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This study aimed to identify organic dairy major farm types (MFTs) in seven European countries, describe these MFTs in an open research database and assess central characteristics of the MFTs. This was conducted in a three-step procedure including (1) Identification of organic MFTs in seven European countries: Austria, Switzerland, Germany, Denmark, Lithuania, Poland and Sweden, based on existing data from dairy databases and consultations with experts within the respective fields of knowledge; (2) Collection of data on farm characteristics, management procedures, production level and herd health from at least 10 farms per MFT and country and (3) Creating an open research database on MFT characteristics, description of essential characteristics of MFTs and assessment of similarities and differences between farms within and across MFTs. The results indicate variations in herd characteristics such as production level, herd size, farm size, housing system, milking system and cow health status between organic dairy farms in these seven European countries. It also indicates variations in management strategies such as feeding, animal health management and recruitment strategies across the organic dairy sector in Europe. These variations seem to be associated with differences between regions and countries in the conditions for organic dairy production, such as topography, land availability and regulations.

Background The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits. This data was used to investigate the genetics underlying fertility and calving traits and to identify potentially causative genomic regions and variants. We performed genome-wide association studies for 13 functional traits related to female fertility as well as for direct and maternal calving ease based on imputed whole-genome sequences. Deregressed breeding values from ~1000–5000 bulls per trait were used to test for associations with approximately 10 million imputed sequence SNPs. Results We identified a QTL on BTA17 associated with non-return rate at 56 days and with interval from first to last insemination. We found two significantly associated non-synonymous SNPs within this QTL region. Two more QTL for fertility traits were identified on BTA25 and 29. A single QTL was identified for maternal calving traits on BTA13 whereas three QTL on BTA19, 21 and 25 were identified for direct calving traits. The QTL on BTA19 co-localizes with the reported BH2 haplotype. The QTL on BTA25 is concordant for fertility and calving traits and co-localizes with a QTL previously reported to influence stature and related traits in Brown Swiss dairy cattle. Conclusion The detection of QTL and their causative variants remains challenging. Combining comprehensive phenotypic data with imputed whole genome sequences seems promising. We present a QTL on BTA17 for female fertility in dairy cattle with two significantly associated non-synonymous SNPs, along with five additional QTL for fertility traits and calving traits. For all of these we fine mapped the regions and suggest candidate genes and candidate variants. Electronic supplementary material The online version of this article (10.1186/s12864-017-4308-z) contains supplementary material, which is available to authorized users.