Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.

Adaptive potential of breeding lines of spring barley in conditions of Kuznetsk Depression

Adaptive properties of spring barley in the conditions of the Kuznetsk depression have been studied. The objects of the research are five medium-ripening breeding lines of spring barley. The breeding lines were studied in a nursery of competitive varietal trials in 2016-2020. The soil of the experimental plot is leached chernozem, heavy loam with a medium granulometric composition. The repetition was fourfold, the seeding rate (optimal for spring barley in the cultivation zone) 450 pcs / m2. The sowing dates were April 29 - May 5, the harvesting was done with a Sampo 130 combine at the stage of full ripeness of spring barley samples (August 12-15). The experiment was carried out in comparison with the standard cultivar Biom. The parameters of environmental plasticity (bj), stability (S2dj), the environmental conditions index (Ij) were calculated according to the method developed by S.A. Eberchart and W.A. Russel, which examines the positive response of the genotype to the improved growing conditions. Under contrasting growing conditions of spring barley in the years of research, it was found that the environment factor had a significant influence on the yield - 82.6%, the share of genotype influence was 1.4%. The average yield over the years of the study of spring barley in the nursery of competitive variety trials was 5.51 t/ha, the maximum average yield has a breeding line KM-198/11 - 6.45 t/ha. Genotypes with the highest adaptive properties were identified: KM-198/11 (bi = 0.24, Si2 = 2.59), Nutans 12/16 (bi = 0.24, Si2 = 2.18) with yield variability of 25.9-29.2% (Biom standard - 46.1%). The medium-maturing selection line of spring barley KM-198/11, having above-average adaptive properties, is prepared for submission for state variety testing in 2021 as the variety Kuzbass Jubilee. The main advantages of the variety were revealed: high drought tolerance, resistance to lodging and blight, high productivity (6.45-8.50 t/ha), large grain size (53.2 g), medium reaction to stress factors (reduced productivity). Grain crude protein content was 13.6-14.1%, the film content 8.4%, the natural weight 620 g/l.

Effects of restricting energy during the gilt development period on growth and reproduction of lines differing in lean growth rate: Responses in reproductive performance and longevity

Longevity and reproductive performance are economically important traits in the swine industry that are largely influenced by nutrition and other environmental factors. Reproductive performance and longevity through 4 parities was assessed in gilts of 2 genetic lines developed on ad libitum access to feed or restricted to 75% of ad libitum intake. A total of 661 gilts were used in a 2 x 2 factorial with half of the gilts allocated to an ad libitum diet (AL; n = 330), while the other half were energy restricted by 25% (R; n = 331) from 123 to 235 d of age. All gilts were sired by an industry maternal line. Dams of the gilts were from either a Large White by Landrace industry maternal line or Nebraska Selection Line 45X, producing gilts designated as W x L (n = 355) and L45X (n = 306), respectively. Daily estrus detection began at 140 d of age to obtain age at puberty (AP). Gilts (n = 510) were mated on their second or later estrus, beginning at 240 d of age. Sow weight and backfat were recorded at 110 d of gestation and weaning of each parity. Number of live-born, stillborn, and mummified pigs per litter and piglet birth and weaning weights were recorded through 4 parities. More L45X than W x L and more AL than R gilts reached puberty by 230 d of age (P < 0.01). Dietary treatment did not affect probability to produce parities 1 to 4 or any litter trait analyzed. The L45X females tended to be more likely to produce parities 1 (P < 0.08) and 3 (P < 0.06), while W x L had heavier litters at birth (P < 0.01) and weaning (P = 0.01). Treatment by parity interactions (P < 0.01) existed for weight and backfat prior to farrowing and backfat at weaning, and weight at weaning exhibited a line by treatment by parity interaction (P = 0.04) as R sows had lower weights and backfats in earlier parities, but caught up to AL sows in later parities. A treatment by parity interaction (P < 0.01) was also present for backfat loss from farrowing to weaning as R gilts lost less backfat than AL in parities 1 and 2, but more in parities 3 and 4. No significant differences were detected between lines or treatments for lifetime production traits. The populations of pigs and data presented here provide a framework for a diverse array of further studies. Alternative approaches to restrict energy have been assessed in addition to methods of marker-assisted and genomic selection for improvement of litter size and sow longevity.

A low-area design of two-factor authentication using DIES and SBI for IoT security

Internet of things (IoTs) is an integration of heterogeneous physical devices which are interconnected and communicated over the physical Internet. The design of secure, lightweight and an effective authentication protocol is required, because the information is transmitted among the remote user and numerous sensing devices over the IoT network. Recently, two-factor authentication (TFA) scheme is developed for providing the security among the IoT devices. But, the performances of the IoT network are affected due to the less memory storage and restricted resource of the IoT. In this paper, the integration of data inverting encoding scheme (DIES) and substitution-box-based inverter is proposed for providing the security using the random values of one-time alias identity, challenge, server nonce and device nonce. Here, the linearity of produced random values is decreased for each clock cycle based on the switching characteristics of the selection line in DIES. Moreover, the linear feedback shift register is used in the adaptive physically unclonable function (APUF) for generating the random response value. The APUF–DIES-IoT architecture is analyzed in terms of lookup table, flip flops, slices, frequency and delay. This APUF–DIES-IoT architecture is analyzed for different security and authentication performances. Two existing methods are considered to evaluate the APUF–DIES-IoT architecture such as TFA-PUF-IoT and TFA-APUF-IoT. The APUF–DIES-IoT architecture uses 36 flip flops at Virtex 6; it is less when compared to the TFA-PUF-IoT and TFA-APUF-IoT.

Identification and Allelic Variants Associated With Cold Tolerance of PmPIAS in Pinctada fucata martensii

The protein inhibitor of activated STAT (PIAS) functions in diverse aspects, including immune response, cell apoptosis, cell differentiation, and proliferation. In the present study, the PIAS in the pearl oyster Pinctada fucata martensii was characterized. The sequence features of PmPIAS were similar to that of other PIAS sequences with PIAS typical domains, including SAP, Pro-Ile-Asn-Ile-Thr (PINIT), RLD domain, AD, and S/T-rich region. Homologous analysis showed that PmPIAS protein sequence showed the conserved primary structure compared with other species. Ribbon representation of PIAS protein sequences also showed a conserved structure among species, and the PINIT domain and RLD domain showed the conserved structure compared with the sequence of Homo sapiens. The expression pattern of PmPIAS in different tissues showed significant high expression in the gonad. PmPIAS also exhibited a significantly higher expression in the 1 and 2 days after cold tolerance stress (17°C) and showed its potential in the cold tolerance. The SNP analysis of the exon region of PmPIAS obtained 18 SNPs, and among them, 11 SNPs showed significance among different genotypes and alleles between cold tolerance selection line and base stock, which showed their potential in the breeding for cold tolerance traits.

The use of A. mellifera drone's olfactory sensitivity towards pathological odours as a selection trait in the breeding against V. destructor

The most effective strategy against brood diseases, such as infestation by the mite Varroa destructor, is the early detection and removal of sick brood. Recent findings suggest that genes associated with worker bees' olfactory perception play a central role in Varroa-sensitive hygiene (VSH). In the following approach, Apis mellifera drones' odour sensitivity was examined through a standardised Proboscis extension response (PER) test. Individuals with a positive/negative conditioning outcome to two parasitised-pupae extracts (extract-low and extract-high) were used for breeding. Twenty-one queens from a VSH selection line (SelQ) and nineteen queens from an unselected line (ConQ) were single-drone-inseminated with drones that showed either a positive (SenD+) or a negative (SenD-) PER test. Individual VSH behaviour of a total of 5072 offspring of these combinations (SelQ x SenD+, SelQ + x SenD-, ConQ x SenD+, ConQ x SenD-) was subsequently observed in a specially designed unit with infrared light. The results from the observation were also separately examined, considering the hygienic status of the participating queens and drones. The results of the PER test of the drones were not significantly reflected in the VSH results of the respective offspring. On the other hand, the participating queens/drones' hygienic status was crucial for the manifestation of VSH.

Design of multiplexing circuit using electro-optic effect based optical waveguides

The multiplexer is a combinational circuit that transfers multiple data inputs over a single output line. The input data are selected and transferred to the output line based on the selection line. In this work, 2 × 1 and 4 × 1 multiplexer is proposed. The proposed multiplexer has been worked out using the electro-optic principle. It is implemented using lithium niobate-based Mach–Zehnder interferometer (LN-MZI). LN-MZI is used as an optical switching device. The performance parameters extinction ratio, contrast ratio and insertion loss have been computed and found 31.31, 28.02 and 0.043 dB respectively.

Direct and correlated responses to selection for autumn lambing in sheep

Background Seasonal reproduction limits productivity, flexibility, and profitability in commercial sheep production. Hormonal and (or) photoperiodic manipulation can be used to control estrous cycles in sheep and reduce limitations that are imposed by the seasonal anestrous but are often impractical or incompatible with the extensive management systems preferred for ruminant livestock. Thus, the current study investigated the use of selection to improve realized fertility (i.e., the proportion of ewes that lambed) following an out-of-season spring joining period (May and June) in a crossbred sheep population. Results Over 17 years, estimated breeding values (EBV) for fertility in selected (S) ewes increased by 0.175 (0.01 per year). The mean EBV for fertility of S ewes was greater than that of control ewes by year 10 (P = 0.02), and the fertility of adult (≥ 3 years old) ewes reached 0.88 ± 0.05 by year 17. Lambing began approximately 140 days after the introduction of rams, and 64% of the S ewes that lambed did so in the first 17 days of the potential lambing season, which indicated that most of the S ewes were cycling at the time of ram introduction and were not induced to cycle by the introduction of breeding males (i.e., the so-called “ram effect”). Animals in the S line had modest increases in body weight and scrotal circumference. A modest negative trend in the additive maternal effect on birth weight was observed but was reversed by additional selection on EBV for maternal birth weight. The heritability of litter size in autumn lambing was low (0.04) and could potentially limit the response to selection for this trait. Conclusions Selection improved realized ewe fertility in out-of-season mating, with absolute increases of approximately 1% per year in the percentage of joined ewes that lambed in the autumn. Genetic antagonisms with other performance traits were generally small. A modest antagonism with maternal breeding values for birth weight was observed but it could be accommodated by selection on EBV for maternal birth weight. Our results support results of previous studies that indicate that these selected ewes had one of the shortest seasonal anestrous periods reported for temperate sheep breeds and that spring-lambing lactating ewes from the selection line were capable of relatively rapid rebreeding in the spring.