Structure and genetic variability of the Costa Rican Paso horse.

The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.

Allelic and genotypic frequencies of SNP related to beef and carcass quality in Romosinuano cattle in Mexico.

Romosinuano is a tropically adapted Bos taurus breed, and some Mexican breeders aim to improve it genetically. The aim was to estimate allelic and genotypic frequencies for SNPs associated with meat quality in a Mexican Romosinuano population. Four hundred ninety-six animals were genotyped using the Axiom©BovMDv3 array. Only SNPs related to meat quality in this array were studied in this analysis. The Calpain, Calpastatin, and Melanocortin-4 receptor alleles were considered. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium were estimated with the PLINK software. Alleles associated with meat tenderness and higher marbling scores were found in the Romosinuano cattle population. CAPN1_4751 was not found in Hardy-Weinberg equilibrium. The rest of the markers could not be affected by selection and inbreeding. Romosinuano cattle in Mexico have similar genotypic frequencies in markers related to meat quality to Bos taurus breeds known for their meat tenderness. Breeders can choose a marker-assisted selection to improve meat quality characteristics.

Expression of PLCZ1 mRNA in spermatozoa of Criollo and European bulls in a low-input system.

Sperm motility and kinematics analysis are important to predict bull fertility. However, there are other molecules in the sperm with the ability to improve the pregnancy rate. For example, PLCZ1 is a sperm protein that plays a unique role in the activation of the zygote and is important for the survival of the embryo. The objective of this work was to compare the expression of PLCZ1 mRNA in sperm cells of Chihuahuan Criollo and European bulls in the winter and summer seasons, under a low-input system. Six (3.33 ± 0.43 years old) bulls (three Criollo, three European) were used. Gross and individual motility were measured in semen obtained by electrostimulation. The cell pack was pelletized by centrifugation and stored in liquid nitrogen. The sperm cells were purified and total RNA was extracted. cDNA was synthesized to perform qPCR and measure the relative level of PLCZ1 transcripts in each bull. There were no differences in individual motility, however, gross motility was lower (P < 0.05) in Criollo bulls, both in the winter (71.1 ± 2.8 vs. 76.6 ± 2.8%) and in the summer season (58.9 ± 2.8 vs. 77.7 ± 2.8%). PLCZ1 expression was 5.3 times higher (P < 0.05) in winter than in summer (5.09 ± 1.09 vs 0.959 ± 1.09). No difference (P>0.05) was found in the expression levels of PLCZ1 between both breeds (4.36 ± 1.09 vs 1.69 ± 1.09), for Criollo and European, respectively. Although the animals presented seminal motility within the recommended limits for insemination, the expression levels of PLCZ1 vary depending on the time of the year and this might impact the rate of successful pregnancies. Therefore, it is important to complement conventional analysis of seminal quality with molecular characteristics.

Assessment of Genetic Diversity, Runs of Homozygosity, and Signatures of Selection in Tropical Milking Criollo Cattle Using Pedigree and Genomic Data.

The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree (FPed), the genomic relationship matrix (FGRM), and runs of homozygosity (FROH) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for FPED, FGRM, and FROH, respectively. Correlation between FPED and FROH was significant only for runs of homozygosity > 4 Mb, indicating the FPED of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program.

Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis.

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate signal transduction, development, metabolism, and stress responses in plants through post-transcriptional degradation and/or translational repression of target mRNAs. Several studies have addressed the role of miRNAs in model plant species, but miRNA expression and function in economically important forage crops, such as Bouteloua gracilis (Poaceae), a high-quality and drought-resistant grass distributed in semiarid regions of the United States and northern Mexico remain unknown. RESULTS: We applied high-throughput sequencing technology and bioinformatics analysis and identified 31 conserved miRNA families and 53 novel putative miRNAs with different abundance of reads in chlorophyllic cell cultures derived from B. gracilis. Some conserved miRNA families were highly abundant and possessed predicted targets involved in metabolism, plant growth and development, and stress responses. We also predicted additional identified novel miRNAs with specific targets, including B. gracilis ESTs, which were detected under drought stress conditions. CONCLUSIONS: Here we report 31 conserved miRNA families and 53 putative novel miRNAs in B. gracilis. Our results suggested the presence of regulatory miRNAs involved in modulating physiological and stress responses in this grass species.