Genomic selection in white lupin

Genomic selection in white lupi

Characterizing the molecular and morphophysiological diversity of Italian red clover

Red clover (Trifolium pratense L.) is the third major forage species in Europe, but there is limited information on the biodiversity and the genetic structure of landraces and natural populations which evolved in this region. The objective of this study was producing such information for Italian germplasm on the ground of molecular and morphophysiological diversity. The study included 16 Italian natural populations from a wide range of environments, four landraces representing the four traditional commercial ecotypes, and two varieties. Eight morphophysiological traits were assessed in a replicated trial under field conditions, whereas two AFLPs primer combinations with 140 polymorphic markers were recorded on a random sample of 13 genotypes per population. Ordination and classification results based on morphophysiological data clearly kept track of the type of germplasm (i.e. landrace or natural population) and its geographic origin, unlike results based on molecular markers. Euclidean distances among populations based on morphophysiological traits were not correlated with Nei’s genetic distances based on molecular markers according to Mantel’s test. Geographical distances among landrace or natural population material was correlated with distances based on morphophysiological traits but not with those based on molecular markers. The average within-population variation stimated via molecular markers was about 2.6-fold higher than that among populations, preventing an acceptable discrimination among most populations. On average, natural populations tended to have within-population variation similar to varieties and somewhat lower than landraces. Our results have implications for collection, conservation, exploitation and registration in a sui generis system of red clover genetic resources.L’articolo è disponibile sul sito dell’editore http://www.springerlink.com

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections - a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding

Detection and exploitation of white lupin (Lupinus albus L.) genetic variation for seed γ-conglutin content

The seed γ-conglutin protein fraction of white lupin has particular pharmacological interest, but its industrial production is hindered by low content in the seed. This study provides an unprecedented assessment of genotypic and environmental variation for seed content and production of γ-conglutin, exploring also the ability of Near-Infrared Spectroscopy (NIRS) to predict seed γ-conglutin content. Significant (P < 0.01) genetic variation for seed γ-conglutin content emerged among ten genotypes (cultivars or breeding lines) across three environments (range: 1.59-2.02 %) and five genotypes in other two environments (range: 1.47-1.80 %). Genotype variation was found also for seed protein content and γ-conglutin proportion on total protein, the latter trait having higher impact than the former on genotype variation for seed γ-conglutin content. The production of γ-conglutin per unit area was affected also by genotype yielding ability beside genotype seed γ-conglutin content. No genotype × environment interaction was detected for any γ-conglutin trait. NIRS-based prediction based on cross-validations was only moderately accurate for seed γ-conglutin content (R2 = 0.66), while being accurate for seed protein content (R2 = 0.95). In conclusion, breeding for higher seed γ-conglutin content is feasible using data from very few test sites and, to some extent, NIRS-based predictions

Alfalfa genomic selection for different stress-prone growing regions

Alfalfa (Medicago sativa L.) selection for stress-prone regions has high priority for sustainable crop–livestock systems. This study assessed the genomic selection (GS) ability to predict alfalfa breeding values for drought-prone agricultural sites of Algeria, Morocco, and Argentina; managed-stress (MS) environments of Italy featuring moderate or intense drought; and one Tunisian site irrigated with moderately saline water. Additional aims were to investigate genotype × environment interaction (GEI) patterns and the effect on GS predictions of three single-nucleotide polymorphism (SNP) calling procedures, 12 statistical models that exclude or incorporate GEI, and allele dosage information. Our study included 127 genotypes from a Mediterranean reference population originated from three geographically contrasting populations, genotyped via genotyping-by-sequencing and phenotyped based on multi-year biomass dry matter yield of their dense-planted half-sib progenies. The GEI was very large, as shown by 27-fold greater additive genetic variance × environment interaction relative to the additive genetic variance and low genetic correlation for progeny yield responses across environments. The predictive ability of GS (using at least 37,969 SNP markers) exceeded 0.20 for moderate MS (representing Italian stress-prone sites) and the sites of Algeria and Argentina while being quite low for the Tunisian site and intense MS. Predictions of GS were complicated by rapid linkage disequilibrium decay. The weighted GBLUP model, GEI incorporation into GS models, and SNP calling based on a mock reference genome exhibited a predictive ability advantage for some environments. Our results support the specific breeding for each target region and suggest a positive role for GS in most regions when considering the challenges associated with phenotypic selection.EEA Santiago del EsteroFil: Annicchiarico, Paolo. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria. Centro di Ricerca Zootecnia e Acquacoltura; ItaliaFil: Nazzicari, Nelson. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria. Centro di Ricerca Zootecnia e Acquacoltura; ItaliaFil: Bouizgaren, Abdelaziz. Institut National de la Recherche Agronomique du Maroc. Centres Régionaux de Marrakech et de Rabat; MarruecosFil: Hayek, Taoufik. Institut des Régions Arides de Médenine; TunezFil: Laouar, Meriem. Ecole Nationale Supérieure Agronomique. Dép. de Productions Végétales. Laboratoire d’Amélioration Intégrative des Productions Végétales; ArgeliaFil: Cornacchione, Monica. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santiago del Estero; ArgentinaFil: Basigalup, Daniel Horacio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi. Grupo de Mejoramiento Genético de Alfalfa; ArgentinaFil: Monterrubio Martin, Cristina. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria. Centro di Ricerca Zootecnia e Acquacoltura; ItaliaFil: Brummer, E. Charles. University of California at Davies. Depeparment of Plant Sciences. Plant Breeding Center,; Estados UnidosFil: Pecetti, Luciano. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria. Centro di Ricerca Zootecnia e Acquacoltura; Itali

Broadening and exploiting the genetic base of white lupin

White lupin is a European crop with a long history of domestication and high potential interest for high-protein food or feedstuff. This report aims to summarize the research steps that were undertaken to (i) verify the extent of genetic diversity exploited by modern breeding, (ii) identify elite bitter-seed landraces and sweet-seed germplasm aimed to broaden the genetic base for European breeding, (iii) assess the genetic variation for tolerance to key abiotic stresses in the germplasm of the novel genetic base, and (iv) verify the potential of genomic models based on genotyping-bysequencing (GBS) SNP data to select simultaneously and cost-efficiently for some complex traits. Molecular diversity patterns of 83 landraces from nine major historical cropping regions and 15 commercial varieties confirmed that modern plant breeding exploited only a modest part of the crop genetic variation. Germplasm evaluation experiments for adaptation to severe drought or calcareous soil revealed substantial genetic variation (Annicchiarico and Thami-Alami, 2012; Annicchiarico et al., 2018), which, along with other information, was exploited to identify four elite landraces and four elite, sweet-seed lines that acted as parents of a broadly-based population. Some 144 sweet-seed lines extracted from this population were evaluated for grain yield under severe drought in a managed environment of Italy and for adaptation to moderately calcareous soil in a spring-sown environment of the Netherlands and an autumn-sown environment of Greece. We report on the observed line variation for these traits, and on the construction of genomic selection models and their ability to predict the line adaptation to drought or lime soil based on cross validations. Genome-enabled models may be used also to select for tolerance to anthracnose and the sweet-seed trait

Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis—A Role Relevant for Seed Vigor Prediction and Plant Robustness

Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)–stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight readyto- use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction

Genetic mapping of anthracnose resistance in white lupin

White lupin (Lupinus albus) is a valuable grain legume with a high protein content and quality, contributing to soil fertility (Monteiro et al., 2014, Lambers et al., 2013). Its high yield potential could make it a sustainable alternative for imported soybean in Europe (Lucas et al., 2015). However, lupin anthracnose, caused by the air- and soilborne fungus Colletotrichum lupini severely limits cultivation as low levels of seed infestation can already cause total yield loss (Talhinhas et al., 2016). Host resistance is crucial for managing anthracnose but a better insight into the genetic basis is required. We developed a high-throughput phenotyping tool that identifies field-relevant anthracnose resistance under controlled conditions. For inoculation, we identified a local, highly virulent C. lupini strain. Phylogenetic analyses revealed that the strain belongs to a globally dispersed genetic group corresponding to Dubrulle et al.’s (2020) C. lupini group II. Using the developed tool we phenotyped a diverse collection of 200 white lupin accessions, revealing a strong segregation between susceptible and resistant plants, potentially holding novel sources of resistance. Genotyping-bysequencing was performed and the generated single-nucleotide polymorphic markers (SNPs) are currently being used for genetic mapping. Quantitative trait loci (QTLs) for anthracnose resistance will be presented aiding to improve and speed up white lupin breeding programs

Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis—A Role Relevant for Seed Vigor Prediction and Plant Robustness

Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)–stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.</p

Open questions and research needs in the adoption of conservation agriculture in the mediterranean area

This article aims to provide a review of major challenges and research needs for the diffusion of conservation agriculture (CA) and the improvement of crop–soil–water conditions in Southern Europe and Northern Africa. A multidisciplinary study and a participatory approach are at the basis of an international project of research and innovation action, “Research-based participatory approaches for adopting conservation agriculture in the Mediterranean Area-CAMA”. It aims to understand the reasons and the research needs that limit a large CA diffusion in the Mediterranean countries. CAMA aims to provide significant advances to CA through multidisciplinary research at the field and farm scales (with main emphasis on smallholder), encompassing a socio-economic analysis of the reasons that obstacle the CA diffusion, legume crop improvement as a component of improved CA cropping systems, and a network of long-term experiments on CA and soil characteristic modification. Its results will be available to scientific and farming communities.This research received the financial funding by PRIMA (Grant Agreement n. 1912), a programme supported by the European Union, research project “Research-based participatory approaches for adopting Conservation Agriculture in the Mediterranean Area – CAMA”, coord. Dott. Michele Rinaldi. Special thanks to Fabrice Dentressangle, CAMA Project Officer and to “Italian PRIMA Secretariate” office