Morphological and molecular characterization of new plant type core set for yield and culm strength traits in rice (Oryza sativa L.)

New plant type core set comprising indica and tropical japonica accessions along with checks were evaluated for yield and culm strength related traits and characterized with gene specific markers viz., Gn1a, DEP1, Ghd7, SPL14, GS5, TGW6 and SCM2. Analysis of variance revealed significant differences as well as presence of variability among the genotypes for all the traits. Seven genotypes (IRGC25510, IRGC1742, Haorei machang, Azhoghi, Thangmoi, BPT5204 and Swarnadhan) do not possess similar allele as that of the assessed genes based on combined analysis for all the traits and genes. Of them, four genotypes IRGC1742, Azhoghi, BPT5204 and Swarnadhan possess ideal trait combination (90–100 days to 50% flowering, 100–120 cm plant height, grain number of > 200, 11–15 productive tillers) but with weak culm can be ideal sources for identification of new genes for yield attributing traits and direct introgression of SCM2. Based on single trait-gene analysis, nine trait wise donors with high value for the trait (also with desirable plant type) but without similar allele of the corresponding gene were identified. One genotype IRGC7486 with high grain number (300), four genotypes (IRGC50448, IRGC43741, IRGC15147 and IRGC39111) with strong culm (1195–2655 g.f), three genotypes viz., IRGC15147, IRGC39111 and IRGC10658 with high panicle weight and one genotype Solumpiket with high 1000-grain weight and high panicle weight can be considered for identification of novel gene(s) for respective traits.

     

Evaluation of blood and milk oxidative status during early postpartum of dairy cows

In dairy cows, the intensity of metabolic activity, associated with the negative energy balance (NEBAL), is responsible for an increased production of reactive oxygen species (ROS) and, subsequently, for the development of the condition of oxidative stress, which may overwhelm the antioxidant potential of the bovine maternal organism, making it prone to the development of many puerperal dysfunctions, as well as to an alteration of colostrum and milk quality. Given these premises, the aims of this study are to evaluate serum and milk concentrations of ROS and lipoperoxides, vitamins A and E, on the 10th, 12th, 14th and 16th day postpartum of dairy cows, a particularly critical period during which the NEBAL reaches its nadir, and to compare the trends of these parameters in two different bovine breeds. The study was performed in pluriparous Italian Friesian and Brown dairy cows. On the 10th day postpartum, all cows underwent a clinical examination to exclude the presence of alterations; furthermore, on the same day, a milk sample was collected from each cow, in order to perform the somatic cell count (SCC; (CE) N. 853/2004) and to establish which of them had an SCC ⩽400 000/ml or >400 000/ml. In this study, among the 110 cows that were initially selected, the evaluation of these parameters allowed the inclusion of 80 animals, which were divided into four groups of 20 subjects each: Group F and F1: Italian Friesian healthy cows, with SCC ⩽400 000/ml and >400 000/ml, respectively; Group B and B1: Italian Brown healthy cows, with SCC ⩽400 000/ml and >400 000/ml, respectively. On the 10th, 12th, 14th and 16th day postpartum, peripheral blood and milk samples were collected. The results obtained show that in group B1 there were higher concentrations of ROS and milk antioxidants compared with Friesian group cows. This datum let us suppose that even in the presence of higher ROS concentrations the antioxidant status found in group B1 seems to be able to counteract the oxidative damage, which is more likely to develop in these cows.     

H2AFZ,RNF4 and NR4A1 loci are associated with boar semen quality by population association studies

Abstract

Spermatogenesis is a complex process regulated by many genes. In this study, H2AFZ, RNF4 and NR4A1 genes were selected as candidate genes for boar semen quality traits based on their functions during spermatogenesis, and the associations of three loci (H2AFZ c.192?+?210–192?+?213delCGAT, RNF4 c.374?+?358 T?>?C and NR4A1 c.956?+?796 A?>?G) with sperm quality traits were analyzed in Duroc (n?=?185), Large White (n?=?87) and Landrace (n?=?49) pig populations. The results showed H2AFZ c.192?+?210–192?+?213delCGAT AA boars produced 1.52% lower abnormal sperm rate (ASR) than AB boars in Landrace pigs (p?<?0.05); RNF4 c.374?+?358?TC boars produced 0.31?×?10⁸/ml higher sperm concentration (SCON) than CC boars (p?<?0.05) in Large White pigs; NR4A1 c.956?+?796 A?>?G was associated with ASR in Duroc and Large White pigs and was associated with sperm motility (MOT) in Large White and Landrace pigs. This study indicated the H2AFZ, RNF4 and NR4A1 loci were the potential molecular markers for improving the semen quality traits in boars.     

Impact of subclinical and clinical mastitis on sensitivity to pain of dairy cows

A total of 90 cows from three commercial farms were used to evaluate the relationship between subclinical mastitis and clinical mastitis and thermal nociceptive threshold. Milk strips from all udder quarters were tested for clinical mastitis with visual inspection of milk and udder alterations and for subclinical mastitis using California Mastitis Test. Milk yield was recorded, milk was sampled and further analyzed for somatic cells count (SCC). Cows were considered healthy when SCC<200 000 cells/ml and no visual alterations in milk and/or udder, with mild subclinical mastitis when SCC>200 000 cells/ml and no visual alterations in milk and/or udder, with moderate subclinical mastitis when SCC>500 000 cells/ml and no visual alterations in milk and/or udder and with clinical mastitis when visual alterations in milk and/or udder were detected. Nociceptive threshold was evaluated with the thermal threshold meter apparatus applied to the rear legs. Thermal threshold (TT) decreased when we compared healthy cows with cows presenting clinical mastitis and tended to decrease when we compare healthy cows with those with moderate subclinical mastitis. TT was lower at the ipsilateral rear leg compared with the contralateral leg to the infected mammary gland. TT linearly decreases as _log10SCC increased and it showed sharp decrease as _log10SCC exceed the value of 6.4. Increase in one unit of _log10SCC increased the odds of low thermal threshold (lower than 55.8°C). Subclinical mastitis might be a welfare issue as it tended to decrease nociceptive thermal threshold.     

Association study of single nucleotide polymorphisms in JAK2 and STAT5B genes and their differential mRNA expression with mastitis susceptibility in Chinese Holstein cattle

The JAK–STAT pathway plays a key role in mediating immune responses. The genetic effects of single nucleotide polymorphisms (SNPs) in JAK2 and STAT5B were investigated for serum cytokines, mastitis indicators and productions traits in a population of 468 Chinese Holstein cattle. Pooled DNA sequencing revealed one SNP (BTA8:g.39645396A>G) in JAK2 and two SNPs (BTA19:g.43673888A>G and BTA19:g.43660093T>C) in STAT5B. A fixed effect model considering the effects of SNPs, parity, herd, season and year of calving was used by way of the general linear model procedure of sas . Genotype frequencies of these SNPs in the population were in Hardy–Weinberg equilibrium (P > 0.05). A novel SNP (g.39645396A>G) in JAK2 was predicted to change the amino acid from lysine to asparagine and was significantly associated with the somatic cell count (SCC) and somatic cell score (SCS), whereas g.43673888A>G in STAT5B was significantly associated with SCC, SCS and interleukin‐4 (IL‐4) (P < 0.05). The dominant effect of g.39645396A>G in JAK2 was significant for SCS, and its additive effect was significant for SCC, whereas the dominant effect of g.43673888A>G in STAT5B was significant for SCS and IL‐4 (P < 0.05). The combination of g.39645396A>G in JAK2 and g.43673888A>G in STAT5B showed a significant effect on SCC, SCS, IL‐4 and TNF‐α (P < 0.05). As for mRNA expression analysis, the AA genotype g.39645396A>G and GG genotype g.43673888A>G indicated higher mRNA expression level and were significantly different from other genotypes (P < 0.05). The results imply that JAK2 and STAT5B genes could be useful candidate genes, and the identified polymorphisms might potentially be strong genetic markers for selection of dairy cattle against mastitis development.     

Microbiological quality and related factors of sheep milk produced in farms of NE Greece

Sheep herds are a significant capital of dairy industry in Greece, but as dairy farming becomes more complex and intense the need to provide assistance to dairy producers on milk quality is critical. In this study, the quality of raw milk produced in sheep farms of NE Greece was surveyed and the role of various factors was explored. In total, 21 dairy ewe’s farms from the regions of Xanthi and Evros, in the north-eastern Greece were monitored. Milk samples were sampled after the morning milking every 15 days throughout the dairy period (March–June). For the study, a questionnaire was also filled by personal interview with the owners in order to collect information about herd characteristics, health status, handling practices etc. From each farm, air was also sampled for microbiological analysis. Milk samples were examined for chemical components: fat content, protein, lactose, non-fat dry matter (NFDM) and somatic cells count (SCC). Microbiological examination involved the estimation of Total Bacterial Counts (TBC), coliform count (CC), Staphylococcus aureus, Streptococcus sp., and preliminary incubation count (PIC). The possible correlation among different bacterial species and their interaction with SCC and chemical components of milk was also considered. It was examined whether farm management practices could influence the hygiene and the quality of milk. Our results show that as an average TBCs were 5.48 log cfu/ml, SCC: 6.05 log cells/ml, CC: 4.49 log cfu/ml, S. aureus: 3.94 log cfu/ml, Streptococcus sp.: 4.95 log cfu/ml and PIC: 5.7 log cfu/ml. The mean fat, protein, lactose and NFDM were 6.17%, 5.28%, 4.73% and 10.95% respectively. The study revealed significant positive correlation between TBC and PIC (0.825), while SCC was marginally positive correlated with protein and NFDM. No statistically significant correlations observed among SCC with any of the bacterial species. Herd size and farm management practices had considerable influence on SCC and bacterial species.     

Incidence of Subclinical Mastitis and Prevalence of Major Mastitis Pathogens in Organized Farms and Unorganized Sectors

Subclinical mastitis (SCM) represents a major proportion of the burden of mastitis. Determining somatic cell count (SCC) and electrical conductivity (EC) of milk are useful approaches to detect SCM. In order to correlate grades of SCM with the load of five major mastitis pathogens, 246 milk samples from a handful of organized and unorganized sectors were screened. SCC (>5 × 10⁵/mL) and EC (>6.5 mS/cm) identified 110 (45 %) and 153 (62 %) samples, respectively, to be from SCM cases. Randomly selected SCM-negative samples as well as 186 samples positive by either SCC or EC were then evaluated for isolation of five major mastitis-associated bacteria. Of the 323 isolates obtained, 95 each were S. aureus and coagulase-negative staphylococci (CoNS), 48 were E. coli and 85 were streptococci. There was no association between the distribution of organisms and (a) the different groups of SCC, or (b) organised farms and unorganised sectors. By contrast, there was a significant difference in the distribution of CoNS, and not other species, between organized farms and unorganized sectors. In summary, bacteria were isolated irrespective of the density of somatic cells or the type of farm setting, and the frequency of isolation of CoNS was higher with organized farms. These results suggest the requirement for fine tuning SCC and EC limits and the higher probability for CoNS to be associated with SCM in organized diary sectors, and have implications for the identification, management and control of mastitis in India.     

Phenotypic and genetic relationships between udder morphology and udder health in dairy ewes

The aim of this paper was studying the phenotypic and genetic relationships between udder morphology traits and udder health in dairy sheep. From 2000 to 2008 udder traits, somatic cell count (SCC) and clinical mastitis cases were recorded in an experimental flock consisting each year of around 900 ewes. A logistic regression was performed to evaluate the risk for a ewe of showing either a mastitis or at least 2 daily SCC records greater than 1 × 10⁶ cells/ml in one of its lactations as function of udder traits scored in 1st lactation. 1587 individual udder scores and 39,950 SCC daily records were used for the analysis. Secondly, genetic correlation between lactation mean of somatic cell score and udder traits were estimated by a REML method applied to four bi-trait animal models, using data from 2251 primiparous ewes. Logistic regression results indicated that the risk of mastitis or high SCC values during the productive life increased as the cistern height increased and the degree of udder suspension and udder depth decreased. This suggests that the appraisal of the udder is a useful tool for culling decision aimed at increasing the sanitary status of the flock. The genetic correlation between lactation SCS and udder traits were favourable for udder depth (−0.50 ± 0.12), teat placement (0.39 ± 0.011) and degree of udder suspension (−0.42 ± 0.011) and closed to zero for the degree of separation of the two halves. Thus selection for udder morphology, already implemented in some dairy sheep breeds with the aim of improving machine milkability, will lead to a favourable correlated genetic response on SCC.     

Association of five candidate genes with fatty acid composition in Korean cattle

Fatty acid composition of meat is becoming more important due to consumer demand for high quality and healthy foods. The present study evaluated the associations of five candidate genes (FABP4, FASN, NR1H3, GH and SCD) with fatty acid composition in Korean cattle (Hanwoo). The g.3691G > A single nucleotide polymorphism (SNP) in the FABP4 gene had significant effects on high myristic acid (C14:0; P < 0.01) and palmitic (C16:0; P < 0.05) in animals having the GG genotype, and high arachidonic acid (C20:4; P < 0.05) in the AA genotype of Hanwoo. The FASN SNP at position g.17924G > A was also significantly associated with myristic acid (P < 0.01). In case of the SCD gene, a significant effect was only observed in myristoleic acid (C14:1; P < 0.01). However, SNPs in GH and NR1H3 genes showed no effects on fatty acid composition. The results indicate that SNPs in three candidate genes, FABP4, FASN and SCD, may be influential in breeding design for fatty acid composition in Hanwoo.     

Natural rubber biosynthesis in plants,the rubber transferase complex,and metabolic engineering progress and prospects

Natural rubber (NR) is a nonfungible and valuable biopolymer, used to manufacture ~50 000 rubber products, including tires and medical gloves. Current production of NR is derived entirely from the para rubber tree (Hevea brasiliensis). The increasing demand for NR, coupled with limitations and vulnerability of H. brasiliensis production systems, has induced increasing interest among scientists and companies in potential alternative NR crops. Genetic/metabolic pathway engineering approaches, to generate NR‐enriched genotypes of alternative NR plants, are of great importance. However, although our knowledge of rubber biochemistry has significantly advanced, our current understanding of NR biosynthesis, the biosynthetic machinery and the molecular mechanisms involved remains incomplete. Two spatially separated metabolic pathways provide precursors for NR biosynthesis in plants and their genes and enzymes/complexes are quite well understood. In contrast, understanding of the proteins and genes involved in the final step(s)—the synthesis of the high molecular weight rubber polymer itself—is only now beginning to emerge. In this review, we provide a critical evaluation of recent research developments in NR biosynthesis, in vitro reconstitution, and the genetic and metabolic pathway engineering advances intended to improve NR content in plants, including H. brasiliensis, two other prospective alternative rubber crops, namely the rubber dandelion and guayule, and model species, such as lettuce. We describe a new model of the rubber transferase complex, which integrates these developments. In addition, we highlight the current challenges in NR biosynthesis research and future perspectives on metabolic pathway engineering of NR to speed alternative rubber crop commercial development.     

Economic consequences of mastitis and withdrawal of milk with high somatic cell count in Swedish dairy herds

The main aim was to assess the impact of mastitis on technical and economic results of a dairy herd under current Swedish farming conditions. The second aim was to investigate the effects obtained by withdrawing milk with high somatic cell count (SCC). A dynamic and stochastic simulation model, SimHerd, was used to study the effects of mastitis in a herd with 150 cows. Results given the initial incidence of mastitis (32 and 33 clinical and subclinical cases per 100 cow-years, respectively) were studied, together with the consequences of reducing or increasing the incidence of mastitis by 50%, modelling no clinical mastitis (CM) while keeping the incidence of subclinical mastitis (SCM) constant and vice versa. Six different strategies to withdraw milk with high SCC were compared. The decision to withdraw milk was based on herd-level information in three scenarios: withdrawal was initiated when the predicted bulk tank SCC exceeded 220 000, 200 000 or 180 000 cells/ml, and on cow-level information in three scenarios: withdrawal was initiated when the predicted SCC in an individual cow's milk exceeded 1 000 000, 750 000 or 500 000 cells/ml. The accuracy with which SCC was measured and predicted was assumed to affect the profitability of withdrawing milk with high SCC and this was investigated by applying high, low or no uncertainty to true SCC. The yearly avoidable cost of mastitis was estimated at €8235, assuming that the initial incidence of mastitis could be reduced by 50%. This cost corresponded to 5% of the herd net return given the initial incidence of mastitis. Expressed per cow-year, the avoidable cost of mastitis was €55. The costs per case of CM and SCM were estimated at €278 and €60, respectively. Withdrawing milk with high SCC was never profitable because this generated a substantial amount of milk withdrawal that was not offset by a sufficient increase in the average price per delivered kg milk. It had the most negative impact on net return when high incidence of mastitis was simulated. Withdrawing milk with high SCC based on low-uncertainty information reduced the amount of withdrawn milk and thus resulted in less negative effect on net return. It was concluded that the current milk-pricing system makes it more profitable for farmers to sell a larger amount of milk with higher SCC than to withdraw milk with high SCC to obtain payment premiums, at least in herds with mastitis incidences within the simulated ranges.     

Cytotoxic activity induced by crude extracts of Ganoderma lucidum (W. Curt.: Fr.) P. Karst. on mouse myeloma cancer cell-line

Ganoderma lucidum powder using hot water and methanol extraction methods indicated a twofold more active cytotoxic activity with IC₅₀ of 44 ± 3.8 μg/ml in the latter method. The representative dose-response curves of the G. lucidum crude extracts on J558 cell-lines revealed that there were great similarities between the curves which reflected rapid killing activities. The percentage viability of the J558 cell exposed to these crude extracts was dose dependent only up to 150 μg/ml. After which, there was no significant reduction when the dose was increased to 200 or 400 μg/ml. The morphological alterations induced by the crude extract were examined under the phase contrast, fluorescent and electron microscopy. When J558 cells were treated with doses higher than 50 μg/ml of the crude extract, obvious morphological changes and apoptosis occurred after 72 h. At 400 μg/ml, most of the cells showed necrosis characterized as small fragments with uniformly stained red nuclei. The apoptotic and necrotic cells increased by 16.5 and 29.1%, respectively whereas the viable cells decreased by as much as 45.6. The mode of cell death via apoptosis was 3.6% higher than necrosis. However, these morphological changes were not observed in the case of 3T3 cells. Results obtained from scanning electron microscopy and transmission electron microscopy further confirmed the occurrence of various apoptotic and necrotic features.     

Stable integration and expression of β-glucuronidase and NPT II genes in mango somatic embryos

Summary Somatic proembryos of mango (Mangifera indica L. cv. Hindi) were co-cultivated withAgrobacterium tumefaciens strain A208 harboring pTiT37-Se::pMON 9749 (9749 ASE). Transformed somatic proembryos capable of growing on selection medium containing 200 μg/ml kanamycin produced the characteristic indigo blue precipitate in the presence of 5-bromo-4-chloro-3-glucuronic acid. These proembryos were chimeral consisting of transformed (blue) and nontransformed (yellow/white) cells. A stepwise selection strategy was found necessary to eliminate chimeras. a) Initial screening at 200 μg/ml kanamycin to enable growth of transformed cells, b) further screening at 400 μg/ml kanamycin to reduce chimeras, and c) recovery of pure transformed clones of proembryos in liquid selection medium with 100 μg/ml kanamycin. The integration of the NPT II and GUS genes into mango genome was confirmed by Southern hybridization.     

Novel SNPs of butyrophilin (<Emphasis Type="Italic">BTN1A1</Emphasis>) and milk fat globule epidermal growth factor (EGF) 8 (<Emphasis Type="Italic">MFG</Emphasis>-<Emphasis Type="Italic">E8</Emphasis>) are associated with milk traits in dairy goat

Butyrophilin (BTN1A1) and milk fat globule epidermal growth factor (EGF) 8 (MFG-E8) genes are both milk fat globule membrane proteins. BTN1A1 plays a key role in the secretion of milk lipid and production which has effects on performance traits, while the MFG-E8 is vital for the development of the mammary gland and phagocytic clearance of apoptotic cells. Therefore, BTN1A1 and MFG-E8 gene are candidate genes for quantitative traits in mammalian animals with respect to milk performance traits. The objective of this study is to investigate variations in goat BTN1A1 and MFG-E8 gene and analyze their associations with growth trait and milk performance. In this study, the goat BTN1A1 gene showed a novel single-nucleotide polymorphism (SNP): XM_001494179:g.8659C>T, resulting in a missense mutation: CTT (Leu)>TTT (Phe) at position 377 aa of the BTN1A1 (526 aa); the goat MFG-E8 gene showed four novel SNPs: NC_007319: g.843delA, 6417delC, 14892T>C and 14996A>C, only the 14892T>C result in a synonymous mutation. The associations between genotypes and production traits were analyzed. Significant statistical results implied that HinfI locus of BTN1A1 gene is associated with milk fat yield (P = 0.004), total solid (P = 0.002), solid-non fat (P = 0.018) and first milk yield (P = 0.030). The DA and EcoRV loci of MFG-E8 gene are associated with milk fat yield (DA locus: P = 0.000; EcoRV locus: P = 0.033) and total solid (DA locus: P = 0.002; EcoRV locus: P = 0.015) in the Xinong Saanen dairy goat.     

Lactoferrin concentrations in goat milk throughout lactation

Lactoferrin is an iron-binding glycoprotein and is considered a major part of the non-specific disease resistance complex in the mammary gland. For cows, the influence of physiological factors on the lactoferrin concentration in milk has been reported. In addition, lactoferrin concentrations have been demonstrated to be proportional to somatic cell counts (SCC) in cows milk. In this study, we aimed to analyse the effects of lactational stage, lactation number and SCC in 19 goats throughout an entire lactational period. Lactoferrin concentrations in weekly composite milk samples were analysed with a competitive ELISA developed for caprine lactoferrin. Maximal lactoferrin concentrations were observed in the colostral samples (387 ± 69 μg/ml). In the following week, less than 20% of these concentrations were observed (62 ± 25 μg/ml) and thereafter until week 32 p.p., the weekly mean concentrations ranged between 10 and 28 μg/ml. Toward the end of lactation, approximately during the 33rd week, the concentrations began to increase and were reaching about 3.2-fold higher values in week 44 (107 ± 19 μg/ml). SCC were only available in monthly intervals and could thus not be directly related to the weekly lactoferrin recordings. When classifying the individual goats according to the median of their SCC values obtained during midlactation, the goats with SCC medians >430,000 had higher lactoferrin milk concentrations during this time than the ones with SCC below this threshold (P < 0.05). In addition, sampling week and parity significantly affected the lactoferrin concentration (P < 0.05 and P < 0.01, respectively). Comparing SCC and lactoferrin, both parameters are significantly affected by various physiological factors. Further studies are needed to clarify if the relationship between Lf and bacterial counts is closer compared to the relationship between SCC and bacterial counts.     

Associations between single nucleotide polymorphisms in 33 candidate genes and meat quality traits in commercial pigs

This study aimed to evaluate the effects of single nucleotide polymorphisms (SNPs) in candidate genes for meat quality using a custom 96‐SNP panel (Illumina Vera Code GoldenGate Assay) on 15 traits collected from 400 commercial pigs. Meat quality measurements included muscle pH, color (L*, a* and b*), drip loss, cooking loss, peak shear force and six sensory traits including appearance (outside and inside), tenderness, juiciness, flavor and overall liking as well as carcass weight and probe yield. Thirty‐five SNPs with minor allele frequencies > 0.10 remained for the multimarker association using the GLM procedure of sas 9.2. Results showed that 20 SNPs were significantly associated with at least one of the traits with either additive or dominance or both effects (P < 0.05). Among these significant SNPs, five of them in ADIPOQ, FTO, TNF, LEPR and AMPD1 had an effect on more than three traits simultaneously; those in MC4R, CAST, DGAT1 and MYF6 had an effect on two traits, while the others were associated with one trait. The results suggest that these markers could be incorporated into commercial pigs for marker‐assisted selection and breeding programs for carcass and meat quality trait improvement.