Following the Permian-Triassic Boundary mass extinction (PTBME), the Early Triassic biotic recovery witnessed several failed recoveries of the nekton and marked changes in the ecological associations of terrestrial plants during its 5 my time span. This period is characterized by a series of profound fluctuations of the global carbon cycle, associated with changes in global climate and closely related changes in sea level, weathering rates, redox conditions, and finally organic carbon burial. However, the pacing and the underlying cause(s) of these changes are not yet well constrained, nor understood. Episodic pulses of volcanism of the Siberian Large Igneous Province (S-LIP) are commonly proposed as a trigger for these Early Triassic climate disturbances. However, S-LIP magmatism does not extend over a sufficiently long period to explain the carbon cycle disturbances and associated biotic setbacks during the Smithian and the Spathian, that is during most of the Early Triassic.This study develops a precise chronological framework for the Early Triassic substages by integrating new and published UPb zircon ages of volcanic ash beds with detailed biostratigraphic and carbon isotope data. The combination of these methods allows for the accurate delineation and bracketing of stage and substage boundaries and provides insights into the timing of biotic and environmental changes. This age-depth model spans from the latest Permian until the earliest Middle-Triassic and is accurately correlated to the carbonate C-isotope record, ammonoid and conodont biochronology of a composite section from the Nanpanjiang Basin (South China). In the studied outer shelf sections, unconformities terminate periods of condensed deposition that coincide with positive shifts in the δ13Ccarb isotope record. Duration of main unconformities is assessed by the age-depth model and are mostly close to biostratigraphic boundaries such as the Permian-Triassic (PTB), Dienerian-Smithian (DSB), Smithian-Spathian (SSB) and Spathian-Anisian (SAB). This approach allows us to define the ages of Early Triassic substage boundaries and the pace of carbon cycle fluctuations more accurately at the millennial timescale. The age of Griesbachian-Dienerian boundary (GDB) is confined between 251.669 + 0.057/−0.057 Ma and 251.657 + 0.057/−0.059 Ma, the DSB between 251.005 + 0.084/−0.075 Ma and 250.772 + 0.067/−0.084 Ma, the SSB between 249.347 + 0.051/−0.053 Ma and 249.326 + 0.055/−0.056 Ma and the SAB between 247.183 + 0.040/−0.044 Ma and 246.883 + 0.082/−0.073 Ma. Furthermore, the durations of the δ13Ccarb cycles and the ages of its excursion peaks (N1-P4) were determined and compared.

This comment addresses the incorrect treatment and presentation of data from laser ablation ICP-MS U–Pb age determinations of two samples of the Třebíč Pluton. This results in inaccurate ages and error assessment, invalidating the age interpretations of the authors. To corroborate our arguments, new high-precision chemical abrasion ID-TIMS data are presented that unequivocally define the emplacement age of the Třebíč pluton.

The connection between volcanic activity of large igneous provinces and the respective feedback from environment and biosphere contributing to the carbon cycle has been investigated at the present temporal resolution of high-precision U/Pb dating. Uncertainties of 0.05 % on the 206Pb/238U age from zircon dating allow a resolution of 30-50 ka pulses of magmatic activity; simultaneously, the duration of carbon isotope excursions (CIE) can be determined, the geological boundaries dated, or global sedimentary gaps can be quantified at the same level of precision. This contribution demonstrates with two case studies that we can refine the contemporaneity and start to reliably infer causality of consecutive events at the 104 year level. Until the Anisian the aftermath of the Permo-Triassic Boundary Mass extinction (PTBME; ~251.94 Ma, Baresel et al., 2017) is characterized by profound fluctuations of the global carbon cycle with amplitudes of up to 8 ‰ in d13Ccarb values. These represent large variations in the global climate and biological crises, in particular during the end-Smithian extinction event (~249.1 Ma). A precise chronology from the southern Nanpanjiang basin (China) allows for a quantification of these fluctuations of Earth climate. Following the volcanic pulse causing the PTBME, several discontinuous episodes of volcanism of the Siberian Large Igneous Province (S-LIP) were generally assumed to have caused the subsequent Early Triassic carbon cycle fluctuations. This is, however, in disagreement with the geochronological database of precise zircon U/Pb dates that put an end to the volcanic activity at 250.6 Ma (Burgess & Bowring, 2015; Augland et al., 2019). Therefore, recurrent S-LIP volcanism is an unlikely explanation for the Early Triassic unstable carbon cycle. The initial intrusive pulse of the Karoo Large Igneous Province (K-LIP) formed the sill/dyke complex of the Karoo basin, South Africa. New, precise U/Pb geochronology confirms its very short duration at around 183.2-182.8 Ma (Burgess et al., 2015; Corfu et al., 2016), as well as its synchronicity with the lower Toarcian oceanic anoxic event (T-OAE), and a carbon cycle disturbance of presumable global importance. Repeated excursions in d13Corg of up to 3 ‰ in the late Pliensbachian (~185.5 Ma) as well as at the Pliensbachian-Toarcian boundary (~183.5 Ma) are therefore at least partly older than any known magmatic activity of the K-LIP (Lena et al., 2019). We therefore, again, must invoke non-volcanic drivers in order to explain the instability of the carbon cycle. These two case histories demonstrate that in order to invoke causality and global importance to carbon cycle instability, as well as for the testing of its correlation with volcanic episodes, we need to rely on geochronology of both sedimentary and volcanic records at the 104 years level of precision. References: Augland et al. (2019) Scientific Reports, 9:18723 ; Baresel et al. (2017) Solid Earth, 8, 361–378, 2017; Burgess & Bowring (2015) Science Advances, 1(7), e1500470–e1500470; Burgess et al. (2015) Earth and Planetary Science Letters, 415(C), 90–99; Corfu, F. et al. (2016) Earth and Planetary Science Letters, 434(C), 349–352; Lena et al. (2019) Scientific Reports, 9:18430.

The conservation status of the Blue-backed Parrot Tanygnathus everetti, a species endemic to the Philippines, has long been obscured by its former taxonomic status as a subspecies of the Azure-rumped Parrot T. sumatranus of Sulawesi, Indonesia. A detailed review of evidence from museum material and birdwatchers' records indicates it is known from Luzon, Polillo Islands, Panay, Negros, Samar, Leyte, Mindanao and the Sulu archipelago. There is no evidence it survives on Luzon, Polillo Islands, Panay, Negros and Leyte. On Samar its numbers have dwindled towards extinction but it is likely to survive in tiny numbers (total <100) in the illegally logged Samar Island Natural Park (SINP). On Mindanao it has virtually disappeared from the only known predictable site, the PICOP logging concession at Bislig, and the few records elsewhere suggest <100 persist on the island. In the Sulu archipelago, it may survive in tiny numbers (<50) on Jolo (Bud Dajo National Park) and Tawi-Tawi in the Malum watershed. Records are mainly from primary lowland forest below 450 m, and it appears much less adapted to more open forest formations than its relative, the Blue-naped Parrot T. lucionensis. The almost total clearance of lowland forest in the Philippines, especially primary formations, is assumed to have greatly constrained its distribution and numbers. However, this has been compounded by a barely documented but evidently relentless trade in wild-caught birds. Legal protection for the last vestiges of forests holding this species is called for. SINP needs immediate protection from rampant logging and any poaching. An intensive survey of anticipated and known key sites is urgent, along with a broadscale community campaign to discourage the catching and keeping of parrots, plus an active search for captive birds to form an ex situ conservation breeding initiative. Any such initiative should keep the population on the Sulu archipelago (subspecies burbidgii) separate from T. everetti found in the rest of the Philippine islands, as they are so different.

The dynamics of the carbon cycle across different timescales is crucial for understanding past and present global climate changes. Following the Permian-Triassic boundary mass extinction (PTBME), the carbon cycle changed profoundly during the following 5.4 Myr, with magnitudes of changes comparable to those of the Precambrian. In pace with the successive cycles of the carbon budget, the recovery of the marine nekton underwent several evolutionary diversification and extinction cycles accompanied by eustatic sea-level changes and profound ecological reorganization of land plants, all indicative of climatic changes. Additional eruptive bursts of the Siberian Large Igneous Province (SLIP) are traditionally called upon as a plausible trigger for these climatic oscillations but firm evidence for coeval SLIP volcanism is still lacking. Based on new precise and accurate U-Pb zircon ages, we establish a high-resolution temporal calibration of the biggest positive carbon isotope excursion (CIE) spanning about 600 kyr in the late Smithian. The age of the Smithian-Spathian boundary (SSB) is established between 249.29 +/- 0.06 and 249.11 +/- 0.09 Ma. Our oldest U-Pb zircon ages indicate no overlap in time between the middle Smithian onset of the thermal maximum and the youngest available U-Pb zircon ages from SLIP volcanism. The constructed time line also indicates a duration of the global unconformity at the SSB that is compatible with glacio-eustatism. Potential cooling mechanisms such as a volcanic winter, the biological pump and the cessation of volcanism are discussed in the light of this new time line. In the low latitudes, the onset of the positive CIE remarkably predates the temperature drop by some 100 to 125 kyr. However, as long as the magnitude of such offset - if any - is unknown for the high latitudes, relations between the CIE and the cooling will remain an open question associated with largest Triassic extinction of the nekton.

The present sub-permil precision of single zircon chemical abrasion, isotope-dilution, thermal ionisation mass spectrometry (CA-ID-TIMS) U-Pb dates often reveals age dispersions that are outside of analytical uncertainty. Interpreting these complex age distributions requires the ability to distinguish between protracted crystallization of zircon over a few 100 kyr, age bias due to radiation damage induced Pb-loss, and analytical artefacts. This is a particularly critical issue when a number of these factors occur together. To ensure geologically meaningful results, the complete eradication of Pb-loss is of paramount importance. The impact of Pb-loss can be removed by chemical abrasion (CA) applied prior to the dissolution of zircon. However, CA is an empirical approach that is used without a detailed understanding of how the temperature applied during the annealing step, or the temperature and duration of the partial dissolution step affect the radiation-damaged zones. In addition, the conditions of the CA procedures differ between laboratories making comparisons of age data problematic. This study presents an experimental approach to quantify how chemical abrasion affects the crystal structure and the chemical composition of zircon as well as its U-Pb age. For this experiment, we have chosen the Plesovice reference zircon, because of its known variation in trace element concentrations and especially the presence of domains rich in actinides. We performed CA experiments under different temperature-time conditions on fragmented Plesovice crystals. These were compared in respect to the changes in trace element concentration, lattice order and U-Pb date. The most reliable U-Pb results are obtained by chemically abrading Plesovice fragments at 210 degrees C for 12 h. Additionally, we demonstrate that the Plesovice zircon cannot be considered homogenous at the current level of precision achieved by CA-ID-TIMS dating due to a natural age variation at the similar to 900 kyr scale.

Following the Permian-Triassic mass extinction (PTME), the Early Triassic is characterized by large short-lived perturbations of the global carbon cycle associated with radiation and extinction pulses of the biota. More stable conditions resumed in the Middle Triassic (Anisian). The exact ages and duration of these short-lived but intense radiation-extinction events as well as carbon cycle perturbations are poorly constrained and a robust intercalibration of U-Pb dates, biochronozones and carbon isotope fluctuations is still lacking. An accurate and precise time frame is essential in order to quantify the dynamics of the underlying mechanistic processes and to assess the validity of the various explanatory scenarios. The most drastic Early Triassic extinction occurred at the Smithian-Spathian boundary (SSB) and is associated with a globally recognized sharp positive excursion of the marine d13C signal. Based on the most recently published ages for the Permian-Triassic boundary (251.938 ± 0.029 Ma, Baresel et al., 2016) and for the Early-Middle Triassic boundary (247.05 ± 0.16 Ma, Ovtcharova et al., 2015), we know the Early Triassic lasted 4.9 myr. However, neither the position of the SSB nor the durations of the major biotic and abiotic events around the SSB are constrained by radiometric dates. Here, we will present new high precision, chemical abrasion, isotope dilution, thermal ionization mass spectrometry (CA-ID-TIMS) U-Pb ages from single zircon crystals, sampled from closely spaced volcanic ash layers that bracket the SSB in the Nanpanjiang Basin (Guizhou province, South China). These ash layers are found in a mixed carbonate–siliciclastic, conodont-rich sedimentary succession (Luolou Formation) that is well calibrated biochronologically. We obtained best estimates of the ages of the SSB and associated events by applying Bayesian age modelling.

Title: The mammalian cervical vertebrae blueprint depends on the T (brachyury) gene 1 2 Andreas Kromik, Reiner Ulrich, Marian Kusenda, Andrea Tipold, Veronika M. Stein, 3 Maren Hellige, Peter Dziallas, Frieder Hadlich, Philipp Widmann, Tom Goldammer, 4 Wolfgang Baumgärtner, Jürgen Rehage, Dierck Segelke, Rosemarie Weikard, Christa 5 Kühn 6 7 Affiliations: 8 * Leibniz-Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196 9 Dummerstorf, Germany 10 § Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, 11 Germany 12 † Clinic for Cattle, University of Veterinary Medicine Hannover, 30173 Hannover, Germany 13 ‡ Department of Small Animal Medicine and Surgery, University of Veterinary Medicine 14 Hannover, 30559 Hannover, Germany 15 ** Clinic for Horses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany 16 §§ Vereinigte Informationssysteme Tierhaltung w.V. (vit), 27283 Verden, Germany 17 ‡‡ Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, 18 Germany 19 20 Genetics: Early Online, published on January 22, 2015 as 10.1534/genetics.114.169680

A key common feature all but three known mammalian genera is the strict seven cervical vertebrae blueprint, suggesting the involvement of strong conserving selection forces during mammalian radiation. This is further supported by reports indicating that children with cervical ribs die before they reach reproductive age. Hypotheses were put up, associating cervical ribs (homeotic transformations) to embryonal cancer (e.g., neuroblastoma) or ascribing the constraint in cervical vertebral count to the development of the mammalian diaphragm. Here, we describe a spontaneous mutation c. 196A.> G in the Bos taurus T gene (also known as brachyury) associated with a cervical vertebral homeotic transformation that violates the fundamental mammalian cervical blueprint, but does not preclude reproduction of the affected individual. Genome-wide mapping, haplotype tracking within a large pedigree, resequencing of target genome regions, and bioinformatic analyses unambiguously confirmed the mutant c. 196G allele as causal for this previously unknown defect termed vertebral and spinal dysplasia (VSD) by providing evidence for the mutation event. The non-synonymous VSD mutation is located within the highly conserved T box of the T gene, which plays a fundamental role in eumetazoan body organization and vertebral development. To our knowledge, VSD is the first unequivocally approved spontaneous mutation decreasing cervical vertebrae number in a large mammal. The spontaneous VSD mutation in the bovine T gene is the first in vivo evidence for the hypothesis that the T protein is directly involved in the maintenance of the mammalian seven-cervical vertebra blueprint. It therefore furthers our knowledge of the T-protein function and early mammalian notochord development.

Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53) and Transforming Growth Factor beta 1 (TGFB1) genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG) I442M (rs109570900) and the Growth /differentiation factor 8 (GDF8) Q204X (rs110344317) loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily energy intake as observed in our study.

A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human height in several large meta-analyses. Furthermore, a mutation within the NCAPG gene was found to affect growth and body frame size in cattle. Together with the results of this study in German Warmbloods, these findings strongly indicate LCORL/NCAPG as a candidate locus for withers height in horses. Further studies are, however, needed to confirm this.

Background Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G ( NCAPG ) and myostatin ( GDF8 ), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight. Results Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH , within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth. Conclusions Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior functional hypothesis was demonstrated by data suggesting that NCAPG might contribute to vascular smooth muscle contraction by indirect effects on the NO pathway via modulation of arginine metabolism. Our study shows for the first time in cattle that integration of genetic, physiological and metabolomics data in a systems biology approach will enable (or contribute to) an improved understanding of metabolic and gene networks and genotype-phenotype relationships.

Abstract. The bovine retinoic acid receptor-related orphan receptor C gene (RORC) is located on bovine chromosome 3 in the vicinity of several QTL for milk production traits, and an association of RORC genetic variants with carcass fatness traits had been confirmed by several studies. In a F2 resource population, a chromosome-wise QTL and association study with 26 genetic markers (microsatellites and SNPs from genes involved in fat metabolism) on BTA3 was performed. In the analysis, 183 first and 152 second lactation records of 183 cows were included. The QTL study revealed five QTL affecting milk yield (MY), fat percentage (FP) and protein percentage (PP) as well as the milk fat/milk protein ratio (FPR), respectively, in the chromosomal region harbouring the RORC gene. The association study displayed a significant association between RORC c.1138+65A>G and MY and also associations between RORC c.934-262T>G and MY, FP and FPR, respectively. A combined QTL association study showed that these SNPs included as fixed effect in the corresponding model resulted in a prominent drop of the QTL test statistic. For the RORC c.934-262T allele, which had been confirmed to increase intramuscular fat deposition, an increasing effect on milk fat content traits was detected. The RORC c.1138+65G allele that had been shown to positively affect rump fat thickness, was associated with increased MY in our study. In conclusion, we found indications that the RORC SNPs, which previously had been highlighted due to their effects on carcass fat deposition, are also associated with milk production traits.

Background The intramuscular fat deposition and the fatty acid profiles of beef affect meat quality. High proportions of unsaturated fatty acids are related to beef flavor and are beneficial for the nutritional value of meat. Moreover, a variety of clinical and epidemiologic studies showed that particularly long-chain omega-3 fatty acids from animal sources have a positive impact on human health and disease. Results To screen for genetic factors affecting fatty acid profiles in beef, we initially performed a microsatellite-based genome scan in a F 2 Charolais × German Holstein resource population and identified a quantitative trait locus (QTL) for fatty acid composition in a region on bovine chromosome 27 where previously QTL affecting marbling score had been detected in beef cattle populations. The long-chain acyl-CoA synthetase 1 (ACSL1) gene was identified as the most plausible functional and positional candidate gene in the QTL interval due to its direct impact on fatty acid metabolism and its position in the QTL interval. ACSL1 is necessary for synthesis of long-chain acyl-CoA esters, fatty acid degradation and phospholipid remodeling. We validated the genomic annotation of the bovine ACSL1 gene by in silico comparative sequence analysis and experimental verification. Re-sequencing of the complete coding, exon-flanking intronic sequences, 3' untranslated region (3'UTR) and partial promoter region of the ACSL1 gene revealed three synonymous mutations in exons 6, 7, and 20, six noncoding intronic gene variants, six polymorphisms in the promoter region, and four variants in the 3' UTR region. The association analysis identified the gene variant in intron 5 of the ACSL1 gene ( c.481-233A>G ) to be significantly associated with the relative content of distinct fractions and ratios of fatty acids (e.g., n-3 fatty acids, polyunsaturated, n-3 long-chain polyunsaturated fatty acids, trans vaccenic acid) in skeletal muscle. A tentative association of the ACSL1 gene variant with intramuscular fat content indicated that an indirect effect on fatty acid composition via modulation of total fat content of skeletal muscle cannot be excluded. Conclusions The initial QTL analysis suggested the ACSL1 gene as a positional and functional candidate gene for fatty acid composition in bovine skeletal muscle. The findings of subsequent association analyses indicate that ACSL1 or a separate gene in close proximity might play a functional role in mediating the lipid composition of beef.

A parallel association study was performed in two independent cattle populations based on 41 validated, targeted single nucleotide polymorphisms (SNPs) and four microsatellite markers to re-evaluate the multiple quantitative trait loci (QTL) architecture for milk performance on bovine chromosome 6 (BTA6). Two distinct QTL located in the vicinity of the middle region of BTA6, but differing unambiguously regarding their effects on milk composition and yield traits were validated in the German Holstein population. A highly significant association of the protein variant ABCG2 p.Tyr581Ser with milk composition traits reconfirmed the causative molecular relevance of the ABCG2 gene in QTL region 1, whereas in QTL region 2, significant and tentative associations between gene variants RW070 and RW023 (located in the promoter region and exon 9 of the PPARGC1A gene for milk yield traits) were detected. For the German Fleckvieh population, only RW023 showed a tentative association with milk yield traits, whereas those loci with significant effects in German Holsteins (ABCG2 p.Tyr581Ser, RW070) showed fixed alleles. Even though our new data highlight two variants in the PPARGC1A gene (RW023, RW070) in QTL region 2, based on the results of our study, currently no unequivocal conclusion about the causal background of this QTL affecting milk yield traits can be drawn. Notably, the German Holstein and Fleckvieh populations, known for their divergent degree of dairy type, differ substantially in their allele frequencies for the growth-associated NCAPG p.Ile442Met locus.

A variety of QTL mapping studies in different dairy cattle populations suggest that there are at least three distinct QTL regions on bovine chromosome 6 (BTA6) affecting milk production traits (http://www.animalgenome.org/cattle/). According to the current version of the bovine genome assembly Btau 4.0 (NCBI), one QTL (37.2-38.2 Mb) with a predominant effect on milk protein and fat content is located proximally of marker BM143, whereas a second QTL particularly affecting milk fat and milk protein yield was identified distally of BM143 (44.1-46.6 Mb). Moreover, a third QTL with effect on milk yield and composition was detected in a region enclosing 88.1-88.8 Mb. The multiple QTL architecture on BTA6 impedes dissecting the distinct QTL on a molecular level. Whereas the third QTL region has a strong focus on the casein gene cluster, fine mapping studies targeted at candidate genes underlying the QTL affecting milk composition in QTL region 1 had indicated conflicting results. Mutations in the ABCG2 (ABCG2 Y581S, Cohen-Zinder et al. 2005; Olsen et al. 2005) and SPP1 (OPN3907, Schnabel et al. 2005) genes have been proposed as putative underlying functional mutation. However, OPN3907 identified in the US Holstein population could be excluded in the Israeli Holstein (Seroussi et al. 2008) and Norwegian dairy (Olsen et al. 2007) cattle populations as causative molecular background in QTL region 1. Because of its chromosomal position and key function in energy metabolism, the PPARGC1A gene was discussed as a positional and functional candidate for the QTL region 2. A noncoding gene variant of the PPARGC1A gene (c.1892+19T>C) was identified to be trait-associated in the German Holstein (GH) population indicating that the PPARGC1A gene could be involved in the genetic variation underlying the QTL for milk fat yield on BTA6 (Weikard et al. 2005). However, it remained to be elucidated whether this gene variant is causal for the QTL or if the trait association is due to linkage disequilibrium (LD) with a yet undetected functional polymorphism in close proximity to the SNP. Therefore, the aim of this study was to re-evaluate the QTL region 2 using a higher density map of SNPs in two independent cattle populations, GH and Fleckvieh (GF).