs capture genetic variation in a stable way. As inbred lines they are amenable to multiple investigations, such as replicated measurement or the accumulation of data over time. There are two disadvantages to RILs: they do not capture information about dominance unless this is recorded in early generations and they segregate only for the alleles that distinguish the two parents. The latter disadvantage is overcome by linkage disequilibrium mapping methods such as Multi-parent Advanced Generation Inter-Cross (MAGIC) populations 2 , Nested Association Mapping (NAM) 3 which, together with Genome-Wide Association Studies (GWAS), enable analyses of diverse populations 4 and can capture the contribution of multiple alleles. Nevertheless, sufficiently large RIL populations can provide a high degree of resolution in genetic mapping and, when the parents are sufficiently divergent, RILs can capture many bi-allelic differences. Here we present a preliminary analysis of two RIL populations derived from two wide crosses in Pisum. A wide cross within P. sativum sativum is represented by RILs derived from the cross between cv Caméor (a French field pea variety, also designated JI3253) and JI0281 (a P. s. sativum accession from Ethiopia, designated 'P. sativum landrace DCG0248' in Kreplak et al. 5). The second is an inter-specific or inter-subspecific cross. One parent of this second wide cross is JI2202 (designated 'P. sativum abyssinicum_Landrace_DCG0563 by Kreplak et al. 5) which represents a closely related group of peas that have been domesticated independently from P. s. sativum 6,7. Sometimes P. s. abyssinicum is regarded as a distinct species rather than a subspecies of P. sativum. The second parent of this population, JI2822, is a genetic stock, a RIL derived from the cross between JI0015 and JI0399, which has been widely used in mutagenesis experiments (see 8 and references therein) or for gene conten