WHOLE-GENOME RE-SEQUENCING OF TWO TOMATO LANDRACES REVEALS SEQUENCE VARIATIONS UNDERPINNING KEY ECONOMICALLY IMPORTANT TRAITS

In the post-genomic era, one of the major challenges is the identification of alleles directly responsible for phenotype variation among different genotypes within the same species. Tomato is a model crop for understanding the development and ripening of climacteric fleshy fruits, and it is also known to be an important source of health-promoting compounds. In addition, cultivated tomato germplasm shows a high phenotypic variation despite its very low genetic diversity. Toward the identification of sequence variations responsible for stress tolerance, high fruit quality and long shelf life, we re-sequenced the genomes of two traditional landraces grown in the Campania region (Southern Italy). Crovarese, belonging to the Corbarino type (COR), and Lucariello (LUC) are typically grown under low water regimes and produce highly appreciated fruits, which can be stored up to 4-8 months. We generated 65.8M and 56.4M of paired-end 30-150 bp reads with an average insert size of 380 bp (± 52bp) and 364 bp (± 49bp) for COR and LUC, respectively. A referenceguided assembly was performed using 'Heinz 1706' as a reference genome. We estimated a mean coverage depth of ~15X for COR and 13X for LUC. Comparing the genomes of COR and LUC with that of 'Heinz 1706' we found a similar distribution of SNPs (68.8% vs. 69.9%, respectively), small deletions (8.9% vs. 8.6%) and small insertions (22.1% vs. 21.3%). Through a de novo assembly of the unmapped reads we identified 29 and 36 new contigs in COR and LUC, respectively. The new contigs could be assigned to the chromosomes thanks to the use of a splitread approach. On average, the contigs inserted in COR were 654bp, whereas those inserted in LUC were 616bp. Using custom RNA-seq data, a total of 43054 and 44576 gene loci were annotated in COR and LUC, corresponding to 62369 and 65094 transcripts, respectively. Among the genes showing a similar structure in COR and LUC compared to 'Heinz 1706', we identified ~2000 and 1700 SNPs causing potentially disruptive effects on the function of 1371 and 1201 genes in COR and LUC, respectively. Interesting GO categories highly represented in genes affected by sequence changes were identified. Major variations were present in stress-responsive genes as well as in fruit quality and development-related genes. From a practical perspective, the identified SNPs and InDels are candidate polymorphisms to track DNA variations associated to key traits of economic interest

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

EFFECT OF TWO DIFFERENT ANTIBIOTIC COMBINATIONS ON FERTILITY OF FROZEN BUFFALO AND SAHIW AL BULL SEMEN

This study was carried out to identify the suitable antibiotic combinations in semen extender for improvement in fertility of frozen semen of buffalo and cow (Sahiwal) bulls to obtain better pregnancy rate through artificial insemination (AI). For this study eight first ejaculates, four each from a buffalo and a cow (Sahiwal) bull were used. The ejaculates were split-sampled and diluted with Tris-citric acid extender (at 37°C; 50x 106 spermatozoa/mI), containing either SP (streptomycin 1000 ~g/ml and penicillin 1000 IU/ml) or GTLS (gentamycin 500 µg/ml, Tylosin 100 µg/ml and linco-spectin 300/600 µg/ml). There was no difference in post-thaw motility for these samples. Fertility test based on 75-days first service pregnancy rate was determined under field conditions. A total of 400 inseminations were recorded, 200 for each buffalo and cow (Sahiwal) with J 00 of each antibiotic combination, respectively. Fertility rates for SP-based frozen semen of buffalo bull were 41.66% and were 55.2% for GTLS-containing frozen semen, respectively. The results for GTLS were higher (P<0.0001) than SP. Similarly, fertility rates were higher (P<0.0001) for GTLS-based frozen semen of Sahiwal bull (78.78%) than SP-containing frozen semen (69.6%) of the same specie. Fertility rates also differed due to species of donor bulls. They were better (P<0.0001 ) for the frozen Sahiwal bull semen than that of the buffalo bull in both SP and GTLS- based frozen semen samples, respectively. In conclusion. seminal quality measured by field fertility trial indicated GTLS combination of antibiotics added to the semen extender was better for improvement in the fertility of frozen buffalo) and Sahiwal bull semen, by yielding better pregnancy rates through AI

FACTORS AFFECTING THE EFFICIENCY OF ARTIFICIAL INSEMINATION IN CATTLE AND BUFFALO IN PUNJAB, PAKISTAN

The main objective of this study was to identify the factors that affect the success of artificial insemination (A.I) services under field conditions. The data from a total of 459 inseminations were analyzed. The effects of farm, animal, semen/bull and A.I. technician on conception rate were studied. Milk progesterone concentration was used as an indicator of conception. Milk samples were collected from animals at day 0, 11 and 22 post-insemination and analysed for progesterone (P4) concentrations using radioimmunoassay (RIA) kits. Results indicated that the overall conception rate through A.I. under field condition was 29%. Among the farm-related factors, only region had a significant effect on conception rate (P0.05). Animals inseminated within 24 hours after the onset of estrus had a higher, though statistically insignificant, conception rate than those inseminated after 24 hours. Among the animal-related factors, species, milk production, body condition score (BCS), lactation state, heat signs and uterine tone had a significant effect on conception rate. The conception rate in buffaloes was higher than in cattle (P<0.05). Animals with the higher BCS had a better conception rate than those having lower condition. Conception rate in the milking animals was more than the dry ones (P<0.05). Animals showing the passage of mucus from external genitalia (P<0.05) and marked uterine tone (P<0.01) showed better conception rate. Among the semen/bull related factors, bull breed, semen type, quality and source had a marked effect on conception rate. The conception rate was higher with the semen of cross bred and buffalo bulls (P<0.05). The conception rate with liquid semen was high and low with frozen semen (P<0.01). Good quality semen yielded higher conception rate than poor quality semen (P<0.01). The conception rate varied significantly due to A.I. technician (P<0.01). In conclusion, there is a tremendous scope to improve the existing A.I. technology in field through improved management of both animal and farm, supply of high quality frozen semen and enhancement in insemination skill of A.I. technicians

EFFECTS OF A NEW ANTIBIOTIC COMBINATION ON POST -THAW MOTION CHRACTERISTICS AND MEMBRANE INTEGRITY OF BUFFALO AND SAHIWAL BULL SPERMATOZOA AND ON THE BACTERIOLOGICAL QUALITY OF THEIR SEMEN

In this study the effects of a new antibiotic combination, i.e., gentamycin, tylosin and linco-spectin (STLS) on post-thaw motion characteristics, plasma membrane integrity, sperm morphology and the total aerobic bacterial counts (TABC) in buffalo and Sahiwal bull semen were investigated. Ten ejaculates, five each from a buffalo and a Sahiwal bull, possessing more than 60% sperm motility were used. These ejaculates were diluted in Tris-citric acid (TCA) extender (at 37 °C; 50 X 106 spermatozoa/mi), containing either GTLS (gentamycin 500 g/ml, tylosin 100 g/ml and linco-spectin 300/600 g/ml), streptomycin 1000 g/ml and penicillin 1000 IU/ml (SP), or negative control with no antibiotics (NCON). Samples were cooled to 4°C in 2 hours, equilibrated at 4°C for 4 hours, filled in 0.5 ml straws, frozen in a controlled rate cell freezer and plunged into liquid nitrogen. Frozen semen was thawed at 37°C for 15 seconds. Post-thaw sperm motion characteristics, plasma membrane integrity and sperm morphology were determined. Total aerobic bacterial counts and the frequency of appearance of bacterial genera were determined in neat semen, after dilution, and after freezing and thawing. Mean motilities (visual; computer-assisted, linear and circular), velocities (straight-line, average path and curvilinear) and lateral head displacement (LHD) in post- thaw semen samples did not differ due to antibiotics or species. Same was true for sperm plasma membrane integrity. Morphologically abnormal spermatozoa were lower (P<0.05) in GTLS and SP than in NCON. Sperm cells possessing normal acrosomes were higher (P<0.01) in GTLS and SP than in NCON. Total aerobic bacterial counts in post-thaw samples were lower (P<0.05) in GTLS than in SP or NCON. Staphylococcus and micrococcus were lower in samples treated with GTLS than that of SP or NCON. Pseudomonas and E.coli were more frequent in buffaloes than Sahiwal bull samples. Proteus and corynebacteria were scarcely present. In conclusion, GTLS was not determintal to post thaw motion characteristics, sperm morphology and membrane integrity of buffalo and Sahiwal bull spermatozoa. Furthermore, it efficiently reduced the number of aerobic micro-organisms in buffalo and Sahiwal bull semen