Genetic Links between Reproductive Traits and Amino Acid Pairwise Distances of Swine Leukocyte Antigen Alleles among Mating Partners in Microminipigs.

Previously, we found that a greater dissimilarity in swine leukocyte antigen (SLA) class I and class II alleles between mating partners resulted in increased farrowing rates in a highly inbred population of Microminipigs (MMPs). In this follow-up study, we have analyzed the effects of dissimilarity in SLA alleles between mating partners for seven different reproductive traits, including litter size and the number of stillborn and live or dead weaned piglets. We determined the relationships among reproductive traits within each mating event and the amino acid distances of SLA alleles as markers of diversity between mating partners. Our results indicate that mating partners with greater amino acid pairwise genetic distances in the SLA-1 class I gene or DQB1 class II gene alleles were associated with significantly larger litter sizes and higher numbers of live piglets at birth and weaning. Also, partners with greater pairwise distances in the SLA-2 class I gene alleles exhibited fewer pre-weaning deaths. These findings suggest that the dissimilarity in SLA class I and class II alleles between mating partners may affect not only farrowing rates but also other key reproductive traits such as litter size and improved piglet survival rates. Consequently, SLA alleles could serve as valuable genetic markers for selecting mating partners in breeding programs and for conducting epistatic studies on various reproductive traits in MMPs.

Genome-wide association study for stayability at different calvings in Nellore beef cattle.

BACKGROUNDING: Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life. RESULTS: The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. CONCLUSION: Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population.

Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods.

Integrated Multi-Tissue Transcriptome Profiling Characterizes the Genetic Basis and Biomarkers Affecting Reproduction in Sheep (Ovis aries).

The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic-pituitary-ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand-receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep.

Evaluating the performance of genomic prediction accounting for effects of single nucleotide polymorphism markers in reproductive traits of Japanese Black cattle.

We examined the prediction accuracies of genomic best linear unbiased prediction (GBLUP), various weighted GBLUP according to the degrees of marker effects (WGBLUP) and machine learning (ML) methods, and compared them with traditional BLUP for age at first calving (AFC), calving difficulty (CD), and gestation length in Japanese Black cattle. For WGBLUP, firstly, BayesC and FarmCPU were used to estimate marker effects. Then, we constructed three weighted genomic relationship matrices from information of estimated marker effects in the first step: absolute value of the estimated marker-effect WGBLUP, estimated marker-variance WGBLUP, and genomic-feature WGBLUP. For ML, we applied Gaussian kernel, random forest, extreme gradient boost, and support vector regression. We collected a total of 2583 animals having both phenotypic records and genotypes with 30,105 markers and 16,406 pedigree records. For AFC, prediction accuracies of WGBLUP methods using FarmCPU exceeded BLUP by 25.7%-39.5%. For CD, estimated marker-variance WGBLUP using BayesC achieved the highest prediction accuracy. Among ML methods, extreme gradient boost, support vector regression, and Gaussian kernel increased prediction accuracies by 28.4%, 19.0%, and 36.4% for AFC, CD, and gestation length compared with BLUP, respectively. Thus, prediction performance could be improved using suitable WGBLUP and ML methods according to target reproductive traits for the population used.

Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits.

BACKGROUND: Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS: We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS: Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.

Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs.

With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.

Effects of dietary supplementation of N-carbamylglutamate on the haematology parameters, secondary sexual characteristics and testicular gene expression in roosters.

A total of 288 11-week-age roosters were used to evaluate the effects of dietary supplementation of N-carbamylglutamate (NCG) on reproductive traits and testicular gene expression. The experimental periods were 12 weeks. All birds were randomly assigned to 4 treatments with 6 replicates per treatment and 12 birds per replicate. Dietary conditions were based on a basal diet and supplemented with 0%, 0.08%, 0.12%, or 0.16% NCG to form C, N1, N2 and N3 groups respectively. Dietary supplementation of NCG had positive effects on the seminiferous tubule parameters, serum gonadotropin-releasing hormone and testosterone levels and the secondary sexual characteristics. Transcriptomics analysis was performed on the testicular tissues between C and N3 groups at the 16-week-age. Genes were mainly enriched in nine pathways, such as cytochrome P450 exogenous metabolism, drug metabolism, steroid hormone synthesis and glutathione metabolism, in which the ZP4 gene, cytochrome P450 family member 11A1 and other genes involved in the maintenance of gonadal function, steroid hormone biosynthesis and metabolism, and so forth, exist differences in expression levels. In summary, dietary supplementation of NCG had positive effects on the reproductive traits of roosters. NCG supplementation improved the development of reproductive traits of roosters by regulating the genes expression in testicular tissues and thus improved the synthesis of reproductive hormones in vivo.

Associations of CALM1 and DRD1 polymorphisms, and their expression levels, with Taihang chicken egg-production traits.

Egg production by hens is an important reproductive performance index in the poultry industry. To investigate the effects of the CALM1 and DRD1 genes on egg production in chicken, their mRNA expression and single nucleotide polymorphisms (SNP) levels were investigated, and bioinformatics and egg-production association analyses were performed. Three SNPs (g.44069941G > A and g.44069889A > G in CALM1 and g.10742639C > T in DRD1) were detected in the exons and introns of CALM1 and DRD1 in 400 Taihang chickens. Among them, g.44069941G > A was significantly associated with Taihang chicken egg production on the 500th day (p < 0.05), whereas g.10742639C > T was significantly associated with the 300th day (p < 0.05). The expression levels of CALM1 and DRD1 in ovarian tissues of a high-yielding Taihang group were greater than in a low-yielding group (p < 0.05). The bioinformatics analysis revealed that the mutations influenced the mRNA secondary structures of CALM1 and DRD1. This study provides new insights into the potential effects of CALM1 and DRD1 polymorphisms on chicken egg production. The two SNPs g.44069941G > A and g.10742639C > T are potential molecular markers for improving the reproductive traits of Taihang chicken.

CALM1 and DRD1 were two important genes for reproduction. In this study, the entire coding regions of both genes were sequenced and mutations were detected in Taihang chickens. The results showed that two single nucleotide polymorphisms (SNPs), g.44069941G > A in the CALM1 gene and g.10742639C > T in the DRD1 gene, were associated with egg-laying traits. g.10742639C > T is a synonymous mutation predicted to affect the secondary structure of mRNA. Therefore, these two mutations might be potential molecular markers for improving reproductive traits in Taihang chickens.

Reproductive Traits Demonstrate How Well the Mediterranean Stripe-Necked Turtle Mauremys leprosa Can Flourish under Highly Degraded-Polluted Conditions.

We measured and compared the reproductive traits of the Mediterranean stripe-necked turtles Mauremys leprosa living in highly degraded-polluted vs. intact natural habitats in Algeria. Data on reproduction were obtained by using X-ray examination of gravid females and examination of nests. The results were opposite to the negative trend confirmed in most freshwater turtles exposed to pollution and suggested the ability of this species to flourish instead in highly degraded-polluted habitats. An optimum development was recorded for several reproductive patterns of the studied freshwater turtle under conditions considered uninhabitable for other vertebrates. Females exhibited record body sizes among conspecifics, which allowed them to carry significantly larger clutches, exceeding by up to 3 eggs the previously largest reported clutch. The mean clutch size (8.79 ± 2.70 eggs) was also higher than findings from previous studies, except for in some other polluted habitats. Furthermore, large females even with large clutches carried large eggs. Egg measurements in the disturbed habitat revealed new records exceeding those previously noted; in egg length (by 3.0 mm), egg width (by 2.8 mm), egg mass (by 1.8 g), and clutch mass (by 18.6 g). In comparison, the usual reproductive performances were observed in the intact natural habitat; female body sizes were significantly smaller and carried fewer eggs of smaller size.

Association analysis and expression level of ACE polymorphisms with egg-laying trait in Taihang chicken.

The number of egg-laying is an important indicator of reproduction performance in poultry breeding. To investigate the relationship between the function of Angiotensin-converting enzyme (ACE) and egg-laying performance of Taihang chicken, the mRNA and protein expression and single nucleotide polymorphism (SNP) of ACE were detected. Analysis of ACE bioinformatics and association analysis of polymorphisms were then performed. The polymorphisms analysis of ACE showed that three SNP loci (g.5066812A>C, g.5080076G>A, and g.5072728A>G) were detected in 800 Taihang chickens with egg-laying records. Association analysis of egg-laying found that ACE g.5066812A>C mutation was significantly associated with the egg-laying performance of Taihang chickens (P < 0.05), and the individuals with the g.5066812A>C mutation showed significantly increasing egg-laying. The mRNA expression was significantly higher in individuals with the AA genotype mutation than those with the AC and CC genotypes (P < 0.01), and the expression of ACE protein levels was consistent with the mRNA expression. Bioinformatics analysis indicated that these mutations affected the secondary and tertiary structure of ACE. This study provides new insights into ACE affecting chicken egg production and some basis for improving the egg production rate of Taihang chickens.

Genetic parameter analysis of reproductive traits in Large White pigs.

OBJECTIVE: 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). METHODS: 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. RESULTS: 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. CONCLUSION: 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.

Source-sink manipulations differentially affect carbon and nitrogen dynamics, fruit metabolites and yield of Sacha Inchi plants.

BACKGROUND: Being a promising tropical woody oilseed crop, the evergreen and recurrent plants of Sacha Inchi (Plukenetia volubilis L.) has complex phenology and source-sink interactions. Carbon source-sink manipulations with control and two treatments (reduce source, ca. 10% mature leaf pruning; reduce sink, 10% fruitlet thinning) were conducted on 2.5-year-old field-grown P. volubilis plantation during the early-wet season in a seasonal tropical area. RESULTS: Leaf photosynthetic rate and specific leaf area largely remained unchanged in response to defoliation or defloration. Compared with control, higher N contents on average were observed in both remaining leaves and branches of the defoliated plants, suggesting that N-mobilization was mainly due to the enhanced N uptake from soil. Carbon, but not N, is a source-driven growth process of P. volubilis plants, as defoliation reduced the contents of non-structural carbohydrates (especially sugar) in branches, although temporally, whereas defloration increased available C reserve. The seasonal dynamic pattern of fruit ripening was altered by source-sink regulations. Total seed yield throughout the growing season, which depends on fruit set and retention (i.e., number of matured fruit) rather than individual fruit development (size), was slightly increased by defloration but was significantly decreased by defoliation. Compared with control, defloration did not enrich the KEGG pathway, but defoliation downregulated the TCA cycle and carbohydrate and lipid metabolisms in fruitlets after 24 days of the applications of source-sink manipulation. CONCLUSION: Carbohydrate reserves serve to buffer sink-source imbalances that may result from temporary adjustment in demand for assimilates (e.g., defloration) or shortfalls in carbon assimilation (e.g., defoliation). Defoliation is disadvantageous for the yield and also for carbohydrate and lipid accumulation in fruits of P. volubilis plants. Although more studies are needed, these results provide new insights to the further improvement in seed yield of the strong source-limited P. volubilis plants by source/sink manipulations.

RFamide-related peptides' gene expression, polymorphism, and their association with reproductive traits in chickens.

RFamide-related peptides (RFRP) are synthesized by the hypothalamus and have a regulatory role in gonad development. The goal of this study was to investigate the association between SNP of the RFRP gene and the reproductive traits and hormone levels of Zhenning yellow chickens. The mRNA expression levels were detected based on different tissues, ages, and genotypes. Eleven mutation sites were detected in the RFRP gene, 4 of which were significantly related to reproductive traits and hormone levels. Association analysis revealed that A276G was associated with egg production at 300 d of age (EP300) and amount of prehierarchical follicles (P < 0.05). G1396A was associated with egg weight at 300 d of age and luteinizing hormone (LH) and prolactin levels (P < 0.05). G1694A showed significant associations with fertilization rate and LH levels (P < 0.05), and A2659G was associated with EP300 (P < 0.05). The results of expression analysis showed that the RFRP mRNA expression levels in the hypothalamus were higher than those in other tissues (P < 0.01). The expression in immature individuals was higher than that in mature ones (P < 0.01). There were also differences in mRNA expression levels between different genotypes (P < 0.05). In summary, the results of this study might provide potential markers and a theoretical basis for the improvement of chicken reproductive traits.

Dietary supplementation with combined extracts from garlic (Allium sativum), brown seaweed (Undaria pinnatifida), and pinecone (Pinus koraiensis) improves milk production in Holstein cows under heat stress conditions.

OBJECTIVE: This study was conducted to examine the effects of a mixture of pinecone oil, garlic, and brown seaweed extracts (PGBE) on milk production traits as well as physiological and ethological parameters in Holstein cows during the summer season (24 May to 03 July 2015, Korea). METHODS: Among the extract combinations tested, we found that the level of 2,2'-azino-bis (3-ethylberzothiazoline-6-sulphonic acid) cation radical scavenging activity of the 0.16% PBGE complex at ratio of 1:1:1 (vol/vol) was comparable to that of the control (ascorbic acid; 1 mg/mL). Additionally, the PBGE complex reduced lipopolysaccharide-induced COX-2 expression in bovine mammary epithelial cells. Based on these findings, 40 lactating Holstein cows were used to measure the effects of PBGE complex at ratio of 1:1:1 (vol/vol) on milk production, immune response, metabolites, and behavior patterns by dividing the cows into two groups fed diets containing PGBE complex (n = 20; 0.016%/kg feed dry matter basis) or not containing PGBE complex (control, n = 20) for 40 d. RESULTS: Results showed that PGBE complex did not influence milk composition, eating and ear surface temperature patterns, immune response, or metabolic parameters but promoted average milk yield throughout the experimental period. Additionally, a tendency of higher total antioxidant capacity and glutathione in the PGBE group was observed compared to the those in the control. When the temperature-humidity index (THI) exceeded 72 (average THI = 73.8), PGBE complex-fed cows experiencing heat stress showed increased milk yield and a tendency of increased rumination compared to the control. CONCLUSION: We suggest that incorporation of a combined mixture of 0.016% PGBE (1:1:1 ratio, vol/vol) to diet has the potential to improve milk yield and health status of cows under mild to moderate heat stress, denoting that it might be useful as an alternative anti-stressor in the diet of dairy cows under hot conditions.

Genomic evaluation for novel stayability traits in Nellore cattle.

Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability traits: STAY42, STAY53 and STAY64, which are measured at 52, 64 and 76 months of cow's age, considering at least 2, 3 and 4 calving, respectively. ssGBLUP yielded the highest prediction accuracy for all traits. The heritability estimates for STAY42, STAY53, STAY63 and STAY64 were 0.090, 0.151, 0.152 and 0.143, respectively. The genetic correlations between traits ranged from 0.899 (STAY42 and STAY53) to 0.985 (STAY53 and STAY63). The high genetic correlation between STAY42 and STAY53 suggests that besides being related to cow longevity, STAY53 is also associated with the early-stage reproductive efficiency. Thus, STAY53 is recommended as a suitable selection criterion for reproductive efficiency due to its higher heritability, favourable genetic correlation with other traits, and measured earlier in life, compared with the conventional stayability trait, that is STAY63.

Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs.

Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5, BMP6, BMP7, ACVR1, INHBA, ZFYVE9, TGFBR2, DCN, ID4, BAMBI, and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9, SLC39A11, SNCA, and UNC5D are candidate genes for reproduction traits.

Inherited dimorphism in cleistogamous flower production in Portulaca oleracea: a comparison of 16 populations growing under different environmental conditions.

BACKGROUND AND AIMS: Cleistogamy is considered to be an adaptive strategy resulting in plasticity in chasmogamous (CH) and cleistogamous (CL) flower production depending on environmental conditions and plant size. The aim of this study was to investigate whether CH and CL flower production in Portulaca oleracea is genetically differentiated among populations in association with climatic conditions. METHODS: First, we conducted growth experiments with P. oleracea seedlings from 16 populations under two temperature conditions. Secondly, we sowed seeds originating from the parents in the first experiment and grew the resulting plants to investigate whether flower production is heritable and whether plants in the same population show the same pattern of flower production. KEY RESULTS: Two types of plants that produced only CH or CL flowers (referred to as CH and CL plants, respectively) were mainly observed, and the growing temperature conditions did not affect flower production. The frequency of CL plants increased with a decrease in the mean temperature in the original population. The CL plants tended to begin reproduction earlier than the CH plants, and the probability that a CH plant would flower decreased under the low growing temperature condition. Thus, CL plants may have some advantages in unfavourable environments in which early reproduction is necessary due to a short growing season and/or when CH flowers cannot open due to low temperatures. The progeny originating from CH and CL plants also produced only CH and CL flowers, respectively, suggesting that there is a genetic basis for the dimorphism in flower production in P. oleracea, represented by CH and CL plants. CONCLUSIONS: In contrast to the previous hypothesis that the production of both CH and CL flowers would be plastic, the genotypes producing either CH or CL flowers occurred at different frequencies under varying climatic conditions.

Variants in BMP7 and BMP15 3'-UTRs Associated with Reproductive Traits in a Large White Pig Population.

Bone morphogenetic protein 7 (BMP7) and BMP15, which encode members of the BMP family, have been identified by whole-genome resequencing as breeding-related genes that overlap with a known quantitative trait locus for reproductive traits. In this study, we investigated the effects of variants at the BMP7 and BMP15 gene loci on sow reproductive traits. We isolated 669 and 1213 bp sequences of the 3'-untranslated region (3'-UTR) of the porcine BMP7 and BMP15 genes, respectively, and detected several RNA regulatory elements, such as miRNA response elements and AU-rich elements. Pooled DNA sequencing identified two novel point mutations (viz., BMP7 c.1569A>G and BMP15 c.2366G>A) in the 3'-UTR. Association analysis showed that the c.1569A>G polymorphism was associated with the litter weight trait in a Large White pig population. Furthermore, analysis of the combined genetic effects revealed that AA/GA and AG/GG were the favorable combined genotypes for the total number of piglets born (TNB) and the total number of piglets born alive (NBA), whereas. Together, our findings confirm that BMP7 and BMP15 are candidate genes for porcine reproductive performance.

Copy number variation of ZNF280AY across 21 cattle breeds and its association with the reproductive traits of Holstein and Simmental bulls.

The mammalian Y chromosome gene families in the ampliconic region are expressed predominantly or exclusively in the testis, and their copy number variations (CNV) are significantly associated with male reproductive traits, suggesting they have important roles in spermatogenesis and testicular development. ZNF280AY (zinc finger protein 280A, Y-linked) is a member of the zinc finger protein family and has been identified as a bovid-specific Y-chromosome gene. The current study applied a reliable quantitative real-time PCR method to estimate the CNV of ZNF280AY in 715 bulls across 21 cattle breeds and to further investigate the association of the CNV of ZNF280AY with bull reproductive traits and ZNF280AY mRNA expression levels in adult testis. The results revealed that the median copy number of ZNF280AY was 47, and the copy number varied from 11 to 154, showing significant CNV between and within the investigated cattle breeds. In addition, all 715 bulls were classified into Y1, Y2, and Y3 lineage groups based on a rapid genotyping method described previously. Pairwise comparisons indicated that bulls belonging to the Y1 lineage had a significantly lower median copy number (40) than bulls belonging to the Y2 (52) and Y3 lineages (57). Association analysis revealed that the CNV of ZNF280AY was correlated negatively with the percentage of normal sperm and sperm concentration in Holstein bulls, whereas no significant correlation was observed with ejaculation volume, total sperm count, sperm motility, postthaw motility (PTM), and scrotal circumference in Holstein and Simmental bulls. Furthermore, no correlation was observed between ZNF280AY copy number and ZNF280AY mRNA expression levels in the testis. The current study suggests that the CNV of the ZNF280AY gene family is associated with male reproductive traits and may serve as a valuable marker for early bull fertility selection in Holstein breeding programs.