A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits

Previous research has found that a quantitative trait locus exists affecting calving and conformation traits on Bos taurus autosome 18 that may be related to increased calf birth weights, which are not routinely recorded in the United States. Birth weight data from large, intensively managed dairies in eastern Germany with management systems similar to those commonly found in the United States were used to develop a selection index predictor for predicted transmitting ability (PTA) of birth weight. The predictor included body depth, rump width, sire calving ease, sire gestation length, sire stillbirth, stature, and strength. Genetic and phenotypic correlations and heritabilities from the United States were substituted for the German values, and birth weight PTA predicted for 31,984 bulls with US genetic evaluations. A genome-wide association study was conducted on the predicted birth weight PTA with the 2-step genomic BLUP procedure used for routine evaluations in the United States. Allele substitution effects were predicted for 43,188 single nucleotide polymorphisms (SNP). Genotypes were available for 53,644 predictor animals. Gene set enrichment analysis was performed on the 100 SNP that had the largest effects expressed in additive genetic standard deviations. Several SNP related to growth and development were found among the 25 SNP with the largest effects, including markers located within or near (≤100 kbp) ABCA12, FLRT2, LHX4, MAP3K5, NRAC, NTNG1, PIGN, and ZNF75A. The gene set enrichment analysis identified the Kyoto Encyclopedia of Genes and Genomes “Regulation of actin cytoskeleton” pathway (bta04810) as being enriched. That pathway includes the ROCK gene, which is involved in placental function in the human, as well as other developmental genes (e.g., FAK and PAK). Prediction equations derived from one population are useful for identifying genes and gene networks associated with phenotypes that are not directly measured in a second population. This approach will identify only genes associated with the traits used to construct the birth weight predictor, and not loci that affect only birth weight.     

A genome scan for quantitative trait loci affecting milk somatic cell score in Israeli and Italian Holstein cows by means of selective DNA pooling with single- and multiple-marker mapping

Mastitis is an important and common dairy cattle disease affecting milk yield, quality, and consumer safety as well as cheese yields and quality. Animal welfare and residues of the antibiotics used to treat mastitis cause public concern. Considerable genetic variation may allow selection for increased resistance to mastitis. Because of high genetic correlation to milk somatic cell score (SCS), SCS can serve as a surrogate trait for mastitis resistance. The present study intended to identify quantitative trait loci (QTL) affecting SCS in Israeli and Italian Holstein dairy cattle (IsH and ItH, respectively), using selective DNA pooling with single and multiple marker mapping. Milk samples of 4,788 daughters of 6 IsH and 7 ItH sires were used to construct sire-family high- and low-tail pools, which were genotyped at 123 (IsH) and 133 (ItH) microsatellite markers. Shadow correction was used to obtain pool allele frequency estimates. Frequency difference between the tails and empirical standard error of D, SE(D), were used to obtain P-values. All markers significant by single marker mapping were also significant by multiple marker mapping, but not vice versa. Combining both populations, 22 QTL on 21 chromosomes were identified; all corresponded to previous reports in the literature. Confidence intervals were set by chi-squared drop method. Heterozygosity of QTL was estimated at 44.2%. Allele substitution effects ranged from 1,782 to 4,930 cells/mL in estimated breeding value somatic cell count units. Most (80%) of the observed variation in estimated breeding value somatic cell score could be explained by the QTL identified under the stringent criteria. The results found here can be used as a basis for further genome-wide association studies for the same trait.     

The Glycemic Index of Rice and Rice Products: A Review,and Table of GI Values

Rice is the principle staple and energy source for nearly half the world's population and therefore has significant nutrition and health implications. Rice is generally considered a high glycemic index (GI) food, however, this depends on varietal, compositional, processing, and accompaniment factors. Being a major contributor to the glycemic load in rice eating populations, there is increasing concern that the rising prevalence of insulin resistance is as a result of the consumption of large amounts of rice. Devising ways and means of reducing the glycemic impact of rice is therefore imperative. This review gathers studies examining the GI of rice and rice products and provides a critical overview of the current state of the art. A table collating published GI values for rice and rice products is also included.     

黑龙江省种植大豆品种遗传多样性分析及与性状关联SSR标记筛选

为从分子水平鉴定黑龙江省种植大豆品种的遗传多样性,并筛选与蛋白质、脂肪、百粒重和水分等大豆主要性状显著关联的SSR分子标记,利用18对SSR引物,采用荧光毛细管电泳法分析黑龙江省75个种植大豆品种遗传多样性,并与性状进行关联分析.结果 表明:18个SSR标记中的10个标记可以实现单对引物准确鉴别42个大豆品种,18个S...     

Genomic analysis of claw lesions in Holstein cows: Opportunities for genomic selection,quantitative trait locus detection,and gene identification

Claw lesions are the third most important health issue in dairy cattle, after mastitis and reproductive disorders, and genomic selection is a key component for long-term improvement of claw health. The objectives of this study were to assess the feasibility of a genomic evaluation for claw health in French Holstein cows, explore possibilities to increase evaluation accuracy, and gain a better understanding of the genetic determinism of claw health traits. The data set consisted of 48,685 trimmed Holstein cows, including 9,646 that were genotyped; 478 genotyped sires were also used. Seven claw lesion traits were evaluated using BLUP, genomic BLUP, BayesC, and single-step genomic BLUP, and the accuracies obtained using these approaches were measured through a validation study. The BayesC approach was used to detect quantitative trait locus (QTL) regions associated with the 7 individual traits (digital dermatitis, heel horn erosion, interdigital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure) based on their Bayes factor. Annotated genes on these regions were reported. Genomic evaluation approaches generally did not allow for greater accuracies than BLUP, except for single-step genomic BLUP. Accuracies were moderate, but best and worst validation animals were correctly discriminated and showed significant differences in lesion frequencies. A total of 192 QTL regions were identified, including 13 with major evidence or involved for 2 of the traits. A high number of genes were present on these regions, and several had functions associated with the immune system. In particular, the EPYC gene is located close to a major evidence QTL for resistance to digital dermatitis that is also a QTL for interdigital hyperplasia (on chromosome 5, around 20.9 MB) and has been associated with Ehlers-Danlos syndrome in cattle. Genomic selection can be used to improve resistance to individual claw lesions, and several possibilities exist to improve accuracies of genomic evaluations.     

A 100-Year Review: Identification and genetic selection of economically important traits in dairy cattle

Over the past 100 yr, the range of traits considered for genetic selection in dairy cattle populations has progressed to meet the demands of both industry and society. At the turn of the 20th century, dairy farmers were interested in increasing milk production; however, a systematic strategy for selection was not available. Organized milk performance recording took shape, followed quickly by conformation scoring. Methodological advances in both genetic theory and statistics around the middle of the century, together with technological innovations in computing, paved the way for powerful multitrait analyses. As more sophisticated analytical techniques for traits were developed and incorporated into selection programs, production began to increase rapidly, and the wheels of genetic progress began to turn. By the end of the century, the focus of selection had moved away from being purely production oriented toward a more balanced breeding goal. This shift occurred partly due to increasing health and fertility issues and partly due to societal pressure and welfare concerns. Traits encompassing longevity, fertility, calving, health, and workability have now been integrated into selection indices. Current research focuses on fitness, health, welfare, milk quality, and environmental sustainability, underlying the concentrated emphasis on a more comprehensive breeding goal. In the future, on-farm sensors, data loggers, precision measurement techniques, and other technological aids will provide even more data for use in selection, and the difficulty will lie not in measuring phenotypes but rather in choosing which traits to select for.     

Prevalence,Genetic Diversity,and Technological Functions of the Lactobacillus sanfranciscensis in Sourdough: A Review

The use of sourdough as a leavening agent in bread making is a very old method that can be traced back to ancient times. Sourdoughs harbor a complex microbiota that is affected by multiple factors including factors related to cereal plants, grains, and sourdough processing techniques. Lactobacillus sanfranciscensis is the key autochthonous bacterium of the traditional sourdough microbiota and it is said to be “sourdough adapted” species. Despite the great dominance of this bacterium in sourdoughs, the origin of this species still remains unclear. Lactobacillus sanfranciscensis positively influences all aspects of sourdough and fermented foods. However, the positive influence of this species on sourdough is a strain‐dependent characteristic. The first purpose of this review was to discuss factors affecting the microbiota of sourdoughs with particular emphasis on reasons behind the remarkable prevalence of L. sanfranciscensis in this ecological niche. The second objective was to discuss the genotypic and phenotypic classification of L. sanfranciscensis strains and the influence of this species on technological and functional characteristics of sourdough including its influence on rheological properties of dough and bread characteristics, texture, aroma, and shelf‐life through the inhibition of fungal growth.     

大米中2-乙酰基-1-吡咯啉检测技术及形成机制研究进展

2-乙酰基-1-吡咯啉是大米中的特征香气成分,其含量高低直接影响大米品质和价格。因此,开展大米中2-乙酰基-1-吡咯啉精准检测方法研究,对于明确呈香机理、提升大米品质及促进进出口贸易都具有重要意义。综述了当前主要的前处理技术和基于GC、GC-MS、GC-O-MS、GC-TOF-MS、GC×GC-TOF-MS、HPLC-MS/MS等仪器检测2-乙酰基-1-吡咯啉的研究进展,分析了各种方法的优缺点,以及2-乙酰基-1-吡咯啉形成机制的研究进展,以期实现大米中2-乙酰基-1-吡咯啉的精准检测及大米品质提升提供借鉴。     

Olive oil traceability by means of chemical and sensory analyses: A comparison with SSR biomolecular profiles

The relationship between genetic diversity and phenotype in olive, instrumental to improve the efficacy of olive clonal selection, is still far from being fully understood. This work reports on a comparison made between plant SSR genetic data and quality of monovarietal olive oils. Nine monovarietal oils produced by selected genotypes were characterised under chemical and sensory profiles. Fatty acid compositions were determined to evaluate quantitative differences among oils; some fatty acids are actually highly correlated with the genetic matrix, and PCA of fatty acids composition explains 85.53% variability. Moreover some oils characterised by high levels of oleic acid appeared interesting from a nutritional standpoint. Organoleptic profiles evidenced differences especially for the attributes defined as “pleasant flavours”; oils obtained by different genetic matrices were characterised by different flavour intensities of tomato or artichoke, almond or aromatic herbs, correspondence analysis among sensory pleasant attributes and olive oil samples explaining 91.68% variability.     

Antimicrobial Resistance on Farms: A Review Including Biosecurity and the Potential Role of Disinfectants in Resistance Selection

Resistance to therapeutic antimicrobial agents is recognized as a growing problem for both human and veterinary medicine, and the need to address the issue in both of these linked domains is a current priority in public policy. Efforts to limit antimicrobial resistance (AMR) on farms have so far focused on control of the supply and use of antimicrobial drugs, plus husbandry measures to reduce infectious disease. In the United Kingdom and some other countries, substantial progress has been made recently against targets on agricultural antimicrobial drug use. However, evidence suggests that resistant pathogenic and commensal bacteria can persist and spread within and between premises despite declining or zero antimicrobial drug use. Reasons for this are likely complex and varied but may include: bacterial adaptations to ameliorate fitness costs associated with maintenance and replication of resistance genes and associated proteins, horizontal transmission of genetic resistance determinants between bacteria, physical transfer of bacteria via movement (of animals, workers, and equipment), ineffective cleaning and disinfection, and co‐selection of resistance to certain drugs by use of other antimicrobials, heavy metals, or biocides. Areas of particular concern for public health include extended‐spectrum cephalosporinases and fluoroquinolone resistance among Enterobacteriaceae, livestock‐associated methicillin‐resistant Staphylococcus aureus, and the emergence of transmissible colistin resistance. Aspects of biosecurity have repeatedly been identified as risk factors for the presence of AMR on farm premises, but there are large gaps in our understanding of the most important risk factors and the most effective interventions. The present review aims to summarize the present state of knowledge in this area, from a European perspective.