Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.

BACKGROUND: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). RESULTS: Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. CONCLUSION: Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments.

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.

A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

BACKGROUND: The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. RESULTS: A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. CONCLUSIONS: This high-density SNP genetic map is the first comprehensive linkage map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny.

Comparative transcriptome analyses reveal conserved and distinct mechanisms in ovine and bovine lactation.

A combined analysis of a bovine and ovine mammary gland transcriptome from two similarly designed microarray experiments suggested a strong positive association between the differentially expressed genes (DEGs) implying that major pathways regulating the lactation process were evolutionarily conserved within the two species. Some distinct pathways identified indicate the physiological differences underlying the species. Novel techniques were established for the combined analysis of the transcriptomes of different species or heterogeneous platforms for comparative gene expression analysis allowing for greater experimental power to detect conserved pathways. Conserved DEGs were mainly related to lipid metabolism, amino acid synthesis, cell proliferation, signaling and immune systems indicating functional processes involved in the regulation of lactation including milk synthesis and lactation persistency. There were no functionally annotated DEGs that show antagonistic expression between sheep and cattle suggesting that the lactation process is essentially the same in the two species. DEGs that were found exclusively in sheep were mostly associated with gland morphogenesis while DEGs exclusively expressed in cattle, indicated that certain immune response and milk composition mechanisms were different in the bovine as compared to sheep. The conserved processes across the two species suggest the use of the ovine as a suitable model for lactation studies, considering the challenges and expense of conducting lactation physiology and genomics studies within the cow.

Association of the single nucleotide polymorphism in CAPN3 gene with growth performance in Merino and Garut (MEGA) backcross sheep.

BACKGROUND: Sheep is one of the commodities of livestock which has been known widely in Indonesia for supporting the national food security. Improvement in genetic quality by selection based on genetic markers for growth is necessary to increase meat production. Quantitative trait loci (QTL) analysis in sheep suggests that Calpain 3 gene (CAPN3) gene might be one of the candidate loci affecting growth traits. CAPN3 is located on chromosome 7 sheep expressed in the skeletal muscles. The aim of this study was to investigate polymorphism CAPN3 intron 11 in Merino × Garut (MEGA) backcross using the PCR-RLFP method and to determine their association with growth traits. RESULTS: SNP intron 11 CAPN3 | BseSI of Merino × Garut (MEGA) backcross sheep was polymorphic and resulted in two alleles of C and T with a frequency of 0.76 and 0.24, respectively, and CC, CT, and TT genotypes with a frequency of 0.54, 0.43, and 0.02, respectively. These loci were found to be in Hardy-Weinberg equilibrium. The SNP CAPN3 | BseSI significantly affected (P < 0.05) the birth weight in Merino × Garut (MEGA) backcross sheep. CONCLUSION: This result suggests that the CAPN3 | BseSI can be used as a genetic marker for birth weight trait in sheep.

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle.

BACKGROUND: We investigated strategies and factors affecting accuracy of imputing genotypes from lower-density SNP panels (Illumina 3K, 7K, Affymetrix 15K and 25K, and evenly spaced subsets) up to one medium (Illumina 50K) and one high-density (Illumina 800K) SNP panel. We also evaluated the utility of imputed genotypes on the accuracy of genomic selection using Australian Holstein-Friesian cattle data from 2727 and 845 animals genotyped with 50K and 800K SNP chip, respectively. Animals were divided into reference and test sets (genotyped with higher and lower density SNP panels, respectively) for evaluating the accuracies of imputation. For the accuracy of genomic selection, a comparison of direct genetic values (DGV) was made by dividing the data into training and validation sets under a range of imputation scenarios. RESULTS: Of the three methods compared for imputation, IMPUTE2 outperformed Beagle and fastPhase for almost all scenarios. Higher SNP densities in the test animals, larger reference sets and higher relatedness between test and reference animals increased the accuracy of imputation. 50K specific genotypes were imputed with moderate allelic error rates from 15K (2.85%) and 25K (2.75%) genotypes. Using IMPUTE2, SNP genotypes up to 800K were imputed with low allelic error rate (0.79% genome-wide) from 50K genotypes, and with moderate error rate from 3K (4.78%) and 7K (2.00%) genotypes. The error rate of imputing up to 800K from 3K or 7K was further reduced when an additional middle tier of 50K genotypes was incorporated in a 3-tiered framework. Accuracies of DGV for five production traits using imputed 50K genotypes were close to those obtained with the actual 50K genotypes and higher compared to using 3K or 7K genotypes. The loss in accuracy of DGV was small when most of the training animals also had imputed (50K) genotypes. Additional gains in DGV accuracies were small when SNP densities increased from 50K to imputed 800K. CONCLUSION: Population-based genotype imputation can be used to predict and combine genotypes from different low, medium and high-density SNP chips with a high level of accuracy. Imputing genotypes from low-density SNP panels to at least 50K SNP density increases the accuracy of genomic selection.

Identification of a null allele in genetic tests for bovine leukocyte adhesion deficiency in Pakistani Bos indicus × Bos taurus cattle.

Two clinically healthy mature Pakistani Bos indicus × Bos taurus cattle were genotyped as homozygous affected for the lethal immunodeficiency disorder bovine leukocyte adhesion deficiency (BLAD) using previously described PCR-RFLP based DNA tests which was confirmed by sequencing. Sequencing of Bos taurus and B. indicus × B. taurus genomic DNA surrounding the disease causing mutation (c.383A > G) in the ITGB2 gene identified numerous variations in exonic and intronic regions within and between species, including substantial variation in primer annealing sites for three PCR-RFLP tests for one of the B. indicus allelic variants. These variations in the primer annealing sites resulted in a null allele in the DNA tests causing the misdiagnosis of some heterozygous B. taurus × B. indicus cattle to be classified as homozygous affected. New primers were designed and a modified test was developed which simultaneously identified the disease mutation and the Pakistani B. indicus allelic variant associated with the null allele in the previous test.

Genetic analysis of digital image derived morphometric traits of black tiger shrimp (Penaeus monodon) by incorporating G × E investigations.

The black tiger shrimp, Penaeus monodon, is the second most economically important aquaculture shrimp species in the world, and in Australia it is one of the most commonly farmed shrimp species. Despite its economic significance, very few studies have reported the genetic evaluation of economically important morphological size and shape traits of shrimp grown in commercial grow-out environments. In this study we obtained genetic parameter estimates and evaluated genotype-by-environment interaction (GxE) for nine body morphological traits of shrimp derived from images. The data set contained image and body weight (BW) records of 5,308 shrimp, from 64 sires and 54 dams, reared in eight grow-out ponds for an average of 133 days. From the images, landmark based morphological distances were computed from which novel morphological traits associated with size and shape were derived for genetic evaluation. These traits included body weight (BW), body length (BL), body size (BS), head size (HS), Abdominal size (AS), abdominal percentage (AP), tail tip (TT), front by back ratio (FBR), condition factor (CF) and condition factor length (CFL). We also evaluated G×E interaction effects of these traits for shrimp reared in different ponds. The heritability estimates for growth related morphological and body weight traits were moderately high (BW: h 2 = 0.32 ± 0.05; BL: h 2 = 0.36 ± 0.06; BS: h 2 = 0.32 ± 0.05; HS: h 2 = 0.31 ± 0.05; AS: h 2 = 0.32 ± 0.05; and TT: h 2 = 0.28 ± 0.05) and low for abdominal percentage and body shape traits (AP: h 2 = 0.09 ± 0.02; FBR: h 2 = 0.08 ± 0.02; CF: h 2 = 0.06 ± 0.02; and CFL: h 2 = 0.003 ± 0.004). G × E interaction were negligible for all traits for shrimp reared in different ponds, suggesting re-ranking is not prevalent for this population. Genetic correlations among growth related morphological traits were high ranging from 0.36 to 0.99, suggesting these traits can be simultaneously improved through indirect genetic selection. However, negative genetic correlations were observed for FBR & CF shape traits with major growth traits (ranged -0.08 to -0.95), suggesting genetic selection for rapid growth will likely result in thick/fatty shrimp over generations. Our study showed image-based landmark data can be successfully employed for genetic evaluation of complex morphological traits of shrimp and is potentially amenable to machine-learning derived parameters in semi-automated high volume phenotyping systems needed under commercial conditions.

Genetic parameters of color phenotypes of black tiger shrimp (Penaeus monodon).

Black tiger shrimp (Penaeus monodon) is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams. The color of uncooked shrimp was subjectively scored on a scale from 1 to 4, with "1" being the lightest/pale color and "4" being the darkest color. For cooked shrimp color, shrimp were graded firstly by subjective scoring using a commercial grading score card, where the score ranged from 1 to 12 representing light to deep coloration which was subsequently found to not be sufficiently reliable with poor repeatability of measurement (r = 0.68-0.78) Therefore, all images of cooked color were regraded on a three-point scale from brightest and lightest colored cooked shrimp, to darkest and most color-intense, with a high repeatability (r = 0.80-0.92). Objective color of both cooked and uncooked color was obtained by measurement of RGB intensities (values range from 0 to 255) for each pixel from each shrimp. Using the "convertColor" function in "R", the RGB values were converted to L*a*b* (CIE Lab) systems of color properties. This system of color space was established in 1976, by the International Commission of Illumination (CIE) where "L*" represents the measure of degree of lightness, values range from 0 to 100, where 0 = pure black and 100 = pure white. The value "a*" represents red to green coloration, where a positive value represents the color progression towards red and a negative value towards green. The value "b*" represents blue to yellow coloration, where a positive value refers to more yellowish and negative towards the blue coloration. In total, eight color-related traits were investigated. An ordinal mixed (threshold) model was adopted for manually (subjectively) scored color phenotypes, whereas all other traits were analyzed by linear mixed models using ASReml software to derive variance components and estimated breeding values (EBVs). Moderate to low heritability estimates (0.05-0.35) were obtained for body color traits. For subjectively scored cooked and uncooked color, EBV-based selection would result in substantial genetic improvement in these traits. The genetic correlations among cooked, uncooked and body weight traits were high and ranged from -0.88 to 0.81. These suggest for the first time that 1) cooked color can be improved indirectly by genetic selection based on color of uncooked/live shrimp, and 2) intensity of coloration is positively correlated with body weight traits and hence selection for body weight will also improve color traits in this population.

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence.

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Mapping quantitative trait loci (QTL) in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep.

BACKGROUND: In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL) for extended lactation and lactation persistency in sheep. METHODS: An (Awassi × Merino) × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. RESULTS: Overall, one highly significant (LOD > 3.0), four significant (2.0 < LOD < 3.0) and five suggestive (1.7 < LOD < 2.0) QTL were detected across all traits in common by both mapping methods. One additional suggestive QTL was identified using maximum likelihood estimation, and four suggestive (0.01 < P < 0.05) and two significant (P < 0.01) QTL using the regression approach only. All detected QTL had effect sizes in the range of 0.48 to 0.64 SD, corresponding to QTL heritabilities of 3.1 to 8.9%. The comparison of the detected QTL with results in cattle showed conserved linkage regions. Most of the QTL identified for lactation persistency and extended lactation did not coincide. This suggests that persistency and extended lactation for the same as well as different milk yield and component traits are not controlled by the same genes. CONCLUSION: This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.

Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates.

BACKGROUND: Recent developments of high-density SNP chips across a number of species require accurate genetic maps. Despite rapid advances in genome sequence assembly and availability of a number of tools for creating genetic maps, the exact genome location for a number of SNPs from these SNP chips still remains unknown. We have developed a locus ordering procedure based on linkage disequilibrium (LODE) which provides estimation of the chromosomal positions of unaligned SNPs and scaffolds. It also provides an alternative means for verification of genetic maps. We exemplified LODE in cattle. RESULTS: The utility of the LODE procedure was demonstrated using data from 1,943 bulls genotyped for 73,569 SNPs across three different SNP chips. First, the utility of the procedure was tested by analysing the masked positions of 1,500 randomly-chosen SNPs with known locations (50 from each chromosome), representing three classes of minor allele frequencies (MAF), namely >0.05, 0.010.05), for validating and checking the quality of a genome assembly, and offers a means for positioning of unordered scaffolds containing SNPs. The LODE procedure will be helpful in refining genome sequence assemblies, especially those being created from next-generation sequencing where high-throughput SNP discovery and genotyping platforms are integrated components of genome analysis.

Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers.

BACKGROUND: At the current price, the use of high-density single nucleotide polymorphisms (SNP) genotyping assays in genomic selection of dairy cattle is limited to applications involving elite sires and dams. The objective of this study was to evaluate the use of low-density assays to predict direct genomic value (DGV) on five milk production traits, an overall conformation trait, a survival index, and two profit index traits (APR, ASI). METHODS: Dense SNP genotypes were available for 42,576 SNP for 2,114 Holstein bulls and 510 cows. A subset of 1,847 bulls born between 1955 and 2004 was used as a training set to fit models with various sets of pre-selected SNP. A group of 297 bulls born between 2001 and 2004 and all cows born between 1992 and 2004 were used to evaluate the accuracy of DGV prediction. Ridge regression (RR) and partial least squares regression (PLSR) were used to derive prediction equations and to rank SNP based on the absolute value of the regression coefficients. Four alternative strategies were applied to select subset of SNP, namely: subsets of the highest ranked SNP for each individual trait, or a single subset of evenly spaced SNP, where SNP were selected based on their rank for ASI, APR or minor allele frequency within intervals of approximately equal length. RESULTS: RR and PLSR performed very similarly to predict DGV, with PLSR performing better for low-density assays and RR for higher-density SNP sets. When using all SNP, DGV predictions for production traits, which have a higher heritability, were more accurate (0.52-0.64) than for survival (0.19-0.20), which has a low heritability. The gain in accuracy using subsets that included the highest ranked SNP for each trait was marginal (5-6%) over a common set of evenly spaced SNP when at least 3,000 SNP were used. Subsets containing 3,000 SNP provided more than 90% of the accuracy that could be achieved with a high-density assay for cows, and 80% of the high-density assay for young bulls. CONCLUSIONS: Accurate genomic evaluation of the broader bull and cow population can be achieved with a single genotyping assays containing ~ 3,000 to 5,000 evenly spaced SNP.

Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers.

BACKGROUND: Genomic selection (GS) uses molecular breeding values (MBV) derived from dense markers across the entire genome for selection of young animals. The accuracy of MBV prediction is important for a successful application of GS. Recently, several methods have been proposed to estimate MBV. Initial simulation studies have shown that these methods can accurately predict MBV. In this study we compared the accuracies and possible bias of five different regression methods in an empirical application in dairy cattle. METHODS: Genotypes of 7,372 SNP and highly accurate EBV of 1,945 dairy bulls were used to predict MBV for protein percentage (PPT) and a profit index (Australian Selection Index, ASI). Marker effects were estimated by least squares regression (FR-LS), Bayesian regression (Bayes-R), random regression best linear unbiased prediction (RR-BLUP), partial least squares regression (PLSR) and nonparametric support vector regression (SVR) in a training set of 1,239 bulls. Accuracy and bias of MBV prediction were calculated from cross-validation of the training set and tested against a test team of 706 young bulls. RESULTS: For both traits, FR-LS using a subset of SNP was significantly less accurate than all other methods which used all SNP. Accuracies obtained by Bayes-R, RR-BLUP, PLSR and SVR were very similar for ASI (0.39-0.45) and for PPT (0.55-0.61). Overall, SVR gave the highest accuracy.All methods resulted in biased MBV predictions for ASI, for PPT only RR-BLUP and SVR predictions were unbiased. A significant decrease in accuracy of prediction of ASI was seen in young test cohorts of bulls compared to the accuracy derived from cross-validation of the training set. This reduction was not apparent for PPT. Combining MBV predictions with pedigree based predictions gave 1.05 - 1.34 times higher accuracies compared to predictions based on pedigree alone. Some methods have largely different computational requirements, with PLSR and RR-BLUP requiring the least computing time. CONCLUSIONS: The four methods which use information from all SNP namely RR-BLUP, Bayes-R, PLSR and SVR generate similar accuracies of MBV prediction for genomic selection, and their use in the selection of immediate future generations in dairy cattle will be comparable. The use of FR-LS in genomic selection is not recommended.

Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep.

An (Awassi x Merino) x Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P < 0.01) and additional 25 suggestive (P < 0.05) QTL were detected across both single QTL methods and all traits. In preparation of a meta-analysis, all QTL results were compared with a meta-assembly of QTL for milk production traits in dairy ewes from various public domain sources and can be found on the ReproGen ovine gbrowser http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight.

A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL) analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE) and is freely available on request. The new analysis package offers the advantage of enabling QTL x fixed effect interactions to be included in the model. Fifty-four putative QTL were identified on nine chromosomes. Significant QTL with sex-specific effects (i.e. QTL x sex interaction) in the range of 0.4 to 0.7 SD were found on ovine chromosomes 1, 3, 6, 11, 21, 23, 24 and 26.

Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel.

BACKGROUND: The extent of linkage disequilibrium (LD) within a population determines the number of markers that will be required for successful association mapping and marker-assisted selection. Most studies on LD in cattle reported to date are based on microsatellite markers or small numbers of single nucleotide polymorphisms (SNPs) covering one or only a few chromosomes. This is the first comprehensive study on the extent of LD in cattle by analyzing data on 1,546 Holstein-Friesian bulls genotyped for 15,036 SNP markers covering all regions of all autosomes. Furthermore, most studies in cattle have used relatively small sample sizes and, consequently, may have had biased estimates of measures commonly used to describe LD. We examine minimum sample sizes required to estimate LD without bias and loss in accuracy. Finally, relatively little information is available on comparative LD structures including other mammalian species such as human and mouse, and we compare LD structure in cattle with public-domain data from both human and mouse. RESULTS: We computed three LD estimates, D', Dvol and r2, for 1,566,890 syntenic SNP pairs and a sample of 365,400 non-syntenic pairs. Mean D' is 0.189 among syntenic SNPs, and 0.105 among non-syntenic SNPs; mean r2 is 0.024 among syntenic SNPs and 0.0032 among non-syntenic SNPs. All three measures of LD for syntenic pairs decline with distance; the decline is much steeper for r2 than for D' and Dvol. The value of D' and Dvol are quite similar. Significant LD in cattle extends to 40 kb (when estimated as r2) and 8.2 Mb (when estimated as D'). The mean values for LD at large physical distances are close to those for non-syntenic SNPs. Minor allelic frequency threshold affects the distribution and extent of LD. For unbiased and accurate estimates of LD across marker intervals spanning < 1 kb to > 50 Mb, minimum sample sizes of 400 (for D') and 75 (for r2) are required. The bias due to small samples sizes increases with inter-marker interval. LD in cattle is much less extensive than in a mouse population created from crossing inbred lines, and more extensive than in humans. CONCLUSION: For association mapping in Holstein-Friesian cattle, for a given design, at least one SNP is required for each 40 kb, giving a total requirement of at least 75,000 SNPs for a low power whole-genome scan (median r2 > 0.19) and up to 300,000 markers at 10 kb intervals for a high power genome scan (median r2 > 0.62). For estimation of LD by D' and Dvol with sufficient precision, a sample size of at least 400 is required, whereas for r2 a minimum sample of 75 is adequate.

A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle.

Analysis of data on 1000 Holstein-Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy-Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05-0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of > or =3 SNPs were identified. The average block length was 69.7 +/- 7.7 kb, which is approximately 5-10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000-100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require approximately 250,000 SNPs in the discovery phase.

Comparative experimental Haemonchus contortus infection of two sheep breeds native to the Canary Islands.

This study compares the susceptibility to Haemonchus contortus infection in two breeds of sheep endemic to the Canary Islands, the Canaria Hair Breed sheep and the Canaria sheep. Sheep were experimentally infected with 20,000 larvae of H. contortus and animals killed on days 7 and 28 post-infection. No difference between sheep breeds were detected in immature worm counts at days 7 or 28 post-infection. However, in comparison to the Canaria sheep breed, the Canaria Hair Breed sheep showed lower mean faecal egg counts, lower adult worm counts, lower number of eggs in utero and female worm stunting. Overall, these data suggest that the Canaria Hair Breed sheep has a greater resistance to H. contortus infection than Canaria sheep, and that this resistance may act at the level of the adult parasite.