Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10

La biohydrogénation (BH) ruminale des acides gras polyinsaturés (AGPI) est à l'origine de la production d'intermédiaires trans retrouvés dans les productions de ruminants (essentiellement le lait). Il existe deux voies de BH produisant des acides gras (AG) trans qui auraient des propriétés différentes : les isomères t11 auraient des effets bénéfiques pour la santé des consommateurs et les isomères t10 seraient responsables d'une forte diminution du taux butyreux du lait, représentant une contrainte majeure pour les éleveurs. Dans des conditions physiologiques normales, la voie t11 est fortement majoritaire, par contre avec des rations à base d'ensilage de maïs, riches en concentrés et surtout si elles comprennent des suppléments lipidiques riches en AGPI, une déviation de la voie t11 à la voie t10 peut se produire avec une augmentation significative des isomères t10 au détriment des isomères t11. L'objectif de cette thèse est d'expliquer les modalités de cette déviation, afin de mieux la maîtriser en élevage. Nos travaux permettent de conclure que les facteurs alimentaires de maîtrise de la déviation de la voie t11 vers la voie t10, sont la teneur en amidon rapidement fermentescible et la teneur en c9,c12-C18:2. Lorsque la quantité de c9,c12-C18:2 présente dans le rumen est faible, même avec une ration riche en amidon et un pH bas dans le rumen, la déviation n'a pas lieu, la voie t11 suffisant à assurer l'hydrogénation des AGPI puisque dans ces conditions, la 9 isomérisation est elle aussi peu efficace à pH bas. En revanche, lorsqu'en plus de l'amidon, du c9,c12-C18:2 est ajouté dans la ration, la voie t11 devient insuffisante et c'est la voie t10 qui prend le relais. Le pyroséquençage 454 couplé à une régression multiple SPLS nous ont permis d'établir des corrélations entre les taxons identifiés et la proportion d'AG (t10 ou t11) dans le rumen. Il s'avère que les genres bactériens corrélés fortement et positivement aux AG t10 sont plus ou moins impliqués dans le métabolisme ruminal du lactate ainsi qu'au faible pH ruminal. Cependant, l'identification des taxons les plus corrélés aux AG t11 était moins précise, elle s'arrête à l'ordre des Clostridiales. Enfin, dans des conditions de déviation de la voie t11 à la voie t10, l'addition de vitamine E dans la ration des vaches n'a pas permis de restaurer un ratio déjà élevé. Ces résultats ont abouti à une meilleure compréhension de cette déviation et orientent vers une meilleure maîtrise en élevage.Rumen biohydrogenation (BH) of polyunsaturated fatty acids (PUFA) is responsible of the production of trans intermediates found in ruminant products (mainly milk). There are two BH pathways leading to trans fatty acids (FA) with different biological properties: t11 isomers have beneficial effects for consumer's health and t10 isomers result in low milk fat content, representing a major constraint for farmers. In most conditions, t11 FA are the major trans FA, but in some conditions, especially with diets based on corn silage and including lipid supplements rich in PUFA, a shift from t11 to t10 pathway can occur with a significant increase of t10 isomers at the expense t11 isomers. The objective of this work was to explain modalities of this shift to better control it in animal production. Our results demonstrated that dietary factors responsible of the shift from t11 to t10 pathway are starch rapidly fermentable and c9, c12-C18:2 contents. When the amount of c9, c12-C18:2 present in the rumen is low, even though the diet is rich in starch and the pH is low in the rumen, the shift does not occur, t11 pathway being sufficient to ensure the hydrogenation of PUFA since in these conditions, the 9 isomerization is also poorly effective at low pH. However, when c9, c12-C18:2 is supplemented to the diet in addition to starch, t11 pathway becomes insufficient for FA BH, and t10 pathway becomes dominant. 454 pyrosequencing coupled to a multiple sPLS regression allowed us to establish correlations between some identified taxa and FA proportions (t10 or t11) in the rumen. It appears that bacterial genera that are strongly and positively correlated with t10 FA are more or less involved in the metabolism of ruminal lactate and also positively correlated with a low ruminal pH. However, identification of taxa correlated with t11 FA was less accurate, stopping at Clostridiales order. Finally, once the shift occurred, the subsequent addition of vitamin E was not able to counteract this process. These results lead to a better understanding of this shift to better control it in animal livestock.TOULOUSE-ENSAT-Documentation (315552324) / SudocSudocFranceF

Characterization of faba bean and chickpea viruses causing yellowing and stunting symptoms in Tunisia

In Tunisia, faba bean (Vicia faba) and chickpea (Cicer arietinum) are considered as strategic crops because of their economic and social relevance and significant direct contribution towards the national food balance. However, production levels of these crops remain quite low which is often attributed to abiotic and biotic stresses that are prevailing in the major growing areas. Viruses causing yellowing and stunting symptoms represent one of the major constraints that reduce the genetic potential of most cultivated species and varieties. To characterize these viruses in Tunisia, field surveys were conducted in five main regions (Béja, Bizerte, Cap-Bon, Jendouba and Kef) during 2018 and 2019 growing seasons. A total of 389 faba bean and 182 chickpea samples with yellowing and stunting symptoms were collected and tested by tissue blot immunoassay (TBIA) using specific monoclonal antibodies (MAbs). Laboratory results showed that Chickpea chlorotic stunt virus (CpCSV) was the most common virus detected in 47.6% of faba bean and 18.7% of chickpea tested samples, followed by Beet western yellows virus (BWYV) (28% in faba bean and 4.4% in chickpea). Whereas, only 8.8% of faba bean samples were infected with Faba bean necrotic yellows virus (FBNYV), and Bean leafroll virus (BLRV) in faba bean (6.7%) and chickpea (9%) samples. To confirm the presence of yellowing viruses in Tunisia, total RNA was extracted from 5 faba bean and 27 chickpea samples that showed positive reaction to BLRV MAb (8 samples: 2 faba bean, 6 chickpea), BWYV MAb (7 samples: 2 faba bean, 5 chickpea) and CpCSV MAb (17 samples: 1 faba bean, 16 chickpea). Reverse transcription-polymerase chain reaction (RT-PCR) was performed using specific luteovirus primer pairs. RT-PCR amplicons of the expected size of each primer were obtained from 32 samples and were sequenced in both directions. Molecular results showed that BWYV and CpCSV (both belong to genus Polerovirus, family Solemoviridae) and BLRV (belong to genus Luteovirus, family Tombusviridae) were identified in Tunisia, and the coat protein nucleotide sequence analysis of the Tunisian isolates showed 99% homology to Moroccan isolate (CpCSV), 97% homology to the French isolate (BWYV), and 98% homology to Argentina isolate (BLRV)

Present status of some virus diseases affecting legume crops in Tunisia, and partial characterization of Chickpea chlorotic stunt virus

Field surveys were conducted in Tunisia during the 2005‒2006, 2006‒2007 and 2009‒2010 growing seasons to identify viruses which produce yellowing, reddening and/or stunting symptoms of chickpea, faba bean and pea crops. Tissue blot immunoassay (TBIA) results showed that Chickpea chlorotic stunt virus (CpCSV) was the most common virus, followed by Faba bean necrotic yellows virus, Bean leafroll virus and Beet western yellows virus. The coat protein (CP) gene nucleotide sequence of seven CpCSV isolates collected from different regions of Tunisia was compared with sequences of five other isolates in the NCBI database. A homology tree of the CP nucleotide sequences was prepared and CpCSV isolates were grouped into two clusters. The first group contained two Tunisian CpCSV chickpea isolates collected from Bizerte and Kef; sequenced regions showed a high nucleotiode homology (95%) to that of the Ethiopian and Sudanese CpCSV isolates. The second group included five Tunisian isolates: two from chickpea, two from pea and one from faba bean, which showed a high homology (96%) when compared with the Moroccan, Egyptian and Syrian CpCSV isolates

Viroid infection and rootstocks affect productivity and fruit quality of the Tunisian citrus cultivar Maltaise demi sanguine

In Tunisia, sweet orange citrus cultivars are usually grafted on sour orange rootstock. However, this rootstock is susceptible to Citrus tristeza virus (CTV). A trial was established in 2005 to evaluate the performance of newly introduced rootstocks compared to sour orange, using the sweet orange cultivar ‘Maltaise demi sanguine’ as the grafted scion. The effect of single or mixed viroid infections were monitored over 12 years. Once established, tree growth, cumulative yield, tree performance and fruit quality of ‘Maltaise sweet orange’ were assessed from 2008. Mixed viroid infections caused significant decreases (39 to 60%) in the canopy volume of ‘Maltaise’ grafted on Carrizo citrange, Swingle citrumelo, Cleopatra mandarin, Rangpur lime, Volkamer lemon and Trifoliate orange. The cumulative yield of trees grafted on’Alemow’ (Citrus macrophylla) and inoculated with Hop stunt viroid (HSVd) was 76% less than the healthy control. Mixed infections caused production decreases of 56% from trees grafted on Swingle citrumelo and 69% from those grafeted on Trifoliate orange. When quality parameters of fruit from trees infected with each viroid, and combinations of viroids were compared, no significant differences were recorded.

Viroid infection and rootstocks affect productivity and fruit quality of the Tunisian citrus cultivar Maltaise demi sanguine

In Tunisia, sweet orange citrus cultivars are usually grafted on sour orange rootstock. However, this rootstock is susceptible to Citrus tristeza virus (CTV). A trial was established in 2005 to evaluate the performance of newly introduced rootstocks compared to sour orange, using the sweet orange cultivar ‘Maltaise demi sanguine’ as the grafted scion. The effect of single or mixed viroid infections were monitored over 12 years. Once established, tree growth, cumulative yield, tree performance and fruit quality of ‘Maltaise sweet orange’ were assessed from 2008. Mixed viroid infections caused significant decreases (39 to 60%) in the canopy volume of ‘Maltaise’ grafted on Carrizo citrange, Swingle citrumelo, Cleopatra mandarin, Rangpur lime, Volkamer lemon and Trifoliate orange. The cumulative yield of trees grafted on’Alemow’ (Citrus macrophylla) and inoculated with Hop stunt viroid (HSVd) was 76% less than the healthy control. Mixed infections caused production decreases of 56% from trees grafted on Swingle citrumelo and 69% from those grafeted on Trifoliate orange. When quality parameters of fruit from trees infected with each viroid, and combinations of viroids were compared, no significant differences were recorded.

Incidence and Molecular Characterization of Citrus psorosis virus in Tunisia

In order to study the current situation of Citrus psorosis virus (CPsV) in Tunisia, field surveys were conducted in commercial orchards in Cap Bon region and 575 citrus trees were sampled. As determined by DAS-ELISA, the CPsV incidence in Tunisia was high, and ranged between 20 and 47%, according to geographical location, citrus species and varieties. cDNA encompassing the full-length RNA3 from Tunisian isolates was synthesized by RT-PCR using specific primers and two isolates were cloned and sequenced. Full length sequences of the coat protein (CP) gene were obtained and deposited in GenBank. Based on CP gene sequences, phylogenetic clustering of isolates revealed two populations, one includes isolates from Spain, Morocco and New Zealand and the other includes those from Tunisia, Spain, Italy, Mexico and Egypt. Genetic haplotype network provided evidence of the existence of two distinct clusters with an ambiguous origin. Selective neutrality test was significantly positive, suggesting a balancing selection of CPsV CP gene

Chapter 6 - Barley

Among 30 viruses have been reported on barley, but only few of them are widespread and cause significant economic damage. Among the most important viruses reported to infect barley are BUDVs (such as BYDV-PAV, BYDV-MAV), cereal yellow dwarf virus (CYPV)-RPV, barely yellow striate mosaic virus (BYSMV), and barley stripe mosaic virus (BSMV)

Barley yellow dwarf virus in barley crops in Tunisia: prevalence and molecular characterization

A field survey was conducted in Tunisia in the North-Eastern regions (Bizerte, CapBon and Zaghouan), the North-Western region (Kef) and the Central-Eastern region (Kairouan) during the 2011/2012 growing season, in order to determine the incidence and the geographic distribution of Barley yellow dwarf virus (BYDVs) in barley fields. Tissue blot immunoassays (TBIA) showed that BYDV was most common in Zaghouan (incidence 14%), Cap Bon (14%) and Bizerte (35%), in randomly collected samples from these three locations.Among the different BYDVs identified, BYDV-PAV (64%) was the most common followed by BYDV-MAV (16%) and CYDV-RPV (3%). The coat protein gene sequences of six isolates collected from different regions shared >98% pairwise similarity. In comparisons with other BYDV sequences from around the world, the Tunisian sequences shared greatest homology with isolates 109 and ASL1 from the United States of America and Germany (≈97%), and <90% with all other isolate sequences available in public databases

Epidemiology and management of legume and cereal viruses in Arab and Mediterranean regions

In the Arab and Mediterranean regions, cool-season food legumes (chickpea, faba bean, lentil and pea) are infected naturally by many viruses, and the number of viruses involved continues to increase. However, at any specific location only a few of these pathogens are of economic concern. Yield losses resulting from virus attack vary widely, from little, as in the case of Broad bean mottle virus in Tunisia and Morocco, to complete crop failure when conditions permit widespread virus infection at the vulnerable early plant growth stage, as with Faba bean necrotic yellows virus in Egypt and Syria. Cereal crops (wheat, barley and oat) in Arab and Mediterranean regions are also affected by viruses, mainly Barley yellow dwarf virus-PAV, and this virus is reported to occur at epidemic levels in only Algeria, Morocco and Tunisia. Epidemic spread of most viral diseases was always associated with high vector populations and activity. Although virus disease management can be achieved through the combined effects of several approaches, development of resistant genotypes is one of the most promising control components. Experience over the last few decades has clearly showed that no single method of virus disease control reduces yield losses in legume crops. Some progress was made on the disease management of some legume and cereal viruses using combinations of healthy seed, host resistance, cultural practices (such as adjustments of planting date and plant density, and roguing of infected plants early in the season) and chemical control virus vectors