Molecular markers and their use in animal breeding

Genetic polymorphisms in HMGCS1 gene and its association with slaughter characteristics, meat quality, and organ coefficients in Guizhou white goats

OBJECTIVE

This study aimed to identify polymorphisms in the gene encoding the 3-hydroxy-3-methylglutaryl-CoA synthase 1, HMGCS1, and analyze their association with slaughter characteristics, meat quality, and organ coefficients in Guizhou white goats.

METHODS

A total of 153 twelve-month-old Guizhou white goats (78 male and 75 female) were included in the study. Slaughter characteristics, meat quality, and organ coefficients were assessed. Association analyses between genotypes and phenotypic traits were conducted using a generalized linear model.

RESULTS

Four polymorphic loci were identified, i.e., g.15523T>C, g.15530G>C, g.18413T>C, g.19711G>A in exons 5, 8, and 9 of the HMGCS1 gene. Across all polymorphic loci, males of the same genotype generally exhibited significantly better slaughter traits compared to females of the same genotype (p<0.05). At the g.18413T>C locus, differences in shear force were observed between males and females of the same genotype and within the same sex across different genotypes (p<0.05). Organ coefficients were significantly higher in males of the same genotype compared to females (p<0.05). The g.15523T>C and g.15530G>C loci were found in strong linkage disequilibrium and significantly associated with intramuscular fat content (p<0.05). Fat content in diploid Hap2/2 individuals was significantly higher than in Hap1/1 and Hap1/2 (p<0.05). At the g.19711G>A locus, female goats with the CC genotype showed significantly higher levels of dry matter compared to male goats of the same genotype and female goats of other genotypes within the group. Organ coefficients for the liver and hooves in male goats were significantly higher than in females of the same genotype (p<0.05).

CONCLUSION

The strongly linked loci g.15523T>C and g.15530G>C were significantly associated with intramuscular fat content and could be used as molecular markers for enhancing this trait in goat breeding programs, fostering the development of goat production.

Strong associations between the FGF-2 gene and productivity traits of Holstein-Friesian dairy cattle

Sustainability in dairy cattle farms depends on the efficiency of milk yield and reproductive traits. Thus, this study aimed to investigate the effect of the FGF-2/Csp6I gene and major environmental factors on these traits in Holstein-Friesian cattle. A total of 212 whole blood samples were collected from the Vena coccygea of cattle and the data obtained from these samples were used in all statistical analyses. Then, the restriction fragment length polymorphism (RFLP) method (determination of genotypes) was conducted and programs including PopGene (allele and genotype frequencies), Minitab (association analyses) and MTDFREML (variance components and genetic parameters) were used. Alleles A (0.4269) and G (0.5731) as well as genotypes AA (0.174), AG (0.505) and GG (0.321) were found, indicating that the population is polymorphic and in Hardy-Weinberg equilibrium (P > 0.05). The effect of the Csp6I polymorphism of FGF-2 gene on peak milk yield (PMY) (P < 0.01); lactation milk yield (LMY), milking time (MT), 305-day and 200-day lactation milk yield (LMY305 and LMY200), average daily milk yield (ADMY) (P < 0.05); 100-day lactation milk yield (LMY100), age of using in first breeding (AUFB) and number of inseminations per conception (NIPC) (P < 0.10) were significant. The heritability of milk yield traits and the correlation between direct and maternal heritability for reproductive traits were high. Furthermore, the breeding value of PMY was higher for the AA genotype (0.745 ± 0.292) than for the AG genotype (-0.268 ± 0.171) (P < 0.05). As a result, the A allele and AA genotype for the FGF-2/Csp6I gene had an increasing effect on milk yield without compromising reproductive performance in Holstein-Friesian dairy cattle.

Omics approaches to understand impact of heat stress on semen quality and fertility in bovines

Recent surge in global climate change poses unprecedented challenges to traditional livestock breeding methods. In tropical countries, where large bovines are vital source of meat and milk, the escalating global warming significantly impact their productivity. Central to this challenge is the resilient ability of the animals, which directly influences the productivity. Artificial insemination (AI) programs, a cornerstone in modern livestock production, have also been severely hampered by climate change-induced heat stress, affecting the quality semen production. This stress not only affects the blood biochemical profiles of the animals but also their testicular physiology, leading to the issues such as low-quality semen with compromised freezability and fertility. Researchers have identified specific markers, including single nucleotide polymorphisms (SNPs), copy number variations (CNV), and epigenetic signatures like histone modifications, DNA methylation, and noncoding RNAs, influencing the semen quality in livestock species. Furthermore, the issue of heat stress has been addressed in a very precise way, and biomarkers have been identified, which can be integrated into the breeding programme to keep up the sire summary. Transcriptomic studies have further illuminated the temporal expression patterns of genes related to sperm quality during heat stress, pinpointing candidate genes for further exploration. This review comprehensively summarizes the progress made in understanding the intricacies of sperm biology in bovines, with a specific focus on cattle and buffalo delving into a spectrum of changes, from biochemical shifts to profound cellular alterations, including genomic, transcriptomic, and epigenetic modifications.

Characterization of the myostatin gene in the neotropical species Piaractus mesopotamicus and the possibility of its use in genetic improvement programs

BACKGROUND

The myostatin gene has played an important role in the genetic improvement of the main species of economic importance; however, it has not yet been described for some Neotropical fish essential for aquaculture. This study aimed to characterize the myostatin gene of pacu, Piaractus mesopotamicus, and investigate the association of a microsatellite marker in this gene with the weight of fish.

METHODS AND RESULTS

The myostatin gene sequence was obtained after following a RACE-PCR strategy based on a partial mRNA sequence available in the GenBank database and the alignment of myostatin sequences from other fish species. The obtained sequence for the P. mesopotamicus gene was analyzed for short tandem repeats, and one dinucleotide was observed at the 3´untranslated region. A short tandem repeat polymorphism was verified in a wild population. Subsequently, the STR was evaluated in a test population of 232 animals in two 220 m² concrete tanks at the Aquaculture Center of Unesp. Eight alleles and 22 genotype combinations were identified. A significant association was observed between microsatellite marker polymorphisms and the weight traits (WEIGHT1 and WEIGHT2). Alleles 210, 222, 226, and 230 were found to favor weight gain.

CONCLUSIONS

In summary, this study contributes to the characterization of the myostatin gene in pacu fish and identifies an association between a STR and weight traits. Thus, this gene could be used as a target for genetic breeding using molecular strategies such as CRISPR and quantitative strategies such as marker-assisted selection, which would contribute to improving the production of the species.

Integrating targeted genetic markers to genotyping-by-sequencing for an ultimate genotyping tool

New selection methods, using trait-specific markers (marker-assisted selection (MAS)) and/or genome-wide markers (genomic selection (GS)), are becoming increasingly widespread in breeding programs. This new era requires innovative and cost-efficient solutions for genotyping. Reduction in sequencing cost has enhanced the use of high-throughput low-cost genotyping methods such as genotyping-by-sequencing (GBS) for genome-wide single-nucleotide polymorphism (SNP) profiling in large breeding populations. However, the major weakness of GBS methodologies is their inability to genotype targeted markers. Conversely, targeted methods, such as amplicon sequencing (AmpSeq), often face cost constraints, hindering genome-wide genotyping across a large cohort. Although GBS and AmpSeq data can be generated from the same sample, an efficient method to achieve this is lacking. In this study, we present the Genome-wide & Targeted Amplicon (GTA) genotyping platform, an innovative way to integrate multiplex targeted amplicons into the GBS library preparation to provide an all-in-one cost-effective genotyping solution to breeders and research communities. Custom primers were designed to target 23 and 36 high-value markers associated with key agronomical traits in soybean and barley, respectively. The resulting multiplex amplicons were compatible with the GBS library preparation enabling both GBS and targeted genotyping data to be produced efficiently and cost-effectively. To facilitate data analysis, we have introduced Fast-GBS.v3, a user-friendly bioinformatic pipeline that generates comprehensive outputs from data obtained following sequencing of GTA libraries. This high-throughput low-cost approach will greatly facilitate the application of DNA markers as it provides required markers for both MAS and GS in a single assay.

Selection and direct biomarkers of reproductive capacity of breeding boars

Efficient management of pig reproduction is paramount for the sustainability and productivity of the global pork industry. Modern artificial insemination (AI) breeding programs have greatly benefited from the integration of advanced selection methods and biomarkers to enhance the reproductive performance of boars. While traditional selection methods have relied soley on boar phenotype, such as growth rate and conformation, modern pig breeding has shifted more and more toward molecular and genetic tools, which are still complemented by phenotypic traits. These methods encompass genomics, transcriptomics, and proteomics. Biomarkers serve as critical indicators of boar reproductive capacity. They can help to identify individuals with superior fertility and aid in the early identification of potential fertility issues, allowing for proactive management strategies. This review summarizes current knowledge of various biomarkers associated with semen quality, sperm function, and overall reproductive fitness in boars. Furthermore, we explore advanced technologies and their potential applications in uncovering novel selection methods and biomarkers for predicting boar fertility. A comprehensive understanding of selection criteria and biomarkers governing boar reproductive capacity is essential for developing effective breeding programs to enhance swine reproductive performance.

Segregation GWAS to linearize a non-additive locus with incomplete penetrance: an example of horn status in sheep

BACKGROUND

The objective of this study was to introduce a genome-wide association study (GWAS) in conjunction with segregation analysis on monogenic categorical traits. Genotype probabilities calculated from phenotypes, mode of inheritance and pedigree information, are expressed as the expected allele count (EAC) (range 0 to 2), and are inherited additively, by definition, unlike the original phenotypes, which are non-additive and could be of incomplete penetrance. The EAC are regressed on the single nucleotide polymorphism (SNP) genotypes, similar to an additive GWAS. In this study, horn phenotypes in Merino sheep are used to illustrate the advantages of using the segregation GWAS, a trait believed to be monogenic, affected by dominance, sex-dependent expression and likely affected by incomplete penetrance. We also used simulation to investigate whether incomplete penetrance can cause prediction errors in Merino sheep for horn status.

RESULTS

Estimated penetrance values differed between the sexes, where males showed almost complete penetrance, especially for horned and polled phenotypes, while females had low penetrance values for the horned status. This suggests that females homozygous for the 'horned allele' have a horned phenotype in only 22% of the cases while 78% will be knobbed or have scurs. The GWAS using EAC on 4001 animals and 510,174 SNP genotypes from the Illumina Ovine high-density (600k) chip gave a stronger association compared to using actual phenotypes. The correlation between the EAC and the allele count of the SNP with the highest -log10(p-value) was 0.73 in males and 0.67 in females. Simulations using penetrance values found by the segregation analyses resulted in higher correlations between the EAC and the causative mutation (0.95 for males and 0.89 for females, respectively), suggesting that the most predictive SNP is not in full LD with the causative mutation.

CONCLUSIONS

Our results show clear differences in penetrance values between males and female Merino sheep for horn status. Segregation analysis for a trait with mutually exclusive phenotypes, non-additive inheritance, and/or incomplete penetrance can lead to considerably more power in a GWAS because the linearized genotype probabilities are additive and can accommodate incomplete penetrance. This method can be extended to any monogenic controlled categorical trait of which the phenotypes are mutually exclusive.

The effects and mechanisms of heat stress on mammalian oocyte and embryo development

The sum of nonspecific physiological responses exhibited by mammals in response to the disruption of thermal balance caused by high-temperature environments is referred to as heat stress (HS). HS affects the normal development of mammalian oocyte and embryos and leads to significant economic losses. Therefore, it is of great importance to gain a deep understanding of the mechanisms underlying the effects of HS on oocyte and embryonic development and to explore strategies for mitigating or preventing its detrimental impacts in the livestock industry. This article provides an overview of the negative effects of HS on mammalian oocyte growth, granulosa cell maturation and function, and embryonic development. It summarizes the mechanisms by which HS affects embryonic development, including generation of reactive oxygen species (ROS), endocrine disruption, the heat shock system, mitochondrial autophagy, and molecular-level alterations. Furthermore, it discusses various measures to ameliorate the effects of HS, such as antioxidant use, enhancement of mitochondrial function, gene editing, cultivating varieties possessing heat-resistant genes, and optimizing the animals'rearing environment. This article serves as a valuable reference for better understanding the relationship between HS and mammalian embryonic development as well as for improving the development of mammalian embryos and economic benefits under HS conditions in livestock production.

Circular RNA circRPS19 promotes chicken granulosa cell proliferation and steroid hormone synthesis by interrupting the miR-218-5p/INHBB axis

Ovarian follicle development is an important physiological activity for females and makes great significance in maintaining female health and reproduction performance. The development of ovarian follicle is mainly affected by the granulosa cells (GCs), whose growth is regulated by a variety of factors. Here, we identified a novel circular RNA (circRNA) derived from the Ribosomal protein S19 (RPS19) gene, named circRPS19, which is differentially expressed during chicken ovarian follicle development. Further explorations identified that circRPS19 promotes GCs proliferation and steroid hormone synthesis. Furthermore, circRPS19 was found to target and regulate miR-218-5p through a competitive manner with endogenous RNA (ceRNA). Functionals investigation revealed that miR-218-5p attenuates GCs proliferation and steroidogenesis, which is opposite to that of circRPS19. In addition, we also confirmed that circRPS19 upregulates the expression of Inhibin beta B subunit (INHBB) by binding with miR-218-5p to facilitate GCs proliferation and steroidogenesis. Overall, this study revealed that circRPS19 regulates GCs development by releasing the repression of miR-218-5p on INHBB, which suggests a novel mechanism in respect to circRNA and miRNA regulation in ovarian follicle development.

Genetic diversity and population structure of Anatolian Hair goats, an ancient breed

This study aimed to investigate the genetic characterization and diversity of Hair goats from 10 regions using 20 microsatellite markers. A total of 522 alleles were observed. The INRA0023 locus exhibited the greatest number of alleles (48), while the DRBP1 locus had the highest effective allele number (16.27), and the BM1818 and DRBP1 loci had the highest polymorphic information content value (0.94). The expected heterozygosity value ranged from 0.85 (ILSTS011) to 0.94 (BM1818, SRCRSP15, and DRBP1). The Hair goat populations in Konya and Hatay displayed the lowest and highest allele numbers, with values of 10.40 and 16.25, respectively. The fixation index (F IS ) values are significant in defining population structures and determining the extent of heterozygosity losses. TheF IS values exhibited a range of 0.031 in Muǧla to 0.226 in Burdur. A total of 107 unique alleles were identified in Hair goat populations. However, it is noteworthy that, out of all the alleles, only 25 had a frequency exceeding 5 %. The results indicate that the microsatellite markers utilized demonstrate sufficient levels of polymorphism, making them appropriate for efficiently investigating the genetic variability of Hair goat populations.

Transcriptome profiling reveals SLC5A5 regulates chicken ovarian follicle granulosa cell proliferation, apoptosis, and steroid hormone synthesis

The egg-laying performance of hens holds significant economic importance within the poultry industry. Broody inheritance of the parent stock of chickens can result in poor options for the improvement of egg production, and is a phenomenon influenced by multiple genetic factors. However, few studies have been conducted to delineate the molecular mechanism of ovarian regression in brooding chickens. Here, we explored the pivotal genes responsible for the regulation of ovarian follicles in laying hens, using RNA-sequencing analysis on the small ovarian follicles from broody and laying chickens. Sequencing data analysis revealed the differential expression of 200 genes, with a predominant enrichment in biological processes related to cell activation and metabolism. Among these genes, we focused on solute carrier family 5 member 5 (SLC5A5), which exhibited markedly higher RNA expression levels in follicles from laying compared with broody chickens. Subsequent cellular function studies with knockdown of SLC5A5 in chicken ovarian follicle granulosa cells (GCs) led to the down-regulation of genes associated with cell proliferation and steroid hormone synthesis, and concurrent promotion of gene expression linked to apoptosis. These findings indicated that SLC5A5 deficiency led to the inhibition of proliferation, steroid hormone synthesis and secretion, and promotion of apoptosis in chicken GCs. Our study demonstrated a pivotal role for SLC5A5 in the development and function of chicken GCs, shedding light on its potential significance in the broader context of chicken ovarian follicle development, and providing a prospective target to improve the egg-laying performance of chickens via molecular marker-assisted breeding technology.

Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle

Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database to understand the biological importance of milk production through gene expression and modules. In this study, we employed CytoNCA and ClusterONE plugins within Cytoscape for network analysis. Moreover, miRWalk software was utilized to detect miRNAs, and DAVID was employed to identify gene ontology and pathways. The results revealed 140 up-regulated genes and 312 down-regulated genes. In addition, we have identified 91 influential genes and 47 miRNAs that are closely associated with milk production. Through our examination of the network connecting these genes, we have found significant involvement in important biological processes such as calcium ion transit across cell membranes, the BMP signaling pathway, and the regulation of MAPK cascade. The conclusive network analysis further reveals that GAPDH, KDR, CSF1, PYGM, RET, PPP2CA, GUSB, and PRKCA are closely linked to key pathways essential for governing milk production. Various mechanisms can control these genes, making them valuable for breeding programs aiming to enhance selection indexes.

Three novel simple sequence repeats (SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig

Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

Association analysis for SNPs of MSTN and IGFBP-3 genes with body size and other production traits in Liaoning Cashmere Goats

Liaoning cashmere goat (LCG) have tall bones, high cashmere production and outstanding meat production performance. In recent years, good breeding progress has not been made in terms of body size, meat yield, milk yield and other properties in terms of production. The study focused on the correlation between the SNPs of MSTN and IGFBP-3 genes with the body size performance, cashmere production and milk performance. The MSTN and IGFBP-3 gene sequence alignment and PCR-Seq polymorphism were used to detect the potential SNPs, and the correlation with production performance was analyzed by SPSS and SHEsis software. The results showed that the TT genotype at the T1662G locus of the MSTN gene is dominant and has significant advantages in body measurements such as sacrum height, chest width, and waist height. The C allele at the C4021T locus of IGFBP-3 gene shows an advantage in the body measurement performance. Among the haplotype combinations, H2H2:TGTC is preponderant combination for body size performance, H2H2:TGTC and H1H2:TGCC are preponderant combinations for cashmere production performance, H1H3:GGCC is preponderant combination for milk production performance. It may be a molecular marker for future selection and breeding.

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website's database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/.

Genetic diversity and population structure of a Peruvian cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and males with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold's distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

Genetic polymorphism of the ovine MAP3K5 gene and its association with body size traits in Hu sheep of China

Abstract. As an excellent local sheep breed in China, Hu sheep have the characteristics of producing more lambs and good motherhood. The purpose of this study was to identify the polymorphism of the mitogen-activated protein kinase 5 (MAP3K5) gene and determine whether it was associated with the body size traits (body height, body length, chest circumference, and cannon circumference) in Hu sheep. The polymorphism of MAP3K5 was identified by using PCR amplification, followed by Sanger sequencing, and KASPar (Kompetitive Allele Specific PCR) technology was used for genotyping subsequently. The results of the association analysis showed that MAP3K5 (g.205261 A > G) was significantly associated with body height at 80, 100, 140, 160, and 180 d; body length at 80 and 160 d; chest circumference at 100, 140, 160, and 180 d; and cannon circumference at 100 and 120 d, respectively. The results of qRT-PCR showed that the expression level of MAP3K5 in the heart was significantly higher (P < 0.05) than in the other 10 tissues. In summary, the MAP3K5 mutation loci may be used as a candidate molecular marker for the body size traits of Hu sheep.

Advances in Mechanism and Application of Molecular Breeding of Medicinal Mushrooms: A Review

With the development of molecular biology and genomics technology, mushroom breeding methods have changed from single traditional breeding to molecular breeding. Compared with traditional breeding methods, molecular breeding has the advantages of short time and high efficiency. It breaks through the restrictive factors of conventional breeding and improves the accuracy of breeding. Molecular breeding technology is gradually applied to mushroom breeding. This paper summarizes the concept of molecular breeding and the application progress of various molecular breeding technologies in mushroom breeding, in order to provide reference for future research on mushroom breeding.

Advanced Practical Strategies to Enhance Table Egg Production

The global demand for table eggs has increased exponentially due to the growing human population. To meet this demand, major advances in hen genetics, nutrition, and husbandry procedures are required. Developing cost-effective and practically applicable strategies to improve egg production and quality is necessary for the development of egg industry worldwide. Consumers have shown a strong desire regarding the improvement of hens' welfare and egg quality. They also become interested in functional and designer foods. Modifications in the nutritional composition of laying hen diets significantly impact egg nutritional composition and quality preservation. According to previous scientific research, enriched egg products can benefit human health. However, producers are facing a serious challenge in optimizing breeding, housing, and dietary strategies to ensure hen health and high product quality. This review discussed several practical strategies to increase egg production, quality, and hens' welfare. These practical strategies can potentially be used in layer farms for sustainable egg production. One of these strategies is the transition from conventional to enriched or cage-free production systems, thereby improving bird behavior and welfare. In addition, widely use of plant/herbal substances as dietary supplements in layers' diets positively impacts hens' physiological, productive, reproductive, and immunological performances.

Association analysis of prolactin and prolactin receptor genes with selected productive and reproductive traits in Egyptian buffalo

A total of 266 records of buffalo raised in two experimental herds in Egypt were assessed to detect prolactin (PRL) and prolactin receptor (PRLR) genes' polymorphism using PCR-Single Strand Conformational Polymorphism (SSCP) and PCR-Restricted Fragment Length Polymorphism (RFLP) techniques as well as to investigate their association with calf birth weight (BW), weaning weight (WW), lactation period (LP), total milk yield (TMY), stillbirth, calving ease (CE), gestation length (GL), postpartum interval to pregnancy (PPIP), calving interval (CI), and age at first calving (AFC). Predicted breeding values were estimated and used in the association with detected genotypes. A monomorphic pattern of the studied PRL 156 bp segment was recorded and absence of its polymorphism in buffalo was corroborated. We also determined polymorphism of PRLR reflected in three loci: PRLR2, PRLR4, and PRLR9. Significant differences among PRLP9 genotypes (AA, AB, and BB) were displayed for all studied traits as well as among PRLR2 genotypes, except for CE, while PRLR4 genotypes significantly differed only in BW, WW, TMY, stillbirth, GL, and AFC. In practice, strong associations among genotypes of the PRLR gene and the traits of interest candidate this gene to be selective in Egyptian buffalo breeding for improving both productive and reproductive traits.

Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle

SIMPLE SUMMARY

As a member of genetic polymorphism, copy number variation has been a commonly used method in the world for investigating effect of genetic polymorphism on gene expression. Effect of genetic polymorphism made on livestock development has been more and more important in beef cattle molecular breeding. The characteristics of Chinese cattle are excellent meat quality, tolerant to rough feeding, good environmental adaptability and so on. But there are some obvious weaknesses still exist in the process of cattle growth and development, such as weak hindquarters and growth slowly. To improve the growth performance and market competitiveness of Chinese cattle, a lot of studies have been made about finding and investigating effective molecular marker. In this study, Q-PCR and data association analysis were used for PLA2G2A gene copy number variation detection and related effect analysis in Chinese cattle. Results showed that PLA2G2A gene has a significant effect on two breeds of Chinese cattle on growth traits, which could be a basic materials and effective information of cattle molecular markers breeding. PLA2G2A, member of secreted phospholipases A2 (sPLA2) in superfamily of phospholipase A2, could catalyze the process of glycerophospholipids hydrolysis from position of sn-2 acyl with the release of free fatty acids and lysophospholipids. Researches about PLA2G2A gene are mostly focus on disease, including tumors and diabetes, the number of study occurred on animal breeding is weak. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for PLA2G2A gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. In QC, XN and GY cattle, the frequencies of Deletion and Duplication are about 40%; in YL cattle, the frequency of Deletion type exceeds 60%; in PN cattle, the frequency of Duplication is closed to 80%. Association analysis indicate that CNV of PLA2G2A gene showed a positive effect in cattle growth: in QC cattle, Chest depth with Normal type copy number possess a increased trend (P < 0.05); individuals with Deletion type copy number have better performance on Height at sacrum, Heart girth and Body height in GY cattle (P < 0.05). The functional role and molecular mechanism of PLA2G2A gene in animal growth and development are still unclear, and it is necessary for processing a further research. This research aims to provide basic materials for molecular breeding of Chinese cattle.

The InDel variants of sheep IGF2BP1 gene are associated with growth traits

Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) plays positive roles in the growth, proliferation of cells and early embryos development by binding mRNA targets. Recently, it had been shown that some polymorphic loci within IGF2BP1 gene were associated with growth traits in animals, especially in goats. Therefore, it has been hypothesized that some variants within IGF2BP1 gene may be also involved in growth traits of sheep. Nine insertion/deletion (InDel) mutations within IGF2BP1 were identified and three loci were polymorphic. Meanwhile, the association analyses between three InDels and growth traits were carried out in 745 sheep. The results showed that all InDels included 5 bp InDel in downstream region, 9 bp InDel in intron 4 and 15 bp InDel in intron 2 within IGF2BP1 were significantly associated with growth traits (p<.05). Furthermore, at 5 and 9 bp InDel loci, the individuals of heterozygous genotype (ID) had superior growing performance especially at body weight (BW). In all, three InDels were crucial variants correlated with growth traits and could be applied in marker-assisted selection (MAS) in sheep.

Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F₂ birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F₂ birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.

The Potential Role of MYOM1 and ATGL Genes in Pig Production Improvement

In the present study, two missense variants within ATGL (rs331307082) and MYOM1 (rs326001585) genes were tested for their potential usage as genetic markers related to pig production traits. The genotyping was performed on 519 pigs representing 990 synthetic sire line. The association analysis indicated that ATGL gene affected the panel of fattening parameters (test daily gain, age at slaughter), meatiness traits (meat percentage in the carcasses; the weight of loin, ham and primary cuts, and loin eye area), and meat quality characteristics (water exudation). In turn, MYOM1 polymorphism was related to loin weight, the weight of primary cuts and weight of loin backfat. Pigs with AA genotype were characterized by significantly higher loin and primary cut weights compared to opposite homozygotes GG (P<0.05). The observed differences were 2.29 kg and 1.2 kg, respectively. Moreover, despite higher meatiness, AA animals together with AG were characterized by lower weight of loin backfat (P<0.05) and average backfat thickness (P<0.1) compared to GG pigs. The MYOM1 polymorphism did not affect pork quality traits. The results allowed us to propose the new genetic markers which may be used in pig selection to obtain appropriate meatiness and fatness level in carcasses without decreasing meat quality.

Lipid profile of sperm cells in Thai native and commercial roosters and its impact on cryopreserved semen quality

Plasma membrane lipids are the key factor in the ability of chicken sperm to be frozen. They ensure fluidity and flexibility of the sperm membrane for effective viability and motility during in vitro storage. The objective of this study was to compare the lipid profiles of different native and commercial chicken breeds: native Thai (Pradu Hang Dam) roosters and commercial (Rhode Island Red) roosters, with respect to their frozen sperm quality. In addition, lipid peroxidation and antioxidant enzymes superoxidase dismutase (SOD) and catalase (CAT) were also examined. Semen was collected from 12 roosters of each breed. For fresh semen, parameters assessed include semen volume, pH, sperm concentration, sperm motility, and viability, while for frozen semen, the parameters assessed were sperm motility and viability. Moreover, other parameters assessed included malondialdehyde (MDA) concentration, activities of SOD and CAT, and fatty acid profile. We found that sperm viability and motility of frozen semen were higher in the commercial breed than in the native breed (P < 0.05). The commercial chicken breed had higher MDA concentration than the native breed (P < 0.05), but antioxidant enzymes remained unchanged in both. Levels of arachidonic acid (AA; C20:4n-6) and docosahexaenoic acid (DHA; C22:6n-3) were significantly higher (P < 0.05) in the commercial than in the native breed; however, n-6 to n-3 ratios were not different. In conclusion, our study found that lipid profiles have an influence on frozen sperm viability and motility between the breeds. Polyunsaturated fatty acids, particularly AA and DHA, are beneficial to sperm quality.

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

A novel (ATC)n microsatellite locus is associated with litter size in an indigenous Chinese pig

Simple sequence repeats (SSRs) are an important part of the genome and have become powerful auxiliary DNA markers in animal breeding using marker-assisted selection (MAS). Based on previous sequencing data of Qinghai Bamei pigs, a total of three novel candidate SSR loci were analysed in this study. Time-of-flight mass spectrometry (TOF-MS) was used for SSR genotyping, and association analyses between SSRs and the litter size of Qinghai Bamei sows was also performed. The results of genotyping showed that the (ATC)_n -P1, (AC)_n -P2 and (AC)_n -P3 loci had 2, 3 and 18 genotypes, respectively; 2, 3 and 8 alleles were also identified at these loci. Except for the (AC)_n -P2 locus, the polymorphism information content (PIC) values of other loci were greater than 0.25. Association analyses indicated that only the (ATC)_n -P1 locus was significantly associated with the litter size of Qinghai Bamei sows (p = .047). Compared to 189-/189- genotype, individuals with the 189-/195- genotype had the senior litter size, which was 9.04 ± 0.21. Our results enrich the data on SSRs in Qinghai Bamei pigs and indicate that (ATC)_n -P1 is a candidate locus for MAS in the pig industry.

Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models

The current changing climate trend poses a threat to the productive efficacy and welfare of livestock across the globe. This review is an attempt to synthesize information pertaining to the applications of various genomic tools and statistical models that are available to identify climate-resilient dairy cows. The different functional and economical traits which govern milk production play a significant role in determining the cost of milk production. Thus, identification of these traits may revolutionize the breeding programs to develop climate-resilient dairy cattle. Moreover, the genotype–environment interaction also influences the performance of dairy cattle especially during a challenging situation. The recent advancement in molecular biology has led to the development of a few biotechnological tools and statistical models like next-generation sequencing (NGS), microarray technology, whole transcriptome analysis, and genome-wide association studies (GWAS) which can be used to quantify the molecular mechanisms which govern the climate resilience capacity of dairy cows. Among these, the most preferred option for researchers around the globe was GWAS as this approach jointly takes into account all the genotype, phenotype, and pedigree information of farm animals. Furthermore, selection signatures can also help to demarcate functionally important regions in the genome which can be used to detect potential loci and candidate genes that have undergone positive selection in complex milk production traits of dairy cattle. These identified biomarkers can be incorporated in the existing breeding policies using genomic selection to develop climate-resilient dairy cattle.

Effects of polymorphism of the GPAM gene on milk quality traits and its relation to triglyceride metabolism in bovine mammary epithelial cells of dairy cattle

Mitochondrial glycerol-3-phosphate acyltransferase (GPAM) catalyses the initial and rate-regulated first-stage pathway of glycerol lipid synthesis and helps to allocate acyl-CoA (acyl-coenzyme A) to triglyceride (TG) synthesis and away from degradation pathways in animal lipometabolism-related pathways. In this study, RNA interference (RNAi) and GPAM gene overexpression were used to examine the correlation between the expression of GPAM and adipogenesis in bovine mammary epithelial cells (bMECs). Additionally, three novel polymorphisms were identified within the bovine key functional domain of GPAM with Sanger sequencing. The relationship between variants of the GPAM gene and milk quality traits of Chinese Holstein cows was then analysed using statistical methods. The results showed that knockdown of the GPAM gene significantly reduced the synthesis of triglycerides in the bMECs (p < 0.05), whereas the overexpression of the GPAM gene significantly increased the synthesis of TG (p < 0.05). In Chinese Holstein dairy cattle, the polymorphic locus of the GPAM gene E20-3386G > A was significantly correlated with fat, protein and somatic cell count (p < 0.05); I18-652A > G was significantly correlated with fat, total fat content, protein, dry matter and somatic cell count (p < 0.05); and I18-726A > G was significantly correlated with protein, milk yield, dry matter and somatic cell count (p < 0.05). Specifically, individuals with the AA genotype of the I18-652A > G and E20-3386G > A polymorphic loci had a higher milk fat percentage (p < 0.05). In summary, GPAM plays a pivotal role in the intracellular regulation of triglyceride, and its mutations could work as a competent molecular marker for selective breeding in dairy cattle.

Comparison of growth performance and biochemical components between parent and hybrid offspring in the oriental river prawn, Macrobrachium nipponense

Macrobrachium nipponense, as one of the large-yield farmed shrimp, is facing germplasm degradation. Genetic improvement through hybridization is one of the effective methods to solve this problem. In this study, using a three-line hybrid strategy, two-hybrid F1 populations were obtained using three local populations of M. nipponense as parents for crossbreeding. Five populations were then cultured for 3 months. Growth rate performance was measured by the hepatosomatic index, weight gain, body length growth rate and special growth rate. Biochemical components were also assessed. The results showed that the survival rate and growth performance of the hybrid progeny were better than those of the parents. The levels of triglycerides, total cholesterol, glycogen and lactic acid of the hybrid population were higher than those of the parents. This was consistent with variation in the activity of four digestive enzymes. Compared with the results of the fatty acid and amino acid analysis, it was found that the contents of polyunsaturated fatty acids such as eicosapentaenoic acid, docosapentaenoic acid and docosahexaenoic acid and eight essential amino acids in the hybrid populations were significantly higher than those of their parents, and the contents of flavor amino acids were higher. The expression level of molting genes related to the growth of the parent populations was lower than that of the hybrids. These results show that crossbreeding is effective for the genetic improvement of M. nipponense germplasm. Hybrids showed advantages in growth and nutrition and multigenerational breeding will be required to form a stable germplasm.

Genetic characterisation of non-descript cattle populations in communal areas of South Africa

Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.

A selection method of chickens with blue-eggshell and dwarf traits by molecular marker-assisted selection

The blue-eggshell and dwarf traits have an important economic value in poultry production. Using a genetic aggregation-based strategy, the molecular marker-assisted selection technology was jointly used to provide a rapid breeding method for pure strain chickens simultaneously with hens exhibiting the blue-eggshell and dwarf traits. Overall, 80 male dwarf chickens and 1,000 hybrid blue-eggshell hens (F0) were used for the hybridization experiment. Subsequently, the crossing of F1 or F2 chicks was performed in succession. The F1 and F2 chicks were respectively detected by the joint molecular markers of the solute carrier organic anion transporter family, namely, 1B3 (SLCO1B3) and the growth hormone receptor (GHR) genes, which relate to blue-eggshell and dwarf traits. Meanwhile, the selection of blue-eggshell and dwarf phenotypes was used to validate the data obtained by the molecular markers. The results showed that F1 chicks included the heterozygous and wild-type of SLCO1B3, as well as the homozygous (hens) and heterozygous (roosters) of GHR. However, F2 chicks included 3 different genotypes of both SLCO1B3 and GHR. Ultimately, 196 F1 roosters (concurrently with heterozygous genotype of SLCO1B3 and GHR) and 1,073 F1 hens (concurrently with heterozygous genotype of SLCO1B3 and homozygous genotype of GHR) were obtained from the initial 10,040 F1 chicks. Further, 27 F2 roosters and 345 F2 hens, which simultaneously carried the homozygous genotype of SLCO1B3 and GHR, were screened from the initial 6,000 F2 chicks. Data obtained on the blue-eggshell and dwarf phenotypes were consistent with the results by molecular markers. Similarly, the purity verification of the strain obtained through 2 crossing experiments (F0♂ × F2♀ and F2♂ × F2♀) revealed that all chickens had the blue-eggshell and dwarf traits, supporting that the obtained F2 strain was pure. In summary, for the first time, we successfully bred a pure strain chicken with blue-eggshell and dwarf traits by jointly using the molecular markers of the SLCO1B3 and GHR genes. Our study provides a new method for the rapid cultivation of new chicken strains.

ACAT-1 gene rs1044925 SNP and its relation with different clinical forms of chronic Chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi (T. cruzi), although discovered more than a century ago, is still a not very well-elucidated aspect. Individuals in the chronic phase of the disease may present asymptomatic clinical form or symptomatologies related to the cardiac, digestive systems, or both (mixed clinical form). SNPs (single nucleotide polymorphisms) have been identified as important markers because they constitute about 90% of the variation in the human genome. One of them is localized to the ACAT-1 gene (cholesterol acyltransferase 1) (rs1044925) and has been linked to lipid disorders. Some studies have suggested the interaction between T. cruzi and the lipid metabolism of the host. Therefore, the objective of the present study was to evaluate the association between the ACAT-1 gene rs1044925 SNP in relation to clinical manifestations in patients with chronic Chagas disease. A total of 135 individuals with chronic Chagas disease, 86 (63.7%) asymptomatic individuals and 49 (36.3%) symptomatic patients (22 with cardiac clinical form, 18 with digestive form and 9 with mixed form) participated in the study. To evaluate the polymorphism, the PCR-RFLP technique were used. There was a significant difference and a higher frequency of AA and AC genotypes (p = 0.047 and p = 0.016, respectively) of the ACAT-1 gene in asymptomatic chagasic individuals. The result suggests a protective character of the AA and AC genotypes of the rs1044925 SNP in relation to the presence of symptomatic clinical manifestations of the disease in chronic chagasic individuals.

From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products

Camels have an important role in the lives of human beings, especially in arid regions, due to their multipurpose role and unique ability to adapt to harsh conditions. In spite of its enormous economic, cultural, and biological importance, the camel genome has not been widely studied. The size of camel genome is roughly 2.38 GB, containing over 20,000 genes. The unusual genetic makeup of the camel is the main reason behind its ability to survive under extreme environmental conditions. The camel genome harbors several unique variations which are being investigated for the treatment of several disorders. Various natural products from camels have also been tested and prescribed as adjunct therapy to control the progression of ailments. Interestingly, the camel employs unique immunological and molecular mechanisms against pathogenic agents and pathological conditions. Here, we broadly review camel classification, distribution and breed as well as recent progress in the determination of the camel genome, its size, genetic distribution, response to various physiological conditions, immunogenetics and the medicinal potential of camel gene products.

Invited review: Reproductive and genomic technologies to optimize breeding strategies for genetic progress in dairy cattle

Abstract. Dairy cattle breeders have exploited technological advances that have emerged in the past in regards to reproduction and genomics. The implementation of such technologies in routine breeding programs has permitted genetic gains in traditional milk production traits as well as, more recently, in low-heritability traits like health and fertility. As demand for dairy products increases, it is important for dairy breeders to optimize the use of available technologies and to consider the many emerging technologies that are currently being investigated in various fields. Here we review a number of technologies that have helped shape dairy breeding programs in the past and present, along with those potentially forthcoming. These tools have materialized in the areas of reproduction, genotyping and sequencing, genetic modification, and epigenetics. Although many of these technologies bring encouraging opportunities for genetic improvement of dairy cattle populations, their applications and benefits need to be weighed with their impacts on economics, genetic diversity, and society.

The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons)

The list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which often little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations of S. cebifrons exist, which originated from two different Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to other Sus species potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well.

The association between polymorphism of the GH1 gene and changes in protein structure and carcass traits in Mehraban sheep (Ovis aries)

The present study indicates an association between carcass traits and genetic polymorphism and changes in the protein structure of the growth hormone 1 (GH1) gene in Mehraban sheep. Polymorphism of the GH1 gene was detected by polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) and DNA sequencing methods in 463 individuals. Two different structures in the GH1 protein and six single nucleotide polymorphisms were identified. The association of these SSCP patterns and protein structures with carcass traits was analysed. The SSCP patterns were shown to be associated with carcass traits. Individuals with AB SSCP pattern and Type B protein structure had significantly higher fat-tail weight and volume (P < 0.05) than did those individuals with CC SSCP pattern and Type A protein structure. Moreover, CC SSCP pattern and Type A protein structure contributed to low concentration of blood triglycerides (P = 0.004). The results confirmed the importance of GH1 as a candidate gene for marker-assisted selection for carcass-trait variations in sheep.

Polymorphisms of heat shock protein 90 (Hsp90) in the sea cucumber Apostichopus japonicus and their association with heat-resistance

Heat shock protein 90 (Hsp90) functions as a molecular chaperone and plays an important role in the resistance of organisms to stress, particularly heat-stress. In our study, 12 exons and 11 introns of hsp90 were identified in the sea cucumber Apostichopus japonicus. Twenty-two single nucleotide polymorphisms (SNPs), including three non-synonymous mutations, were detected in the exons. Susceptible and resistant individuals were distinguished using a high-temperature (32 °C) challenge experiment. Three blocks with high linkage disequilibrium were detected among these SNPs. Five of the twenty-two SNPs were shown to be significantly associated with susceptibility/resistance to high temperature by correlation analysis (chi-square test, P < 0.05). To confirm the importance of these five SNPs, a heat-resistance strain (HRS) was selected through three generations. Using the common population as the control group, it was shown that the distributions of genotypes and alleles of SNP e10-1 and e11-6 were significantly different between the two groups (P < 0.05). SNP e10-1 was trimorphic, with three alleles (A, C and T) and five genotypes (AA, CC, AT, CT and AC). The allele frequency of SNP e2-3 was also significantly associated with this trait (P < 0.05). This is the first demonstration of SNPs related to heat-resistance in A. japonicus and supports the use of SNP markers in the selective breeding of sea cucumbers.