Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds.

Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its "year-round estrus and multiple births" and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep's high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

Effect of SNPs on Litter Size in Swine.

Although sows do not directly enter the market, they play an important role in piglet breeding on farms. They consume large amounts of feed, resulting in a significant environmental burden. Pig farms can increase their income and reduce environmental pollution by increasing the litter size (LS) of swine. PCR-RFLP/SSCP and GWAS are common methods to evaluate single-nucleotide polymorphisms (SNPs) in candidate genes. We conducted a systematic meta-analysis of the effect of SNPs on pig LS. We collected and analysed data published over the past 30 years using traditional and network meta-analyses. Trial sequential analysis (TSA) was used to analyse population data. Gene set enrichment analysis and protein-protein interaction network analysis were used to analyse the GWAS dataset. The results showed that the candidate genes were positively correlated with LS, and defects in PCR-RFLP/SSCP affected the reliability of candidate gene results. However, the genotypes with high and low LSs did not have a significant advantage. Current breeding and management practices for sows should consider increasing the LS while reducing lactation length and minimizing the sows' non-pregnancy period as much as possible.

4D label-free quantitative proteomic analysis identifies CRABP1 as a novel candidate gene for litter size in rabbits†.

In commercial rabbit breeding, litter size is a crucial reproductive trait. This trait directly determines the reproductive ability of female rabbits and is crucial for evaluating the production efficiency. We here compared differentially expressed proteins of in the ovary tissue from New Zealand female rabbits with high (H) and low (L) litter sizes by using 4D label-free quantitative proteomic technology and identified 92 differential proteins. The biological functions of these proteins were revealed through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Most distributions of GO and KEGG were related to reproduction, growth development, and metabolism. Furthermore, a novel candidate gene cellular retinoic acid binding protein-1 (CRABP1), which was highly expressed in the L group, was selected for further biological function verification. The Cell Counting Kit-8 (CCK-8) assay and flow cytometry analysis revealed that CRABP1 can promote granulosa cell (GC) apoptosis and inhibit GC proliferation. Furthermore, qRT-PCR and western blotting analysis revealed that CRABP1 regulates the genes (HSD17B1, Wnt-10b, FSHR, TAF4B, BMP15, and BMP6) and protein (Wnt-10b) associated with steroid hormone synthesis and follicle development. The PCR product direct sequencing method revealed single nucleotide polymorphisms in the core promoter region of CRABP1. Luciferase activity assays revealed that the transcriptional activity of the GG genotype was significantly higher than that of the TT or TG genotype. Different genotypes are accompanied by changes in transcription factors, which indicates that T-359G polymorphism can regulate CRABP1 expression. In general, we identified litter size-related genes and revealed the mechanism underlying the effect of CRABP1 on litter size. CRABP1 serves as a key factor in the reproductive capacity of rabbits and can act as a molecular biomarker for the breeding of New Zealand rabbits.

The novel C268A variant of BMP2 is linked to the reproductive performance of Awassi and Hamdani sheep.

BACKGROUND: Prolificacy-associated genetic markers can be utilized to enhance litter size in the sheep breeding industry. Sheep reproduction is influenced by a multitude of genes, including bone morphogenetic protein 2 (BMP2). This study aimed to explore the potential relationship between variability in the BMP2 gene and reproductive performance in Awassi and Hamdani ewes. METHODS AND RESULTS: The genomic DNA was extracted from 99 single-progeny ewes and 101 twin ewes. Polymerase chain reaction (PCR) was employed to produce an amplicon consisting of four sequence fragments: 277 bp, 251 bp, 331 bp, and 340 bp, from exons 1, 2, 3, and 4 of the BMP2 gene, respectively. Three genotypes were identified for amplicons in exon 4 with 340-bp lengths: CC, CA, and AA. Upon analyzing the sequence of the CA genotype 382 C > A, a novel mutation was discovered in this genotype. A robust association was identified between the single nucleotide polymorphisms (SNP) 382 C > A and reproductive performance through statistical analysis. An important distinction was discovered between ewes carrying SNP 382 C > A and those carrying CC in terms of litter sizes, twinning rates, lambing rates, and days to lambing. An analysis of logistic regression revealed a significant association between litter size and the 382 C > A SNP. There was a decrease in lamb production among ewes with the CC genotype compared to those with the CA and AA genotypes. CONCLUSIONS: These results indicate that the SNP variant 382 C > A has a positive influence on the reproductive performance of Awassi and Hamdani sheep. Sheep carrying the 382 C > A SNP exhibit increased litter size and overall productivity compared to those without the SNP.

Impact of litter size on the hematological and iron status of gilts, sows and newborn piglets: a comparative study of domestic pigs and wild boars.

BACKGROUND: The critically low hepatic iron stores of newborn piglets are considered to be a major cause of neonatal iron deficiency in modern breeds of domestic pig (Sus domestica). The main factor believed to contribute to this phenomenon is large litter size, which has been an objective of selective breeding of pigs for decades. As consequence, iron transferred from the pregnant sow has to be distributed among a greater number of fetuses. RESULTS: Here, we investigated whether litter size influences red blood cell (RBC) indices and iron parameters in Polish Large White (PLW) piglets and gilts. Small and large litters were produced by the transfer of different numbers of embryos, derived from the same superovulated donor females, to recipient gilts. Piglets from large litters obtained following routine artificial insemination were also examined. Our results clearly demonstrated that varying the number of piglets in a litter did not affect the RBC and iron status of 1-day-old piglets, with all showing iron deficiency anemia. In contrast, gilts with small litters displayed higher RBC and iron parameters compared to mothers with large litters. A comparative analysis of the RBC status of wild boars (having less than half as many piglets per litter as domestic pigs) and PLW pigs, demonstrated higher RBC count, hemoglobin level and hematocrit value of both wild boar sows and piglets, even compared to small-litter PLW animals. CONCLUSIONS: These findings provide evidence that RBC and iron status in newborn PLW piglets are not primarily determined by litter size, and indicate the need to study the efficiency of iron transport across the placenta in domestic pig and wild boar females.

Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats.

Litter size is a key indicator of production performance in livestock. However, its genetic basis in goats remains poorly understood. In this work, a genome-wide selection sweep analysis (GWSA) on 100 published goat genomes with different litter rates was performed for the first time to identify candidate genes related to kidding rate. This analysis was combined with the public RNA-sequencing data of ovary tissues (follicular phase) from high- and low-yielding goats. A total of 2278 genes were identified by GWSA. Most of these genes were enriched in signaling pathways related to ovarian follicle development and hormone secretion. Moreover, 208 differentially expressed genes between groups were obtained from the ovaries of goats with different litter sizes. These genes were substantially enriched in the cholesterol and steroid synthesis signaling pathways. Meanwhile, the weighted gene co-expression network was used to perform modular analysis of differentially expressed genes. The results showed that seven modules were reconstructed, of which one module showed a very strong correlation with litter size (r = -0.51 and p-value <0.001). There were 51 genes in this module, and 39 hub genes were screened by Pearson's correlation coefficient between core genes > 0.4, correlation coefficient between module members > 0.80 and intra-module connectivity ≥5. Finally, based on the results of GWSA and hub gene Venn analysis, seven key genes (ACSS2, HECW2, KDR, LHCGR, NAMPT, PTGFR and TFPI) were found to be associated with steroid synthesis and follicle growth development. This work contributes to understanding of the genetic basis of goat litter size and provides theoretical support for goat molecular breeding.

Detection of polymorphisms in six genes and their association analysis with litter size in sheep.

Litter size in sheep is a complex trait controlled by micro-effective polygenes. APAF1, CLSTN2, CTH, PLCB1, PLCB4, and CHST11 are all involved in mammalian reproduction. However, the effects of these genes on litter size in sheep are still unclear. Therefore, in this study, we used Sequenom MassARRAY® SNP assay technology to type the single nucleotide polymorphisms (SNPs) loci of six genes in five sheep breeds. The results showed that most sheep breeds contain three genotypes at each locus. Then, we conducted population genetic analysis on the SNPs of six genes and found that the polymorphic information content in all sheep breeds ranged from 0 to 0.37, and most sheep breeds were in Hardy-Weinberg equilibrium (p > 0.05). In addition, association analysis in Small Tail Han sheep indicated that the rs399534524 locus in CLSTN2 was highly associated with first parity litter size, and litter size in ewes with CT genotype was higher than that in ewes with CC genotype or TT genotype. Furthermore, the rs407142552 locus in CTH was highly associated with second parity litter size in Small Tail Han sheep, and litter size in ewes with CT genotype was higher than that in ewes with TT genotype. Finally, we predicted the CTH and CLSTN2 protein interaction network and found that HTR1E, NOM1, CCDC174 and ALPK3 interact with CLSTN2 and have been reported as candidate genes related to litter size in sheep. These results suggest that they may be useful genetic markers for increasing litter size in sheep.

Genetic variant of the sheep E2F8 gene and its associations with litter size.

The economic efficiency of sheep breeding, aiming to enhance productivity, is a focal point for improvement of sheep breeding. Recent studies highlight the involvement of the Early Region 2 Binding Factor transcription factor 8 (E2F8) gene in female reproduction. Our group's recent genome-wide association study (GWAS) emphasizes the potential impact of the E2F8 gene on prolificacy traits in Australian White sheep (AUW). Herein, the purpose of this study was to assess the correlation of the E2F8 gene with litter size in AUW sheep breed. This work encompassed 659 AUW sheep, subject to genotyping through PCR-based genotyping technology. Furthermore, the results of PCR-based genotyping showed significant associations between the P1-del-32bp bp InDel and the fourth and fifth parities litter size in AUW sheep; the litter size of those with genotype ID were superior compared to those with DD and II genotypes. Thus, these results indicate that the P1-del-32bp InDel within the E2F8 gene can be useful in marker-assisted selection (MAS) in sheep.

Factors affecting birth weight and stillbirth in sows housed in a tropical environment.

This study analysed data from a commercial swine herd in Thailand equipped with a free-farrowing housing system, comprising 17,196 piglets from 1318 litters, to explore the impact of sow and litter characteristics on the piglet birth weight and the incidence of stillbirth. The piglets were classified into four groups based on the total number of piglets born per litter (TB): ≤9 (n = 1434), 10-12 (n = 3232), 13-15 (n = 6537) and ≥16 (n = 5993). Sows were classified into four groups based on parity number: 1, 2-4, 5-7 and ≥8. The piglets were categorized into quartiles based on their birth order ranking: Q1 (n = 4786), Q2 (n = 4143), Q3 (n = 3808) and Q4 (n = 4456). Piglet birth weight was individually measured before colostrum ingestion. On average, TB, the number of live-born piglets and the incidence of stillbirth were 13.1 ± 3.7, 11.5 ± 3.8 and 6.3%, respectively. Among these litters, 26.6% had TB numbers ≥16. The average piglet birth weight was 1.37 ± 0.36 kg, with 18.3% of piglets weighing ≤1.0 kg at birth. Piglet birth weight was influenced by birth order ranking, as Q4 piglets were found to be heavier than piglets born in Q1-Q3 (p < .001). Moreover, the percentage of piglets with a birth weight of ≤1.0 kg increased from 5.9% in litters with TB of ≤9-25.3% in litters with TB of ≥16 (p < .001). Additionally, primiparous sows had lower piglet birth weights compared to sows with parity numbers 2-4, 5-7 and ≥8 (p < .001). Piglets born in the fourth quartile (Q4) had a higher risk of stillbirth compared to those born in the first (Q1), second (Q2) and third (Q3) quartiles (12.5% vs. 2.2%, 4.1% and 6.6%, respectively, p < .001). The incidence of stillbirth in litters with TB ≥16 was also higher than that in litters with TB ≤9 and 10-12 (p < .05). Furthermore, sows with parity numbers ≥8 had a higher incidence of stillbirth (9.7%) compared to primiparous sows (4.0%, p < .001), sows with 2-4 parity (5.2%, p < .001) and sows with 5-7 parity (7.6%, p = .003). In summary, a high incidence of stillbirth was found in piglets born in the last quartile of litters, in litters with >16 piglets and for sows with parity numbers ≥8. Piglets born in the last quartile of litters were heavier than those born in the first to third quartiles.

Anti-Müllerian hormone as a promising novel biomarker for litter size in Romanov sheep.

Anti-Müllerian hormone (AMH) is a hormone produced by growing preantral and antral follicles of the ovary. AMH is accepted as an important biomarker for fertility and superovulation parameters in livestock species. This study aimed to evaluate changes in serum AMH level in the oestrous cycle, repeatability of AMH, the effect of age on serum AMH level and the effects of AMH on litter size in Romanov sheep. In the study, a total of 36 Romanov sheep were used as animal material. First blood samples (0th day) were collected from 36 ewes to evaluate AMH and progesterone levels. Second blood samples were collected randomly from 20 ewes 9 days after first sampling to compare AMH levels at two different periods of the oestrous cycle in Romanov ewes. The ewes were categorized into three groups as low, medium and high AMH based on their first AMH levels. Results indicated that serum AMH level did not change during the oestrous and dioestrous phases of the oestrous cycle and two random time points of the oestrous cycle (p > .05). Pearson correlation analysis revealed that there is a high (r = .95) and significant (p < .001) correlation between AMH levels at the 0th (AMH-1) and 9th (AMH-2) days. The effect of AMH level on litter size was found to be significant. Litter size was significantly higher in the high AMH group than in the low AMH group (p < .05). In addition, the age of ewes did not affect serum AMH levels (p > .05). ROC analysis indicates that AMH cut-off value >320 pg/mL with 70% sensitivity and 100% specificity can be used for litter size in Romanov ewes. In conclusion, AMH is highly repeatable and its serum AMH level did not change during the oestrous cycle in Romanov sheep. In addition, AMH affects litter size and can be reliably used as a marker for litter size in Romanov sheep.

Sheep litter size heredity basis using genome-wide selective analysis.

Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-ß (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.

Factors contributing to stillbirth in young hyper-prolific sows in a tropical free-farrowing system.

The present study investigated factors associated with the incidence of stillbirth in young hyper-prolific sows within free farrowing systems in tropical environments. A total of 714 live-born and 54 stillborn piglets from 57 Landrace × Yorkshire sows, with an average parity of 2.7 ± 1.0 (range: 1 - 4), were comprehensively investigated. Reproductive variables of the sows, including gestation length, farrowing duration, the total number of piglets born per litter, and the birth order and status of each piglet, were recorded. Differences in the physiological characteristics of live-born and stillborn piglets, such as birth interval, cumulative birth interval, body weight at birth, crown-rump length, body mass index (BMI), ponderal index (PI), meconium staining score, and the percentage of piglets with a broken umbilical cord, were analysed. Piglets were divided into four groups based on the quartiles of birth order (Q1-Q4). On average, the duration of farrowing was 173.3 ± 85.9 min, and the total number of piglets born and number of piglets born alive-per litter were 14.1 ± 3.8 and 12.5 ± 3.5, respectively. The incidence of stillbirth was 6.7% (54/801 piglets). The higher percentages of stillbirths were detected in sows with large litter sizes (≥17 piglets, 10.9%) compared to those with small (≤13 piglets, 6.1%) and moderate (14 - 16 piglets, 2.8%) litter sizes (p < .001). The incidences of stillbirth in Q3 and Q4 of the litters were higher than in Q1 and Q2 (p < .001). Compared to live-born piglets, stillborn piglets had higher cumulative birth interval (103.0 ± 3.71 vs. 142.4 ± 9.35 min, p < .001), BMI (17.1 ± 0.15 vs. 18.4 ± 0.39 kg/m2, p = .002), PI (63.7 ± 0.59 vs. 70.8 ± 1.59 kg/m3, p < .001), meconium staining scores (1.78 ± 0.04 vs. 2.04 ± 0.10, p = .021), and the percentage of piglets born with a ruptured umbilical cord (45.2% vs. 66.0%, p = .004). An increase in the incidence of stillbirth was detected at 60, 120, 150, 180, and ≥ 210 min after the first piglet was born, compared to those born within the first 30 min of farrowing (p < .05). In conclusion, the study found that stillbirths in young, hyper-prolific sows were linked to several factors: large litter sizes (≥17 piglets per litter), prolonged cumulative birth intervals (142.4 min), elevated BMI of 18.4 kg/m2, high PI values of 70.8 kg/m3, increased meconium staining scores, and a higher occurrence of ruptured umbilical cords. To reduce the risk of stillbirth, particularly among piglets with high body indices born later in the birthing process, it is recommended to enhance farrowing supervision for young sows, starting at a cumulative birth interval of 60 min.

Association of polymorphism in the promotor area of the caprine BMPR1B gene with litter size and body measurement traits in Damani goats.

This study aimed to explore polymorphisms in the promoter region of the caprine BMPR1B (Bone morphogenetic protein receptor 1 beta) gene and its association with body measurement and litter size traits in Damani does. A total of 53 blood samples were collected to analyze the association between the BMPR1B gene polymorphism and 11 phenotypic traits in Damani female goats. The results revealed that three novel SNPs were identified in the promoter region of the caprine BMPR1B gene, including g.67 A > C (SNP1), g.170 G > A(SNP2), and g.501A > T (SNP3), among which the SNP1 and SNP2 were significantly (p < 0.05) associated with litter size and body measurement traits in Damani goats. In SNP1 the AC genotype could be used as a marker for litter size, and the CC genotype for body weight in Damani goats. In SNP2, the genotype GG was significantly (p < 0.05) associated with ear and head length. Therefore, we can conclude from the present study, that genetic variants AC and CC of the caprine BMPR1B gene could be used as genetic markers for economic traits through marker-assisted selection for the breed improvement program of the Damani goat.

Managing prolific sows in tropical environments.

Litter size in modern sows has been dramatically improved in recent decades by genetic selection for highly prolific sows. In a tropical environment, the average total number of pigs born and number born alive are reported to be as high as 17.2 and 15.1 piglets per litter, respectively. Therefore, the new production target in many herds aims to achieve 30-40 pigs weaned per sow per year. Despite the improvements in litter size, the mean preweaning piglet mortality rate remains high, at between 10% and 20%, in major pig-producing countries. A sufficient daily feed intake by lactating sows is important for high milk production as sow milk yield is the limiting factor for piglet growth rate. Heat stress, which can occur when the ambient temperatures rise above 25°C, is one of the major problems that decreases daily feed intake and compromises milk yield. Therefore, it is necessary to encourage high feed intakes to achieve high milk yields. However, even with high nutrient intakes, productivity can be constrained by intestinal barrier function, limiting digestive ability, and allowing potential pathogens and/or toxins to become systemic. This is more likely greater under tropical conditions because of heat stress, exacerbating sow fertility problems. Underpinning sow herd performance, including responses to environmental challenges, is the selection of appropriate gilts, for example, selection and management for early puberty, thus presumably selecting the more fertile gilts and the correct management of lactation to improve the number of weaned piglets are some of the key factors for future reproductive efficiency of the farm under tropical conditions.

Selecting the optimal strategies when using nurse sows for supernumerous piglets.

Hyper-prolific sows frequently do not have a sufficient number of functional teats for their piglets to nurse which has led to the use of nurse sows to manage these surplus piglets. This review discusses strategies for using nurse sows and factors that influence preweaning survival and weight gain of their litters, as well as those that affect their subsequent rebreeding performance. Rearing piglets using a nurse sow can be as successful as piglets reared with their biological mother and is thus a powerful management tool to decrease preweaning piglet mortality. Selecting a young sow as nurse sow is beneficial for piglet survival; however, piglets nursing first parity sows often have a lower daily weight gain than piglets nursing multiparous sows. A litter of uniform surplus piglets is preferably handled using the two-step nurse sow strategy. A consequence of nonuniform litters will most likely be an increased mortality and decreased weaning weight among the smallest piglets within a litter. The subsequent fertility of nurse sows is not compromised. There is an increased risk of lactational oestrus when using nurse sows leading to an increased weaning-to-oestrus interval; however, litter size in nurse sows is identical or even moderately higher in the subsequent parity compared with nonnurse sows.

Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits.

Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.

Identification of risk factors for ewe mortality during the pregnancy and lambing period in extensively managed flocks.

BACKGROUND: Ewe mortality during pregnancy and lambing is an issue for sheep producers globally, resulting in reduced productivity and profitability, compromised ewe welfare, and poor consumer perception. Despite these negative consequences, there was little investigation into factors associated with ewe death during this time. Therefore, this study aimed to assess associations between ewe body condition score (BCS), weight, reproductive parameters, and risk of mortality during pregnancy and lambing. METHODS: Four cohorts from three commercial New Zealand farms participated, with 13,142 ewe lambs enrolled and followed over time. Data were collected for five consecutive lambings. Visits aligned with key on-farm management times, specifically: prior to breeding, at pregnancy diagnosis (PD), prior to lambing (set-stocking), and, at weaning of their lambs. At each visit, ewes were weighed, BCS assessed and reproductive status was recorded when relevant (litter size at PD and lactation status after lambing). Ewes that died or were culled were recorded, and any ewes that were absent from consecutive visits were presumed dead. Logistic regressions were developed to assess the relationship between weight and BCS at each visit, PD result (single or multiple-bearing) and lactation status (wet or dry) in each year, and, risk of mortality during the pregnancy and lambing period in each year. RESULTS: In the PD to weaning period, mortality incidence ranged from 6.3 to 6.9% for two-tooth (18-months-old at breeding) to mixed-age (54-months-old at breeding) ewes. For ewe lambs (7 to 8-months-old at breeding), mortality was 7.3% from set-stocking to weaning. Heavier ewe lambs at PD were less likely to die during lambing (OR: 0.978, p = 0.013), as were those with greater set-stocking BCS. In subsequent years, BCS was a predictor of ewe death, with odds of mortality greatest for ewes < BCS 2.5. Additionally, for poorer BCS ewes, increasing weight reduced risk of mortality, but there was no impact of increasing weight in greater BCS ewes. CONCLUSIONS: This study identified risk factors associated with ewe mortality during the pregnancy and lambing period. Flock owners can use these to either cull at-risk ewes or proactively intervene to reduce likelihood of mortality, thereby improving flock productivity, profitability and welfare.

Effect of NLR family pyrin domain containing 9 gene polymorphism on litter size in large white pigs.

NLR family pyrin domain containing 9 (NLRP9) is a mammalian reproduction-related gene. In this study, we researched the associations between polymorphisms located in the coding sequence (CDS) of the NLRP9 gene, and both the total number of piglets born per litter (TNB) and the number of piglets born alive per litter (NBA) in Canada Large White pigs (CLW). We detected a single nucleotide polymorphism (SNP) within exon 3 (g.10910C > T). The allele frequencies at the NLRP9 locus were 0.474 for the C allele and 0.526 for the T allele. Three genotypes, CC, CT, and TT, occurred with frequencies of 0.216, 0.515, and 0.269, respectively. Sows with the CC genotype had the largest TNB and NBA, sows with TT had the smallest, and those with CT were in-between. This difference was statistically significant (p < 0.05). Furthermore, CC females grew faster than CT or TT females, and there was a significant relationship between NLRP9 polymorphism and the average daily gain (p < 0.05). Here, we provide the first evidence for a novel SNP in NLRP9 associated with litter size in CLW sows, which could be used as a genetic marker to improve litter size in pig breeding and production.

Genetic polymorphisms in ESR and FSHß genes and their association with litter traits in Large White pigs.

The estrogen receptor (ESR) gene and follicle-stimulating hormone ß (FSHß) gene are responsible for litter traits. The present study aimed to verify the polymorphisms of ESR and FSHß and assess their effects on the litter traits in 201 Large White pigs. Four SNPs (g.C669T, g.A1296G, g.C1665T and g.A1755G) were found in ESR. The TT genotype at g.C1665T locus and AA genotype at g.A1755G locus could significantly increase the total litter size of the first litter of American Large White pigs (p < 0.05). Eight SNPs were found in exon 3 of FSHß. The AA genotype at g.A511G locus, AA and AG genotypes at g.A617G locus, CC and CT genotypes at g.C630T locus, CT and TT genotypes at g.C652T locus, CT and TT genotypes at g.C735T locus, AA and AG genotypes at g.A746G, AA and AG genotypes at g.A921G and CT genotype at g.C678T could significantly increase the litter size of different strains of Large White pigs (p < 0.05). Our study revealed that the genetic variations of ESR and FSHß were closely related to the litter trait of Large White pigs. Therefore, ESR and FSHß genes could be used as molecular markers for the genetic selection of Large White pigs.

Comparative analysis of genome-wide copy number variations between Tibetan sheep and White Suffolk sheep.

The DNA copy number variations (CNVs) are widely involved in affecting various kinds of biological functions, such as environmental adaptation. Tibetan sheep and White Suffolk sheep are two representative indigenous and exotic breeds raised in Sichuan, China, and both of them have many contrasting biological characteristics. In this study, we employed high-throughput sequencing approach to investigate genome-wide CNVs between the two sheep breeds. A total of 11,135 CNV regions (CNVRs) consisting of 6,488 deletions and 4,647 duplications were detected, whose length ranged from 1,599 bp to 0.56 Mb with the mean of 4,658 bp. There were 281 CNVRs segregated between Tibetan sheep and White Suffolk sheep, and 18 of them have been fixed within both breeds. Functional analyses of candidate genes within the segregating CNVRs revealed the thyroid hormone signaling pathway and CTNNB1 gene that would be responsible for differential biological characteristics of breeds, such as energy metabolism, seasonal reproduction, and litter size. Furthermore, the segregating CNVRs identified in this study were overlapped with many known quantitative trait loci that are associated with growth, testis weight, and reproductive seasonality. In conclusion, these results help us better understanding differential biological characteristics between Tibetan sheep and White Suffolk sheep.