First Report of 'Candidatus Phytoplasma solani' Infecting Parsnip in Serbia

The parsnip is a biennial plant native to Eurasia. During August and September 2016, typical phytoplasma yellows symptoms were observed on parsnip plants grown in Serbia. To our knowledge, this is the first report of phytoplasma infecting parsnip in Serbia

Encuesta de datos demográficos y fenotípicos de razas locales de cerdos del proyecto TREASURE

The paper reports the results of a survey on the demographic and phenotypic characterization of 20 European local pig breeds involved in the H2020 TREASURE project including information on: demographic parameters, main morphological features, reproductive information, additional information collected at herd-level (i.e. temperament, holding, mating practices), origins and development of the breeds. Almost all the breeds (18 out of 20) possess a herd book even if the starting year is highly variable (from 1980 to 2006). Number of breeding females ranged from 24 (Moravka) to over 200,000 heads (Ibérico). Male/female ratio varied greatly with the highest values for the Italian breeds probably due to the different policy of animal recording. Almost all the breeds undergo a conservation program whereas really few are interested by other conservation techniques and for less than five breeds data related to effective number and inbreeding coefficient are easily available. Average values for teat number, litter size and weaned piglets are 12, 8 and 6 respectively with a great potential for their improvement. The depicted scenario is highly diversified and the data collected represent the starting point for the achievement of a collective trademark under the umbrella of the TREASURE project

Genome‐wide detection of copy number variants in European autochthonous and commercial pig breeds by whole‐genome sequencing of DNA pools identified breed‐characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.info:eu-repo/semantics/acceptedVersio

Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Krskopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'de-domestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed

Survey of demographic and phenotypic data of local pig breeds of TREASURE project

The paper reports the results of a survey on the demographic and phenotypic characterization of 20 European local pig breeds involved in the H2020 TREASURE project including information on: demographic parameters, main morphological features, reproductive information, additional information collected at herd-level (i.e. temperament, holding, mating practices), origins and development of the breeds. Almost all the breeds (18 out of 20) possess a herd book even if the starting year is highly variable (from 1980 to 2006). Number of breeding females ranged from 24 (Moravka) to over 200,000 heads (Ibérico). Male/female ratio varied greatly with the highest values for the Italian breeds probably due to the different policy of animal recording. Almost all the breeds undergo a conservation program whereas really few are interested by other conservation techniques and for less than five breeds data related to effective number and inbreeding coefficient are easily available. Average values for teat number, litter size and weaned piglets are 12, 8 and 6 respectively with a great potential for their improvement. The depicted scenario is highly diversified and the data collected represent the starting point for the achievement of a collective trademark under the umbrella of the TREASURE project

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production system

Interdependence of morphological characters of onion bulbs (Allium cepa L.)

The paper presents morphologic characters of the bulb of the onion populations. As these populations have different origin, we studied basic characters of bulbs and their interdependence; number of opened juicy leaves, number of closed juicy leaves, number o hearts, number of buds and onion shape. Results are processed according to variance analysis and interdependence was determined by correlation's coefficient. It was found that he populations with a higher number of opened juicy leaves have more hearts and more buds in the bulb. Consequently, positive correlation between these characters was found Negative correlation was obtained between the number of closed juicy leaves, number of hearts and buds in the bulb. The share index of the studied populations ranged from 0.63 (flattened round) to 1.54 (cylindrićal bulbs), which means that this character of the bulb is in negative correlation with the number of hearts and buds in the bulb