Landrace Research Articles

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner's strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams' methods included quantitative genetics, classical machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.

Transcriptomic analysis reveals molecular insights into lactation dynamics in Jakhrana goat mammary gland

BackgroundGoat milk is gaining popularity as a superior alternative to bovine milk due to its closer resemblance to human milk. Understanding the molecular processes underlying lactation is crucial for improving milk quality and production in goats. However, the genetic mechanisms governing lactation in goats, particularly in indigenous breeds like the Jakhrana, remain largely unexplored.ResultsIn this study, we performed a comprehensive transcriptomic analysis of Jakhrana goat mammary glands during early and late lactation stages. We isolated milk somatic cells and conducted RNA sequencing, followed by transcript quantification and mapping against the ARS1.2 Capra hircus reference assembly. Our analysis identified differentially expressed genes (DEGs) and commonly expressed genes (CEGs) across the lactation phases. Early lactation showed enrichment of genes encoding antimicrobial peptides and lubrication proteins, while late lactation exhibited heightened expression of genes encoding major milk proteins. Additionally, DEG analysis revealed upregulation of pivotal genes, such as the ABC transporter gene MRP4, implicated in modulating milk composition and quality.ConclusionOur findings provide insights into the genetic mechanisms underlying lactation dynamics in the Jakhrana goat. Understanding these mechanisms could help in improving milk production and quality in goats, benefiting both the dairy industry and consumers.

The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability.

There is evidence that Murciano Granadina (MG), the most important caprine dairy breed in Spain, has been introgressed by African goats, but the precise geographic origin of such introgression has not been identified yet. Moreover, an accurate estimate of the magnitude of this African introgression is lacking, since current estimates are based on small numbers of sampled individuals. The aim of our work was to tackle these two issues by genotyping 500 MG goats with the Goat SNP50 BeadChip and comparing their genotypes with those of reference populations from Spain (Bermeya), France (Saanen), Morocco (Barcha, Draa, Ghazalia, Noire de Atlas, Nord, Moroccan), Egypt (Barki, Oasis, Saidi), Algeria (Arabia, Makatia, M'Zabite, Kabyle), Tunisia (Tunisian native breeds) and Sudan (Desert, Nilotic, Taggar). The population of 500 MG goats was subdivided into 10 datasets of 50 individuals to ensure that sample sizes of the target (MG) and reference populations are balanced. Performance of an unsupervised ADMIXTURE analysis demonstrated that MG goats have a North African ancestry, with an average proportion of 4.4 ± 2.3%. Next, we did a supervised ADMIXTURE analysis that revealed that the Moroccan genetic component reaches a proportion of 4.01 ± 3.9% in MG goats, while the Algerian (0.001 ± 0.001%), Egyptian (0.2 ± 0.1%), Sudanese (0.1 ± 0.1%) and Tunisian (0.3 ± 0.4%) components are present in extremely small proportions. The historical circumstances of this introgression event are currently unknown, but several plausible scenarios are outlined. Moreover, our results show considerable inter-individual heterogeneity regarding the magnitude of the Moroccan introgression of MG goats (0%- 12% depending on the MG data set under analysis). This result implies that reliable estimates about the introgression of autochthonous livestock by exotic breeds can only be obtained by extensively sampling target populations.

Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom

BackgroundSheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.ResultsIn this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.ConclusionOur results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.

Characterization, registration and gazette notification

The first animal to be domesticated by the man was dog which probably occurred at least 14,000 years ago- the animals being used for hunting and as watchdogs. In India many exotic dog breeds (mainly German Shepherd, Labrador, Doberman, Pomeranian etc) are kept as pet but little emphasis has been given to the native dog breeds. Some Indian breeds of dogs reported in India are Caravan Hound, Combai, Chippiparai, Rajapalayam, Rampur Hound, Kanni, Mudhol Hound, Indian Mastiff (Bulli), Himalayan sheep dog, Bhutia dogs, Bhakarwal dogs etc. ICAR-NBAGR has developed methodology for characterization of dog breeds of Indian through systematic survey in the area of its distribution along with Breed Descriptors format for dog breeds. Phenotypic characterization of two indigenous dog breeds viz Rajapalayam and Chippiparai were completed by ICAR-NBAGR. Rajapalayam and Chippiparai dogs are exclusively reared for guarding the farm and farm houses. Chippiparai dogs are even given to brides during marriage. There is huge demand for the pups of these dog breeds. State of Karnataka has also completed the characterization of Mudhol hound breed. All three dog have been registered by ICAR & Gazette notified by Govt. of India.

Deciphering genomic signatures in different Indian milch cattle breeds

In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, four statistical tools (Tajima’s D, CLR, ROH, and iHS) were used on four indigenous cattle breeds. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). Our findings serve as a foundation for identifying selective sweeps responsible for the genetic variation of traits. These sweeps could hold functional significance for multiple cattle breeds across various subcontinents. However, to enhance the robustness of the results, further studies with high-density arrays or whole-genome sequencing, employing greater resolution and larger sample sizes, are warranted.

Genetic variations in HsP90AA1 chaperone gene across diverse Indian native cattle (<i>Bos indicus</i>) breeds adapted to varied agroclimatic regions

Indian zebu cattle during their separate evolution from Bos taurus, have acquired certain changes in a set of genes that regulate the body temperature in response to heat stress. Heat shock proteins (HSPs), the abundant and ubiquitous molecular chaperones play essential role in many cellular biological processes, and are preferentially transcribed in response to heat stress. The objective of this study was to comparatively screen variants/ single nucleotide polymorphisms (SNPs) in the HSP90AA1 gene in cattle breeds, viz., Gir, Kankrej, Ladakhi, Nagori, Nimari, Ongole, Rathi and Sahiwal, adapted to different agroclimatic regions of India including the exotic breed Holstein Friesian and yak (Bos grunniens). Sanger sequencing was carried out in all the translatable exons of the gene. The analysis revealed 6 SNPs – 3 were located in exon 3, 1 SNP each in exon 4 and 6, and another SNP in exon 9. We also identified a novel SNP 2937 (G>T) nucleotide position of exon 9. Interestingly, 2 variants detected at position 1924 (A>G) of exon 3 and 2343 (T>C) of exon 6 with a frequency of 0.9 and 0.73, respectively, were found to be almost fixed in nearly all of the Indian native cattle breeds. These SNPs could potentially be utilized to undertake genotype-phenotype association studies for superior heat stress tolerance trait in Indian native cattle.

СТРУКТУРЫ ИСПОЛЬЗОВАНИЯ ПАХОТНЫХ ЗЕМЕЛЬ В ЛЕСОСТЕПНОЙ ЗОНЕ БАШКИРСКОГО ЗАУРАЛЬЯ СО ВТОРОЙ ПОЛОВИНЫ 20 ВЕКА

We analyzed modern use of arable lands of 1985 in forest-steppe zone of Post-Ural of the Republic of Bashkortostan. Climate is temperate continental. An average annual temperature is 1.6℃ and an average annual precipitation of 427.9 mm. The hottest month is July with an average temperature of 17.5 and the coldest month is January with an average temperature of -14.8℃. Modern agricultural lands usually are used as a hay (43%). Use can be caused with local cattle breeding as traditional horse breeding. Overgrowth captures by 25% of Pinus silvestris. Scot’s pine is growing better on dry lands because it captures more area of overgrowth.

Epigenetic Regulation for Heat Stress Adaptation in Plants: New Horizons for Crop Improvement under Climate Change

Global warming poses a significant threat to plant ecosystems and agricultural productivity, primarily through heat stress (HS), which disrupts photosynthesis, respiration, and overall plant metabolism. Epigenetic modifications, including DNA methylation, histone modifications, and RNA modifications, enable plants to dynamically and heritably adjust gene expression in response to environmental stressors. These mechanisms not only help plants survive immediate stress but also confer stress memory, enhancing their resilience to future HS events. This review explores the mechanisms underlying plant thermotolerance, emphasizing the critical role of epigenetic regulation in adapting to HS. It also highlights how DNA methylation modulates stress-responsive genes, histone modifications facilitate transcriptional memory, and RNA modifications influence mRNA stability and translation. Recent advancements in genome editing technologies, such as CRISPR-Cas9, have enabled precise modifications of epigenetic traits, offering new avenues for breeding climate-resilient crops. The integration of these modern tools with traditional breeding methods holds significant promise for developing crops with enhanced thermotolerance. Despite the potential, challenges such as the stability and heritability of epigenetic marks and the complex interplay between different epigenetic modifications need to be addressed. Future research should focus on elucidating these interactions and identifying reliable epigenetic markers for selection. By leveraging the insights gained from epigenetic studies, we can develop innovative breeding strategies to improve crop resilience and ensure sustainable agricultural productivity in the face of global warming. This review underscores the importance of epigenetic regulation in plant adaptation to heat stress and its potential to revolutionize crop breeding, offering a pathway to secure food production and sustainability under changing climatic conditions.

PSVII-6 Gender prediction in Hanwoo cattle using custom SNP arrays

Abstract Hanwoo is one of the indigenous cattle breeds in South Korea, and genetic evaluation at the national level is conducted using custom Illumina SNP arrays. Accurate gender assignment is essential in genetic evaluation and breeding programs for livestock species. In this study, we described a method for using custom single nucleotide polymorphism (SNP) array data to predict gender of Hanwoo cattle using logistic regression model. We analyzed a set of 958 SNPs, with 947 located on the X chromosome and 11 on the Y chromosome, focusing on heterozygosity rates from the X chromosome and missing rates from Y chromosome SNPs. Using a training dataset comprising 5,000 bulls and 2,005 cows with accurately recorded genders, we built a prediction model. Subsequently, we evaluated the performance of the model on test datasets consisting of 6,657 bulls, 27 steers, and 8,418 cows. The concordance between predicted gender and recorded gender were 99.98%, 100.00% and 99.98% for bulls, steers, and cows, respectively. This result showed better accuracy of gender prediction compared with the GENOMESTUDIO tool that uses only the heterozygosity rate of SNPs in X chromosome in the case of restricted number of SNPs in sex chromosomes. Overall, our findings could be used as an effective method for more precise genetic evaluation by correcting potential gender errors in Hanwoo cattle breeding programs.

PSXII-11 Impact of pre-breeding and breeding supplementation in May-born range heifers on growth rates and reproductive performance

Abstract Our objectives were to determine the impact rumen undegradable protein (RUP) supplementation prior to and during the breeding season had on growth rates and reproductive performance in May-born yearling range heifers. This study was conducted over a 3-yr period at the University of Nebraska, Gudmundsen Sandhills Laboratory (GSL) near Whitman, NE and utilized May-born Red Angus x Simmental crossbred heifers [n = 192; weaning body weight (BW) = 200 kg ± 28 kg]. Heifers were randomly assigned by pre-breeding BW to one of two treatments: 1) received 0.908 kg of a dried distillers grain supplement (DDGS; Supp, n = 66) pre-breeding through the breeding season or 2) received no supplement (NoSupp, n = 138). Each year, treatments were initiated in July and ended in August (55 ± 3 d). Using a C-Lock Smart Feeder (Rapid City, SD) heifers had individual access to their allotted DDGS supplementation. On average, NoSupp heifers consumed 0.09 kg/d (yr 1) and 0.02 kg/d (yr 2 and 3); whereas, Supp heifers averaged 0.59, 0.74, and 0.76 kg/d in yr 1, 2, and 3, respectively. Heifer BW was collected pre-trial (May), pre-breeding (July), breeding (August), pregnancy diagnosis (October), and pre-calving (April). Body condition score (BCS) was collected at pregnancy diagnosis (October) and pre-calving (April; Yr 1 and 2). Before each breeding season, two blood samples were collected 10 d apart to determine pubertal status. Heifers were synchronized with a single 5 mL intramuscular injection of prostaglandin F2 alpha (Lutalyse, Zoetis, Parsippany, NJ) 5 d after bull turnout during a 30 d natural service breeding season. Pregnancy diagnosis was determined via rectal ultrasound in October. No differences (P > 0.12) in BW were noted among treatments for all measurement timepoints. Moreover, SUPP heifers had greater (P < 0.02) average daily gain (ADG) from pre- trial to pregnancy diagnosis compared with NoSUPP heifers. However, there was no differences (P = 0.11) in ADG from pregnancy diagnosis to pre- calving. At pregnancy diagnosis (October), a treatment x year interaction (P = 0.02) for BCS was present where Supp heifers had a greater BCS than NoSupp heifers in yr 3. Heifer BCS pre-calving was not affected (P = 0.12) by treatment. There was a greater percentage (P < 0.01) of SUPP heifers cycling compared with NoSUPP heifers. However, there were no differences (P > 0.24) in pregnancy rates, the percentage that calved in the first 21 d, calf birth BW, or subsequent calving date. Ultimately, this study implies that providing a RUP supplement prior to and during the breeding season will increase the percentage of heifers that are cycling before breeding and have a greater ADG through pregnancy diagnosis; however, supplementation will not impact other reproductive parameters or BW gains.

NMR-Based Metabolomic Analysis of Biotic Stress Responses in the Traditional Korean Landrace Red Pepper (Capsicum annuum var. annuum, cv. Subicho).

Korean landrace red peppers (Capsicum annuum var. Subicho), such as the traditional representative Subicho variety, are integral to Korean foods and are often consumed raw or used as a dried powder for cuisine. However, the known vulnerability of local varieties of landrace to biotic stresses can compromise their quality and yield. We employed nuclear magnetic resonance (NMR) spectroscopy coupled with a multivariate analysis to uncover and compare the metabolomic profiles of healthy and biotic-stressed Subicho peppers. We identified 42 metabolites, with significant differences between the groups. The biotic-stressed Subicho red peppers exhibited lower sucrose levels but heightened concentrations of amino acids, particularly branched-chain amino acids (valine, leucine, and isoleucine), suggesting a robust stress resistance mechanism. The biotic-stressed red peppers had increased levels of TCA cycle intermediates (acetic, citric, and succinic acids), nitrogen metabolism-related compounds (alanine, asparagine, and aspartic acid), aromatic amino acids (tyrosine, phenylalanine, and tryptophan), and γ-aminobutyric acid. These findings reveal the unique metabolic adaptations of the Subicho variety, underscoring its potential resilience to biotic stresses. This novel insight into the stress response of the traditional Subicho pepper can inform strategies for developing targeted breeding programs and enhancing the quality and economic returns in the pepper and food industries.

Analysis of the Genetic Diversity and Genetic Structure of Jiangshan Black Pigs Using Single Nucleotide Polymorphism (SNP) Chips.

The Jiangshan black pig is an indigenous pig breed in China, renowned for its superior meat quality and adaptability to roughage. However, the population of Jiangshan black pigs has dwindled due to the introduction of cosmopolitan pig breeds and the outbreak of African swine fever, putting them at risk of extinction. To offer insights into the conservation and breeding of Jiangshan black pigs, this study involved 118 Jiangshan black pigs as the research subjects and employed the Zhongxin-1 Porcine Breeding Array PLUS chip to detect whole-genome SNPs. Additionally, various software tools were utilized to accurately analyze the genetic diversity, phylogenetic relationship, inbreeding coefficient, and pedigree structure of the Jiangshan black pig conservation population. The findings indicated that the effective population size (Ne) of the Jiangshan black pig was 4.9, with an average inbreeding coefficient of 0.253 within the population. A genetic relationship analysis identified that the 16 male pigs were clustered into four families, and the 100 female pigs were also assigned to these familial groups. Furthermore, two female pigs were classified as "other" due to their distant genetic relatedness to all the males. These results contribute to a better understanding of the current status of the conservation of the Jiangshan black pig population and offer a theoretical foundation for the development of conservation strategies.

A study on the diversity of phlebotomine sand flies (Diptera, Psychodidae) in karstic limestone areas in Vientiane Province, Laos, with a description of two new species of Sergentomyia França and & Parrot

BackgroundSoutheast Asia is well known as a hotspot of biodiversity. However, very little is known about cave-dwelling hematophagous insects that are medically important. Taxonomic knowledge and ecology of phlebotomine sand flies are very poorly studied in Laos, as well as in other countries in the region. Herein, we report species diversity data and some notes on the ecology of the detected species from these karstic limestone areas of Laos.MethodsPhlebotomine sand flies were collected using Centers for Disease Control and Prevention (CDC) light traps from limestone cave locations in three districts of Vientiane Province, Laos. Both morphological and molecular techniques were used for sand fly identification. Species diversity and abundance were analyzed according to sites, locations, collection seasons, and trapping positions.ResultsA total of 6564 sand flies, of which 5038 were females and 1526 were males, were morphologically identified into 20 species belonging to five genera (Chinius, Idiophlebotomus, Phlebotomus, Sergentomyia, and Grassomyia). The most abundant species were Chinius eunicegalatiae, Phlebotomus stantoni, Sergentomyia hivernus, Se. siamensis, and Idiophlebotomus longiforceps. Cytochrome b analysis results supported the morphological identification and revealed that Se. siamensis was separated from other members of the Se. barraudi group. Two new species, Se. dvoraki n. sp. and Se. marolii n. sp., were described. Sand fly density was generally high except in a cave in Vangvieng, with species richness ranging from 14 to 18 across different caves. Outside caves had higher species richness (R = 20) and diversity (H = 2.50) than cave entrances (R = 18, H = 2.41) and interiors (R = 16, H = 2.13). Seasonal variations showed high sand fly density in Feung and Hinheup during both dry and rainy seasons, while Vangvieng had a notable decrease in density during the dry season (D = 6.29).ConclusionsThis study revealed that the diversity of phlebotomine sand fly fauna in Laos, particularly in karstic limestone areas, is greater than previously known. However, the taxonomic status of many species in Laos, as well as Southeast Asia, still needs more in-depth study using both morphological characters and molecular methods. Many species could be found from inside, at the entrance, and outside of caves, indicating a wide range of host-seeking behavior or possible natural breeding in the karstic cave areas.Graphical abstract

A novel codominant plumage color pattern of white breast patches in WugangTong geese was controlled by EDNRB2

Two basic plumage color patterns are observed in adult geese: solid grey (G) or colorless white (W). However, a Chinese indigenous breed, the Wugangtong goose (WGT), continues to be subject to selective breeding efforts as it displays segregation of plumage colors, including G, W, and a novel color pattern designated Wb (G with white breast circles). The underlying genetic mechanisms responsible for the Wb phenotype are yet to be determined. The current study employed the population differentiation index (FST) to analyze 90 geese exhibiting diverse plumage colors, identifying the fifth intron of EDNRB2 as a particularly noteworthy region with the highest FST values. Sanger sequencing of the region surrounding the EDNRB2 gene identified a 14-bp insertion within exon 3 as the causal mutation. The heterozygosity of this 14-bp insertion and wild-type alleles was completely associated with the Wb phenotype, thereby substantiating the codominant nature of the G and W phenotypes. An inter-species corroborated this finding cross between the graylag (no 14-bp insertion) and the swan goose (homozygous for the 14-bp insertion) breeds, as hybrids from this cross exhibited the Wb phenotype. Transcriptomes from white breast patches and gray dorsal skins of 4 Wb geese were compared. A significant downregulation of genes involved in melanin synthesis and melanocyte development was observed, including EDRNB2 and MLANA. The downregulation of MLANA indicated that the mutated EDNRB2 resulted in melanocyte loss in specific body regions, as MLANA is a marker gene for melanocytes. The findings were corroborated by melanin staining using the Mansson-Fontana method, which revealed no melanin particles deposited in the white breast patches. In summary, the gray plumage color was codominant to the white color in WGT geese, and plumage color variations were controlled by EDNRB2. The findings of our study offer valuable and practical guidance for the purification of plumage colors among WGT, whether through traditional phenotype selection or molecular breeding methods.

Geographic patterns and ecological adaptations of Manila clam (Ruditapes philippinarum) along the Chinese coast: Insights from migration dynamics and gene flow

The Manila Clam (Ruditapes Philippinarum) is one of the most economically significant marine bivalves along the China coast. In recent years, due to the escalating scale of aquaculture, the artificial activities of "cross-regional introduction" have to some extent exerted an influence on the genetic diversity and structure of clam larvae, leading to an ongoing occurrence of genetically mixed clam larvae populations and ambiguous genetic foundation of germplasm resources in China. Therefore, there is an imperative need to gain profound insights into the lineage, genetic structure, and assess the adaptability potential of clams originating from both northern and southern regions. We use Specific Locus Amplified Framents technology to simplify genome sequencing of wild clams along the coast of China. Through genetic diversity, genetic structure, gene flow, and selection elimination analysis, the results show that clams can be divided into distinct north-south lineages, with Wafangdian in Liaoning (RPLW), Zhangzi Island in Liaoning (RPLZ), and Laizhou in Shandong (RPSL) comprise the northern lineage, while Lianjiang in Fujian (RPFL) constitutes the southern lineage. The artificial relocation of clams in China has resulted in a blended population structure among local clams. The genetic functional differences between clams from the north and south are primarily manifest in energy metabolism, and the adaptive evolution of clams is mainly associated with temperature. This integrative research not only furnishes valuable insights into the genetic structure of clam populations, thereby contributing to the advancement of natural conservation and genetic breeding efforts for clams but also establishes the groundwork for a comprehensive exploration of clam adaptive evolution.

Effect of Ash, Crude Protein and Nitrogen in Traditional Varieties of Rice Against Sitophilus oryzae (L.) Infestation in Storage

Effect of Ash, Crude Protein and Nitrogen in Traditional Varieties of Rice Against Sitophilus oryzae (L.) Infestation in Storage

Genomic and Conventional Inbreeding Coefficient Estimation Using Different Estimator Models in Korean Duroc, Landrace, and Yorkshire Breeds Using 70K Porcine SNP BeadChip.

The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. Sus scrofa chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between FROH total and FROH1-2Mb, showing that short ROH were the primary contributors to overall FROH values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (FROH) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes.

Effect of Dietary Supplementation of Buffer and Application of Herbal Teat Dip on the Milk Composition of Lactating Rathi Cattle

Background: Nowadays, there is an increasing demand among the consumers for clean milk or superior quality milk and milk products. The current scenario of dairy sector in India showcases a low productivity among the indigenous dairy breeds which requires the employment of nutritional and managemental interventions to improve the milk quality as well as performance of lactating cattle. The use of buffers like trisodium citrate and herbal post milking herbal teat dip are part of such interventions. The current study is aimed at evaluating the effect of such interventions on the milk quality of lactating Rathi cattle. Methods: Twenty-four cattle were selected at LRS, Bikaner and divided into four treatment groups consisting of six cattle each. The experiment was conducted for 60 days, where T1 group was used as control, T2 group was given the basal diet along with oral supplementation of buffer trisodium citrate @ 30 mg/kg body weight, T3 group received the basal diet along with the topical application of herbal teat dip (aloe vera, turmeric, lemon extract and castor oil) and T4 group was given the basal diet along with a combination of oral supplementation of trisodium citrate @ 30 mg/kg body weight as well as the topical application. The milk samples of the experimental animals were examined for milk fat per cent, milk SNF per cent, milk lactose per cent and milk protein per cent. Result: The results of the study revealed that there was a significant effect (P less than 0.05) of buffer supplementation and application of herbal teat dip on milk fat per cent, whereas it was highly significant (P less than 0.01) for milk SNF per cent between the control and treatment groups. There was no significant effect observed in milk lactose percent or milk protein per cent.

Elucidating the Genetic Regulation of Reproductive Prolificacy in Tibetan Sheep Through Ovarian Tissue Sequencing

Background: This study aims to unravel the genetic intricacies regulating the reproductive prolificacy of Tibetan sheep, an indigenous breed prominently found in the Qinghai-Tibet Plateau. Methods: We employed meticulous sequencing and analytical strategies to discern the differential expressions of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in the ovarian tissues of ewes with varying lambing numbers. Result: In our study, we identified 817 genes with differential expression in twin-bearing ewes compared to those bearing single lambs. This group comprised 495 upregulated and 322 downregulated genes, featuring key candidates like COL1A1, COL1A2, BMPRIB, GDF9, BMP15 and TGFB2. Furthermore, we discovered a notable difference in the expression of long non-coding RNAs (lncRNAs) in ewes birthing twins as opposed to singles, with 210 differentially expressed lncRNAs identified, including 91 upregulated and 119 downregulated. Key genes and lncRNAs associated with reproductive efficiency were identified, contributing valuable insights into the underlying molecular mechanisms and offering a robust foundation for enhancing breeding strategies and overall livestock productivity.