Isolates from the Fusarium fujikuroi species complex, mainly F. sacchari, have been reported to be the causal agents of pokkah boeng in sugarcane in Brazil. However, inadequate information was ...available on the occurrence and genetic diversity of F. sacchari in Northeast Brazil, which is a limiting factor on management. Thus, isolates of F. subglutinans sensu lato from sugarcane plants with symptoms of pokkah boeng were evaluated using the sexual cross‐fertility to determine species. All the isolates produced black perithecia when they were crossed with the test isolates of F. sacchari. Three weeks after the crossing, the formation of fertile ascospores cirri was observed. Thirty‐four isolates were self‐sterile hermaphrodites, while 21 were fertile only as males. Five isolates were homothallic. The effective size Ne(f) of the population as a function of the frequency of hermaphrodites and female sterile strains was 95.5%. The F. sacchari isolates were separated into four genetic groups independent of geographic location. The mean of polymorphism among all populations was 79%, and the average unbiased genetic diversity (uh) was considered moderate (0.31). This study in addition to confirming that F. sacchari as the main species associated with pokkah boeng in sugarcane in Northeast Brazil, reveals the relationship of mating type and genetic diversity of F. sacchari. The unrestricted gene flow between regions is probably the best explanation for the low geographic correlation. This knowledge will help in the adoption of management measures with fungicides or resistant cultivars.
The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the efficiency of ...including genomic information in the analyses.
There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses.
The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from -0.65±0.31 to 0.59±0.19, using A, and from -0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses.
The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses.
Cajui (Anacardium spp.) is a native fruit tree (small cashew) of the Brazilian Cerrado and possesses the potential for commercialization. However, cajui exploitation occurs exclusively through ...extractivism in the absence of conservation strategies. The lack of conservation strategies may lead to a decrease in genetic diversity of Anacardium. In this work, the genetic diversity and population structure of three natural populations in Sete Cidades National Park (PNSC; PI, Brazil) were assessed using ISSR analysis of 56 cajui accessions and two A. occidentale accessions (outgroup) from Pacajus (CE, Brazil). A total of 112 markers were obtained, 93 (83.04%) of which were polymorphic. The diversity indices of these populations indicated moderate levels of genetic diversity. According to AMOVA, 96.17% of the genetic variability lay within populations, with low genetic differentiation among populations (ΦST = 0.03828). Furthermore, STRUCTURE analysis indicated the existence of four connected genetic groups. The findings show that the individuals from the three collection sites did not represent different subpopulations, likely due to the high gene flow (Nm = 6.7) favored by the floral biology of Anacardium, pollinators and small-animal seed dispersers. This research identifies genetically divergent individuals (C-03, C-05, C-22, C-26, C-34 and C-39), which should be considered priority individuals for conservation and can inform conservation programs for Anacardium spp.
Lecithin-cholesterol acyltransferase (LCAT), an enzyme that participates in lipoprotein metabolism, plays an important role in cholesterol homeostasis. Mutations in the LCAT gene can cause two rare ...genetic disorders: familial LCAT deficiency (FLD), which is characterized by corneal opacities, normocytic anemia, dyslipidemia, and proteinuria progressing to chronic renal failure, and fish-eye disease (FED), which causes dyslipidemia and progressive corneal opacities. Herein, we report six suspected cases of FLD in the backlands of Piauí, located in northeast Brazil. A genetic diagnosis was performed in index cases. Among these, a further investigation was performed to identify new cases in the families. In addition, molecular analyses were performed to verify the levels of consanguinity within families and the existence of a genetic relationship between them. All six index cases were confirmed as FLD with an identical mutation (c.803G > A, p.R268H). The genetic investigation confirmed another 7 new cases of FLD, 52 heterozygous and 6 individuals without mutations. The rate of consanguinity revealed that marriages within the family did not contribute to the high number of FLD cases within the restricted region. The elders of each family (patriarchs and matriarchs) were subjected to a kinship analysis and were more genetically related to each other than the control group. Bayesian analysis was implemented to confirm the hypothesis of connectivity among patriarchs and matriarchs and indicated that they were genetically more related to each other than would be randomly expected, thus suggesting the occurrence of a possible founder effect in these families.
The production of animal-based foods from native breeds have a synergistic relationship with the regional culture, the local climate, and mainly the maintenance of alternative genetic resources for a ...system with a lower environmental impact. Thus the efficiency of conservation and production depends on assessing the variability of these local breeds. In the case of Curraleiro Pé-duro cattle, the most adapted individuals have undergone natural selection over five hundred years in the Brazilian savannas, mating with little or no human interference. The peculiarities of these biomes, where the regional flora is the food base and cattle is raised in extensive areas, likely influenced the genetic composition of the different groups that make up the first cattle breed of Brazil.
To evaluate the composition, diversity, variation, differentiation, and genetic structure of the populations studied, samples of hair follicles from 474 individuals of different animal categories (calves, yearlings, heifers, cows, and bulls) from three farms, defined as subpopulations "A", "B", and "C", were collected. The animals were genotyped for 17 microsatellite markers using a DNA sequencer. After verification of monomorphic alleles, alleles outside the expected size range, and for the presence of stutter bands, the results were subjected to statistical analysis.
The markers used were suitable for the proposed application with a mean Polymorphism Information Content (PIC) of 0.62. On average, the effective alleles were 4.25 per marker, with mean heterozygosities of 0.74 (observed and expected), which was lower in herd A (0.70) in comparison to herds B (0.77) and C (0.74). The analysis of molecular variance (AMOVA) revealed a higher rate of variation within herds (98.5%) and lower among herds (1.5%) (F
ranging from 0.00723 and 0.03198;
-values < 0.05). However no significant differences among herds where found with the Mantel test based on geographic distances. The formation of genetic clusters of all animals sampled with the software Structure resulted in minimum cluster values, with two main genetic groups (
= 2) observed among the evaluated animals. Therefore, based on PIC and heterozygosity values, a wide genetic diversity was observed, despite little differences in population structure (AMOVA, F
, and Structure results) among sampling sites.
Abstract
Infection by Haemonchus contortus is the gastrointestinal parasitosis of greatest economic and social importance in the production of goats, being the leading cause of mortality in the ...Brazilian goat industry. Genetic selection for resistance to parasites in Anglo-Nubian goats has proven to be a viable alternative to traditional methods of controlling gastrointestinal nematodes, producing animals genetically superior in resistance to parasites. This study aimed to evaluate
the impact of including genomic information on the estimation of variance components, genetic parameters, and predictive accuracy of genetic values for the new trait Parasitic Resistance (PR) in Anglo-Nubian goats. The PR is generated by measuring Body Condition Score, FAMACHA chart (ranging from 1 to 5), and Fecal Egg Count on a regular scale. These three traits were used as input variables in the CAPRIOVI software, which uses fuzzy logic to create the PR score, ranging from 0 to 10. Animals with lower scores are more likely to be parasitized and require treatment, while animals with higher scores are less likely to be infected. We used information from 352 animals, totaling 3,855 repeated measurements of PR over the years (2001 to 2020) and 1,500 animals in the pedigree. Animals with less than three measurements for any of the three input traits were removed from the dataset. Contemporary groups were built from information from the year of birth, data collection season, birth season, and physiological stage of the animal, considered as fixed effects, and age at the time of data collection as a covariate in an animal repeatability model. A total of 89 animals were genotyped using the Bead Chip Goats SNP50. After quality control, the remaining 38,659 SNPs (Table 1) were used to build the hybrid matrix (H). The variance components (VC) were estimated using the Bayesian Gibbs Sampling method, and breeding values were predicted using the Best Linear Unbiased Prediction (BLUP) and single-step Best Linear Unbiased Prediction (ssGBLUP) methods. The additive genetic variance and heritability estimation ranged from 0.13 to 0.14 and 0.04 to 0.05, respectively (Table 2). The accuracies obtained for PR with BLUP and ssGBLUP were 0.12 and 0.14, respectively, representing a gain of 16.7%. The genomic information (25 % of all animals with phenotypes) with the repeated records improved the predictive model capability based on accuracy. It also improved the VC estimation for PR in Anglo-Nubian goats raised in the Brazilian semi-arid region. These results highlight the positive impact of genetic evaluation of goats for PR, even with few phenotypes and genotyped animals. In addition to elucidating the additive genetic influence of parasite resistance, it can be a great source of information on the selection and production of Anglo-Nubian goats.
Cattle weight development is highly correlated with some body measurements. Based on the relationship between morphometric measurements and body mass, our aim was to develop regression equations to ...estimate the body weight of Curraleiro Pé-Duro (CPD) cattle to be used in farms that lack access to weighting scales. Data from 1023 animals from four farms on withers height (WH), body length (BL), body score (BS), heart girth (HG), permanent teeth (PT), scrotal perimeter (SP), and live weight were used. The animals were classified into five categories depending on age and/or sex: newborns (NB), calves, weaned animals, cows, and bulls. The best models are GLM with Gamma, Gamma, inverse Gaussian, Gaussian, and Gamma distributions for NB, calves, weaned animals, cows, and bulls, respectively. Predictive modeling for bulls was the best performing overall, with a correlation of 0.97 between the estimated by the model and the obtained with a weighting scale. For NB, calves, weaned animals, and cows, the correlation (
r
) was 0.85, 0.90, 0.95, and 0.87, respectively. The evaluated models are adequate to be used as a technical solution to estimate weight in a cattle production system.
•Moderate genomic parameters for ultrasound-based carcass traits were obtained for hair sheep adapted to harsh environments.•Carcass traits evaluated in vivo are feasible for selection in Santa Inês ...sheep.•Genetic evaluation for carcass traits is favored by adding genomic information.•Single-step GBLUP outperforms BLUP based on the accuracy of genomic breeding values.
Santa Inês is a locally adapted hair sheep breed that is under large expansion in Brazil and other Tropical countries. This study aimed to evaluate the effect of different relationship matrices (A or H) on the estimation of genetic parameters and accuracy of (genomic) breeding values (G)EBVs for carcass traits measured in vivo in Santa Inês sheep. A total of 977, 890, 894, and 882 records for loin eye area (LEA), marbling score (MLE), subcutaneous fat thickness (SFT), and leg circumference (LEC), respectively, were included in this study. There were 1637 animals in the numerator relationship matrix (A). A total of 389 animals with phenotypic information were genotyped using the OvineSNP50 BeadChip. After the genotyping quality control, 388 samples and 42,748 SNPs remained in the dataset. The (co)variance components were estimated via Bayesian inference through single- and multi-trait analyses using the animal model with either the A or H matrix. The theoretical accuracies of (G)EBVs, Pearson correlation between breeding values estimated including or not genomic information, and Spearman rank correlation were used to evaluate the feasibility of incorporating genomic information in the analyses. Heritability estimates ranged from 0.12 ± 0.06 (SFT, using the A matrix) to 0.29 ± 0.07 (LEA, using the H matrix), in the single-trait analyses, and from 0.17 ± 0.05 (SFT, using A) to 0.33 ± 0.07 (LEA, using H), in a multi-trait setting. Direct genetic additive variance and heritability estimates were higher when including genomic information. Unfavorable and high genetic correlation was observed between LEA and SFT. The estimates of theoretical accuracy of (G)EBVs were higher in all the scenarios when genomic information was incorporated in the model. Gains in accuracy ranged from 0.013 to 0.039 units when genomic information was included in the analyses. Thus, if available, genomic information should be incorporated in the estimation of genetic parameters and breeding values for carcass traits measured in vivo in Santa Inês sheep.
Gastrointestinal nematode infections have caused expressive losses in sheep production worldwide. The improvement of host genetic resistance to worms has been used as a strategy to mitigate this ...problem. In this sense, the inclusion of genomic information has shown potential to increase the accuracy of prediction of breeding values and speed up selection. In this study, we aimed to compare estimates of genetic parameters and breeding values for traits that indicate the resistance to gastrointestinal nematode infection in Santa Inês sheep using the pedigree-based BLUP or including genomic information. There were 1478 animals in the pedigree, of which 271 were genotyped using the OvineSNP50 BeadChip (Illumina, Inc.). The host resistance was assessed using the following traits: fecal nematode egg counts (FEC); FAMACHA score (FAMACHA); and resistance to gastrointestinal nematode infection (RGNI) as a combination of FEC, FAMACHA, body condition score, and hematocrit. The genetic parameters and breeding values were estimated using single- and multi-trait analyses. For RGNI, the heritability estimates ranged from 0.25 using the single-trait genomic model (S-H) to 0.54 using the traditional multi-trait model (M-A). The heritability estimates for FEC ranged from 0.06 to 0.36, using the single-trait pedigree-based model (S-A) and the multi-trait genomic model (M-H), respectively. For FAMACHA, the heritability estimates ranged from 0.46 (M-H) to 0.54 (M-A). Estimates of genetic correlation ranged from 0.22 to 0.69. The inclusion of genomic information provided gain in accuracy for all traits. All estimates of predictive ability obtained using genomic data in a multi-trait setting were higher than those obtained using single-trait models. The estimates of predictive ability ranged from 0.03 (S-A) to 0.46 (M-H). The heritability estimates obtained using genomic information showed that all traits evaluated are suitable for genomic selection. Despite the low accuracies obtained, the use of the genomic model provided more accurate estimates of breeding values in comparison to the pedigree-based model.
Objective: The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the ...efficiency of including genomic information in the analyses. Methods: There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses. Results: The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from -0.65±0.31 to 0.59±0.19, using A, and from -0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses. Conclusion: The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses.
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