Progress on CRISPR/Cas9 system in the genetic improvement of livestock and poultry

CRISPR/Cas9 gene editing technology, as a highly efficient genome editing method, has been extensively employed in the realm of animal husbandry for genetic improvement. With its remarkable efficiency and precision, this technology has revolutionized the field of animal husbandry. Currently, CRISPR/Cas9-based gene knockout, gene knock-in and gene modification techniques are widely employed to achieve precise enhancements in crucial production traits of livestock and poultry species. In this review, we summarize the operational principle and development history of CRISPR/Cas9 technology. Additionally, we highlight the research advancements utilizing this technology in muscle growth and development, fiber growth, milk quality composition, disease resistance breeding, and animal welfare within the livestock and poultry sectors. Our aim is to provide a more comprehensive understanding of the application of CRISPR/Cas9 technology in gene editing for livestock and poultry.

Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs

Tibetan pigs are indigenous to the Qinghai-Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.

Comparative analyses of functional traits based on metabolome and economic traits variation of Bletilla striata: Contribution of intercropping

The intercropping practice has been regarded as a practical land-use selection to improve the management benefits of Bletilla striata plantations. The reports about the variety of economic and functional traits of Bletilla pseudobulb under intercropping systems were limited. The present study investigated the variation of economic and functional traits of Bletilla pseudobulb under different intercropping systems (the deep-rooted intercropping system: B. striata - Cyclocarya paliurus, CB; and the shallow-rooted intercropping system: B. striata - Phyllostachys edulis, PB). The functional traits were analyzed through non-targeted metabolomics based on GC-MS. The results indicated that the PB intercropping system significantly decreased the yield of Bletilla pseudobulb while significantly increasing the total phenol and flavonoids compared with the control (CK). However, there were no significant differences in all economic traits between CB and CK. The functional traits among CB, PB, and CK were separated and exhibited significant differences. Under different intercropping systems, B. striata may adopt different functional strategies in response to interspecific competition. The functional node metabolites (D-galactose, cellobiose, raffinose, D-fructose, maltose, and D-ribose) were up-regulated in CB, while the functional node metabolites (L-valine, L-leucine, L-isoleucine, methionine, L-lysine, serine, D-glucose, cellobiose, trehalose, maltose, D-ribose, palatinose, raffinose, xylobiose, L-rhamnose, melezitose, and maltotriose) were up-regulated in PB. The correlation between economic and functional traits depends on the degree of environmental stress. Artificial neural network models (ANNs) accurately predicted the variation in economic traits via the combination of functional node metabolites in PB. The correlation analysis of environmental factors indicated that Ns (including TN, NH₄ ⁺-, and NO₃ ^--), SRI (solar radiation intensity), and SOC were the main factors that affected the economic traits (yield, total phenol, and total flavonoids). TN, SRI, and SOC were the main factors affecting the functional traits of the Bletilla pseudobulb. These findings strengthen our understanding of the variation of economic and functional traits of Bletilla pseudobulb under intercropping and clarify the main limiting environmental factors under B. striata intercropping systems.

Leaf trait association in relation to herbivore defense, drought resistance, and economics in a tropical invasive plant

PREMISE

Exploring how functional traits vary and covary is important to understand plant responses to environmental change. However, we have limited understanding of the ways multiple functional traits vary and covary within invasive species.

METHODS

We measured 12 leaf traits of an invasive plant Chromolaena odorata, associated with plant or leaf economics, herbivore defense, and drought resistance on 10 introduced populations from Asia and 12 native populations from South and Central America, selected across a broad range of climatic conditions, and grown in a common garden.

RESULTS

Species' range and climatic conditions influenced leaf traits, but trait variation across climate space differed between the introduced and native ranges. Traits that confer defense against herbivores and drought resistance were associated with economic strategy, but the patterns differed by range. Plants from introduced populations that were at the fast-return end of the spectrum (high photosynthetic capacity) had high physical defense traits (high trichome density), whereas plants from native populations that were at the fast-return end of the spectrum had high drought escape traits (early leaf senescence and high percentage of withered shoots).

CONCLUSIONS

Our results indicate that invasive plants can rapidly adapt to novel environmental conditions. Chromolaena odorata showed multiple different functional trait covariation patterns and clines in the native and introduced ranges. Our results emphasize that interaction between multiple traits or functions should be considered when investigating the adaptive evolution of invasive plants.

Phenotypic Trait Subdivision Provides New Sight Into the Directional Improvement of Eucommia ulmoides Oliver

Eucommia ulmoides Oliver has been used extensively in many fields. To satisfy increasing demand, great efforts must be made to further improve its traits. However, limited information is available on these traits, which is a factor that restricts their improvement. To improve traits directionally, nine clones were assigned to six sites to analyze the effect of different variation sources (the genotype, site, and genotype × environment interaction) on the phenotypic trait. In addition, a mixed linear model was used to assess the contribution of variations. In general, for most traits, the site effect accounted for a larger proportion of the variance, followed by the genotype and genotype × environment interaction effects. All the studied genotypes and sites had a significant effect, indicating that they could be improved by selecting preferable genotypes or cultivation areas, respectively. Interestingly, growth traits or economic traits could be improved simultaneously. Trait performance and stability are necessary when selecting genotypes. Moreover, the discriminating ability of genotypes should be considered in selecting cultivation areas. Annual mean temperature and annual sunshine duration proved to be crucial factors that affected the traits. They were correlated positively with economic traits and leaf yield and correlated negatively with growth traits. These findings contributed to selecting a wider range of cultivation areas. Regarding the genotype × environment interaction effect, there were significant differences only in the gutta-percha content, the total number of leaves, and the chlorogenic acid content. These traits could also be improved by choosing appropriate genotypes for the local environment. The research has provided preliminary data on the main factors that affect the traits of E. ulmoides and offered solutions for trait improvement. This information could be a reference for the trait improvement of other plants.

Variations in the insulin receptor substrate 1 (IRS1) and its association with growth traits in Chinese black Tibetan sheep (Ovis aries)

This paper presented the results on the study of insulin receptor substrate 1 (IRS1) polymorphisms in Chinese black Tibetan sheep. Via DNA direct sequencing, four variations within 3' untranslated region (UTR) of IRS1, including g.9382T > G, g.9569T > G, g.9572C > T and g.9695A > C were detected in the black Tibetan sheep population. Based on the χ² test, those four loci deviated from Hardy-Weinberg equilibrium (p < 0.05). In g.9569T > G locus, genotype of GG possessed advantage on body weight (p < 0.05). In g.9572C > T locus, individuals with genotype of TT homozygous mutation decreased significantly on body weight, withers height, body length and chest circumference (p < 0.05 or p < 0.01). In g.9695A > C locus, the body weight and chest circumference were also higher in AA carriers than in CC carriers (p < 0.05). Our results provided evidence that polymorphisms in IRS1 were associated with growth efficiency traits by quantitative genetic analysis, and may be used for marker-assisted selection in Chinese indigenous sheep.

A 51 bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits

Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G-protein-coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4-8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding.

Accuracies of genomic prediction for twenty economically important traits in Chinese Simmental beef cattle

Genomic prediction has been widely utilized to estimate genomic breeding values (GEBVs) in farm animals. In this study, we conducted genomic prediction for 20 economically important traits including growth, carcass and meat quality traits in Chinese Simmental beef cattle. Five approaches (GBLUP, BayesA, BayesB, BayesCπ and BayesR) were used to estimate the genomic breeding values. The predictive accuracies ranged from 0.159 (lean meat percentage estimated by BayesCπ) to 0.518 (striploin weight estimated by BayesR). Moreover, we found that the average predictive accuracies across 20 traits were 0.361, 0.361, 0.367, 0.367 and 0.378, and the averaged regression coefficients were 0.89, 0.86, 0.89, 0.94 and 0.95 for GBLUP, BayesA, BayesB, BayesCπ and BayesR respectively. The genomic prediction accuracies were mostly moderate and high for growth and carcass traits, whereas meat quality traits showed relatively low accuracies. We concluded that Bayesian regression approaches, especially for BayesR and BayesCπ, were slightly superior to GBLUP for most traits. Increasing with the sizes of reference population, these two approaches are feasible for future application of genomic selection in Chinese beef cattle.

Characteristics of Pig Carcass and Primal Cuts Measured by the Autofom Ⅲ Depend on Seasonal Classification

The objective of this study was to investigate slaughtering performance, carcass grade, and quantitative traits of cuts according to seasonal influence by each month in pigs slaughtered in livestock processing complex (LPC) slaughterhouse in Korea, 2017. A total of 267,990 LYD (Landrace×Yorkshire×Duroc) pig data were used in this study. Results of slaughter heads, sex distribution, carcass weight, backfat thickness, grading class, total weight, and fat and lean meat percentages of each cut predicted by Autofom Ⅲ were obtained each month. The number of slaughtered pigs was the highest in early and late fall but the lowest in midsummer. Only in midsummer that the number of females was higher than that of castrates. During 2017, carcass weight was the lowest in late summer. Backfat thickness was in the range of 21–22 mm. In mid and late spring, pigs showed high 1+ grade ratio (37.05% and 36.15%, respectively). For traits of 11 cuts predicted by Autofom Ⅲ, porkbelly showed lower total weight, lean weight, and fat weight in midsummer to early fall but higher lean meat percentage compared to other seasons. Weights of deboned neck, loin, and lean meat were the highest in midfall compared to other seasons (p<0.05). In conclusion, characteristics of slaughtering, grading, and economic traits of pigs seemed to be highly seasonal. They were influenced by seasons. Results of this study could be used as basic data to develop seasonal specified management ways to improve pork production.

Genotype-environment interaction for age at first calving in buffaloes, using the reaction norm model

The objective of this study was to evaluate the genotype-environment interaction effect on age at first calving in buffaloes. The records were analysed using two approaches: (a) standard animal model and (b) reaction norm model. For the reaction norm analysis, two environmental gradients were formed, using age of first calving or milk yield group contemporary average. The results showed differences in the heritability estimates when using the two approaches. The reaction norm model indicated high heritability in more favourable environments and low magnitude genetic correlations between extreme environments. Based on our findings, we verified the significance of the genotype-environment interaction effect on age at first calving in buffaloes.

Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.

The effect of bovine milk on the growth of Bombyx mori

Bombyx mori L. (Lepidoptera: Bombycidae) is a well-studied Lepidopteran model system because of its morphology, life cycle, and economic importance. Many scientists have placed importance on enhancing the economic traits of B. mori because it's larvae, silkworms, are vital in the production of silk. In this study, the effect of bovine milk on B. mori growth was tested. Bovine milk contains several components that aid in healthy growth. The treatment was given to fifth instar B. mori larvae because the fifth instar period is when B. mori eats voraciously and shows maximum growth among all its larval stages. The larvae were treated with fresh mulberry, Morus L. (Rosales: Moraceae), leaves and mulberry leaves dipped in milk from the first day of the fifth instar. Treatments were given on alternate days, and the silkworms were weighed every day to determine whether milk had any role in enhancing the weight of the larvae. Cocoon weights were measured, as the weight indicates the approximate amount of silk that can be reeled. The results showed that larvae gained 82.5% more weight by the end of fifth instar larval when fed with mulberry leaves dipped in milk than when fed with fresh mulberry leaves without milk. The larvae fed with milk-treated leaves gained 310% weight from day 1 to day 7 of the fifth instar, while the larvae fed with fresh leaves gained 153% weight in the same timespan. In addition, cocoon weight increased by 8% when milk was added compared to when it was not. These results suggest that B. mori larvae can be fed mulberry leaves treated with bovine milk for better growth rate and increased silk production.