scholarly journals Phenotypic and genomic relationships between vulva score categories and reproductive performance in first-parity sows

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Flor-Anita Corredor ◽  
Leticia P. Sanglard ◽  
Jason W. Ross ◽  
Aileen F. Keating ◽  
Richard J. Leach ◽  
...  

Abstract Background One of the biggest challenges in the swine industry is to increase female reproductive efficiency. Recently, vulva score categories (VSC), assessed prior to puberty, has been proposed as an indicator trait of efficient reproductive performance in sows. The objective of this study was to validate the use of VSC as an indicator trait for reproductive performance, and to perform genetic and genomic analyses for VSC. Methods The phenotypic relationship of VSC, using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), on reproductive performance was evaluated on three farms. VSC was measured at 15 weeks of age, for farms 1 and 2, and at 14 weeks of age for farm 3 on 3981 Yorkshire gilts, in which 1083 had genotypes (~ 50 K SNPs). Genetic parameters for VSC with reproductive traits were estimated using ssGBLUP. A Genome-wide association study (GWAS) for VSC was performed using BayesB. Results For the phenotypic analysis of VSC across datasets, differences in performance were identified there was a significant effect (P ≤ 0.05) for the interaction between Farm and VSC for total number dead (TND), and a trend (P < 0.10) for total number born (TNB). There were significant (P ≤ 0.05) pre-defined contrasts of VSC-S versus VSC-M + L on TNB, number born alive (NBA), TND, number of stillborn (NSB), and number of mummies (MUM). Heritability estimates for VSC as a categorical trait (VSCc) and a quantitative trait (VSCq) were 0.40 ± 0.02 and 0.83 ± 0.02, respectively, for across farm, 0.13 ± 0.07 and 0.20 ± 0.10, respectively, for Farm1, 0.07 ± 0.07 and 0.09 ± 0.09, respectively, for Farm2, and 0.20 ± 0.03 and 0.34 ± 0.05, respectively, for Farm3. For across farms, favorable genetic correlations estimates were found for TNB (0.28 ± 0.19) and NBA (0.26 ± 0.17). Within farms, moderate genetic correlations between VSC with reproductive traits were found for TNB (0.61 ± 0.47) and MUM (0.69 ± 0.47) for farm 1, for number of services until first farrow (NS; 0.69 ± 0.38) and unique service with successful first farrow (SFS; − 0.71 ± 0.38) for farm 3. Multiple genomic regions associated with VSCc were identified. Of these, a QTL located on chromosome 3 at 33–34 Mb accounted for about 7.1% of the genetic variance for VSCc and VSCq. This region harbors the gene PRM1 that has been associated with early embryonic development in pigs. Conclusions The results support potential of VSC for improved reproductive efficiency on first-parity performance, but the results might depend on the interaction between environmental factors and VSC, as well as potentially additive genetics.

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 27-28
Author(s):  
Flor-Anita Corredor ◽  
Letícia P Sanglard ◽  
Jason W Ross ◽  
Aileen F Keating ◽  
Nick Serão

Abstract Reproductive efficiency is critical to maximizing productivity in the swine industry. A recent study indicated that vulva score (VSC) assessed prior to puberty may be predictive of reproductive performance in sows, in which gilts with greater VSC had greater reproductive performance. The objective of this study was to validate the effect of VSC on reproductive performance, to estimate genetic parameters, and to perform genomic analysis of VSC. A total of 5494 phenotypes and 1326 genotypes (~50K SNPs) from two farms were available for this study. Measurements included VSC assessed using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), at 15 and 14 weeks of age, for Farm 1 and 2, respectively, and subsequent first parity performance. Genetic parameters were estimated using single-step GBLUP. Genome-wide association study (GWAS) was performed for VSC using BayesB (p=0.999). For Farm1, VSC-L was associated with a greater (P-value=0.04) farrow rate (0.68±0.03) than VSC-S (0.53±0.07). For Farm2, VSC-L was associated with greater (P-value=0.04) number of piglets born alive (NBA; 11.4±0.17) and less mummified fetuses (P-value=0.03; 0.09±0.01) than VSC-S (10.9±0.14; 0.14±0.01). Heritability estimates of VSC were 0.35±0.06 for Farm1 and 0.34±0.05 for Farm2. Moderate genetic correlations between VSC with reproductive traits were found for total number born (0.61±0.21) and NBA (0.62±0.19). The GWAS identified multiple genomic regions associated with VSC. Of these, a QTL located on chromosome 1 at 85Mb accounted for &gt;3% of the genetic variance. This region harbors ADAM21, a gene that has been associated with early embryonic development in pigs. These results validated the use of VSC for prediction of first-parity performance, identified genomic regions controlling VSC, and indicate that selection for increased VSC is possible and could improve reproductive efficiency in swine. We are grateful to Fast Genetics for providing the data and the Iowa Pork Industry Center for financial support.


2020 ◽  
Author(s):  
Margaretha Snyman ◽  
Sunika Süllwald ◽  
Willem Olivier ◽  
Carina Visser

Abstract Background: Reproductive performance and body weight are of the utmost economic importance in determining the efficiency of sheep production. Simultaneous selection for increased reproductive performance and early growth traits is a common strategy in many flocks, but ambiguous results regarding the relationship between reproduction and body weight have been reported. The objective of this study was to perform a genome-wide association study (GWAS) in two South African Merino flocks and an Afrino sheep flock that were selected for both reproduction and body weight over decades. The GWAS aimed to identify SNPs associated with genes affecting the traits number of lambs born (NLB), number of lambs weaned (NLW), total weight of lamb weaned (TWW) and body weight (BW) and thus to ascertain which genes were targeted through directional selection.Results: In the GWAS, 16 SNP markers associated with reproductive traits were identified among the three populations, while 15 SNPs were associated with body weight. These SNPs were linked respectively to 26 and 21 documented genes in the sheep genome. Most of these genes were previously associated in literature with reproduction related, as well as with growth related traits in various farm animal species. This study, supported by results from previous studies performed on sheep and cattle, identified the following genes that warrant further investigation as to their functions and processes relating to growth and reproduction in sheep: MAP7D1, TRAPPC3, THRAP3, TRMP8, SPP2, HDAC9, ZFHX3, SIX6, C14orf39, TAF4B, TRSP1 EYA2, RBMS3, STL38L, BSPH1, LIG1, CABP5 and ELSPBP1. Conclusions: Long-term selection in the flocks for both body weight and reproductive traits, and especially on the composite trait TWW, have favoured genes with pleiotropic effects influencing both groups of traits. SNPs associated with these pleiotropic genes were detected in the association analyses for the various traits.


2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 19-20
Author(s):  
Felipe Hickmann ◽  
José Braccini Neto ◽  
Luke M Kramer ◽  
Kent A Gray ◽  
Yijian Huang ◽  
...  

Abstract Previous studies proposed the use of antibody response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), measured as sample-to-positive (S/P) ratio, as a potential indicator trait to improve the reproductive performance of PRRSV-infected Landrace sows. However, this indicator trait has not yet been validated in Landrace sows or evaluated in a terminal sire line, such as Duroc. The main objective of this work was to perform host-genetic analyses of S/P ratio and reproductive traits during a PRRSV outbreak in maternal and terminal breeds. The data consisted of 690 Duroc and 541 Landrace multiparous sows (1.9±1.2 and 2.3±1.5, respectively) with S/P ratio collected at approximately 54 days after the predicted beginning of the outbreak. Of these, 644 Duroc and 528 Landrace sows also had reproductive data recorded during the PRRSV outbreak comprising number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NBM), number born dead (NBD; sum of NSB and NBM), total number born (TNB; sum of NBA and NBD), and number weaned (NW). All animals had genotype data on ~30K SNPs common across both breeds. Heritability estimates (± standard error) of S/P ratio during the PRRSV outbreak were moderate, with 0.33±0.06 for Duroc and 0.28±0.07 for Landrace. Reproductive traits during the PRRSV outbreak had overall low heritability estimates (≤0.18). Favorable genetic correlations of S/P ratio with NBA (0.65±0.33), in accordance with previous studies, and NBD (-0.33±0.28) were observed for Landrace sows only. Estimates of genetic correlation with other traits were -0.21±0.30 (NBM), -0.12±0.29 (NSB), 0.10±0.38 (NW), and 0.54±1.29 (TNB) for Landrace. For Duroc, these estimates were weaker: -0.33±0.40 (NBA), 0.26±0.27 (NBA), and 0.28±0.30 (NW), with convergence issues for mortality traits. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRSV outbreak in Landrace sows.


2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 18-18
Author(s):  
Leticia P Sanglard ◽  
Felipe Hickmann ◽  
Yijian Huang ◽  
Kent A Gray ◽  
Daniel Linhares ◽  
...  

Abstract Immunoglobulin G antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been proposed as an indicator trait for improved reproductive performance in PRRSV-infected purebred sows and PRRSV-vaccinated crossbred gilts. In this study, we investigated the genetic correlations (rg) of S/P ratio following a PRRSV outbreak and PRRSV-vaccination with performance in non-exposed and PRRSV-exposed sows. PRRSV outbreak phase was defined based on previously described methodologies after the detection of typical clinical signs of PRRSV infection. 541 Landrace sows had S/P ratio measured at ~54 days after the beginning of the PRRSV outbreak (S/Poutbreak), and 906 Landrace x Large White naïve F1 gilts had S/P ratio measured at ~50 days after vaccination with a commercial modified live PRRSV vaccine (S/PVx). 711 and 428 Landrace sows had reproductive performance recorded before and during the PRRSV outbreak, respectively. 811 vaccinated F1 animals had farrowing performance for up to 3 parities. All animals were genotyped for ~28K SNPs. The estimate of rg of S/Poutbreakwith S/PVx was high (rg±SE = 0.72±0.18). Estimates of rg of S/Poutbreak with reproductive performance in F1 sows were low to moderate, ranging from 0.05±0.23 (number stillborn) to 0.30±0.20 (total number born). Estimates of rg of S/PVxwith reproductive performance in non-infected purebred sows were moderate and favorable with number born alive (0.50±0.23), but low (0 to -0.11±0.23) with litter mortality traits. Estimates of rg of S/PVx were moderate and negative (-0.47±0.18) with the number of mummies in PRRSV-infected purebred sows and low with other traits (-0.29±0.18 for total number born to 0.05±0.18 for number stillborn). These results indicate that selection for antibody response following a PRRSV outbreak collected in purebred sows and to PRRSV vaccination collected in commercial crossbred gilts may increase litter size of non-infected and PRRSV-exposed purebred and commercial crossbred sows.


1981 ◽  
Vol 96 (1) ◽  
pp. 107-113 ◽  
Author(s):  
T. G. Martin ◽  
D. Nicholson ◽  
C. Smith ◽  
D. I. Sales

SUMMARYData on 902 ewes (1755 records) bom over 7 years in the synthetic ABRO Dam Line were analysed by least squares. Reproductive traits of the ewe were not affected by whether she was a single or a twin or by the age of her dam. Ewe age had major effects on all reproductive traits. Litter weight traits were affected by the sex distribution and the age of the litter when weighed.Heritability estimates, both by half sib and regression methods, were low for litter size, low to moderate for litter weights, and higher for ewe and fleece weights. Genetic correlations among the litter-weight traits were high. Together with the heritability estimates, they indicated that selection on litter weight at birth (and perhaps other traits) might give a greater change in total litter weight at weaning, the main measure of ewe productivity and the objective in improvement, than would direct selection.


Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 732 ◽  
Author(s):  
Zhang ◽  
Chen ◽  
Ye ◽  
He ◽  
Huang ◽  
...  

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.


2014 ◽  
Vol 54 (1) ◽  
pp. 1 ◽  
Author(s):  
D. J. Johnston ◽  
S. A. Barwick ◽  
G. Fordyce ◽  
R. G. Holroyd ◽  
P. J. Williams ◽  
...  

Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 ± 0.18 and 0.26 ± 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 ± 0.06 and 0.07 ± 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were –0.62 ± 0.24 in Brahman and –0.87 ± 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.


2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Leticia P. Sanglard ◽  
Yijian Huang ◽  
Kent A. Gray ◽  
Daniel C. L. Linhares ◽  
Jack C. M. Dekkers ◽  
...  

Abstract Background The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance. Results There was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP. Conclusions Specific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.


2021 ◽  
Author(s):  
Asher I Hudson ◽  
Sarah G Odell ◽  
Pierre Dubreuil ◽  
Marie-Helene Tixier ◽  
Sebastien Praud ◽  
...  

Genotype by environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype by environment interaction in a maize multi-parent advanced generation intercross population grown across five environments. We found that genotype by environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. In order to understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype by environment variance. We also performed a genome-wide association study to identify markers associated with genotype by environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype by environment interactions in this population.


2021 ◽  
Vol 12 ◽  
Author(s):  
Felipe M. W. Hickmann ◽  
José Braccini Neto ◽  
Luke M. Kramer ◽  
Yijian Huang ◽  
Kent A. Gray ◽  
...  

Porcine Reproductive and Respiratory Syndrome (PRRS) is historically the most economically important swine disease worldwide that severely affects the reproductive performance of sows. However, little is still known about the genetic basis of reproductive performance in purebred herds during a PRRS outbreak through the comparison of maternal and terminal breeds. Thus, the objective of this work was to explore the host genetics of response to PRRS in purebred sows from two breeds. Reproductive data included 2546 Duroc and 2522 Landrace litters from 894 and 813 purebred sows, respectively, which had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). The data were split into pre-PRRS, PRRS, and post-PRRS phases based on standardized farrow-year-week estimates. Heritability estimates for reproductive traits were low to moderate (≤0.20) for Duroc and Landrace across PRRS phases. On the other hand, genetic correlations of reproductive traits between PRRS phases were overall moderate to high for both breeds. Several associations between MARC0034894, a candidate SNP for response to PRRS, with reproductive performance were identified (P-value &lt; 0.05). Genomic analyses detected few QTL for reproductive performance across all phases, most explaining a small percentage of the additive genetic variance (≤8.2%, averaging 2.1%), indicating that these traits are highly polygenic. None of the identified QTL within a breed and trait overlapped between PRRS phases. Overall, our results indicate that Duroc sows are phenotypically more resilient to PRRS than Landrace sows, with a similar return to PRRS-free performance between breeds for most reproductive traits. Genomic prediction results indicate that genomic selection for improved reproductive performance under a PRRS outbreak is possible, especially in Landrace sows, by training markers using data from PRRS-challenged sows. On the other hand, the high genetic correlations with reproductive traits between PRRS phases suggest that selection for improved reproductive performance in a clean environment could improve performance during PRRS, but with limited efficiency due to their low heritability estimates. Thus, we hypothesize that an indicator trait that could be indirectly selected to increase the response to selection for these traits would be desirable and would also improve the reproductive performance of sows during a PRRS outbreak.


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