Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

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BOVISOL Project: Breeding and Management Practices of Indigenous Bovine Breeds: Solutions towards a Sustainable Future

Sustainability ◽

10.3390/su12239891 ◽

2020 ◽

Vol 12 (23) ◽

pp. 9891

Author(s):

Sofiane Boudalia ◽

Samia Ben Said ◽

Dimitrios Tsiokos ◽

Aissam Bousbia ◽

Yassine Gueroui ◽

...

Keyword(s):

Climate Change ◽

Rural Areas ◽

Management Practices ◽

National Level ◽

Farming Systems ◽

World Population ◽

Livestock Farming ◽

Slow Food ◽

Sustainable Future ◽

Mediterranean Countries

In order to deal with the effects of globalization, urbanization, increase in world population, global warming, and climate change; and according to the Sustainable Development Goals (SDG) 2 targets, which aim to end hunger, achieve food security and improved nutrition and promote sustainable agriculture, it is urgently needed to transform our agriculture and livestock farming systems by taking into account the environmental considerations. The Breeding and management practices of indigenous bovine breeds: Solutions towards a sustainable future (BOVISOL) project is a scientific cooperation between three Mediterranean countries (Greece, Tunisia and Algeria) supported and funded by the European Commission under the European Research Area Networks (ERA-NET) scheme of the 7th Framework Programme. This project has been formed around the hypothesis that the local bovine breeds must be preserved since they possess a valuable genetic pool, and they are a part of the landscape and the biodiversity of rural areas. Moreover, their products (milk, cheese, meat, etc.) could contribute significantly to the local economies as they could easily be associated with recent food trends like “local” and “slow food”, which are considered today, as, not only a mean of nutrition, but also a way of living and a part of people’s identity. BOVISOL project aims to: (i) identify the local breeds and populations in a national level, (ii) describe the existing farm and breeding practices, (iii) analyze the quality of the main local animal products, (iv) propose solutions that will promote the sustainability of the traditional farming systems, especially nowadays that climate change proposes new challenges on animal production, and (v) disseminate the solutions on all the levels of the sector (farmers, scientists, local communities, governmental agencies).

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Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

10.1101/703439 ◽

2019 ◽

Cited By ~ 1

Author(s):

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Hubert Pausch

Keyword(s):

Whole Genome Sequencing ◽

Meat Quality ◽

Genome Sequencing ◽

Genomic Diversity ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Cattle Breeds ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

BMC Genomics ◽

10.1186/s12864-020-6446-y ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 8

Author(s):

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Hubert Pausch

Keyword(s):

Whole Genome Sequencing ◽

Meat Quality ◽

Genome Sequencing ◽

Genomic Diversity ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Cattle Breeds ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle

Animals ◽

10.3390/ani10122233 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2233

Author(s):

Yoel Rodríguez-Valera ◽

Dominique Rocha ◽

Michel Naves ◽

Gilles Renand ◽

Eliecer Pérez-Pineda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Nucleotide Polymorphisms ◽

Runs Of Homozygosity ◽

Effective Population ◽

Single Nucleotide ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Management And Conservation

Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.

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Regime of soil humus rural residential areas organic farming systems

Interdepartmental thematic scientific collection "Agriculture" ◽

10.31073/zem.95.78-81 ◽

2018 ◽

Vol 2 (95) ◽

pp. 78-81

Author(s):

L.I. Shkarivska

Keyword(s):

Organic Farming ◽

Rural Areas ◽

Humus Content ◽

Farming Systems ◽

Farming System ◽

Organic Substrates ◽

Residential Areas ◽

Typical Chernozem ◽

Podzolic Soils ◽

Organic Farming System

The changes of the soil’s humus soil within the rural areas are investigated for the organic farming system. The most significant impact of organic agriculture on humus content over 55% was observed on soddy podzolic soils (V>75%), the lowest –7,5% on typical chernozem (V≈16%). Changes in the qualitative composition of humus for the introduction of various types of organic substrates are analyzed.

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Good Management Practices in Managing the Most Important Factors to Ensure Dureble Soil Quality

Revista de Chimie ◽

10.37358/rc.17.10.5884 ◽

2017 ◽

Vol 68 (10) ◽

pp. 2350-2357

Author(s):

George Ungureanu ◽

Gabriela Ignat ◽

Eduard Boghita ◽

Luiza Costuleanu ◽

Catalin Razvan Vintu ◽

...

Keyword(s):

Sustainable Development ◽

Management Practices ◽

Programming Model ◽

Farming Systems ◽

Economic Incentives ◽

Silage Maize ◽

Cash Crops ◽

Raising Awareness ◽

Fodder Grass ◽

Alfalfa Silage

The importance of sustainable development has started to be acknowledged in Romania as well, once the various pollution sources and the restrictions affecting industrial and agricultural pollution were identified, from an economic and ecological standpoint. Sustainable development represents the need of raising awareness about environmental protection and educating people, and this aspect is reflected by the evolution of communal policies in recent years, policies marked by a shift from an approach based on constraints and sanctions to a higher level of flexibility, based on incentives. The purpose of this paper is to make a recommendation for improving existing policy by making an assessment of economic incentives in order to stimulate farmers to adopt sustainable farming systems of a viable, sustainable agriculture, capable to apply the newest technologies and lead to profit and efficiency, to the economical and organizational consolidation. To analyse the effects of different zone packages on income of farmers and the environment a linear programming model is developed for a typical, 192 ha mixed farm in the Iasi region plain pilot area. The major activities of the farm is keeping dairy cattle, growing fodder (grass, alfalfa, silage maize) and cash crops (winter wheat and maize).

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Nitrate Leaching to a Shallow Mid-Atlantic Coastal Plain Aquifer as Influenced by Conventional No-Till and Low-Input Sustainable Grain Production Systems

Water Science & Technology ◽

10.2166/wst.1993.0475 ◽

1993 ◽

Vol 28 (3-5) ◽

pp. 691-700 ◽

Cited By ~ 7

Author(s):

J. P. Craig ◽

R. R. Weil

Keyword(s):

Management Practices ◽

Production Systems ◽

Cropping Systems ◽

Cropping System ◽

Atlantic Coastal Plain ◽

Grain Production ◽

Nitrogen And Phosphorus ◽

Mineral N ◽

Low Input ◽

No Till

In December, 1987, the states in the Chesapeake Bay region, along with the federal government, signed an agreement which called for a 40% reduction in nitrogen and phosphorus loadings to the Bay by the year 2000. To accomplish this goal, major reductions in nutrient loadings associated with agricultural management practices were deemed necessary. The objective of this study was to determine if reducing fertilizer inputs to the NT system would result in a reduction in nitrogen contamination of groundwater. In this study, groundwater, soil, and percolate samples were collected from two cropping systems. The first system was a conventional no-till (NT) grain production system with a two-year rotation of corn/winter wheat/double crop soybean. The second system, denoted low-input sustainable agriculture (LISA), produced the same crops using a winter legume and relay-cropped soybeans into standing wheat to reduce nitrogen and herbicide inputs. Nitrate-nitrogen concentrations in groundwater were significantly lower under the LISA system. Over 80% of the NT groundwater samples had NO3-N concentrations greater than 10 mgl-1, compared to only 4% for the LISA cropping system. Significantly lower soil mineral N to a depth of 180 cm was also observed. The NT soil had nearly twice as much mineral N present in the 90-180 cm portion than the LISA cropping system.

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The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genomics ◽

10.1016/j.ygeno.2021.03.005 ◽

2021 ◽

Author(s):

Maryam Nosrati ◽

Hojjat Asadollahpour Nanaei ◽

Arash Javanmard ◽

Ali Esmailizadeh

Keyword(s):

World Wide ◽

Runs Of Homozygosity ◽

Genomic Inbreeding

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Rural Roads Are Paving the Way for Land-Use Intensification in the Uplands of Laos

Land ◽

10.3390/land10030330 ◽

2021 ◽

Vol 10 (3) ◽

pp. 330

Author(s):

Jean-Christophe Castella ◽

Sonnasack Phaipasith

Keyword(s):

Land Use ◽

Management Practices ◽

Management Strategies ◽

Farming Systems ◽

Long Term Effects ◽

Group Discussions ◽

Rural Roads ◽

External Resources ◽

Hybrid Maize ◽

The Impact

Road expansion has played a prominent role in the agrarian transition that marked the integration of swidden-based farming systems into the market economy in Southeast Asia. Rural roads deeply altered the landscape and livelihood structures by allowing the penetration of boom crops such as hybrid maize in remote territories. In this article, we investigate the impact of rural road developments on livelihoods in northern Laos through a longitudinal study conducted over a period of 15 years in a forest frontier. We studied adaptive management strategies of local stakeholders through the combination of individual surveys, focus group discussions, participatory mapping and remote-sensing approaches. The study revealed the short-term benefits of the maize feeder roads on poverty alleviation and rural development, but also the negative long-term effects on agroecosystem health and agricultural productivity related to unsustainable land use. Lessons learnt about the mechanisms of agricultural intensification helped understanding the constraints faced by external interventions promoting sustainable land management practices. When negotiated by local communities for their own interest, roads may provide livelihood-enhancing opportunities through access to external resources, rather than undermining them.

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Homegarden agroecosystems managed by Salar people on Qinghai-Tibet Plateau

Journal of Ethnobiology and Ethnomedicine ◽

10.1186/s13002-021-00448-x ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Mingjing Zhu ◽

Binsheng Luo ◽

Ben La ◽

Ruijie Chen ◽

Fenggui Liu ◽

...

Keyword(s):

Plant Species ◽

Rural Areas ◽

Production Systems ◽

Farming Systems ◽

Field Investigation ◽

Tibet Plateau ◽

Ecosystem Functions ◽

Structured Interviews ◽

Services Research ◽

Qinghai Tibet Plateau

Abstract Background Salar is a Turkic-speaking Islamic ethnic group in China living mainly in Xunhua Salar Autonomous County (Xunhua or Xunhua County), Qinghai-Tibet Plateau. Salar people are skilled in horticulture and their homegarden (HG) management. They are regarded as the first people on the Qinghai-Tibet Plateau to practice horticulture, especially manage their HGs, traditional farming systems, and supplementary food production systems. Traditional knowledge of Salar people associated with their HGs always contributes significantly to the local livelihood, food security, ornamental value, and biodiversity conservation. The cultivation of different plants in HGs for self-sufficiency has a long tradition in China’s rural areas, especially in some mountainous areas. However, Salar traditional HGs have not been described. The present paper aims to report the features of Salar HGs mostly based on agrobiodiversity and its ecosystem services. Methods The methods used in this work included semi-structured interviews and participatory observation. A total of 60 households in three townships, 9 villages were surveyed. There are 4–12 family members in each household, aged from 20 to 86 years old. The homestead size is between 200 and 1200 m2. Plant species cultivated in Salar HGs were identified according to Flora of China. Based on a comprehensive survey of Salar HGs and related to background data, we identified and characterized the most important services and functions provided by Salar HGs. Results According to primary production systems, there are 4 different types of Salar HGs, including ornamental focus, product focus, dual-purpose and multi-purpose. In total, 108 (excluding weeds and bonsai) plant species were recorded in Salar HGs, within 43 plant families. The most important and frequently used plants are Rosa chinensis, Armeniaca vulgar, Prunus salicina, and Ziziphus jujuba. About 4 to 32 plant species were recorded in each homegarden. We found that the Salar HGs, as a typical agroecosyste, prossess multiple servcices and functions that directly benefit households according to the field investigation. Conclusion This paper reveals the floristic diversity of Salar HGs. It presents useful information in the homegarden agroecosystem of Salar people, such as HG types and species diversity in Salar HGs. Ecosystem functions and services research suggested that the Salar HG agroecosystem provides agroecosystem services mainly related to supply and culture services. Salar HGs are important as food supplement resources, aesthetics symbol, and cultural spaces.

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