Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Background: Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods: 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results: Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions: Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.

Numerical techniques for modeling Doppler ultrasound spectra systems

Evaluation of blood-flow Doppler ultrasound spectral content is currently performed on clinical diagnosis. Since mean frequency and bandwidth spectral parameters are determinants on the quantification of stenotic degree, more precise estimators than the conventional Fourier transform should be seek. This paper summarizes studies led by the author in this field, as well as the strategies used to implement the methods in real-time. Regarding stationary and nonstationary characteristics of the blood-flow signal, different models were assessed. When autoregressive and autoregressive moving average models were compared with the traditional Fourier based methods in terms of their statistical performance while estimating both spectral parameters, the Modified Covariance model was identified by the cost/benefit criterion as the estimator presenting better performance. The performance of three time-frequency distributions and the Short Time Fourier Transform was also compared. The Choi-Williams distribution proved to be more accurate than the other methods. The identified spectral estimators were developed and optimized using high performance techniques. Homogeneous and heterogeneous architectures supporting multiple instruction multiple data parallel processing were essayed. Results obtained proved that real-time implementation of the blood-flow estimators is feasible, enhancing the usage of more complex spectral models on other ultrasonic systems.