Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

A review of porcine skeletal muscle plasticity and implications for genetic improvement of carcass and meat quality

Skeletal muscle is characterized by a remarkable plasticity to adapt to stimuli such as contractile activity, loading conditions, substrate supply or environmental factors. The existing knowledge of muscle plasticity along with developed genetic and genomic technologies, have enabled creating animal breeding strategies and allowed for implementing agriculturally successful porcine genetic improvement programs. The primary focus of this review paper is on pig skeletal muscle plasticity as it relates to genetic improvement of desirable carcass composition and pork quality traits. Biological constraints between practically realized breeding objectives, pig skeletal muscle biology, and pork quality are also discussed. Future applications of genetic and genomic technologies and plausible focus on new breeding objectives enhancing pork production sustainability are proposed as well.

Comprehensive characterization of the differences in metabolites, lipids, and volatile flavor compounds between Ningxiang and Berkshire pigs using multi-omics techniques

This study was conducted to comprehensively characterize, metabolites, lipids, and volatile flavor compounds of NingXiang (NX) pigs, Berkshire (BKS) pigs, and their crossbred (Berkshire × Ningxiang, BN) pigs using multi-omics technique. The results showed that NX had high intramuscular fat (IMF) content and meat redness. The metabolite and lipid compositions were varied greatly among three pig breeds. The NX pigs exhibited distinctive sweet, fruity, and floral aroma while BN pigs have inherited this flavor profile. 2-pentylfuran, pentanal, 2-(E)-octenal, and acetic acid were the key volatile flavor compounds (VOC) of NX and BKS pork. The VOCs were influenced by the composition and content of metabolites and lipids. The NX pigs have excellent meat quality traits, unique flavor profiles, and high degree of genetic stability regarding flavor. The study deepens our understanding of the flavor of Chinese indigenous pigs, providing theoretical basis to understand the meat flavor regulation under different feeding conditions.

Identification of genomic regions associated with fatty acid metabolism across blood, liver, backfat and muscle in pigs

BACKGROUND

The composition and distribution of fatty acids (FA) are important factors determining the quality, flavor, and nutrient value of meat. In addition, FAs synthesized in the body participate in energy metabolism and are involved in different regulatory pathways in the form of signaling molecules or by acting as agonist or antagonist ligands of different nuclear receptors. Finally, synthesis and catabolism of FAs affect adaptive immunity by regulating lymphocyte metabolism. The present study performed genome-wide association studies using FA profiles of blood, liver, backfat and muscle from 432 commercial Duroc pigs.

RESULTS

Twenty-five genomic regions located on 15 Sus scrofa chromosomes (SSC) were detected. Annotation of the quantitative trait locus (QTL) regions identified 49 lipid metabolism-related candidate genes. Among these QTLs, four were identified in more than one tissue. The ratio of C20:4n-6/C20:3n-6 was associated with the region on SSC2 at 7.56-14.26 Mb for backfat, liver, and muscle. Members of the fatty acid desaturase gene cluster (FADS1, FADS2, and FADS3) are the most promising candidate genes in this region. Two QTL regions on SSC14 (103.81-115.64 Mb and 100.91-128.14 Mb) were identified for FA desaturation in backfat and muscle. In addition, two separate regions on SSC9 at 0 - 14.55 Mb and on SSC12 at 0-1.91 Mb were both associated with the same multiple FA traits for backfat, with candidate genes involved in de novo FA synthesis and triacylglycerol (TAG) metabolism, such as DGAT2 and FASN. The ratio C20:0/C18:0 was associated with the region on SSC5 at 64.84-78.32 Mb for backfat. Furthermore, the association of the C16:0 content with the region at 118.92-123.95 Mb on SSC4 was blood specific. Finally, candidate genes involved in de novo lipogenesis regulate T cell differentiation and promote the generation of palmitoleate, an adipokine that alleviates inflammation.

CONCLUSIONS

Several SNPs and candidate genes were associated with lipid metabolism in blood, liver, backfat, and muscle. These results contribute to elucidating the molecular mechanisms implicated in the determination of the FA profile in different pig tissues and can be useful in selection programs that aim to improve health and energy metabolism in pigs.

Genome-Wide Analysis Reveals Copy Number Variant Gene TGFBR3 Regulates Pig Back Fat Deposition

BFT is closely related to meat quality and lean meat percentage in pigs. The BFT traits of European LW pigs significantly differ from those of Chinese indigenous fatty MZ pigs. CNV is a prevalent genetic variation that plays an important role in economically important traits in pigs. However, the potential contribution of CNV to BFT in LW and MZ pigs remains unclear. In this study, whole-genome CNV detection was performed using next-generation sequencing data from LW and MZ pigs, and transcriptome data from back fat tissue of 180-day-old LW and MZ pigs were integrated for expression quantitative trait loci (eQTL) analysis. We identified a copy number variation in the TGFBR3 gene associated with BFT, showing a dose effect between the genome and transcriptome levels of the TGFBR3 gene. In porcine preadipocytes, TGFBR3 expression continuously increased during differentiation. Knockdown of TGFBR3 using specific siRNA inhibited preadipocyte differentiation and proliferation. Our study provides insights into the genetic regulation of pork quality and offers a theoretical basis for improving carcass quality by modulating BFT in pigs.

Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs

Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.

Haplotype-resolved 3D chromatin architecture of the hybrid pig

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison)

Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case-control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770-98,281 kb and chr1:114,133-120,473) and one on chromosome 6 (chr6:37,953-44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.

Genomic signatures reveal selection in Lingxian white goose

Lingxian white goose (LXW) is a goose breed indigenous to China that is famous for its meat quality and fast growth. However, the genomic evidence underlying such excellent breeding characteristics remains poorly understood. Therefore, we performed whole-genome resequencing of 141 geese from 3 indigenous breeds to scan for selection signatures and detect genomic regions related to breed features of LXW. We identified 5 reproduction-related genes (SYNE1, ESR1, NRIP1, CCDC170, and ARMT1) in highly differentiated regions and 11 notable genes in 26 overlapping windows, some of which are responsible for meat quality (DHX15), growth traits (LDB2, SLIT2, and RBPJ), reproduction (KCNIP4), and unique immunity traits (DHX15 and SLIT2). These findings provide insights into the genetic characteristics of LXW and identify genes affecting important traits in LXW, which extends the genetic resources and basis for facilitating genetic improvement in domestic geese breeds.

Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis

This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.

Carcass Quality Profiles and Associated Genomic Regions of South African Goat Populations Investigated Using Goat SNP50K Genotypes

Simple Summary

South Africa is one of the major goat producing countries on the African continent. However, despite a large number of goats being produced, there is still a growing demand for chevon, which leads to producers being unable to reach demand, resulting in an absence of chevon in retail markets. Carcass quality is an important economic trait that plays a major role in influencing consumer preferences and high nutrient provision. Even though chevon is an easily accessible meat for smallholder farmers and has health benefits, it is still less preferred due to perceptions of low meat quality attributes such as toughness, off-odours and flavour, and unappealing colour. The majority of goat populations are village ecotypes whose genetic potential for meat and carcass quality is unknown.

Abstract

Carcass quality includes a battery of essential economic meat traits that play a significant role in influencing farmer breed preferences. A preliminary study was undertaken to investigate the carcass quality and the associated genomic regions in a small nucleus of animals that are representative of South African goat genetic resources. Samples of the South African Boer (n = 14), Northern Cape Speckled (n = 14), Eastern Cape Xhosa Lob ear (n = 12), Nguni/Mbuzi (n = 13), and Village (n = 20) were genotyped using the Illumina goat SNP50K and were phenotyped for carcass quality traits. SA Boer goats had heavier warm and cold carcass weights (17.2 ± 2.3 kg and 16.3 ± 2.3 kg). Pella village goats raised under an intensive system had significantly (p < 0.05) heavier warm and cold carcass weights (9.9 ± 1.1 kg and 9.2 ± 1.2 kg) compared to the village goats that are raised extensively (9.1 ± 2.0 kg and 8.4 ± 1.9). A total of 40 SNPs located on chromosomes 6, 10, 12, 13, 19, and 21 were significantly associated with carcass traits at (−log10 [p < 0.05]). Candidate genes that were associated with carcass characteristics (GADD45G, IGF2R, GAS1, VAV3, CAPN8, CAPN7, CAPN2, GHSR, COLQ, MRAS, and POU1F1) were also observed. Results from this study will inform larger future studies that will ultimately find use in breed improvement programs.

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Pigs are strategically important animals for the agricultural industry. An assessment of genetic differentiation between pigs, undergone and not undergone to selection intensification, is of particular interest. Our research was conducted on two groups of Large White pigs grown on the same farm but in different years. A total of 165 samples were selected with 78 LW_А (n = 78, the Russian selection) and LW_B (n = 87, a commercial livestock). For genotyping, we used GeneSeek^® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). To define breeding characteristics of selection, we used smoothing FST and segment identification of HBD (Homozygous-by-Descent). The results of smoothing FST showed 20 areas of a genome with strong ejection regions of the genome located on all chromosomes except SSC2, SSC3, and SSC8. The average realized autozygosity in Large White pigs of native selection was in (LW_A)—0.21, in LW_В—0.29. LW_А showed 13,338 HBD segments, 171 per one animal, and LW_B—15,747 HBD segments, 181 per one animal. The ejections found by the smoothing FST method were partially localized in the HBD regions. In these areas, the genes ((NCBP1, PLPPR1, GRIN3A, NBEA, TRPC4, HS6ST3, NALCN, SMG6, TTC3, KCNJ6, IKZF2, OBSL1, CARD10, ETV6, VWF, CCND2, TSPAN9, CDH13, CEP128, SERPINA11, PIK3CG, COG5, BCAP29, SLC26A4) were defined. The revealed genes can be of special interest for further studying their influence on an organism of an animal since they can act as candidate genes for selection-significant traits.

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.

Detection of whole genome selection signatures of Pakistani Teddy goat

BACKGROUND

Natural and artificial selection tend to cause variability that contributes to shape the genome of livestock in a way that differentiates them among the animal kingdom. The particular aim here is to identify positive selection signatures with whole genome pooled-sequence data of Pakistani Teddy goat.

METHODS AND RESULTS

Paired-end alignment of 635,357,043 reads of Teddy goat with (ARS1) reference genome assembly was carried out. Pooled-Heterozygosity (Hp) and Tajima's D (TD) are applied for validation and getting better hits of selection signals, while pairwise F_ST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation, moreover annotation of regions under positive selection was also performed. Hp score with - ZHp > 5 detected six windows having highest hits on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, - ZTD value of > 3.3 showed 4 windows with very strong hits on Chr.5 & 9 which harbor STIM1 and ADM genes related to body mass and weight. Lastly, - ZF_ST < - 5 generated four strong signals on Chr.5 & 12 harbor LOC102183233 gene. Other significant selection signatures encompass genes associated with wool production, prolificacy and coat colors traits in this breed.

CONCLUSIONS

In brief, this study identified the genes under selection in Pakistani Teddy goat that will be helpful to refining the marker-assisted breeding policies and converging required production traits within and across other goat breeds and to explore full genetic potential of this valued species of livestock.

The identification of a nuclear factor Akirin with regulating the expression of antimicrobial peptides in red swamp crayfish (Procambarus clarkii)

Akirin is a highly conserved nuclear factor among different species. It is closely related to skeletal muscle development, innate immune response, and tumorigenesis in a variety of animals. In invertebrates, Akirin is mainly involved in gene transcription and NF-κB dependent natural immune response. In the present study, a nuclear factor Akirin was identified from Procambarus clarkii. The Akirin protein of crayfish consists of 204 amino acids and is conserved among its family members, especially the nuclear localization signal peptide motif (KRRR). PcAkirin was highly expressed in stomach, intestines, and hepatopancreas. After A. hydrophila challenge, the transcription level of Akirin significantly increased in hemocyte and hepatopancreas. In addition, the recombinant Akirin protein was produced successfully and helpful to resist WSSV infection by increasing the expression level of some immune related genes. On the contrary, after interfering with Akirin gene by dsRNA, the crayfish increased the sensitivity to A. hydrophila and WSSV infections. The results are more obvious in the accumulated mortality of P. clarkii infected with A. hydrophila and WSSV. All these results suggested that Akirin played a significant role in innate immune responses and protected it from WSSV and bacterial infection in crayfish.

Akirin proteins in development and disease: critical roles and mechanisms of action

The Akirin genes, which encode small, nuclear proteins, were first characterized in 2008 in Drosophila and rodents. Early studies demonstrated important roles in immune responses and tumorigenesis, which subsequent work found to be highly conserved. More recently, a multiplicity of Akirin functions, and the associated molecular mechanisms involved, have been uncovered. Here, we comprehensively review what is known about invertebrate Akirin and its two vertebrate homologues Akirin1 and Akirin2, highlighting their role in regulating gene expression changes across a number of biological systems. We detail essential roles for Akirin family proteins in the development of the brain, limb, and muscle, in meiosis, and in tumorigenesis, emphasizing associated signaling pathways. We describe data supporting the hypothesis that Akirins act as a "bridge" between a variety of transcription factors and major chromatin remodeling complexes, and discuss several important questions remaining to be addressed. In little more than a decade, Akirin proteins have gone from being completely unknown to being increasingly recognized as evolutionarily conserved mediators of gene expression programs essential for the formation and function of animals.

A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs

Feed efficiency (FE) traits in pigs are of utmost economic importance. Genetic improvement of FE related traits in pigs might significantly reduce production cost and energy consumption. Hence, our study aimed at identifying SNPs and candidate genes associated with FE related traits, including feed conversion ratio (FCR), average daily gain (ADG), average daily feed intake (ADFI), and residual feed intake (RFI). A genome-wide association study (GWAS) was performed for the four FE related traits in 296 Landrace pigs genotyped with PorcineSNP50 BeadChip. Two different single-trait methods, single SNP linear model GWAS (LM-GWAS) and single-step GWAS (ssGWAS), were implemented. Our results showed that the two methods showed high consistency with respect to SNP identification. A total of 32 common significant SNPs associated with the four FE related traits were identified. Bioinformatics analysis revealed eight common QTL regions, of which three QTL regions related to ADFI and RFI traits were overlapped. Gene ontology analysis revealed six common candidate genes (PRELID2, GPER1, PDX1, TEX2, PLCL2, ICAM2) relevant for the four FE related traits. These genes are involved in the processes of fat synthesis and decomposition, lipid transport process, insulin metabolism, among others. Our results provide, new insights into the genetic mechanisms and candidate function genes of FE related traits in pigs. However, further investigations to validate these results are warranted.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs

BACKGROUND

Porcine respiratory disease is one of the most important health problems which causes significant economic losses.

OBJECTIVE

To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data.

METHODS

Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma.

RESULTS

Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility.

CONCLUSION

These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

Pigs were domesticated independently in the Near East and China, indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide. Therefore, 12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome. As a result, 72.5 Mb of non-redundant sequences (∼3% of the genome) were found to be absent from the reference genome (Sscrofa11.1) and were defined as pan-sequences. Of the pan-sequences, 9.0 Mb were dominant in Chinese pigs, in contrast with their low frequency in European pigs. One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3 (TIG3) gene which is involved in fatty acid metabolism. Using flanking sequences and Hi-C based methods, 27.7% of the sequences could be anchored to the reference genome. The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure. A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

Evaluation of the four breeds in synthetic line of Jiaxing Black Pigs and Berkshire for meat quality traits, carcass characteristics, and flavor substances

To investigate breed characteristics and the effect of hybridization of Jiaxing Black Pig (JBP) with Western breeds, the carcass and meat quality traits and flavor substances such as inosinic acids (IMP), intramuscular fat (IMF) in longissimus muscle (LM) from five breeds including JBP, Berkshire, Berkshire × JBP (BJBP), Duroc × Berkshire × JBP (DBJBP), Duroc × Landrace × JBP (DLJBP) were compared in this study. It was found that water holding capacity (WHC) of LM in JBP was significantly higher than that in the other strains (p < 0.01). Dressing out percentage and lean percentage of JBP were both significantly lower than those in the others (p < 0.01) in connection with their lighter carcass weight and higher subcutaneous fat percentage (p < 0.01). Heterosis was realized in DJBP, DBJBP, and DLJBP since their carcass weight, lean percentage, and loin eye muscle area (LEMA) were markedly higher when compared to JBP, whereas lower than those in Berkshire. Among the breeds, the content of IMF and IMP in the LM of JBP were the highest. These traits were also palpably improved in the crossbreds, especially for DBJBP, of which pork was considered outstanding for containing the most abundant essential amino acids (EAA) and total amino acids (TAA).

Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding

Inflorescence capacity plays a crucial role in reproductive fitness in plants, and in production of hybrid crops. Maize is a monoecious species bearing separate male and female flowers (tassel and ear, respectively). The switch from open-pollinated populations of maize to hybrid-based breeding schemes in the early 20th century was accompanied by a dramatic reduction in tassel size, and the trend has continued with modern breeding over the recent decades. The goal of this study was to identify selection signatures in genes that may underlie this dramatic transformation. Using a population of 942 diverse inbred maize accessions and a nested association mapping population comprising three 200-line biparental populations, we measured 15 tassel morphological characteristics by manual and image-based methods. Genome-wide association studies identified 242 single nucleotide polymorphisms significantly associated with measured traits. We compared 41 unselected lines from the Iowa Stiff Stalk Synthetic (BSSS) population to 21 highly selected lines developed by modern commercial breeding programs, and found that tassel size and weight were reduced significantly. We assayed genetic differences between the two groups using three selection statistics: cross population extended haplotype homozogysity, cross-population composite likelihood ratio, and fixation index. All three statistics show evidence of selection at genomic regions associated with tassel morphology relative to genome-wide null distributions. These results support the tremendous effect, both phenotypic and genotypic, that selection has had on maize male inflorescence morphology.

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by F_st within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.

Convergent and divergent genetic changes in the genome of Chinese and European pigs

Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs. And these genes belong predominantly to categories related to the nervous system, muscle development, and especially to metabolic diseases. In addition, 35 genes, representing different breeding preference, were found under bidirectional selection for the distinct leanness and reproduction traits between CHD and EUD. The convergent genetic changes, contributing physical and morphological adaption, represent the common concerns on pig domestication. And the divergent genetic changes reflect distinct breeding goals between Chinese and European pigs. Using ITPR3, AHR and NMU as examples, we explored and validated how the genetic variations contribute to the phenotype changes.

Comparison of growth performance of Berkshire purebreds and crossbreds sired by Hereford and Tamworth breeds raised in alternative production system

Objective

The objective of the present study was to compare growth performance of Berkshire purebred pigs (BB), Hereford (HB) and/or Tamworth (TB) sired Berkshire crossbred pigs reared in a hoop structure in two experiments.

Methods

In the first experiment, BB was compared to TB while HB and TB were compared in the second. Body weights (BW) were recorded at 3 days of age and every 28 days from birth until 140 days of age. There was no significant difference between the BW of BB and TB, but HB was heavier than TB by 84 days of age. Least square means of average daily gain (ADG) were evaluated using one-way analysis of variance.

Results

The mean parity (±standard deviation) of the sows was 3.42±2.14 and a total of 45 farrowing occurred from year 2012 to 2014. The mean number of total born, number born alive, number of mummies, and number weaned were 9.23±2.52, 7.87±2.53, 0.04±0.21, and 5.94±2.74, respectively. Parity did not have a significant effect on the growth performance of the pigs. For BB and TB, there was only one time frame in which there was a significant difference in the ADG: between 28 and 56 days of age. For HB and TB, the overall ADG of HB was significantly greater than the total ADG of TB.

Conclusion

The breed of the sire did not affect the growth performance of the progeny between Berkshire purebreds and Tamworth×Berkshire crossbreds. The breed of the sire did have an effect between Hereford and Tamworth sired Berkshire crossbreds (p<0.05). The Hereford sired pigs were found to have increased growth performance compared to Tamworth sired.

Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs

In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism was analysed in 111 Iberian x Landrace backcross animals. The eGWAS identified 92 eSNPs located in seven chromosomal regions and associated with eight genes: CROT, CYP2U1, DGAT1, EGF, FABP1, FABP5, PLA2G12A, and PPARA. Remarkably, cis-eSNPs associated with FABP1 gene expression which may be determining the C18:2(n-6)/C18:3(n-3) ratio in backfat through the multiple interaction of DNA variants and genes were identified. Furthermore, a hotspot on SSC8 associated with the gene expression of eight genes was identified and the TBCK gene was pointed out as candidate gene regulating it. Our results also suggested that the PI3K-Akt-mTOR pathway plays an important role in the control of the analysed genes highlighting nuclear receptors as the NR3C1 or PPARA. Finally, sex-dimorphism associated with hepatic lipid metabolism was identified with over-representation of female-biased genes. These results increase our knowledge of the genetic architecture underlying fat composition traits.

Genomic analysis reveals selection in Chinese native black pig

Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.

A decade of pig genome sequencing: a window on pig domestication and evolution

Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.