Herd clustering strategies and corresponding genetic evaluations based on social–ecological characteristics for a local endangered cattle breed

Abstract. The accuracy of breeding values strongly depends on the population and herd structure, i.e., the number of animals considered in genetic evaluations and the size of contemporary groups (CGs). Local breeds are usually kept in small-sized family farms under alternative husbandry conditions. For such herd structure, consideration of classical herd or herd-test-day effects in CG modeling approaches implies only a few records per effect level. In consequence, the present study aimed on methodological evaluations of different herd clustering strategies, considering social–ecological and herd characteristics. In this regard, we considered 19 herds keeping cows from the small local population of German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind; DSN), 10 herds keeping Holstein Friesian (HF) cows and one mixed herd with HF and DSN cows. Herds were characterized for 106 variables, reflecting farm conditions, husbandry practices, feeding regime, herd management, herd fertility status, herd health status and breeding strategies as well as social–ecological descriptors. The variables were input data for different clustering approaches including agglomerative hierarchical clustering (AHC), partition around medoids (PAM), fuzzy clustering (FZC) and a clustering of variables combined with agglomerative hierarchical clustering (CoVAHC). The evaluation criterion was the average silhouette width (ASW), suggesting a CoVAHC application and consideration of four herd clusters (HCs) for herd allocation (ASW of 0.510). HC1 comprised the larger, half organic and half conventional DSN family farms, which generate their main income from milk production. HC2 consisted of small organic DSN family farms where cows are kept in tie stables. HC3 included the DSN sub-population from former East Germany, reflecting the large-scale farm types. The specialized HF herds were well separated and allocated to HC4. Generalized linear mixed models with appropriate link functions were applied to compare test-day and female fertility traits of 5538 cows (2341 DSN and 3197 HF) from the first three lactations among the four HCs. Least squares means for milk, fat and protein yield (Mkg, Fkg and Pkg) significantly differed between HC. The significant differences among the four HCs clearly indicate the influence of varying herd conditions on cow traits. The similarities of herds within HC suggested the application of HCs in statistical models for genetic evaluations for DSN. In this regard, we found an increase of accuracies of estimated breeding values of cows and sires and of heritabilities for milk yield when applying models with herd-cluster-test-day or herd-cluster-test-month effects compared to classical herd-test-day models. The identified increase for the number of cows and cow records in CG due to HC effects may be the major explanation for the identified superiority.

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Family Farms Versus Large-Scale Farms in Rural Development

Artha Vijnana Journal of The Gokhale Institute of Politics and Economics ◽

10.21648/arthavij/1963/v5/i3/116860 ◽

1963 ◽

Vol 5 (3) ◽

pp. 225 ◽

Cited By ~ 2

Author(s):

Raanan Weitz

Keyword(s):

Rural Development ◽

Large Scale ◽

Family Farms

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Characteristics of Models of Farms in the European Union

Sustainability ◽

10.3390/su13094772 ◽

2021 ◽

Vol 13 (9) ◽

pp. 4772

Author(s):

Hanna Klikocka ◽

Aneta Zakrzewska ◽

Piotr Chojnacki

Keyword(s):

European Union ◽

Minimum Wage ◽

Large Scale ◽

The European Union ◽

Family Farms ◽

Agricultural Income ◽

Commercial Farms ◽

Standard Output ◽

Definition Of ◽

The Eu

The article describes and sets the definition of different farm models under the categories of being family, small, and large-scale commercial farms. The distinction was based on the structure of the workforce and the relationship between agricultural income and the minimum wage. Family farms were dominated by the farming family providing the labour and their income per capita exceeded the net minimum wage in the country. The larger commercial farms feature a predominance of hired labour. Based on surveys, it was found that in 2016 in the EU-28 there were 10,467,000 farms (EU-13—57.3%, EU-15—42.7%). They carried out agricultural activities on an area of 173,338,000 ha (EU-13—28.5%, EU-15—71.5%). Countries of the EU-28 generated a standard output (SO) amounting to EUR 364,118,827,100 (EU-13—17.2% and EU-15—82.8%). After the delimitation, it was shown that small farming (70.8%) was the predominant form of management in the European Union (EU-13—88.2% and EU-15—79.8%) compared to family farming (18.4%) (EU-13—10.5% and EU-15—29%). In most EU countries the largest share of land resources pertains to small farms (35.6%) and family farms (38.6%) (UAA—utilised agricultural area of farms).

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Introducing Twitter Daily Estimates of Residents and Non-Residents at the County Level

Social Sciences ◽

10.3390/socsci10060227 ◽

2021 ◽

Vol 10 (6) ◽

pp. 227

Author(s):

Yago Martín ◽

Zhenlong Li ◽

Yue Ge ◽

Xiao Huang

Keyword(s):

Large Scale ◽

Local Population ◽

External Validation ◽

Population Estimates ◽

County Level ◽

Internal Validation ◽

Population Movements ◽

Dynamic Component ◽

Home Location ◽

Non Local

The study of migrations and mobility has historically been severely limited by the absence of reliable data or the temporal sparsity of available data. Using geospatial digital trace data, the study of population movements can be much more precisely and dynamically measured. Our research seeks to develop a near real-time (one-day lag) Twitter census that gives a more temporally granular picture of local and non-local population at the county level. Internal validation reveals over 80% accuracy when compared with users’ self-reported home location. External validation results suggest these stocks correlate with available statistics of residents/non-residents at the county level and can accurately reflect regular (seasonal tourism) and non-regular events such as the Great American Solar Eclipse of 2017. The findings demonstrate that Twitter holds the potential to introduce the dynamic component often lacking in population estimates. This study could potentially benefit various fields such as demography, tourism, emergency management, and public health and create new opportunities for large-scale mobility analyses.

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Hesitant Fuzzy Linguistic Agglomerative Hierarchical Clustering Algorithm and Its Application in Judicial Practice

Mathematics ◽

10.3390/math9040370 ◽

2021 ◽

Vol 9 (4) ◽

pp. 370

Author(s):

Shuangsheng Wu ◽

Jie Lin ◽

Zhenyu Zhang ◽

Yushu Yang

Keyword(s):

Hierarchical Clustering ◽

Clustering Algorithm ◽

Clustering Algorithms ◽

Agglomerative Hierarchical Clustering ◽

Research Gaps ◽

Judicial Practice ◽

Linguistic Term ◽

Clustering Effect ◽

Hierarchical Clustering Algorithm ◽

Fuzzy Linguistic

The fuzzy clustering algorithm has become a research hotspot in many fields because of its better clustering effect and data expression ability. However, little research focuses on the clustering of hesitant fuzzy linguistic term sets (HFLTSs). To fill in the research gaps, we extend the data type of clustering to hesitant fuzzy linguistic information. A kind of hesitant fuzzy linguistic agglomerative hierarchical clustering algorithm is proposed. Furthermore, we propose a hesitant fuzzy linguistic Boole matrix clustering algorithm and compare the two clustering algorithms. The proposed clustering algorithms are applied in the field of judicial execution, which provides decision support for the executive judge to determine the focus of the investigation and the control. A clustering example verifies the clustering algorithm’s effectiveness in the context of hesitant fuzzy linguistic decision information.

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38 Using pooled data for single-step genomic prediction: Impact of within-pool variance and size

Journal of Animal Science ◽

10.1093/jas/skaa278.017 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 9-9

Author(s):

Johnna L Baller ◽

Stephen D Kachman ◽

Larry A Kuehn ◽

Matthew L Spangler

Keyword(s):

Phenotypic Variation ◽

Equal Opportunity ◽

Cost Effective ◽

Single Step ◽

Pool Size ◽

Individual Data ◽

Phenotypic Data ◽

Breeding Values ◽

Mean Values ◽

Genetic Evaluations

Abstract Economically relevant traits (ERT) are routinely collected within commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, which would be costly; pooling DNA and phenotypic data provides a cost-effective solution. A simulated beef cattle population consisting of 15 generations was genotyped with approximately 50k markers (841 quantitative trait loci were located across the genome) and phenotyped for a moderately heritable trait. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step GBLUP model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when no gap between genotyped parents and pooled offspring occurred. The EBV accuracies resulting from pools were greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. Pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared to individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to EBV accuracies that were statistically different than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible, although differences exist depending on pool size and pool formation strategy. The USDA is an equal opportunity employer.

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Threat of arsenic contamination, salinity and water pollution in agricultural practices of Sundarban Delta, India, and mitigation strategies

SN Applied Sciences ◽

10.1007/s42452-021-04544-1 ◽

2021 ◽

Vol 3 (5) ◽

Author(s):

Anirban Nath ◽

Sourav Samanta ◽

Saon Banerjee ◽

Anamitra Anurag Danda ◽

Sugata Hazra

Keyword(s):

Plant Breeding ◽

Rural Population ◽

Large Scale ◽

Local Population ◽

Agricultural Practices ◽

Mitigation Strategies ◽

Saline Stress ◽

Freshwater Resources ◽

Catchment Areas ◽

The Sundarbans

AbstractThe paper through a critical appraisal of the agricultural practices in the Indian Sundarban deltaic region explores the tripartite problems of arsenic biomagnification, salinity of arable lands and ingress of agrochemical pollutants into the freshwater resources, which endanger the health, livelihood and food security of the rural population inhabiting the delta. The threefold problem has rendered a severe blow to the agrarian economy consequently triggering large-scale outmigration of the rural population from the region. Although recent studies have addressed these issues separately, the inter-connectivity among these elements and their possible long-term impact upon sustainability in the Sundarbans are yet to be elucidated. In the current scenario, the study emphasizes that the depleting freshwater resources is at the heart of the threefold problems affecting the Sundarbans. Owing to the heavy siltation of the local river systems, freshwater resources from the local ravines have salinized beyond the point of being used for agricultural purposes. At the same time, increasing salinity levels resulting from fluctuation of pre- and post-monsoon rainfall, frequent cyclones and capillary movement of salinized groundwater (primarily during the Rabi season) have severely hampered the agricultural practices. Salinization of above groundwater reserves has forced the farmers toward utilization of groundwater, which are lifted using STWs, especially for rice and other cultivations in the Rabi season. The Holocene aquifers of the region retain toxic levels of arsenic which are lifted during the irrigation process and are deposited on to the agricultural fields, resulting in bioaccumulation of As in the food products resourced from the area. The compound effect of consuming arsenic-contaminated food and drinking water has resulted in severe health issues recorded among the local population in the delta. Furthermore, due to the sub-optimal conditions for sustaining agriculture under saline stress, farmers often opt for the cultivation of post-green revolution high-yielding varieties, which require additional inputs of nitrogen-based fertilizers, organophosphate herbicides and pesticides that are frequently washed away by runoff from the watershed into the low-lying catchment areas of the biosphere reserve. Such practices have endangered the vulnerable conditions of local flora and fauna. In the present situation, the study proposes mitigation strategies which necessitate the smart use of locally obtainable resources like water, adaptable cultivars and sustainable agronomic practices like organic farming. The study also suggests engaging of conventional plant breeding strategies such as “Evolutionary plant breeding” for obtaining cultivars adapted to the shifting ecological conditions of the delta in the long run.

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Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves

Genes ◽

10.3390/genes12050708 ◽

2021 ◽

Vol 12 (5) ◽

pp. 708

Author(s):

Moran Gershoni ◽

Joel Ira Weller ◽

Ephraim Ezra

Keyword(s):

Weight Gain ◽

Milk Fat ◽

Variance Components ◽

Complete Data ◽

Variance Component Analysis ◽

Coefficient Of Determination ◽

Birth Date ◽

Analysis Model ◽

Data Set ◽

Genetic Evaluations

Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the analysis of both sexes and similar in the single sex analyses. The regression of yearling weight gain on birth date in the complete data set was −0.96 kg/year. The complete data set was also analyzed by the same model as the variance component analysis, including both sexes and accounting for differing variance components for each sex. The genetic trend for yearling weight gain, including both sexes, was 1.02 kg/year. Genetic evaluations for yearling weight gain was positively correlated with genetic evaluations for milk, fat, protein production, and cow survival but negatively correlated with female fertility. Yearling weight gain was also correlated with the direct effect on dystocia, and increased yearling weight gain resulted in greater frequency of dystocia. Of the 1749 Israeli Holstein bulls genotyped with reliabilities >50%, 1445 had genetic evaluations. As genotyping of these bulls was performed using several single nucleotide polymorhphism (SNP) chip platforms, we included only those markers that were genotyped in >90% of the tested cohort. A total of 40,498 SNPs were retained. More than 400 markers had significant effects after permutation and correction for multiple testing (pnominal < 1 × 10−8). Considering all SNPs simultaneously, 0.69 of variance among the sires’ transmitting ability was explained. There were 24 markers with coefficients of determination for yearling weight gain >0.04. One marker, BTA-75458-no-rs on chromosome 5, explained ≈6% of the variance among the estimated breeding values for yearling weight gain. ARS-BFGL-NGS-39379 had the fifth largest coefficient of determination in the current study and was also found to have a significant effect on weight at an age of 13–14 months in a previous study on Holsteins. Significant genomic effects on yearling weight gain were mainly associated with milk production quantitative trait loci, specifically with kappa casein metabolism.

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146 Survey of residual feed intake in Katahdin and Texel lambs in a feedlot environment

Journal of Animal Science ◽

10.1093/jas/skz397.177 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 75-76

Author(s):

Camren l Maierle ◽

Andrew R Weaver ◽

Eugene Felton ◽

Scott P Greiner ◽

Scott A Bowdridge

Keyword(s):

Feed Intake ◽

Feed Efficiency ◽

Large Scale ◽

Residual Feed Intake ◽

Production Traits ◽

Meaningful Improvement ◽

Average Intake ◽

Test Population ◽

Feeding Trials ◽

Genetic Evaluations

Abstract Residual feed intake (RFI) is quickly becoming the preferred measurement of efficiency in many species due to its inherent independence of most other important production traits. Making meaningful improvement in feed efficiency of sheep will require a consistent methodology to accurately identify efficient individuals. Due to difficulty in measuring this trait efforts must be made to incorporate efficiency data in large-scale genetic evaluations. The aim of this study was to evaluate lambs in a feedlot with large-scale genetic evaluations for feed efficiency calculated by residual feed intake (RFI) utilizing a Growsafe™ system. RFI was calculated by subtracting expected intake from actual intake. Expected intake was determined by regressing metabolic body size of mid-test weight. Regression determined ADG on actual intake for individuals in the population. Texel (n = 58) and Katahdin (n = 118) lambs were placed in a feedlot and fed in separate feeding trials, a complete pellet ad libitum as the sole source of nutrition. In this environment Texel and Katahdin lambs had expected ADG values (0.27 kg/day, 0.32 kg/day respectively) and actual intake data (2154.17 g/day, 1909.33 g/day respectively. After a period of adaptation, Texel average intake was determined over a period of 27 consecutive days and used to calculate individual RFI within the test population. Observable ranges of RFI (-0.62 – +0.62) were seen in the Texel lambs. At the start of the Katahdin trial lambs were separated by sex and FEC treatment. After a period of adaptation, Katahdin average intake was determined over a period of 42 consecutive days and used to calculate individual RFI within the test population. Observable ranges of RFI (-0.53 – +0.50) were seen in the Katahdin lambs as well. In both feeding trials RFI appeared to be normally distributed. Use of this technology may be useful in identifying superior individuals for feed efficiency.

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