Traits Of Economic Importance Research Articles

PSXII-11 Comparison of Egg-Laying Ability Among Eight Lines Including Korean Native Chicken (KNC)

Abstract Chicken egg production capacity is an important economic trait in the poultry industry. To improve the usability of Korean Native chicken (KNC), we measured the egg traits [age of first egg (AFE), first egg weight (FEW), egg number (EN), egg weight (EW)] and performed a comparative analysis. Age of first egg is the number of days an individual starts producing eggs. FEW is the weight of the first egg produced. EN and EW are the number of eggs produced between 20 and 40 weeks old and the weight of the eggs. The chicken breeds we used in our study were KNC (GBY, GWY, CNB, CNW, CNY, CNK), Ameraucana (AMR) and Leghorn (LEG). The CNK line started laying eggs at 140.75 ± 6.23 days. The AFE of CNK was faster than LEG (142.35 ± 7.20, P < 0.05). The weight of the first egg after starting egg production AMR line (44.1 ± 5.20g) produced the heaviest egg among the investigative groups (P < 0.05). The CNY line laid the lightest egg (31.9 ± 3.80g). FEW of KNC was less than that of both LEG and AMR breeds (P < 0.05). The AFE was late and FEW was the greatest in the AMR breed. The LEG which is a representative laying hen laid the most EN between 20 and 40 weeks of age (118.35 ± 10.07). LEG was greater than the CNK (106.85 ± 14.66), which laid the second most (P < 0.05). The CNB (82.45 ± 20.68) showed the least EN. The EW of the AMR (54.20 ± 4.30) was the heaviest (P < 0.05). On the contrary, Six KNC (CNK: 45.70 ± 3.00, GBY: 45.20 ± 3.10, GWY: 45.20 ± 2.20, CNB: 44.60 ± 3.20, CNY: 43.70 ± 3.90, CNW: 43.50 ± 3.40) lines produced lighter eggs than LEG (51.50 ± 3.50) and AMR (P < 0.05). In conclusion, the average egg production performance of the KNC six lines was generally less than that of the LEG and AMR breeds. However, some lines of KNC confirmed that the start date of egg production was faster than other breeds. These results will be used to investigate the genomic pattern of egg production in KNC population and provide fundamental data for gene-based selection to improve egg production.

112 Definition and Genetic Parameters Estimation for Climatic Resilience Indicators Derived from Longitudinal Vaginal Temperature Records in Lactating Sows Under Heat Stress Conditions

Abstract Climatic resilience (CR) can be defined as the ability of an animal to maintain euthermia under thermally stressful conditions. However, CR based on longitudinal physiological variables has not been included in current swine genetic selection schemes. This is the first study deriving novel CR indicators using automatically recorded vaginal temperatures (TV) and estimating genetic parameters for them. Therefore, the study objectives were to: 1) derive novel indicators of CR based on automatically recorded vaginal temperature (TV); and 2) estimate (co)variance components and genetic parameters for these indicators. TV of 1,381 lactating sows (parities 2 to 7; Landrace × Large White) were measured automatically every 10 minutes from June 5th, 2021 to July 30th, 2021 using a vaginally implanted thermochron data recorder. A total of 1,639 F1 (Landrace x Large White) sows within the studied population were genotyped using the PorcineSNP50K Bead Chip. A total of 18 HS indicators derived from Tv, their definitions, heritability estimates, and mean genomic estimated breeding value (GEBV) accuracies are shown in Table 1. Multi-trait animal models were fitted for estimating the (co)variance components, considering the effects of week of data collection, parity, and location (barn and room within barn) as fixed. Heritability estimates for these resilience traits ranged from 0.0004 ± 7.16E-6 (SlopeDe) to 0.291 ± 0.047 (HSAB). Most traits derived directly from vaginal temperature (e.g., Duration: 0.201 ± 0.033, MaxTv: 0.203 ± 0.032) are moderately heritable with substantial additive genetic variance. Besides, LnVar(Med) that is derived from the deviation between the real and predicted value had moderate heritability (0.196 ± 0.041) and high mean GEBV accuracy (0.616 ± 0.042). The indicators defined based on the slope of Tv and time had low heritability estimates, which are close to zero, and low mean GEBV accuracy (0.106 ± 0.050 – 0.337 ± 0.065). Among all the CR indicators, Duration, MaxTv, Nor_medvar, Nor_avevar, HSAA, and HSAB outperformed the other indicators with moderate heritability estimates and high average GEBV accuracies. Genetic correlations were estimated among the six indicators with moderate heritability and high mean GEBV accuracy. Moderate to high positive genetic correlations (0.508 ± 0.034 to 0.992 ± 0.025) were estimated among Duration, MaxTv, Nor_medvar, HSAB, and HSAA. LnVar(Med) showed low negative genetic correlations (-0.218 ± 0.028 to -0.039 ± 0.018) with the traits Duration, MaxTv, HSAA, and HSAB, except with Nor_medvar, which was positive (0.156 ± 0.022). Thus, Duration, LnVar(Med), MaxTv, Nor_medvar, HSAB, and HSAA might be promising CR indicator and contribute toward improving lactating sows’ resilience to thermal stress through genetic selection. New studies about the relationship between these new indicators and other economic important traits in pigs are required before including them in selection indexes.

72 The AG2pi Vision for Resources in Agricultural Genomics and Phenomics: How Asas Can Contribute

Abstract To meet the challenges of an increasing global population and multiple environmental stressors on agricultural production, it is essential to better understand how genotype (G) and environment (E) influence phenotype for traits of economic importance in agriculture. To accomplish this requires interdisciplinary teams consisting of researchers from crop and livestock sciences, genetics, genomics, computational and data sciences, and engineering. Towards this end, in 2020, Congress established the Agricultural Genome to Phenome Initiative (AG2PI). An important objective of this presentation is to encourage strong participation of animal science researchers and industry in ongoing AG2PI activities. The purpose of the initial AG2PI project, awarded to Iowa State University and the Universities of Arizona, Idaho and Nebraska, was to assemble and prepare a community to conduct AG2P research across the plant and animal kingdoms. The AG2PI project aims to: a) identify research gaps and opportunities, b) foster community solutions to these challenges, and c) rapidly disseminate findings for community use. Training workshops, field days, conferences, community surveys, and seed grants have all contributed to these goals. Opinions and ideas from the crop and livestock genetics communities are key to advancing AG2P science and related work. AG2PI has used online community surveys and in-person conferences to gather these and to facilitate transdisciplinary communications. In September 2022, AG2PI held a conference titled “Thinking Big: Visualizing the Future of AG2PI”, in which attendees participated in focused small group discussions to identify which agricultural G2P-related topics are most critical for future R&D funding and which may be the most difficult to achieve. These discussions are summarized in a concept paper for the community, shared with USDA-NIFA, and submitted for publication. A follow-up conference was held June 14-15, 2023, in Kansas City, where people working in both the animal and plant genetics research communities and industry stakeholders attended. Outcomes from this conference will be summarized in this presentation, and requests for animal scientists to provide further input will be made. The future of agricultural genomics will be shaped by both the participants in AG2PI and the solutions developed by the AG2PI community. Funding for this work comes from USDA NIFA awards 2022-70412-38454, 2021-70412-35233, and 2020-70412-32615.

Polymorphism of ADAM12, DPP6 and PRKN genes and their associations with milk production traits in Holstein.

Milk production traits as the most important economic traits of dairy cows, they directly reflect the benefits of breeding and the economic benefits of pasture. In this study, A disintegrin and metalloproteinase-12 (ADAM12), Parkinson's disease gene 2 (PRKN) and dipeptidyl peptidase-like protein subtype 6 (DPP6) polymorphism in 384 Chinese Holstein cows were detected by time-of-flight mass spectrometry and through statistical analysis using software such as Popgene 32, SAS 9.4 and Origin 2022, the relationship between single nucleotide polymorphisms (SNPs) of three genes with four milk production traits such as daily milk yield (DMY), milk fat percentage (MFP), milk protein percentage (MPP) and somatic cell score (SCS) was verified at molecular level. The results showed that four polymorphic loci (116,467,133, 116,604,487, 116,618,268 and 116,835,111) of DPP6 gene, two polymorphic loci (97,665,052 and 97,159,837) of PRKN gene and two polymorphic loci (45,542,714 and 45,553,888) of ADAM12 gene were detected. PRKN-97665052, DPP6-116467133, ADAM12-45553888, DPP6-116604487 and DPP6-116835111 were all in Hardy-Weinberg equilibrium state (p > .05). ADAM12-45542714, PRKN-97159837 and PRKN-97665052 were moderately polymorphic (0.25 ≤ PIC <0.50) in Holstein. It is evident that the selection potential and genetic variation of these five loci are relatively large, and the genetic richness is relatively high. The correlation analysis of different genotypes between these eight loci and milk production traits of Holstein showed that ADAM12-45542714 and DPP6-116835111 (p < .01) had an extremely significant effects on the DMY of Chinese Holstein in Ningxia, while PRKN-97665052 had an extremely significant effect on MFP (p < .01). The effect of PRKN-97665052 and DPP6-116467133 on MPP of Holstein were extremely significant (p < .01). DPP6-116618268 had an extremely significant effect on the SCS of Holstein in Ningxia (p < .01), and AA genotype individuals showed a higher SCS than GG genotype individuals; the other two loci (ADAM12-45553888 and DPP6-116604487) had no significant effects on milk production traits of Holstein (p > .05). In addition, through the joint analysis of DPP6, PRKN and ADAM12 gene loci, it was found that the interaction effect between the three gene loci could significantly affect the DMY, SCS (p < .01) and MPP (p < .05). In conclusion, several different loci of DPP6, PRKN and ADAM12 genes can affect the milk production traits of Holstein to different degrees. PRKN, DPP6 and ADAM12 genes can be used as potential candidate genes for milk production traits of Holstein for marker-assisted selection, providing theoretical basis for breeding of Holstein.

Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons

Plumage color is an important economic trait for breed feature identification and consumer's requirement in pigeons. The domestic pigeon has multiple type of plumage color, thereby providing a unique opportunity for identify the genetic basis of plumage coloration. White feather color is common for meat and medicinal use. To investigate the genetic variation associated with white plumage color in pigeons, we use genome resequencing and population genomics to identify the genomic regions with strong selective signature between pigeons with brown and white plumage color. Meanwhile, we obtained some candidate genes with melanin or melanosome biosynthesis in selected region. Finally, we identified a missense mutation p.E256K in the EDNRB2 completely associated with white plumage color. These findings provide a basis for genetic variation in pigeons with plumage color phenotype.

179 Identification of Regulatory Mutations Affecting Complex Traits

Abstract Understanding genetic bases controlling complex traits of economic importance is fundamental to improve breeding programs. Recent efforts from FAANG consortium resulted in significant progress in the identification of regulatory regions in farm animals. However, most studies in cattle have focused on Bos taurus, and limited information is available for Bos indicus. Considering that Bos indicus is the predominant subspecies in tropical regions, the objective of this work was to identify regulatory variants associated with meat quality by combining information from whole genome sequence (WGS), gene expression (RNA-seq), and open chromatin regions (ATAC-seq). For genome wide association study (GWAS), an imputed panel of SNPs was obtained from WGS of 26 sires, a Bovine HD 770K panel of 374 progenies, and SNPs called from RNA-seq data of Longissimus thoracis muscle (LT) of 192 progenies. The SNPs were identified using GATK4, and the dataset included almost 4.5 million variants that were pruned to 553,581 tag-SNPs (PLINK, r2 = 0.8). ATAC-seq data was obtained from duplicated samples of LT collected from two animals. Phenotype data included back fat thickness (BFT), intramuscular fat (IMF), ribeye area (REA) and shear force (SF). Association of genotypes (553,581 SNPs) and gene expression (12,991 genes), performed in Matrix eQTL resulted in 36,916 cis-eQTL and 14,408 trans-eQTL (FDR &amp;lt; 0.05). For GWAS analysis of the eQTLs with phenotypic traits, we used a linear model in PLINK program (considering population stratification, contemporary group and hot carcass weight). GWAS resulted in 24 eQTLs associated with IMF, three with BFT, 12 with REA, and eight with SF (FDR &amp;lt; 0.10). ATAC-seq analysis (using nfcore/atacseq pipeline implemented in Nextflow) resulted in 33,734 consensus peaks with a mean size of 2.4 kb. The overlap analyses among GWAS, eQTL, and ATAC-seq positions resulted in two, four and one putative regulatory regions that control gene expression and are associated with BFT, IMF and SF, respectively. Functional studies are still necessary to establish if identified mutations are the causal mutation. In conclusion, integration of GWAS, RNAseq, and ATAC-Seq data can result in identification of regulatory mutations associated with phenotypes of economic importance.

Transcriptome analysis of divergent residual feed intake phenotypes in the M. longissimus thoracis et lumborum of Wannan Yellow rabbits

Introduction: Feed efficiency is an important economic trait in rabbit meat production. The identification of molecular mechanisms and candidate genes for feed efficiency may improve the economic and environmental benefits of the rabbit meat industry. As an alternative to the conventional feed conversion ratio, residual feed intake (RFI) can be used as an accurate indicator of feed efficiency.Methods: RNA sequencing was used to identify the differentially expressed genes (DEGs) in the M. longissimus thoracis et lumborum of eight Wannan Yellow rabbits with excessively high or low RFIs (HRFI or LRFI, respectively). Thereafter, Gene Ontology (GO) analysis, enrichment using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, gene set enrichment analysis (GSEA), and protein–protein interaction (PPI) network analysis was conducted.Results: In total, 445 DEGs were identified in the M. longissimus thoracis et lumborum of rabbits with high and low RFIs. The significantly enriched GO terms identified in these two groups were primarily involved in energy and mitochondrial metabolism and oxidation–reduction processes. KEGG analysis identified 11 significantly enriched pathways, including oxidative phosphorylation, PI3K-Akt signaling, and extracellular matrix-receptor interaction pathways. According to GSEA, the expressions of genes and pathways related to mitochondrial function were upregulated in HRFI rabbits, whereas genes with upregulated expressions in LRFI rabbits were related to immune response and energy metabolism. Additionally, PPI network analysis revealed five potential candidate genetic markers.Conclusion: Comparative analysis of the M. longissimus thoracis et lumborum transcriptomes in HRFI and LRFI rabbits revealed FOS, MYC, PRKACB, ITGA2, and FN1 as potential candidate genes that affect feed efficiency in rabbits. In addition, key signaling pathways involved in oxidative phosphorylation and PI3K-Akt and ECM-receptor interaction signaling impact rabbit feed efficiency. These findings will aid in breeding programs to improve feed efficiency and optimize RFI selection of rabbits for meat production.

Analysis of liver miRNA in Hu sheep with different residual feed intake.

Feed efficiency (FE), an important economic trait in sheep production, is indirectly assessed by residual feed intake (RFI). However, RFI in sheep is varied, and the molecular processes that regulate RFI are unclear. It is thus vital to investigate the molecular mechanism of RFI to developing a feed-efficient sheep. The miRNA-sequencing (RNA-Seq) was utilized to investigate miRNAs in liver tissue of 6 out of 137 sheep with extreme RFI phenotypic values. In these animals, as a typical metric of FE, RFI was used to distinguish differentially expressed miRNAs (DE_miRNAs) between animals with high (n = 3) and low (n = 3) phenotypic values. A total of 247 miRNAs were discovered in sheep, with four differentially expressed miRNAs (DE_miRNAs) detected. Among these DE_miRNAs, three were found to be upregulated and one was downregulated in animals with low residual feed intake (Low_RFI) compared to those with high residual feed intake (High_RFI). The target genes of DE_miRNAs were primarily associated with metabolic processes and biosynthetic process regulation. Furthermore, they were also considerably enriched in the FE related to glycolysis, protein synthesis and degradation, and amino acid biosynthesis pathways. Six genes were identified by co-expression analysis of DE_miRNAs target with DE_mRNAs. These results provide a theoretical basis for us to understand the sheep liver miRNAs in RFI molecular regulation.

Looking back at five decades of embryo technology in practice

This paper covers developments from International Embryo Technology Society (IETS) meetings over the past 50 years. The IETS was officially ‘born’ at a meeting in Denver, Colorado on Sunday 26 May 1974. There have been 51 IETS meetings (the first was in May 1974), and the first conference at which papers were presented was in 1975. The name of the IETS was changed from International Embryo Transfer Society to International Embryo Technology Society in 2016. The annual IETS conferences are held once a year in January. Embryo technology advanced from the laborious and slow techniques of surgical recovery and transfer of bovine embryos to non-surgical recovery and transfer in many species. Cryopreservation of embryos was initially a slow process that met with only moderate technical success before the development of technology that resulted in high embryo survival rates. The polymerase chain reaction was used to determine the sex of embryos following laminar flow cytology, which came into use to separate X- and Y-bearing spermatozoa. IVF has grown to become widely used, and several factors make it more useful than superovulation and embryo recovery/transfer. Perhaps the most important tool of all was the system that allowed the genetic ‘mapping’ of the genomic sequence of Bos taurus cattle. Charting key DNA differences by scientists, ‘haplotypes’ are now used routinely to identify animals with desirable traits of economic importance, discover new genetic disorders, and track carrier status of genotyped animals. Future technology is discussed.

Genome-wide association study reveals candidate genes for traits related to meat quality in Colombian Creole hair sheep

Genome-wide association studies (GWAS) allow identifying genomic regions related to traits of economic importance in animals of zootechnical interest. The objective of this research was to conduct a genome-wide association study on meat quality traits using the Illumina OvineSNPs50 BeadChip array. The animals were sampled in the departments of Córdoba, Cesar, and Valle del Cauca. The genotypes obtained with the Illumina OvineSNP50 BeadChip microarray were analyzed SNP (single-nucleotide polymorphism) data to conduct a GWAS for pH and water-holding capacity (WHC) traits measured after 7 days of maturation, in the Longissimus dorsi (LD) muscle, in 167 Creole hair sheep of 12 months old belonging to Pelibuey (CHSP, n = 60), Ethiopian (CHSE, n = 44), and Sudan (CHSS, n = 63) breeds. The GWAS was done using a mixed linear model (MLMA) and based on the Ovis aries v3.1 genome. The CHSE showed the lowest meat juice release and, consequently, the highest water-holding capacity (WHC = 30.6 ± 0.1), suggesting that this breed has better performance in the meat industry compared with CHSS (WHC = 41.7 ± 0.1) and CHSP (WHC = 36.8 ± 0.1), since there is a relationship between WHC and juiciness. For the character pH, it was not possible to annotate genes related to meat quality, while, for the WHC, they have obtained 11 candidate genes associated (ELOVL2, ARAP2, LOC101102527, SHOC2, AIPL1, CSRNP3, IFRD, KDM8, NANS, DAPK1, IBN2, TPM2). Particularly, ELOVL2, ARAP2, IBN2, and TPM2 genes are involved in muscle contraction and fatty acid composition in sheep. In this study, we generated a baseline for GWAS related to meat quality traits in Colombian Creole hair sheep that can be used for future genomic selection plans.

Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep

Copy number variation (CNV) is a genetic structural polymorphism important for phenotypic diversity and important economic traits of livestock breeds, and it plays an important role in the desired genetic variation. This study used whole genome sequencing to detect the CNV variation in the genome of 6 local Tibetan sheep groups. We detected 69,166 CNV events and 7230 copy number variable regions (CNVRs) after merging the overlapping CNVs, accounting for 2.72% of the reference genome. The CNVR length detected ranged from 1.1 to 1693.5 Kb, with a total length of 118.69 Mb and an average length of 16.42 Kb per CNVR. Functional GO cluster analysis showed that the CNVR genes were mainly involved in sensory perception systems, response to stimulus, and signal transduction. Through CNVR-based Vst analysis, we found that the CACNA2D3 and CTBP1 genes related to hypoxia adaptation, the HTR1A gene related to coat color, and the TRNAS-GGA and PIK3C3 genes related to body weight were all strongly selected. The findings of our study will contribute novel insights into the genetic structural variation underlying hypoxia adaptation and economically important traits in Tibetan sheep.

Integrated Analysis of the Effects of Cecal Microbiota and Serum Metabolome on Market Weights of Chinese Native Chickens.

The gut microbiota plays an important role in the physiological activities of the host and affects the formation of important economic traits in livestock farming. The effects of cecal microbiota on chicken weights were investigated using the Guizhou yellow chicken as a model. Experimental cohorts from chickens with high- (HC, n = 16) and low-market-weights (LC, n = 16) were collected. Microbial 16S rRNA gene sequencing and non-targeted serum metabolome data were integrated to explore the effect and metabolic mechanism of cecal microbiota on market weight. The genera Lachnoclostridium, Alistipes, Negativibacillus, Sellimonas, and Ruminococcus torques were enriched in the HC group, while Phascolarctobacterium was enriched in the LC group (p < 0.05). Metabolomic analysis determined that pantothenic acid (vitamin B5), luvangetin (2H-1-benzopyran-6-acrylic acid), and menadione (vitamin K3) were significantly higher in HC serum, while beclomethasone dipropionate (a glucocorticoid) and chlorophene (2-benzyl-4-chlorophenol) were present at higher levels in the LC group. The microbes enriched in HC were significantly positively correlated with metabolites, including pantothenic acid and menadione, and negatively correlated with beclomethasone dipropionate and chlorophene. These results indicated that specific cecal bacteria in Guizhou yellow chickens alter the host metabolism and growth performance. This study provides a reference for revealing the mechanism of cecal microbe actions that affect chicken body weight.

Genome-Wide Association Mapping of Processing Quality Traits in Common Wheat (Triticum aestivum L.).

Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2-42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection.

Investigation for Mutation in BMPR-1B (FecB) Fecundity Gene in Awassi Sheep

Reproduction related traits in sheep such as ovulation rate and litter size are traits of high economic importance but as these traits are only expressed in one sex and in mature animals, thus inclusion of them in selection strategies is limited. Therefore, studying genes associated with reproductive events provides genotypic data, which is more useful in genetic improvement of sheep in a short period of time. Such reproductive traits in sheep are genetically controlled by genes having both additive and major effects. Booroola is the first gene identified in Booroola Merino sheep in Australia has major effects on ewe’s reproduction and has gained much popularity in sheep breeding for its immense economic value. Booroola or Bone Morphogenetic Protein Receptor -1B (BMPR-1B) gene is in chromosome 6 and FecB allele is the result of a single mutation in this gene where one copy of this allele results in a significant increase in ovulation rate thus outcome as increased lambing per parturition. The Awassi sheep is an indigenous breed of Turkey and identifying major genes for fecundity could greatly improve their breeding program. To identify the FecB gene in Awassi sheep, 88 blood samples were taken, and DNA was extracted by salting out method. After PCR amplification and AvaΠ digestion, the samples were analyzed for FecB mutation and all of 88 samples were found not to carry the mutant allele (FecB).

Development and characterization of F1 hybrids involving cultivated and related species of okra

Related species of any crop posses the traits of economic importance. It is important to involve the related wild species in the breeding programme to transfer the traits of economic importance to the cultivated species of crop plants. Further, the characterization of interspecific F1 hybrids is required to know the expression of various traits in both parents and their interspecific hybrid. Cultivated species of okra Abelmoschus esculentus was used to develop two interspecific F1 hybrids independently with two wild species, namely A. moschatus and A. tuberculatus. Both the related species were used as the pollen parent and the cultivated okra as the female parent. The interspecific hybrids were intermediate for days to 50% flowering, first flowering node, flower length, fruit length, fruit diameter, internodal length and plant height. The characteristics like early plant vigor, plant growth habit, flower petal color, fruit color and apex shape of fruit for both the interspecific hybrids were similar to cultivated okra parent.

Predicting some Milk Constituents from Linear Body Measurements and Udder Characteristics of Bunaji Cows Utilizing Machine Learning Techniques

Machine Learning techniques are capable of being used in agriculture since they are powerful, fast and flexible tools for classification and predictions of traits of economic importance, particularly those involving nonlinear systems. This study aimed to show how well machine learning methods could predict milk's crude protein and fat content based on the Bunaji cows' linear body measurements and udder characteristics. Forty (40) lactating Bunaji cows from two dairy farms in Yola South Local Government Area, Adamawa State, were purposefully selected for the study. Milk samples were collected from the cows (one-off measurement). The crude protein and fat content of the milk were determined in percentage. An ensemble model consisting of the random forest (RF), support vector machine (SVM) and neural network (NN) algorithms were created using the Orange Software. The models were cross-validated using five folds to assess their robustness. Mean squared error (MSE), root mean squared error (RMSE), mean absolute error (MAE) and coefficient of determination (R2 ) are the metrics utilized for the evaluation. Using the udder features, the approach was used to construct demonstrative models for the prediction of milk protein content. The SVM and RF learners had MSE that was lower than that of NN, showing that the two were superior to NN. The lower performance of NN in this study can be explained on the basis of extremely low data that was available for this study. RF learners exhibited a low likelihood of mistakes in predicting crude protein from udder traits despite the study's small data set. Large data sets were needed for machine learning techniques. As a result, these models must be improved with lots of data.

Promoter variations in a homeobox gene, BrLMI1, contribute to leaf lobe formation in Brassica rapa ssp. chinensis Makino.

Key message BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage, and cis-regulatory variations lead to the phenotype of lobed or entire leaf margins.Abstract Leaves are the main consumed organ in leafy non-heading Chinese cabbage (Brassica rapa L. ssp. chinensis Makino), and the shape of the leaves is an important economic trait. However, the molecular regulatory mechanism underlying the lobed-leaf trait in non-heading Chinese cabbage remains unclear. Here, we identified a stable incompletely dominant major locus, qLLA10, for lobed leaf formation in non-heading Chinese cabbage. Based on map-based cloning strategies, BrLMI1, a LATE MERISTEM IDENTITY1 (LMI1)-like gene, was predicted as the candidate gene for qLLA10. Genotyping analysis showed that promoter variations of BrLMI1 in the two parents are responsible for elevating the expression in the lobed-leaf parent and ultimately causing the difference in leaf shape between the two parents, and the promoter activity of BrLMI1 was significantly affected by the promoter variations. BrLMI1 was exclusively localized in the nucleus and expressed mainly at the tip of each lobe. Leaf lobe development was perturbed in BrLMI1-silenced plants produced by virus-induced gene silencing assays, and ectopic overexpression of BrLMI1 in Arabidopsis led to deeply lobed leaves never seen in the wild type, which indicates that BrLMI1 is required for leaf lobe formation in non-heading Chinese cabbage. These findings suggested that BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage and that cis-regulatory variations lead to the phenotype of lobed or entire leaf margins, thus providing a theoretical basis for unraveling the molecular mechanism underlying the lobed leaf phenotype in Brassica crops.

Quantitative and molecular aspects of water intake in meat-type chickens

Even though water is the most essential nutrient for poultry production, adequate data on individual water intake in broiler chickens and its relationship with other traits of economic importance is scant. Water is provided to chickens in an unrestricted manner in spite of being a finite resource. Climate change continues to affect water sources and efficient bird use of water is long overdue. Understanding the biological basis of water intake is essential for sustainability of the poultry industry. Individual water and feed intake, and growth data was collected on 520 commercial broilers aged 14 to 42 days. We introduced the concepts of water conversion ratio (WCR) and residual water intake (RWI) as parameters that can be used to assess water intake efficiency. Water conversion ratio was defined as the amount of water consumed per unit of body weight gain, and RWI was defined as the difference between the actual water intake (WI) of a given bird and the expected WI by an average bird from the population with the same metabolic body weight, feed intake (FI) and body weight gain (BWG). The correlation between WI and FI was positive (r=0.77; P<0.0001), and the correlation between WI and BWG was positive (r=0.80; P<0.0001). Based on the distribution of RWI, the bottom 5 birds (LRWI) and the top 5 birds (HRWI) for RWI were selected for mRNA expression differences. The average broiler consumed about 7.8 L (± 1L) of water from 14 to 42 days of age. The mRNA expression of arginine vasopressin (AVP) antidiuretic hormone, calcium sensing receptor (CasR), sodium channel epithelial 1 subunit alpha (SCNN1A) and SCNN1D in the hypothalamus was upregulated in the LRWI group compared to the HRWI group. Similarly, kidney aquaporins (AQP) 2, 3, and 4 were upregulated in the LRWI group compared with the HRWI group. Given that water was provided ad libitum, the up-regulation of AVP and AQP gene mRNA expressions seem to indicate that the LRWI birds were more efficient in water reabsorption in the kidney compared to their HRWI counterparts. Increased water reabsorption will reduce the amount of water consumed to attain hydration. The water reabsorption potential was reflected in the excreta moisture levels as the LRWI birds had significantly lower excreta moisture than the HRWI birds. Excreta moisture level require further studies and could be considered as a potential proxy trait for water intake.

A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance.

Haliotis midae or "perlemoen" is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in minimising the pressure on the wild populations. Here, the draft genome of H. midae has been sequenced, assembled, and annotated. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238Mb, scaffold N50 of 0. 238Mb and GC level of 40%. Gene annotation, combining ab initio and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (H. laevigata, H. rubra, H. discus hannai and H. rufescens) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that H. midae is closely related to the Australian Greenlip (H. laevigata) and Blacklip (H. rubra). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

An important stage in any breeding activity is selection of suitable individuals for further breeding. Thus, the main goal of breeders becomes such a selection of parental forms that leads to the consolidation and maximization of the value of traits of significant utility and economic importance. Heterosis and specific combining ability are very important parameters in plant and animal breeding. The ability to predict their value and relevance could significantly shorten the breeding process. One way to predict the effects of heterosis and specific combining ability is to select parental forms for crosses. This selection can be made on the basis of variation in parental forms. An analysis was made of publicly available data that contain information about the effects of heterosis, the effects of specific combining ability, and phenotypic and genetic diversity of parental forms. Preliminary studies show that the best approach for obtaining favorable hybrids would be selection of parental forms that are very genetically diverse while being phenotypically equal.