Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows.

BACKGROUND: Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement. RESULTS: A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows. CONCLUSIONS: The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.

Meta-analyses of reproductive changes in angiosperm populations in response to elevation reveal a lack of global patterns.

BACKGROUND AND AIMS: Elevation is a major factor shaping plant populations on a global scale. At the same time, reproductive traits play a major role in plant fitness. With increasing altitude and increasingly harsh conditions, decreases in pollinator visitation rates, sexual investment, seed set, and heterozygosity (due to increased selfing) are expected. In response, selection and/or phenotypic plasticity could lead to an increase in plants' floral displays to increase their attractiveness to pollinators and compensates for the negative fitness impacts of reduced pollinator activity. A large body of literature tests these hypotheses at the among-species level, but empirical evidence at the population level (i.e., wihin-species), where adaptive change may occur, is still limited to species-specific studies. Unravelling the global patterns of change in the reproductive traits, flower visitation rates and heterozygosity of plant populations across variable environmental conditions, especially climate can help us to understand how species are able to cope with shifting conditions associated with global change, particularly in mountains. Here, we used meta-analytic approaches to assess the reproductive changes of plant populations in response to elevation on a global scale. METHODS: We used a data set with 243 paired populations of plants at 'lower' and 'higher' elevations, spanning an elevation range of 0-4380 m asl and taken from 121 angiosperm species and 115 published studies. We analyzed changes in flower number, size and longevity, pollen production, flower visitation rate, seed set and expected heterozygosity.We then tested whether the observed patterns for each trait were dependent upon plant phylogeny and various ecogeographical factors and species traits. KEY RESULTS: We found no evidence of elevation having a global effect on the reproductive traits of angiosperm populations. This null global pattern was not affected by geograph or phylogenetics. CONCLUSIONS: Our results suggest that changes in reproductive traits, flower visitation rates, and heterozygosity in plant populations across elevations are specific to each species and ecosystem. Hence, macroevolutionary (across species) and macroecological patterns of elevation of plant reproduction reported previously are apparently not simply the outcome of microevolutionary changes (within species). This apparent specificity of response across plant species poses difficulties in predicting the effects of global changes and, specifically, climatic changes, on the fate of plant species, populations, and communities.

Identifying causal associations between women's reproductive traits and risk of schizophrenia: a multivariate validated two-sample Mendelian randomization analysis.

BACKGROUND: A significant association between women's reproductive traits and the risk of schizophrenia (SCZ) has been discovered, but the causalities remain unclear. We designed a two-sample univariate Mendelian randomization (MR) study using female-specific SNPs collected from a large-scale genome-wide association study as a genetic tool to explore the causal effect of female reproductive traits on the risk of SCZ, and conducted a multivariate MR study to re-validate the above findings. METHODS: From extensive genome-wide association studies (GWAS) of people with European ancestry (n = 176,881 to 418,758 individuals), summary-level data on five female reproductive variables were extracted. Summary-level information on SCZ was taken from a GWAS meta-analysis involving 320,404 people with European ancestry. The inverse variance weighting estimations for both univariable MR (UVMR) and multivariable MR (MVMR) were presented as the primary results. MR-Egger, weighted median, simple mode, and weighted mode regression methods for UVMR, and MVMR-Egger, MVMR-Lasso, and MVMR-median methods for MVMR were used for sensitivity analyses. RESULTS: The UVMR produced compelling proof for a connection between genetically predicted later age at first sexual intercourse (AFS) (OR, 0.632; 95% CI, 0.512-0.777; P < 0.01) and decreased SCZ risk. Pleiotropy analysis of the AFS-SCZ association confirmed the robustness of the MR results (P > 0.05). Consistent, substantial causal effects of AFS (OR, 0.592; 95%CI, 0.407-0.862; P < 0.01) on the risk of SCZ were demonstrated after adjusting for body mass index, years of schooling, and smoking initiation using MVMR. CONCLUSIONS: Our findings provide convincing evidence that early AFS is a risk factor for SCZ. SCZ risk may be decreased by raising awareness of reproductive healthcare for women.

An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population.

Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.

Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design.

Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify QTL related to economic traits. The aim of this study was to identify genomic regions inherited by Gir sire families and genes associated with number of viable oocytes (VO), total number of oocytes (TO), and number of embryos (EMBR) based on a daughter design approach. In total, 15 Gir sire families were selected. The number of daughters per family ranged from 26 to 395, which were genotyped with different SNP panels and imputed to the Illumina BovineHD BeadChip (777K) and had phenotypes for oocyte and embryo production. Daughters had phenotypic data for VO, TO, and EMBR. The search for QTL was performed through GWAS based on GBLUP. The QTL were found for each trait among and within families based on the top 10 genomic windows with the greatest genetic variance. For EMBR, genomic windows identified among families were located on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16, and BTA17, and they were most frequent on BTA7 within families. For VO, genomic windows were located on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23, and BTA27 among families, being most frequent on BTA8 within families. For TO, the top 10 genomic windows were identified on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26, and BTA27, being most frequent on BTA7 and BTA8 within families. Considering all results, the greatest number of genomic windows was found on BTA7, where the VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3 genes were identified in the common regions. In conclusion, 15 Gir sire families with 26 to 395 daughters per family with phenotypes for oocyte and embryo production helped to identify the inheritance of several genomic regions, especially on BTA7, where the EDIL3, HAPLN1, and VCAN candidate genes were associated with number of oocytes and embryos in Gir cattle families.

Assessing genetic parameters for first parity reproductive traits for early selection in Saanen × Beetal goats of India.

The present study aimed to evaluate the genetic parameters of first parity reproductive traits. Information on 762 reproductive records on Saanen × Beetal (S × B) goats reared for approximately five decades was collected from ICAR-National Dairy Research Institute, Karnal, Haryana (1973-2020). For genetic analysis, single-trait and multiple-trait animal models were used. Gibbs sampler for animal model (GSAM) approach was used for estimating (co)variance components of reproductive traits. Six different single-trait animal models (with or without maternal and environmental effects) were used and the deviance information criterion (DIC) determined the best model. The least squares mean for age at first service (AFS), age at first kidding (AFK), service period (SP), dry period (DP), gestation length (GL), kidding interval (KI), litter weight (LW), number of kids born (NKB) and number of female kids born (NFKB) in first parity were 526.99 ± 4.86, 662.96 ± 5.03, 219.11 ± 6.25, 109.38 ± 6.00, 150.48 ± 0.27, 356.63 ± 4.80 days, 3.87 ± 0.05 kg, 1.27 ± 0.02 and 0.67 ± 0.03, respectively. Lower heritability estimates for these reproductive traits revealed a sparse scope for genetic improvement. Multivariate analysis using Model 1 was carried out to evaluate the genetic and phenotypic correlation of these nine reproductive traits. The genetic correlation of DP and SP was negatively with LW, NKB and NFKB, which is favourable as reduction in SP and DP can improve these economically important traits through indirect selection. Consistent efforts towards genetic improvement of these goat flock poses a promising future for meat industry owing to high prolificacy and good reproductive potential in this flock.

Impact of reproductive traits on productive life in Iranian Holstein dairy cows.

Enhancing reproductive performance is a key strategy to mitigate involuntary culling rates, thereby extending productive life (PL) and ultimately improving profitability in dairy cattle herds. A piecewise Weibull proportional hazards model was used to investigate the effect of several important reproductive traits on PL in Holstein dairy cows. Data comprised 200,747 lactation records from 82,505 cows sired by 1952 bulls across 36 dairy herds. PL was defined as the number of days from the first calving to the last milk record or censoring. The statistical model accounted for the time-dependent fixed effects of changes in herd size, year-season, milk production, fat and protein contents, and the time-independent fixed effect of age at first calving. Herd-year and sire effects were also included as random effects. Reproductive traits include calving traits such as calving ease (CE), calf size (CZ), and calf survival (CS), as well as female fertility traits such as number of inseminations per conception (NI), days from calving to first service (CFS), days from first service to conception (FSC), and days open (DO). All reproductive traits had a significant effect on PL (p < 0.001). Each reproductive trait was analysed separately. The relative risk (RR) of being culled increased as the severity of calving difficulties increased in both primiparous and multiparous cows. Cows that calved small or large calves showed a higher risk of being culled compared with those that calved medium size calves. The increased RR of culling was observed only for primiparous cows that gave birth to dead calves. In addition, cows that required more NI, a longer CFS, FSC, and DO had shorter longevity. These insights can deepen our comprehension of the factors affecting PL and provide information for refining management and breeding strategies, which could lead to increased profitability and sustainability in Iranian dairy farming.

Research Progress on the Role of M6A in Regulating Economic Traits in Livestock.

Reversible regulation of N6-methyladenosine (m6A) methylation of eukaryotic RNA via methyltransferases is an important epigenetic event affecting RNA metabolism. As such, m6A methylation plays crucial roles in regulating animal growth, development, reproduction, and disease progression. Herein, we review the latest research advancements in m6A methylation modifications and discuss regulatory aspects in the context of growth, development, and reproductive traits of livestock. New insights are highlighted and perspectives for the study of m6A methylation modifications in shaping economically important traits are discussed.

Genome-wide association research on the reproductive traits of Qianhua Mutton Merino sheep.

Objective: Qianhua Mutton Merino sheep is a new breed of meat wool sheep cultivated independently in China. In 2018, it was approved by the state and brought into the national list of livestock and poultry genetic resources. Qianhua Mutton Merino sheep has the common characteristics of typical meat livestock varieties with rapid growth and development in the early stage and high meat production performance.The objective of this research is to investigate the Genome-wide association of the reproductive traits of Qianhua Mutton Merino sheep. Methods: Qianhua Mutton Merino sheep from the breeding core group were selected as the research object, GWAS was conducted on genes associated with the reproductive traits (singleton or twins, birth weight, age [in days] for sexual maturity, weaning weight, and daily gain from birth to weaning) of Qianhua mutton merino. Results: Our study findings showed that 151 loci of SNPs were detected, among which 3 SNPs related to birth weight and weaning weight occupied a significant portion of the wide genome. The candidate genes preliminarily obtained were SYNE1, SLC12A4, BMP2K, CAMK2D, IMMP2L, DMD, and BCL2. Conclusion: 151 SNP loci were detected for five traits related to reproduction (including singleton or twins, birth weight, age [in days] at sexual maturity, weaning weight, and daily weight gain from birth to weaning). The functions of these candidate genes were mainly enriched in nucleotide metabolism, metal ion binding, oxytocin signaling pathway, and neurotrophin signaling pathway.

Estimation of genetic correlations and genomic prediction accuracy for reproductive and carcass traits in Hanwoo cows.

This study estimated the heritabilities (h2) and genetic and phenotypic correlations between reproductive traits, including calving interval (CI), age at first calving (AFC), gestation length (GL), number of artificial inseminations per conception (NAIPC), and carcass traits, including carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) in Korean Hanwoo cows. In addition, the accuracy of genomic predictions of breeding values was evaluated by applying the genomic best linear unbiased prediction (GBLUP) and the weighted GBLUP (WGBLUP) method. The phenotypic data for reproductive and carcass traits were collected from 1,544 Hanwoo cows, and all animals were genotyped using Illumina Bovine 50K single nucleotide polymorphism (SNP) chip. The genetic parameters were estimated using a multi-trait animal model using the MTG2 program. The estimated h2 for CI, AFC, GL, NAIPC, CWT, EMA, BF, and MS were 0.10, 0.13, 0.17, 0.11, 0.37, 0.35, 0.27, and 0.45, respectively, according to the GBLUP model. The GBLUP accuracy estimates ranged from 0.51 to 0.74, while the WGBLUP accuracy estimates for the traits under study ranged from 0.51 to 0.79. Strong and favorable genetic correlations were observed between GL and NAIPC (0.61), CWT and EMA (0.60), NAIPC and CWT (0.49), AFC and CWT (0.48), CI and GL (0.36), BF and MS (0.35), NAIPC and EMA (0.35), CI and BF (0.30), EMA and MS (0.28), CI and AFC (0.26), AFC and EMA (0.24), and AFC and BF (0.21). The present study identified low to moderate positive genetic correlations between reproductive and CWT traits, suggesting that a heavier body weight may lead to a longer CI, AFC, GL, and NAIPC. The moderately positive genetic correlation between CWT and AFC, and NAIPC, with a phenotypic correlation of nearly zero, suggesting that the genotype-environment interactions are more likely to be responsible for the phenotypic manifestation of these traits. As a result, the inclusion of these traits by breeders as selection criteria may present a good opportunity for developing a selection index to increase the response to the selection and identification of candidate animals, which can result in significantly increased profitability of production systems.

Application of RNA-Seq Technology for Screening Reproduction-Related Differentially Expressed Genes in Tibetan and Yorkshire Pig Ovarian Tissue.

The purpose of this study was to explore and verify genes that regulate the reproductive traits of Tibetan pigs at the mRNA level. The ovarian tissues of Tibetan pigs (TPs) and Yorkshire pigs (YPs) were selected as research objects, and cDNA libraries of the ovarian tissue transcripts of Tibetan pigs and Yorkshire pigs were successfully constructed by the RNA-Seq technique. A total of 651 differentially expressed genes (DEGs) were screened, including 414 up-regulated genes and 237 down-regulated genes. Through GO and KEGG enrichment analysis, it was found that these differentially expressed genes were significantly enriched in cell process, reproductive process, reproduction, cell proliferation, binding, and catalytic activity, as well as oxidative phosphorylation, endocrine resistance, thyroid hormone, Notch, and other signal transduction pathways. Genes significantly enriched in pathways closely related to reproductive regulation were analyzed and selected, and the AR, CYP11A1, CYP17A1, INHBA, ARRB2, EGFR, ETS1, HSD17B1, IGF1R, MIF, SCARB1, and SMAD4 genes were identified as important candidate genes. Twelve differentially expressed genes related to reproduction were verified by RT-qPCR. The results showed that the expression of the AR, CYP17A1, EGFR, ETS1, IGF1R, and SMAD4 genes was significantly higher in Tibetan pigs than in Yorkshire pigs, while the expression of the CYP11A1, INHBA, ARRB2, HSD17B, MIF, and SCARB1 genes in Tibetan pigs was significantly lower than in Yorkshire pigs. The purpose of this study is to provide a theoretical basis for exploring the molecular mechanism of reproductive trait effect genes and the application of molecular breeding in Tibetan pigs.

How Effective Is Environmental Protection for Ensuring the Vitality of Wild Orchid Species? A Case Study of a Protected Area in Italy.

Orchids are among the plants most threatened by anthropic impact and environmental changes. Therefore, all known orchid species are protected in several countries by regional, national and international legislation. Several studies have cast doubts on the effectiveness of legislation to ensure the protection of wild orchids. We assessed the vitality of four orchid populations in a coastal area in Northern Italy, by monitoring the vegetative and reproductive traits of the orchid populations growing both in the protected sites comprising the Natura 2000 network, and in non-protected sites. We also monitored the level of environmental threat to orchid vitality. The early-flowering deceptive species (Ophrys sphegodes and Anacamptis morio) exhibited high vegetative vitality and experienced similar levels of environmental threat in the protected and non-protected areas. However, their reproductive success was strongly jeopardized, probably by a failed pollination that impeded the fruit set. The late-flowering, partially or totally rewarding species (Anacamptis pyramidalis and Anacamptis coriophora) were more strongly impacted by spring mowing and ungulate herbivory and alien species. Only for A. coriophora were the herbivory and alien species invasions lower at the protected vs. non-protected sites, which ensured a higher population vitality at the protected sites. We conclude that the environmental protection in our study area is ineffective for preserving orchids without targeted actions against specific environmental threats.

Comprehensive genome-wide analysis of genetic loci and candidate genes associated with litter traits in purebred Berkshire pigs of Korea.

Objective: The objective of this study was to identify genomic regions and candidate genes associated with the total number of piglets born (TNB), number of piglets born alive (NBA), and total number of stillbirths (TNS) in Berkshire pigs. Methods: : This study used a total of 11,228 records and 2,843 single-nucleotide polymorphism (SNP) data obtained from Illumina porcine 60 K and 80 K chips. The estimated genomic breeding values (GEBVs) and SNP effects were estimated using weighted single-step genomic BLUP (WssGBLUP). Results: : The heritabilities of the TNB, NBA, and TNS were determined using single-step genomic best linear unbiased prediction (ssGBLUP). The heritability estimates were 0.13, 0.12, and 0.015 for TNB, NBA, and TNS, respectively. When comparing the accuracy of breeding value estimates, the results using pedigree-based BLUP (PBLUP) were 0.58, 0.60, and 0.31 for TNB, NBA, and TNS, respectively. In contrast, the accuracy increased to 0.67, 0.66, and 0.42 for TNB, NBA, and TNS, respectively, when using WssGBLUP, specifically in the last three iterations. The results of weighted single-step genome-wide association studies (WssGWAS) showed that the highest variance explained for each trait was predominantly located in the Sus scrofa chromosome 5 (SSC5) region. Specifically, the variance exceeded 4% for TNB, 3% for NBA, and 6% for TNS. Within the SSC5 region (12.26 to 12.76 Mb), which exhibited the highest variance for TNB, 20 SNPs were identified, and five candidate genes were identified: TIMP3, SYN3, FBXO7, BPIFC, and RTCB. Conclusion: : The identified SNP markers for TNB, NBA, and TNS were expected to provide valuable information for genetic improvement as an understanding of their expression and genetic architecture in Berkshire pigs. With the accumulation of more phenotype and SNP data in the future, it is anticipated that more effective SNP markers will be identified.

Predicting the Threat Status of Mosses Using Functional Traits.

Mosses are an early lineage of the plant kingdom, with around 13,000 species. Although an important part of biodiversity, providing crucial ecosystem services, many species are threatened with extinction. However, only circa 300 species have so far had their extinction risk evaluated globally for the IUCN Red List. Functional traits are known to help predict the extinction risk of species in other plant groups. In this study, a matrix of 15 functional traits was produced for 723 moss species from around the world to evaluate the potential of such predictability. Binary generalized linear models showed that monoicous species were more likely to be threatened than dioicous species, and the presence of a sporophyte (sexual reproduction), vegetative reproduction and an erect (straight) capsule instead of a pendent (immersed) one lowers the risk of species extinction. A longer capsule, seta and stem length, as well as broader substrate breadth, are indicative of species with a lower risk of extinction. The best-performing models fitted with few traits were able to predict extinction risks of species with good accuracy. These models applied to Data Deficient (DD) species proved how useful they may be to speed up the IUCN Red List assessment process while reducing the number of listed DD species, by selecting species most in need of a full, detailed assessment. Some traits tested in this study are a novelty in conservation research on mosses, opening new possibilities for future studies. The traits studied and the models presented here are a significant contribution to the knowledge of mosses at risk of extinction and will help to improve conservation efforts.

Potential coconut (Cocos nucifera L.) genotypes for farmers: Evaluation of agronomic traits in a lethal yellowing disease endemic zone in Ghana.

A four-year study was conducted to evaluate selected vegetative and reproductive characteristics in four coconut genotypes namely: Niu Leka Dwarf (NLD), New Guinea Brown Dwarf (NGBD), Malayan Green Dwarf (MGD), Indonesian Brown Dwarf (IBD), and a hybrid between Sri Lankan Green Dwarf and Vanuatu Tall (SGDVTT), which was used as a control. The study was located at Anwea in the Western Region of Ghana, an endemic zone to the lethal yellowing disease. This experiment was laid out in a randomized complete block design (RCBD) in three replications. Results showed a significant higher growth for NGBD, IBD, and NLD in stem girth, leaf length, petiole length, and number of leaflets. NGBD, IBD, and SGDVTT also recorded significantly higher reproductive characteristics. Time taken for first flowering was noticed in IBD (41.30 months). NGBD recorded the highest number of female flowers (27.80), number of spikelets with female flowers (17.20), and total number of spadix (12.50) seasonally. Significant and positive correlations were observed between the number of leaves emitted, and the number of female flowers produced in the coconut genotypes except for MGD. The highest correlation between these vegetative and reproductive characteristics was expressed in IBD while the least was observed in the MGD genotype. MGD also recorded the least number of spikelets with female flowers, suggesting that this genotype is not likely to produce high number of fruits and should not be included in future breeding programs. Low and less robust characteristics were expressed in both SGDVTT, and MGD in the growing period, which could be ascribed to the rather low number of leaflets observed in these genotypes. Conclusions from this study suggest that NGBD, IBD, and NLD are potential genotypes to be integrated into further breeding programs across coconut-growing regions in Ghana.

Dissection of the E8 locus in two early maturing Canadian soybean populations.

Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.

Genome-Wide Association Analysis of Reproductive Traits in Chinese Holstein Cattle.

This study was to explore potential SNP loci for reproductive traits in Chinese Holstein cattle and identify candidate genes. Genome-wide Association Study based on mixed linear model was performed on 643 Holstein cattle using GeneSeek Bovine 50 K SNP chip. Our results detected forty significant SNP loci after Bonferroni correction. We identified five genes (VWC2L, STAT1, PPP3CA, LDB3, and CTNNA3) as being associated with pregnancy ratio of young cows, five genes (PAEP, ACOXL, EPAS1, GLRB, and MARVELD1) as being associated with pregnancy ratio of adult cows, and nine genes (PDE1B, SLCO1A2, ARHGAP26, ADAM10, APBB1, MON1B, COQ9, CDC42BPB, MARVELD1, and HPSE2) as being associated with daughter pregnancy rate. Our study may provide valuable insights into identifying genes related to reproductive traits and help promote the application of molecular breeding in dairy cows.

Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits.

This study aimed to predict the accuracy of genomic estimated breeding values (GEBVs) for reproductive traits in Hanwoo cows using the GBLUP, BayesB, BayesLASSO, and BayesR methods. Accuracy estimates of GEBVs for reproductive traits were derived through fivefold cross-validation, analyzing a dataset comprising 11,348 animals and employing an Illumina Bovine 50K SNP chip. GBLUP showed an accuracy of 0.26 for AFC, while BayesB, BayesLASSO, and BayesR demonstrated values of 0.28, 0.29, and 0.29, respectively. For CI, GBLUP attained an accuracy of 0.19, whereas BayesB, BayesLASSO, and BayesR scored 0.21, 0.24, and 0.25, respectively. The accuracy for GL was uniform across GBLUP, BayesB, and BayesR at 0.31, whereas BayesLASSO showed a slightly higher accuracy of 0.33. For NAIPC, GBLUP showed an accuracy of 0.24, while BayesB, BayesLASSO, and BayesR recorded 0.22, 0.27, and 0.30, respectively. The variation in genomic prediction accuracy among methods indicated Bayesian approaches slightly outperformed GBLUP. The findings suggest that Bayesian methods, notably BayesLASSO and BayesR, offer improved predictive capabilities for reproductive traits. Future research may explore more advanced genomic approaches to enhance predictive accuracy and genetic gains in Hanwoo cattle breeding programs.

Breeding biology in a population of Rufous-collared Sparrow (Zonotrichia capensis, Statius Müller, 1776) at different elevations in the Tropical Andes / Biología reproductiva en una población de Gorrión Copetón (Zonotrichia capensis, Statius Müller, 1776) a diferente elevación en los Andes tropicales

Abstract: Breeding biology in a population of Rufous-collared Sparrow (Zonotrichia capensis, Statius Müller, 1776) at different elevations in the Tropical Andes. Elevation strongly influences the evolution of life history traits associated with bird physiology and reproduction. Since life history traits in birds are modulated by environmental factors that vary with elevation, we expected to find changes in breeding biology traits of Z. capensis at different elevations. In this study, we compared the breeding biology (clutch size, egg volume, and reproductive activity) of a non-migratory population of Z. capensis in two localities at different elevations (low and high elevations, 1 800 m a.s.l., and 3 800 m a.s.l., respectively) and same latitude in the Colombian Tropical Andes for a one-year period. We found no differences in clutch size between the localities; however, egg volume was higher at high elevation. Furthermore, the reproductive activity differed significantly between localities. We propose that clutch size is likely conserved throughout the altitudinal distribution of Z. capensis since the species evolved in Tropical lowlands. On the other hand, the larger egg volume at high elevation could obey local environmental factors that may favor the reproductive success of the population.

Resumen: Biología reproductiva en una población de Gorrión Copetón (Zonotrichia capensis, Statius Müller, 1776) a diferente elevación en los Andes tropicales. La elevación influye fuertemente en la evolución de los rasgos de historia de vida asociados con la fisiología y reproducción de las aves. Dado que los rasgos de historia de vida en las aves están modulados por factores ambientales que varían con la elevación, esperábamos encontrar cambios en los rasgos de la biología reproductiva de Z. capensis a diferentes elevaciones. En este estudio, comparamos la biología reproductiva (tamaño de puesta, volumen del huevo y actividad reproductiva) de una población no migratoria de Z. capensis en dos localidades a diferente elevación (elevación baja 1 800 m snm, y elevación alta 3 800 m snm,) y a la misma latitud en los Andes tropicales colombianos por un período de un año. No encontramos diferencias en el tamaño de puesta entre las localidades; sin embargo, el volumen del huevo fue mayor en elevación alta. Además, la actividad reproductiva difirió entre las localidades. Proponemos que el tamaño de puesta probablemente se conserve en toda la distribución altitudinal de Z. capensis, ya que la especie evolucionó en las tierras bajas tropicales. Por otro lado, el mayor volumen del huevo a elevación alta podría obedecer a factores ambientales locales que pueden favorecer el éxito reproductivo de la población.

Environmental influence on the reproductive strategy of Helogenes marmoratus (Siluriformes: Cetopsidae) in the Amazonian streams

RESUMEN La estrategia reproductiva de una especie debe ajustarse a las variaciones de las condiciones ambientales para garantizar el equilibrio poblacional. En los riachos amazónicos de tierra firme las fluctuaciones hidrológicas están controladas principalmente por las lluvias locales, predominando especies de peces de pequeño porte. Investigamos la estrategia reproductiva de Helogenes marmoratus y la influencia de variables ambientales (e.g., lluvia, conductividad, descriptores del hábitat) en su actividad reproductiva. Colectamos mensualmente entre marzo de 2019 y marzo de 2020 en una microcuenca del río Guamá, en la Amazonia oriental brasileña. Identificamos un período reproductivo prolongado entre julio de 2019 y marzo de 2020. Los machos comienzan a reproducirse con un menor tamaño ( = 27.41; = 31.36 mm). Confirmamos desove parcial, baja fecundidad (59.55 ± 22.76 ovócitos) y ovócitos grandes (1.24 ± 0.15 mm). La estrategia reproductiva de H. marmoratus ocupa un lugar intermedio entre el gradiente oportunista y de equilibrio. Regresiones múltiples destacan la importancia de la profundidad, la conductividad eléctrica, los bancos de hojas y la lluvia como reguladores de la actividad reproductiva de las hembras, explicando 32% de la variación del IGS. Nuestro estudio proporciona evidencia de una respuesta reproductiva diferenciada entre los sexos a las variables ambientales.

ABSTRACT The reproductive strategy of a species must be adjusted to variations in environmental conditions to guarantee population balance. Hydrological fluctuations in Amazonian streams of terra firme (non-flooded) are controlled primarily by local rainfall. Fish assemblages are composed predominantly of species of small size. We investigated the reproductive strategy of the cryptic catfish Helogenes marmoratus and assessed the influence of environmental variables (e.g., rainfall, conductivity, habitat descriptors) on its reproductive activity in a catchment of the Guamá River in the eastern Brazilian Amazon. Through monthly collections between March 2019 and March 2020, we identified an extended reproductive period between July 2019 and March 2020. Males mature at smaller sizes than females ( = 27.41 mm; = 31.36 mm). We confirmed batch spawning, low fecundity (59.55 ± 22.76 stage IV oocytes), and large oocytes (1.24 ± 0.15 mm). Our results indicated that H. marmoratus strategy occupies an intermediate place between opportunistic and equilibrium gradient. Multiple regressions showed that thalweg depth, electrical conductivity, leaf litter, and rainfall are important drivers of reproductive activity of females of H. marmoratus, explaining 32% of the variation of the GSI. Our study provides evidence of differentiated reproductive response between the sexes to environmental variables.