Number Born Alive Research Articles

Enhancing paternal rabbit line’s litter size through backcrossing strategy

After 39 generations of selection, a commercial paternal rabbit line, utilised by farmers through artificial inseminations with sperm from males in a three-way crossbreeding scheme based on average daily weight gain merit (ADG), present a deleterious effect on the reproductive performance. This poses a challenge for the continuation of the breeding program. To address this, our study employed repeated backcrossing, a strategy widely used in the recovery of endangered breeds, to improve the litter size traits of this paternal line. For this purpose, we used a maternal line characterised by its reproductive robustness merit (LP line). The study was conducted in two phases: initially, elite males from the R line were crossed with females from the LP line, and female offspring (BC1) were backcrossed twice with elite males from the R line to create the RLP population (BC3). The best sires and dams from the BC3 population were selected for breeding based on two phenotypically criteria: more than 50 g/day in ADG and being part of a litter with at least 7 live kits at weaning, over three generations. With this experimental design, the ADG merit of sires and dams in the G3 was more than 51 g/day. Regarding litter traits, significant improvements were observed due to heterosis, which diminished as the frequency of R line genes increased. Comparisons between BC1 and BC3 backcrosses showed 9.94 vs. 7.80 for litter size at birth (NB), 9.13 vs. 6.53 for number born alive (NBA), 7.19 vs. 4.99 for litter size at weaning (NW), and 5.65 vs. 4.54 for litter size at marketing (NM), respectively. Nevertheless, after three generations of selection (G3), the litter trait merit showed values of 7.46 for NB and 6.15 for NBA, with heritability of 0.12 and 0.11, respectively, resulting in an improvement of nearly 1 kit per parity (a 25% increase) compared to the R line. Our study illustrated the possibility of improving a rabbit paternal line in terms of litter size merit by integrating genes from a maternal line through three backcrosses, without compromising the ADG merit. This is crucial for extending our breeding program beyond the current 39 generations. HIGHLIGHTS Three backcrossing resulting in an improvement of nearly 1 kit per parity Backcrossing can enhance litter size merit without affecting growth rates. Progeny average daily gain merit remains stable across backcrossing efforts.

Genomic Regions Associated with Growth and Reproduction Traits in Pink-Eyed White Mink.

In mink breeding, balanced selection for growth and reproductive features is essential because these traits are contradictory. The variables of total number born (TNB), number born alive (NBA), and body weight (BW) are highly valuable in terms of their importance in mink production. A comprehensive understanding of the molecular mechanisms that drive these features could offer vital insights into their genetic compositions. In the present study, the single-nucleotide polymorphism (SNP) genotypes of 219 minks were obtained via double digest restriction-site associated DNA sequencing (ddRAD-seq). Following several rounds of screening, about 2,415,121 high-quality SNPs were selected for a genome-wide association study (GWAS). The GWAS was used to determine BW and reproductive traits in pink-eyed white mink. It was suggested that SLC26A36, STXBP5L, and RPS 29 serve as potential genes for the total number of kits born (TNB), while FSCB, PDPN, NKX 2-1, NFKB 1, NFKBIA, and GABBR1 are key genes for the number born alive (NBA). Moreover, RTTN, PRPF31, MACROD1, and KYAT1 are possible BW genes based on association results and available functional data from gene and mammalian phenotype databases. These results offer essential information about the variety of mink and theoretical principles for applying mink breeds.

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs.

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

ZALEŻNOŚCI POMIĘDZY POLIMORFIZMAMI GENÓW RBP4, FSHB I EGF A CECHAMI ROZRODCZYMI U ŚWIŃ

Genes encoding retinol binding protein 4 (RBP4), follicle stimulating hormone subunit beta (FSHB) and epidermal growth factor (EGF) have been proposed as candidate genes for reproduction traits in pigs. The study presented in this work aimed to find associations between variants of these genes and reproduction traits in pigs reared in Poland. Investigation included Polish Large White x Polish Landrace (n = 288) crossbreed and Yorkshire (n = 195) breed sows. Insertion-deletion polymorphism (indel) in EGF gene was determined by means of PCR (polymerase chain reaction) method, however single nucleotide polymorphism (SNP) in RBP4 and FSHB genes by means of PCR-RFLP (restriction fragment length polymorphism) method. Obtained results showed that total number born (TNB) and number born alive (NBA) in 1st, 2nd and 5th parities were associated with RBP4 gene variants, TNB and NBA in first two parities with FSHB variants, however both traits in all parities with EGF variants (p ≤ 0.05 or p ≤ 0.01). In case of RBP4 gene, heterozygous genotype (AB) was favorable for analyzed traits, however in relation to FSHB and EGF genes homozygous genotypes, AA and BB respectively. Obtained results indicate that polymorphism in three analyzed genes is associated with important reproductive traits of pigs kept in Poland.

Plateau-linear reaction norm model analysis of number born alive in purebred Landrace pigs using meteorological data in Japan.

We performed a plateau-linear reaction norm model (RNM) analysis of number born alive (NBA) in purebred Landrace pigs, where breeding value changes according to maximum temperature at mating day, using public meteorological observation data in Japan. We analysed 52,668 NBA records obtained from 10,320 Landrace sows. Pedigree data contained 99,201 animals. Off-farm daily temperature data at the nearest weather station from each of the farms were downloaded from the Japan Meteorological Agency website. A plateau-linear RNM analysis based on daily maximum temperature on mating day (threshold temperature of 16.6°C) was performed. The percentage of the records with daily maximum temperatures at mating days of ≤16.6, ≥25.0, ≥30.0 and ≥35.0°C were 34.3%, 33.6%, 14.0% and 0.8%, respectively. The value of Akaike's information criterion for the plateau-linear RNM was lower than that for a simple repeatability model (RM). With the plateau-linear RNM, estimated value of heritability ranged from 0.14 to 0.15, while that from the RM analysis was 0.15. Additive genetic correlation between intercept and slope terms was estimated to be -0.52 from the plateau-linear RNM analysis. Estimated additive genetic correlations were >0.9 between NBA at different temperatures ranging from 16.6 to 37.6°C. For the 10,320 sows, average values of prediction reliability of the intercept and slope terms for breeding values in the plateau-linear RNM were 0.47 and 0.16, respectively. Increasing weight for slope term in linear selection index could bring positive genetic gain in the slope part, but prediction accuracy would decrease. Our results imply that genetically improving heat tolerance in sows reared in Japan focusing on NBA using RNM is possible, while RNM is more complex to implement and interpret. Therefore, further study should be encouraged to make genetic improvement for heat tolerance in sows more efficient.

228 The effect of temperature-humidity index in different pregnancy stages on litter traits in Taiwan Landrace sows

Abstract Because of climate change, annual average temperatures are gradually rising. Hence, increasing heat stress can impair the litter traits of Taiwanese sows located in tropical and subtropical zones. However, some pregnancy stages may be impacted more by heat stress than other periods. Thus, the purpose of this study was to demonstrate the effect of temperature-humidity index (THI) in different pregnancy stages on total number born (TNB), number born alive (NBA), and stillborn rate (STB). Data were collected in two Taiwanese farms from 2008 to 2021 for TNB, NBA, and STB, while weather data were collected from the closest respective weather station. There were 4,247 and 6,812 pure line Landrace record from farm 1 and farm 2, respectively. Pregnancy stages included 28 d before mating (BEFORE), mating to 30 d of pregnancy (EARLY), 31 to 70 d of pregnancy (MIDDLE), and 71 d of pregnancy to farrowing (LATE). Average THI was calculated in each pregnancy stage and regression coefficients were estimated by linear mixed models within ASReml. A two-trait analysis was used to estimate regression coefficients and genetic correlations among TNB, NBA, and STB. Results showed THI impacted (P &amp;lt; 0.05) TNB and NBA BEFORE and EARLY, while THI influenced (P &amp;lt; 0.05) STB EARLY and MIDDLE. Regression coefficients for TNB were -0.0069 and -0.0228 for BEFORE and EARLY, respectively. For NBA, regression coefficients were 0.0106 and -0.0391 for BEFORE and EARLY, respectively. Regression coefficients for STB were -0.0651 and 0.1332 for EARLY and MIDDLE, respectively. Heritability estimates for TNB, NBA, and STB were 0.168, 0.113, and 0.069, respectively. Genetic correlations between TNB with NBA and STB were 0.913 and 0.539, respectively. While the genetic correlation between NBA and STB was 0.158. In conclusion, THI impacted BEFORE and EARLY stages for TNB and NBA, while the stages of EARLY and MIDDLE were impacted by THI for STB. Hence, control of the environments in these specific stages for sows could improve the performance of litter traits.

Connectedness rating among commercial pig breeding herds in Korea.

This study aims to estimate the connectedness rating (CR) of Korean swine breeding herds. Using 104,380 performance and 83,200 reproduction records from three swine breeds (Yorkshire, Landrace and Duroc), the CR was estimated for two traits: average daily gain (ADG) and number born alive (NBA) in eight breeding herds in the Republic of Korea (hereafter, Korea). The average CR for ADG in the Yorkshire breed ranges from 1.32% to 28.5% depending on the farm. The average CR for NBA in the Yorkshire herd ranges from 0% to 12.79%. A total of 60% of Yorkshire and Duroc herds satisfied the preconditions suggested for genetic evaluation among the herds. The precondition for the genetic evaluation of CR for ADG, as a productive trait, was higher than 3% and that of NBA, as a reproductive trait, was higher than 1.5%. The ADG in the Yorkshire herds showed the highest average CR. However, the average CR of ADG in the Landrace herds was lower than the criterion of the precondition. The prediction error variance of the difference (PEVD) was employed to assess the validation of the CR, as PEVDs exhibit fluctuations that are coupled with the CR across the herds. A certain degree of connectedness is essential to estimate breeding value comparisons between pig herds. This study suggests that it is possible to evaluate the genetic performance together for ADG and NBA in the Yorkshire herds since the preconditions were satisfied for these four herds. It is also possible to perform a joint genetic analysis of the ADG records of all Duroc herds since the preconditions were also satisfied. This study provides new insight into understanding the genetic connectedness of Korean pig breeding herds. CR could be utilized to accelerate the genetic progress of Korean pig breeding herds.

Estimation of genotype by environmental interaction for litter traits by reaction norm model in Taiwan Landrace sows.

The negative effects of heat stress on swine reproduction have been well documented and the recent global warming trend caused by climate change is leading to more days with high temperatures every year. This has caused a reduction in litter trait performance of Landrace sows in Taiwan, a country extending across tropical and subtropical oceanic zones. Therefore, this study developed a modified model to determine which stages of pregnancy, before, early, middle, and late, had the largest impacts of heat stress on litter traits. A reaction norm model (RNM) was used to identify sows with high resilience to heat stress for litter traits followed by analysis of the modified model. Data from Landrace sows were collected from 2 farms in Taiwan between 2008 and 2021. A total of 11,059 records were collected for total number born (TNB), number born alive (NBA), and stillborn rate (STBR). The results showed that the heritabilities of TNB, NBA, and STBR were 0.170, 0.115, and 0.077, respectively. These results were similar between the conventional model and the modified model. In the modified model, the before and early stages of sow pregnancy were the significant periods for TNB and NBA (P < 0.05), while the early and middle stages were significant for STBR (P < 0.05). According to the RNM results, the heritability estimates for TNB, NBA, and STBR were 0.23 to 0.11, 0.18 to 0.08, and 0.10 to 0.04, respectively, showing a decrease from low temperature-humidity index (THI) to high THI. The minimum genetic correlations between the highest and the lowest THI for TNB, NBA, and STBR were 0.85, 0.64, and 0.80, respectively. The results of the RNM for breeding value showed re-ranking across THI values. In conclusion, similar results were obtained for heritability when the model was modified for heat stress estimation. Yet re-ranking of breeding values across THI could help farmers to select not only for improved litter trait performance but also for heat stress resilience of Landrace sows in Taiwan.

Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population.

The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and . Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (NKAIN2, IGF1R, KISS1R, TYRO3, SPINT1, ADGRF5, APC2, PTBP1, CLCN3, CBR4, HPF1, FAM174A, SCP2, CLIC1, ZFYVE9, SPATA33, KIF5C, EPC2, GABRA2, and GABRA4) were identified. These findings provide novel insights into the genetic basis of pig litter traits and will be helpful for improving the reproductive performances of sows in pig breeding.

PSV-6 The Impacts of Heat Stress on Litter Traits of Landrace Population in Taiwan

Abstract Global warming becomes a serious issue in the swine industries of most countries. Sow reproduction suffers the brunt of heat stress problems in tropical and subtropical zones, such as in Taiwan. Litter traits, total number born (TNB) and number born alive (NBA), are essential for sow stability and farm economics. However, these traits are influenced by management, facilities, and environmental conditions. Adjustments to management practices and facilities must be considered environmental conditions, including temperature and relative humidity, particularly in Taiwan under oceanic climates. Such specific climate with high temperature and relative humidity caused heat stress for sows around Taiwan over six months in a year. Therefore, the impact of heat stress at different stages of pregnancy in sows had been analyzed using the best linear unbiased prediction model with heterogeneous residuals. A total of 11,074 records for TNB and NBA from 3,080 Landrace sows were collected from two farms between 2008 and 2021. Simultaneously, weather data were obtained from those weather stations closest to the farms. Sows from mating to farrowing, about four months, had been classified into cool (C) or hot (H) climate condition in each month based on temperature-humidity index equals 70. Hence, there were eight combinations (CCCC, CCCH, CCHH, CHHH, HHHH, HHHC, HHCC, HCCC) of the climate effect in this study. The results of climate effect showed that there was not significant difference among the groups of CCCC, CCCH, CCHH, and CHHH in TNB and NBA, while no significant difference (P &amp;gt; 0.05) was found among the groups of HHHH, HHHC, HHCC, and HCCC in both traits. However, the climate effects of CCCH, CCHH, and CHHH were greater (P &amp;lt; 0.05) than those of HHHC, HHCC, and HCCC in TNB. The climate effects of CCCH and CCHH were greater than those of HHHH, HHHC, HHCC, and HCCC in NBA (P &amp;lt; 0.05). These fluctuations generally indicated when sows experience heat stress on mating and early stage of pregnancy (HHHH, HHHC, HHCC, HCCC), could decrease litter sizes. In the heterogeneous residual variances, the groups of CCCC, CCCH, CCHH, and CHHH were less than the groups of HHHH, HHHC, and HHCC in TNB, significantly, while the groups of CCCC, CCCH, and CHHH were less than the groups of HHHH, HHHC, and HHCC in NBA (P &amp;lt; 0.05). The greatest estimated residual variances were shown in HHCC in both TNB and NBA. These changing of trends indicated high heterogeneous residual variance was discovered when heat stress happened during mating and early pregnancy of sows (HHHH, HHHC, HHCC). In conclusion, heat stress at mating and early stage of sow pregnancy decreased the average and increased the residual variances of TNB and NBA.

Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs.

Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.

Identifying Early-Life Behavior to Predict Mothering Ability in Swine Utilizing NUtrack System.

Early indicator traits for swine reproduction and longevity support economical selection decision-making. Activity is a key variable impacting a sow's herd life and productivity. Early-life activities could contribute to farrowing traits including gestation length (GL), number born alive (NBA), and number weaned (NW). Beginning at 20 weeks of age, 480 gilts were video recorded for 7 consecutive days and processed using the NUtrack system. Activity traits included angle rotated (radians), average speed (m/s), distance traveled (m), time spent eating (s), lying lateral (s), lying sternal (s), standing (s), and sitting (s). Final daily activity values were averaged across the period under cameras. Parity one data were collected for all gilts considered. Data were analyzed using linear regression models (R version 4.0.2). GL was significantly impacted by angle rotated (p = 0.03), average speed (p = 0.07), distance traveled (p = 0.05), time spent lying lateral (p = 0.003), and lying sternal (0.02). NBA was significantly impacted by time spent lying lateral (p = 0.01), lying sternal (p = 0.07), and time spent sitting (p = 0.08). NW was significantly impacted by time spent eating (p = 0.09), time spent lying lateral (p = 0.04), and time spent sitting (p = 0.007). This analysis suggests early-life gilt activities are associated with sow productivity traits of importance. Further examination of the link between behaviors compiled utilizing NUtrack and reproductive traits is necessitated to further isolate behavioral differences for potential use in selection decisions.

Does the climate influence the variance of residual in litter traits of Taiwan Landrace sows?

Heat stress adversely affects the litter traits of Landrace, the primary dam breed in Taiwan. This study aimed to evaluate the effects of heat stress during sow pregnancy with homogeneous and heterogeneous residuals to estimate the genetic parameters of the Taiwan Landrace. Performance records for 11 657 litters and weather data from 2008 to 2021 were collected. The climate effect was defined proportionally from cool to hot for climates 1 to 5. The homogeneous residual analysis showed that the heritabilities of the total number born (TNB) and number born alive (NBA) were 0.164 ± 0.014 and 0.111 ± 0.014 with residual variances of 10.338 and 9.164, respectively. The heterogeneous residual analysis showed that the residual variances for TNB and NBA were 8.934–11.113 and 8.196–9.810, respectively. For TNB, the residual variance in the herd–year–climate effect differed significantly in climate 1 from climates 3 to 5 ( p &lt; 0.01). In NBA, the residual variance was significantly lower in climates 1 and 2 than in climates 3 and 5 ( p &lt; 0.01). In conclusion, heritability was estimated for TNB and NBA. In addition, residual variances could interact with the climate effect in heterogeneous residual analysis.

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs.

Reproductive traits have a key impact on production efficiency in the pig industry. It is necessary to identify the genetic structure of potential genes that influence reproductive traits. In this study, a genome-wide association study (GWAS) based on chip and imputed data of five reproductive traits, namely, total number born (TNB), number born alive (NBA), litter birth weight (LBW), gestation length (GL), and number of weaned (NW), was performed in Yorkshire pigs. In total, 272 of 2844 pigs with reproductive records were genotyped using KPS Porcine Breeding SNP Chips, and then chip data were imputed to sequencing data using two online software programs: the Pig Haplotype Reference Panel (PHARP v2) and Swine Imputation Server (SWIM 1.0). After quality control, we performed GWAS based on chip data and the two different imputation databases by using fixed and random model circulating probability unification (FarmCPU) models. We discovered 71 genome-wide significant SNPs and 25 potential candidate genes (e.g., SMAD4, RPS6KA2, CAMK2A, NDST1, and ADCY5). Functional enrichment analysis revealed that these genes are mainly enriched in the calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. In conclusion, our results help to clarify the genetic basis of porcine reproductive traits and provide molecular markers for genomic selection in pig breeding.

Relationships between gilt development and herd production efficiency are revealed by simulation

<br />The gilt development level is a critical factor for profitability in the pig industry. To evaluate the impact of different gilt development levels on the age structure and production efficiency of female herds we used the performance data of a pig farm that was simulated over a ten-year period, with current production statistics from the Chinese pig industry as a basis for the model. In a herd of 600 breeding sows, we compared age structure, number born alive (NBA), longevity and sow lifetime productivity in three scenarios with gilt culling rates of 10%, 20%, and 30%. The results show that the gilt development has no significant effects on the age structure. The gilt development had no significant effects either on sow reproductive performance or production efficiency. However, the annual replacement rate, longevity, and sow lifetime productivity varied significantly in the three levels of gilt development (<i>P </i>< 0.01). We conclude that the gilt development is closely related to herd turnover and reproductive performance, and ultimately affects the cost of pig production. Gilt development is, therefore, an extremely important factor in an integrated pig production system.

Genome-wide association study reveals the candidate genes for reproduction traits in Yunong black pigs.

Enhancing pig reproductive efficiency has the potential to have a significant positive economic impact on the pig business. We collected four reproduction records of 734 Yunong black pigs in this study, including the total number of piglets born (TNB), the number born alive (NBA), the average birth interval of piglets (ABI) and the average birth weight (ABW). A total of 453 Yunong black pigs were genotyped with Porcine 50K SNP BeadChip. Twenty-five SNPs and 35 genomic areas were found to have a substantial impact on the reproductive performance of Yunong black pigs by single-locus GWAS and single-step GWAS (ssGWAS). For the ssGWAS, we found that the two genomic regions (12.67-13.85 and 14.26-15.01Mb) on Sus scrofa chromosome X were associated with TNB, NBA and ABI. It is worth noting that CNC10110530 and CNC100141254 significantly affected the TNB by both GWAS methods. Finally, we further determined the gene functions by enrichment analysis and a literature search, and identified 28 of them as candidate genes affecting the reproductive performance of Yunong black pigs, including RET, EIF1AX, NELL2, CTPS2, S100G, RBBP7 and PDHA1. This study further promotes understanding of the genetic mechanism of porcine reproductive performance, and also provides more molecular markers for pig breeding.

Genetic parameter analysis of reproductive traits in Large White pigs.

The primary objective of this study was to determine the genetic parameters for reproductive traits among Large White pigs, including the following traits: total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), gestation length (GL), age at first service (AFS) and age at first farrowing (AFF). The dataset consisted of 19,036 reproductive records from 4,986 sows, and a multi-trait animal model was used to estimate genetic variance components of seven reproductive traits. The heritability estimates for these reproductive traits ranged from 0.09 to 0.26, with the highest heritability for GL and AFF, and the lowest heritability for NBA. The repeatabilities for TNB, NBA, LWB, ABW, and GL were ranged from 0.16 to 0.34. Genetic and phenotypic correlations ranged from -0.41 to 0.99, and -0.34 to 0.98, respectively. In particular, the correlations between TNB, NBA and LBW, between AFS and AFF, exhibited a strong positive correlation. Furthermore, for TNB, NBA, LBW, ABW, and GL, genetic correlations of the same trait between different parities were moderately to strongly correlated (0.32 to 0.97), and the correlations of adjacent parities were higher than those of nonadjacent parities. All the results in the present study can be used as a basis for the genetic assessment of the target population. In the formulation of dam line selection index, AFS or AFF can be considered to combine with TNB in a multiple trait swine breeding value estimation system. Moreover, breeders are encouraged to increase the proportion of sows at parity 3-5 and reinforce the management of sows at parity 1 and parity ≥8.

Genome-wide association studies uncover genes associated with litter traits in the pig

Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods—pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)—and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits.

Meta-Analysis of SNPs Determining Litter Traits in Pigs.

Nearly 2000 SNPs associated with pig litter size traits have been reported based on genome-wide association studies (GWASs). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birth weight (LWT), and corpus luteum number (CLN), in order to evaluate their common genetic background and to perform a meta-analysis (MA) of GWASs for total number born (TNB) recorded for animals from five pig populations. In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation, the most interesting candidate gene is PRKD1, which has an association with SB and TNB traits. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, which have not been previously reported, were found to be associated with the TNB trait. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene, associated with lower male fertility in rats. We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate gene comparison. PRKD1 could be an interesting candidate gene with a wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene was SOSTDC1, which was confirmed to affect male fertility in other mammals. This is an important finding, as litter traits are by default linked with females rather than males.

Identification of Genomic Regions and Candidate Genes for Litter Traits in French Large White Pigs Using Genome-Wide Association Studies.

Simple SummarySow reproductive performance is crucial in the entire pig industry. However, the heritability of reproductive traits is slowthat it is difficult to make great genetic progress by traditional breeding methods. Therefore, in this study, we performed genome-wide association analyses of litter traits in French White sows to explore genes related to sow reproductive traits and we finally detected a notable region (10.72–11.06 Mb on chromosome 7) and four promising genes (JARID2, PDIA6, FLRT2 and DICER1). The results of this study provide a theoretical basis for subsequent molecular breeding.The reproductive traits of sows are one of the important economic traits in pig production, and their performance directly affects the economic benefits of the entire pig industry. In this study, a total of 895 French Large White pigs were genotyped by GeneSeek Porcine 50K SNP Beadchip and four phenotypic traits of 1407 pigs were recorded, including total number born (TNB), number born alive (NBA), number healthy piglets (NHP) and litter weight born alive (LWB). To identify genomic regions and genes for these traits, we used two approaches: a single-locus genome-wide association study (GWAS) and a single-step GWAS (ssGWAS). Overall, a total of five SNPs and 36 genomic regions were identified by single-locus GWAS and ssGWAS, respectively. Notably, fourof all five significant SNPs were located in 10.72–11.06 Mb on chromosome 7, were also identified by ssGWAS. These regions explained the highest or second highest genetic variance in the TNB, NBA and NHP traits and harbor the protein coding gene ENSSSCG00000042180. In addition, several candidate genes associated with litter traits were identified, including JARID2, PDIA6, FLRT2 and DICER1. Overall, these novel results reflect the polygenic genetic architecture of the litter traits and provide a theoretical reference for the following implementation of molecular breeding.