Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marke

Analysis of wild Lactuca accessions: identification of redundancies and conservation

Germplasm accessions of wild Lactuca species are maintained worldwide in ex situ collections as gene reservoirs for quality and disease resistance traits for cultivated lettuce. Accessions of 12 Lactuca species from 6 genebanks were compared via morphological characterization and AFLP (Amplified Fragment Length Polymorphism)-based profiling to estimate the extent of duplication. A method of assessing redundancy within very similar, but not identical accessions, is proposed, based on 352 polymorphic AFLP products. Seven duplication groups showed a high level of AFLP similarity, and one pair of Lactuca saligna accessions displayed identical AFLP profiles. In several cases, the morphological assessment indicated that a taxonomic reclassification of accessions was necessary. Candidate duplicates were identified using population parameters and inter- and intra-accession variability. The implications of these findings on the conservation of wild species are discusse

The effect of time of maturation and CaCl2 on quality of young beef

Investigations were carried out on four muscles (M. longissimus dorsi, M. semimembranosus, M. semitendinosus, M. biceps femoris) taken from five young cattle (crosses Domestic Spotted x Limousine) of average body mass prior to slaughtering of 587 kg. On all muscles, 24 h after slaughtering, sensory evaluation was carried out and the following parameters determined: pH value, colour, water binding ability, cooking loss and tenderness (initial values). The remaining part of each muscle was divided into 6 parts, 3 were packaged in plastic foil (control samples), and other 3 were soaked in solution containing 0,4% CaCl2 and 0,4% NaCl and packaged in plastic foil. Pieces of meat prepared in this way were left on temperature of + 40C 7, 14 and 21 days to mature. After this period, all mentioned analyses were carried out on meat samples. It was established that pH value during maturation increased, that meat packaged in plastic foil after 14 days of maturation becomes unusable, whereas the increase of pH values of meat whose maturation occurred in solution CaCl2 and NaCl was slower and therefore meat was still usable after 21 days. Color of meat in control samples was slightly lighter compared to initial condition, whereas the color of meat whose maturation occurred in solutions of salt was statistically considerably lighter (P (lt) 0,05 after 7 days, a P (lt) 0,001 after 14 and 21 days). Water binding ability in control samples was slightly better (P>0,05) after 7 days and after 14 days it was statistically significantly better (P (lt) 0,05) compared to initial state, whereas in meat whose maturation occurred in salt solution this ability was at initial level even after 21 days. Cooking loss in control samples was lower compared to initial values whereas in meat soaked in salt solution cooking loss was higher. Meat tenderness in control samples was statistically considerably better after 14 days of maturation (when meat was not fit for use) and in meat soaked in salt solution it was statistically highly significantly better after 14 and 21 days. According to sensory evaluation, control samples of meat, after 14 days of maturation are not fit for use, whereas meat whose maturation occurred in solution of CaCl2 and NaCl even after 21 days is acceptable from the sensory aspect.Ispitivanja su obavljena na četiri mišića (M. longissimus dorsi, M. semimembranosus, M. semitendinosus, M. biceps femoris) uzetih od pet junadi (melezi domaće šareno goveče x limuzin), prosečne mase pred klanje 587 kg. Na svim mišićima 24 sata posle klanja obavljena je senzorna ocena i određeni su: pH vrednost, boja, sposobnost vezivanja dodate vode, kalo kuvanja i mekoća (početne vrednosti). Ostatak svakog mišića podeljen je na 6 delova od kojih su po 3 upakovani u plastičnu foliju (kontrolni uzorci), a ostala 3 dela su potopljena u rastvor koji sadrži 0,4% CaCl2 i 0,4% NaCl i upakovani u plastičnu foliju. Ovako pripremljeni komadi mesa ostavljeni su pri temperaturi od + 40C 7, 14 i 21 dan na zrenju. Posle isteka zadatog vremena urađena su na komadima od svih mišića navedena ispitivanja.Utvrđeno je da se pH vrednost tokom zrenja povećava i da u mesu koje je upakovano u plastičnu foliju posle 14 dana zrenja dospeva u oblast kad je meso neupotrebljivo, dok je povećanje pH vrednosti kod mesa čije se zrenje odvijalo u rastvoru CaCl2 i NaCl sporije tako da je meso i posle 21 dan upotrebljivo. Boja mesa kod kontrolnih uzoraka bila je neznatno svetlija u odnosu na početno stanje, dok je boja mesa čije se zrenje odvijalo u rastvoru soli bila statistički značajno svetlija (P (lt) 0,05 nakon 7 dana, a P (lt) 0,001 nakon 14 i 21 dan). Sposobnost vezivanja vode kod kontrolnih uzoraka bila je neznatno (P>0,05) bolja nakon 7 dana dok je nakon 14 dana bila statistički značajno bolja (P (lt) 0,05) u poređenju sa početnim stanjem, dok je kod mesa čije se zrenje odvijalo u rastvoru soli i posle 21 dan bila na nivou početnog stanja. Kalo kuvanja kod kontrolnih uzoraka bio je manji u poređenju sa vrednostima na početku ogleda dok je kod mesa potopljenog u rastvor soli bio veći. Mekoća mesa kod kontrolnih uzoraka bila je statistički značajno bolja nakon 14 dana zrenja (kad je meso bilo neupotrebljivo) dok je kod mesa potopljenog u rastvor soli bila statistički visoko značajno bolja posle 14 i 21 dan. Prema senzornoj oceni kontrolni uzorci mesa nakon 14 dana zrenja postaju neupotrebljivi, dok je meso čije se zrenje odvijalo u rastvoru CaCl2 i NaCl i nakon 21 dan zrenja senzorno veoma prihvatljivo

Cattle production: Current situation and future directions of development in Republic of Serbia

Number of heads of cattle in the last 11 years is constantly decreasing. In this period, number of cattle is reduced by 18%. Number of cows and pregnant heifers reduced by 14%. Data indicate that at the end of 2006 1,096.000 heads of cattle were registered. It should be pointed out that number of cows and pregnant heifers of 710.000 heads at the end of 2006 which are included in reproduction represent the future of Serbian cattle production in future. Dominant breeds are Domestic Spotted and Simmental cattle, participating by about 70% in total number, then crossbreds of Domestic Spotted and Simmental and Busha cattle participating with about 25%, and about 5% goes to Black and Red-White cattle of European White-Black and Holstein races. Production of cow's milk is in slight constant increase. This can be explained by increased production of milk per cow. Genetic progress in milk traits was achieved by utilization of progeny tested bulls on milk and increased scope of artificial insemination of cows and heifers. Production of meat is in constant decrease which is consequence of reduction of total number of cattle as well as insufficient number of slaughterhouses with EU certificate. Of total quantity of produced meat, in Central Serbia 69.000 t and in Vojvodina 21.000 t of meat is produced. Starting from the current situation in cattle production, and on basis of previous practice, domestic and international, and development of cattle breeding, fast and efficient transformation of cattle production is necessary, enlargement of agricultural farms and forming of specialized farmers for production of meat and milk. Systems of certification and registration which would increase the product value should be introduced on specialized farms. Milk produced in this way can have added value on the market through special dairy products (hard cheeses, semi hard cheeses, white-soft cheeses and milk beverages). Agricultural households/farms specializing in meat production have objective - production of beef for domestic needs and export. Future of export of Serbian meat is first of all in production of beef of high quality which complies with demands of specific markets (Italy, Greece, etc.).Na osnovu zvaničnih statističkih podataka stanje u govedarstvu se ocenjuje kao nepovoljno. Broj grla poslednjih deset godina konstantno opada. U ovom periodu broj goveda je smanjen za 18%. Dok je broj krava i steonih junica smanjen za 14,3%. Podaci o brojnom stanju i kategorijama goveda takodje ukazuju na značajno smanjenje, tako da kategorija junadi od 1-2 godine je smanjen za 24.5% dok broj teladi je smanjen za 29.2%. Podaci pokazuju da je na kraju 2006. godine evidentirano 1,096.000 grla goveda. Posebno treba imati u vidu da broj krava i steonih junica od 710.000 grla na kraju 2006. godine koja ulaze u reprodukciju predstavljaju budućnost srpske govedarske proizvodnje u narednom periodu. Dominantne rase su domaća šarena i simentalska rasa, sa učešćem od oko 70% u ukupnom broju goveda, zatim melezi goveda domaće šarene i simentalske rase i buša goveda sa oko 25%, i 5% čine crno-bela goveda i crveno-bela goveda evropskih crnobelih i holštajn rasa. Proizvodnja kravljeg mleka je u blagom stalnom porastu. Ovo se može objasniti povećanom proizvodnjom mleka po kravi. Genetski napredak u osobinama mlečnosti postignut je korišćenjem progeno testiranih bikova na mleko i povećanom obimu veštačkog osemenjavanja krava i junica. Proizvodnja mesa je u stalnom opadanju što je posledica opadanja ukupnog broja goveda kao i nedovoljan broj klanica koje imaju sertifikat EU. U 2006. godini registrovane su samo 4 klanice sa EU sertifikatima. Od ukupne kolićine proizvedenog mesa u Centralnoj Srbiji se proizvede 69.000 t dok u Vojvodini 21.000 t. Polazeći od postojećeg stanja u govedarskoj proizvodnji, kao i na osnovu dosadašnje domaće i međunarodne prakse i razvoja govedarstva neophodna brza i efikasna transformacija govedarske proizvodnje u cilju ukrupnjavanja zemljišnih poseda i stvaranja specijalizovanih farmera za proizvodnju mleka i mesa. Na specijalizovanim farmama treba uvesti sisteme certifikacije i registracije koje povećavaju vrednost proizvoda. Ovako proizvedeno mleko može se dalje valorizovati na tržištu preko specijalnih proizvoda od mleka (tvrdi sirevi, polutvrdi sirevi, beli sir i mlečni napitci). Gazdinstva ( farmeri ) specijalizovani za proizvodnju mesa imaju za cilj proizvodnju junećeg mesa za domaće potrebe i za izvoz. Budućnost srpskog izvoza mesa leži pre svega u proizvodnji junećeg mesa takvog kvaliteta koji odgovara zahtevima odgovarajućeg tržišta (Italija, Grčka i dr)

Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marker