Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle

Genetic Association of Interleukin 16 Gene Polymorphisms (rs11556218 & rs4778889) with Type 1 Diabetes in Egyptian Children: A Case-Control Study

BACKGROUND

Type 1 diabetes (T1D) is a serious chronic autoimmune condition. Even though the underlying reason for the onset of T1D is unknown, due to their effector and regulatory roles in immune responses, cytokines are essential in developing autoimmune disorders. Interleukin (IL)16 is an immunomodulatory cytokine implicated in several inflammatory and autoimmune diseases.

OBJECTIVE

This study was designed to examine the association of IL16 gene polymorphisms, rs11556218 T > G and rs4778889 T > C, with the risk of T1D in Egyptian children.

METHODS

Using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, we analyzed rs11556218 T > G and rs4778889 T > C polymorphisms of the IL16 gene in 100 T1D subjects and 93 controls.

RESULTS

Rs11556218 T > G polymorphism of the IL16 gene was not associated with the risk of developing T1D. Analysis of IL16 gene rs4778889 T > C showed that the TT genotype had a considerably higher risk of T1D than the TC genotype [OR = 2.195 (1.205-3.999)]. In comparison to patients with the C allele [OR = 0.6914 (0.38-1.2569)], patients with the T allele [OR = 1.45 (0.7956-2.6296)] were notably more likely to have T1D. A significant decrease was found in the frequency of GT (OR = 0.43, p = .03) and TC (OR = 0.32, p = .011) haplotypes of IL16 gene rs11556218 T > G and rs4778889 T > C polymorphisms in T1D patients compared with controls.

CONCLUSION

IL16 gene rs4778889 T > C polymorphism might be associated with susceptibility to T1D. Egyptians with TT genotypes are more likely to develop T1D. However, GT and TC haplotypes of IL16 gene rs11556218 T > G and rs4778889 T > C polymorphisms highlight their protective role againstT1D disease.

Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.

GWABLUP: genome-wide association assisted best linear unbiased prediction of genetic values

BACKGROUND

Since the very beginning of genomic selection, researchers investigated methods that improved upon SNP-BLUP (single nucleotide polymorphism best linear unbiased prediction). SNP-BLUP gives equal weight to all SNPs, whereas it is expected that many SNPs are not near causal variants and thus do not have substantial effects. A recent approach to remedy this is to use genome-wide association study (GWAS) findings and increase the weights of GWAS-top-SNPs in genomic predictions. Here, we employ a genome-wide approach to integrate GWAS results into genomic prediction, called GWABLUP.

RESULTS

GWABLUP consists of the following steps: (1) performing a GWAS in the training data which results in likelihood ratios; (2) smoothing the likelihood ratios over the SNPs; (3) combining the smoothed likelihood ratio with the prior probability of SNPs having non-zero effects, which yields the posterior probability of the SNPs; (4) calculating a weighted genomic relationship matrix using the posterior probabilities as weights; and (5) performing genomic prediction using the weighted genomic relationship matrix. Using high-density genotypes and milk, fat, protein and somatic cell count phenotypes on dairy cows, GWABLUP was compared to GBLUP, GBLUP (topSNPs) with extra weights for GWAS top-SNPs, and BayesGC, i.e. a Bayesian variable selection model. The GWAS resulted in six, five, four, and three genome-wide significant peaks for milk, fat and protein yield and somatic cell count, respectively. GWABLUP genomic predictions were 10, 6, 7 and 1% more reliable than those of GBLUP for milk, fat and protein yield and somatic cell count, respectively. It was also more reliable than GBLUP (topSNPs) for all four traits, and more reliable than BayesGC for three of the traits. Although GWABLUP showed a tendency towards inflation bias for three of the traits, this was not statistically significant. In a multitrait analysis, GWABLUP yielded the highest accuracy for two of the traits. However, for SCC, which was relatively unrelated to the yield traits, including yield trait GWAS-results reduced the reliability compared to a single trait analysis.

CONCLUSIONS

GWABLUP uses GWAS results to differentially weigh all the SNPs in a weighted GBLUP genomic prediction analysis. GWABLUP yielded up to 10% and 13% more reliable genomic predictions than GBLUP for single and multitrait analyses, respectively. Extension of GWABLUP to single-step analyses is straightforward.

Genome-wide association study for stayability at different calvings in Nellore beef cattle

BACKGROUNDING

Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life.

RESULTS

The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant.

CONCLUSION

Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

Association of Variants in Innate Immune Genes TLR4 and TLR5 with Reproductive and Milk Production Traits in Czech Simmental Cattle

Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal p-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The TLR4 variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the TLR4 variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the TLR5 data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three TLR5 polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data.

Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.

Optimizing genomic selection in soybean: An important improvement in agricultural genomics

Fast-paced yield improvement in strategic crops such as soybean is pivotal for achieving sustainable global food security. Precise genomic selection (GS), as one of the most effective genomic tools for recognizing superior genotypes, can accelerate the efficiency of breeding programs through shortening the breeding cycle, resulting in significant increases in annual yield improvement. In this study, we investigated the possible use of haplotype-based GS to increase the prediction accuracy of soybean yield and its component traits through augmenting the models by using sophisticated machine learning algorithms and optimized genetic information. The results demonstrated up to a 7% increase in the prediction accuracy when using haplotype-based GS over the full single nucleotide polymorphisms-based GS methods. In addition, we discover an auspicious haplotype block on chromosome 19 with significant impacts on yield and its components, which can be used for screening climate-resilient soybean genotypes with improved yield in large breeding populations.

Novel Insight Into the Role of ACSL1 Gene in Milk Production Traits in Buffalo

Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism and was highly expressed in the lactating mammary gland epithelial cells (MGECs). The objectives of the present study were to detect the polymorphisms within ACSL1 in Mediterranean buffalo, the genetic effects of these mutations on milk production traits, and understand the gene regulatory effects on MGECs. A total of twelve SNPs were identified by sequencing, including nine SNPs in the intronic region and three in the exonic region. Association analysis showed that nine SNPs were associated with one or more traits. Two haplotype blocks were identified, and among these haplotypes, the individuals carrying the H2H2 haplotype in block 1 and H5H1 in block 2 were superior to those of other haplotypes in milk production traits. Immunohistological staining of ACSL1 in buffalo mammary gland tissue indicated its expression and localization in MGECs. Knockdown of ACSL1 inhibited cell growth, diminished MGEC lipid synthesis and triglyceride secretion, and downregulated CCND1, PPARγ, and FABP3 expression. The overexpression of ACSL1 promoted cell growth, enhanced the triglyceride secretion, and upregulated CCND1, PPARγ, SREBP1, and FABP3. ACSL1 was also involved in milk protein regulation as indicated by the decreased or increased β-casein concentration and CSN3 expression in the knockdown or overexpression group, respectively. In summary, our present study depicted that ACSL1 mutations were associated with buffalo milk production performance. This may be related to its positive regulation roles on MGEC growth, milk fat, and milk protein synthesis. The current study showed the potential of the ACSL1 gene as a candidate for milk production traits and provides a new understanding of the physiological mechanisms underlying milk production regulation.

Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel

KEY MESSAGE

Significant QTL for sucrose concentration have been identified using a historical soybean genomic panel, which could aid in the development of food-grade soybean cultivars. Soybean (Glycine max (L.) Merr) is a crop of global importance for both human and animal consumption, which was domesticated in China more than 6000 years ago. A concern about losing genetic diversity as a result of decades of breeding has been expressed by soybean researchers. In order to develop new cultivars, it is critical for breeders to understand the genetic variability present for traits of interest in their program germplasm. Sucrose concentration is becoming an increasingly important trait for the production of soy-food products. The objective of this study was to use a genome-wide association study (GWAS) to identify putative QTL for sucrose concentration in soybean seed. A GWAS panel consisting of 266 historic and current soybean accessions was genotyped with 76 k genotype-by-sequencing (GBS) SNP data and phenotyped in four field locations in Ontario (Canada) from 2015 to 2017. Seven putative QTL were identified on chromosomes 1, 6, 8, 9, 10, 13 and 14. A key gene related to sucrose synthase (Glyma.06g182700) was found to be associated with the QTL located on chromosome 6. This information will facilitate efforts to increase the available genetic variability for sucrose concentration in soybean breeding programs and develop new and improved high-sucrose soybean cultivars suitable for the soy-food industry.

Validation of somatic cell score-associated SNPs from Holstein cattle in Sudanese Butana and Butana × Holstein crossbred cattle

The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, P_BF = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: P_BF = 0.003, Butana × Holstein: P_BF = 6.2 × 10⁻¹⁶). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci.

A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz)

MOTIVATION

Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery.

RESULTS

In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BACKGROUND

German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement.

RESULTS

Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%.

CONCLUSION

The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle

The aim of this study was to estimate genotype by time-lagged heat stress (HS) variance components as well as main and interaction SNP-marker effects for maternal HS during the last eight weeks of cow pregnancy, considering milk production traits recorded in the offspring generation. The HS indicator was the temperature humidity index (THI) for each week. A dummy variable with the code = 1 for the respective week for THI ≥ 60 indicated HS, otherwise, for no HS, the code = 0 was assigned. The dataset included test-day and lactation production traits from 14,188 genotyped first parity Holstein cows. After genotype quality control, 41,139 SNP markers remained for the genomic analyses. Genomic animal models without (model VC_nHS) and with in-utero HS effects (model VC_wHS) were applied to estimate variance components. Accordingly, for genome-wide associations, models GWA_nHS and GWA_wHS, respectively, were applied to estimate main and interaction SNP effects. Common genomic and residual variances for the same traits were very similar from models VC_nHS and VC_wHS. Genotype by HS interaction variances varied, depending on the week with in-utero HS. Among all traits, lactation milk yield with HS from week 5 displayed the largest proportion for interaction variances (0.07). For main effects from model GWA_wHS, 380 SNPs were suggestively associated with all production traits. For the SNP interaction effects from model GWA_wHS, we identified 31 suggestive SNPs, which were located in close distance to 62 potential candidate genes. The inferred candidate genes have various biological functions, including mechanisms of immune response, growth processes and disease resistance. Two biological processes excessively represented in the overrepresentation tests addressed lymphocyte and monocyte chemotaxis, ultimately affecting immune response. The modelling approach considering time-lagged genotype by HS interactions for production traits inferred physiological mechanisms being associated with health and immunity, enabling improvements in selection of robust animals.

Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle

Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide association studies (GWAS) have identified multiple loci associated with somatic cell score (SCS) and mastitis in cattle. However, most of the studies have been conducted in different parts of the world on various breeds, and none of the investigations have studied the genetic architecture of mastitis in Romanian dairy cattle breeds up to this point in time. In this study, we report the first GWAS for SCS in dairy cattle breeds from Romania. For GWAS, we used an Axiom Bovine v3 SNP-chip (>63,000 Single Nucleotide Polymorphism -SNPs) and 33,330 records from 690 cows belonging to Romanian Spotted (RS) and Romanian Brown (RB) cattle. The results found one SNP significantly associated with SCS in the RS breed and 40 suggestive SNPs with -log₁₀ (p) from 4 to 4.9 for RS and from 4 to 5.4 in RB. From these, 14 markers were located near 12 known genes (AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55) in RB cattle, 3 markers were close to ZDHHC19, DAPK1 and MMP7 genes, while one SNP overlapped the HERC3 gene in RS cattle. Four genes (HERC3, LUZP2, AKAP8 and MEGF10) associated with SCS in this study were previously reported in different studies. The most significant SNP (rs110749552) associated with SCS was located within the HERC3 gene. In both breeds, the SNPs and position of association signals were distinct among the three parities, denoting that mastitis is controlled by different genes that are dependent according to parity. The current results contribute to an expansion in the body of knowledge regarding the proportion of genetic variability explained by SNPs for SCS in dairy cattle.

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

The objectives of the current study were to detect putative genomic loci and to identify candidate genes associated with milk production traits in Egyptian buffalo. A total number of 161 479 daily milk yield (DMY) records and 60 318 monthly measures for fat and protein percentages (FP and PP, respectively), along with fat and protein yields (FY and PY, respectively) from 1670 animals were used. Genotyping was performed using Axiom® Buffalo Genotyping 90 K array. Genome-wide association study (GWAS) for each trait was performed using PLINK. After Bonferroni correction, 47 SNPs were associated with one or more milk production traits. These SNPs were distributed over 36 quantitative trait loci (QTL) and located on 20 buffalo chromosomes (BBU). For the 47 SNPs, one was overlapped for three traits (DMY, FY, and PY), six were associated with two traits (one for PP and PY and five for FY and PY) while the rest were associated with only one trait. Out of 36 identified QTL, eleven were overlapped with previously reported loci in buffalo and/or cattle populations. Some of these SNPs are placed within or close to potential candidate genes, for example: TPD52, ZBTB10, RALYL and SNX16 on BBU15, ADGRD1 on BBU17, ESRRG on BBU5 and GRIP1 on BBU4. This is the first reported study between genome-wide markers and milk components in Egyptian buffalo. Our findings provide useful information to explore the genetic mechanisms and relevant genes contributing to the variation in milk production traits. Further confirmation studies with larger population size are necessary to validate the findings and detect the causal genetic variants.

Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats.

Association analysis between constructed SNPLDBs and GCA effects of 9 quality-related traits in parents of hybrid rice (Oryza sativa L.)

BACKGROUND

The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F₂ bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F₁ plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis.

RESULTS

Among the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26.

CONCLUSIONS

Thirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.

Association of TLR gene variants in a Czech Red Pied cattle population with reproductive traits

The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.

Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing

A production herd of Czech Simmental cattle (Czech Red Pied, CRP), the conserved subpopulation of this breed, and the ancient local breed Czech Red cattle (CR) were screened for diversity in the antibacterial toll-like receptors (TLRs), which are members of the innate immune system. Polymerase chain reaction (PCR) amplicons of TLR1, TLR2, TLR4, TLR5, and TLR6 from pooled DNA samples were sequenced with PacBio technology, with 3- 5 ×  coverage per gene per animal. To increase the reliability of variant detection, the gDNA pools were sequenced in parallel with the Illumina X-ten platform at low coverage ( 60 × per gene). The diversity in conserved CRP and CR was similar to the diversity in conserved and modern CRP, representing 76.4 % and 70.9 % of its variants, respectively. Sixty-eight (54.4 %) polymorphisms in the five TLR genes were shared by the two breeds, whereas 38 (30.4 %) were specific to the production herd of CRP; 4 (3.2 %) were specific to the broad CRP population; 7 (5.6 %) were present in both conserved populations; 5 (4.0 %) were present solely for the conserved CRP; and 3 (2.4 %) were restricted to CR. Consequently, gene pool erosion related to intensive breeding did not occur in Czech Simmental cattle. Similarly, no considerable consequences were found from known bottlenecks in the history of Czech Red cattle. On the other hand, the distinctness of the conserved populations and their potential for resistance breeding were only moderate. This relationship might be transferable to other non-abundant historical cattle breeds that are conserved as genetic resources. The estimates of polymorphism impact using Variant Effect Predictor and SIFT software tools allowed for the identification of candidate single-nucleotide polymorphisms (SNPs) for association studies related to infection resistance and targeted breeding. Knowledge of TLR-gene diversity present in Czech Simmental populations may aid in the potential transfer of variant characteristics from other breeds.

Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Genetic Selection for Mastitis Resistance

Mastitis is a prevalent and costly disease on dairy farms. Improved management and hygiene can reduce the risk of infection by contagious or environmental pathogens, and genetic selection can confer permanent improvement in mastitis resistance. National veterinary recording systems in the Nordic countries have allowed direct selection for sire families with low incidence of clinical mastitis for 3 decades, whereas other countries have practiced indirect selection for lower somatic cell count. Recently, pooling of producer-recorded data from on-farm herd management software programs has enabled selection for reduced incidence of clinical mastitis in the United States and other leading dairy countries.

Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle

Background

Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involved in multiple processes, including the response to infection, inflammation, and post-infection healing. Low genetic heritability, environmental variations, and farm management differences further complicate the identification of links between genetic variants and mastitis resistance. Consequently, studies of the genetics of variation in mastitis resistance in dairy cattle lack agreement about the responsible genes.

Results

We associated 15,552,968 imputed whole-genome sequencing markers for 5147 Nordic Holstein cattle with mastitis resistance in a genome-wide association study (GWAS). Next, we augmented P-values for markers in genes in the associated regions using Gene Ontology terms, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and mammalian phenotype database. To confirm results of gene-based analyses, we used gene expression data from E. coli-challenged cow udders. We identified 22 independent quantitative trait loci (QTL) that collectively explained 14% of the variance in breeding values for resistance to clinical mastitis (CM). Using association test statistics with multiple pieces of independent information on gene function and differential expression during bacterial infection, we suggested putative causal genes with biological relevance for 12 QTL affecting resistance to CM in dairy cattle.

Conclusion

Combining information on the nearest positional genes, gene-based analyses, and differential gene expression data from RNA-seq, we identified putative causal genes (candidate genes with biological evidence) in QTL for mastitis resistance in Nordic Holstein cattle. The same strategy can be applied for other traits.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5050-x) contains supplementary material, which is available to authorized users.

Association of udder traits with single nucleotide polymorphisms in crossbred Bos indicus-Bos taurus cows

The size, support, and health of udders limit the productive life of beef cows, especially those with background, because, in general, such cows have a reputation for problems with udders. Genomic association studies of bovine udder traits have been conducted in dairy cattle and recently in Continental European beef breeds but not in cows with background. The objective of this study was to determine associations of SNP and udder support scores, teat length, and teat diameter in half (Nellore), half (Angus) cows. Udders of cows ( = 295) born from 2003 to 2007 were evaluated for udder support and teat length and diameter ( = 1,746 records) from 2005 through 2014. These included a subjective score representing udder support (values of 1 indicated poorly supported, pendulous udders and values of 9 indicated very well-supported udders) and lengths and diameters of individual teats in the 4 udder quarters as well as the average. Cows were in full-sibling or half-sibling families. Residuals for each trait were produced from repeated records models with cow age category nested within birth year of cows. Those residuals were averaged to become the dependent variables for genomewide association analyses. Regression analyses of those dependent variables included genotypic values as explanatory variables for 34,980 SNP from a commercially available array and included the genomic relationship matrix. Fifteen SNP loci on BTA 5 were associated (false discovery rate controlled at 0.05) with udder support score. One of those was also detected as associated with average teat diameter. Three of those 15 SNP were located within genes, including one each in (), (), and (). These are notable for their functional role in some aspect of mammary gland formation or health. Other candidate genes for these traits in the vicinity of the SNP loci include () and (). Because these were detected in Nellore-Angus crossbred cows, which typically have very well-formed udders with excellent support across their productive lives, similar efforts in other breeds should be completed, because that may facilitate further refinement of genomic regions responsible for variation in udder traits important in multiple breeds.

Validating genome-wide associated signals for clinical mastitis in German Holstein cattle

A validation study for six genomic regions previously identified by a genome-wide association study for somatic cell score was conducted with data of clinical mastitis in German Holstein cattle. Out of 10 tested SNPs, five on chromosomes 6, 13 and 19 were significantly associated with clinical mastitis (P < 0.05). Three SNPs on chromosomes 6 and 19 had the same direction of effect as those previously reported in the initial genome-wide association study for somatic cell score. The other two SNPs on chromosome 13 had opposite effects. As well as validating associations within known QTL from previous studies, e.g. chromosomes 6 and 19, novel loci on chromosome 13 were confirmed. Promising candidate genes are, for example: deoxycytidine kinase, immunoglobulin J chain, vitamin D binding protein, forkhead box K2, sodium/hydrogen exchanger 8 and cytoplasmic nuclear factor of activated T-cells 2. Our confirmation study provides additional evidence for the functional role of the linked genomic regions to immune response. This information can be used as a basis for further functional studies for those potential genes.

Genome-wide association mapping for flowering and maturity in tropical soybean: implications for breeding strategies

Knowledge of the genetic architecture of flowering and maturity is needed to develop effective breeding strategies in tropical soybean. The aim of this study was to identify haplotypes across multiple environments that contribute to flowering time and maturity, with the purpose of selecting desired alleles, but maintaining a minimal impact on yield-related traits. For this purpose, a genome-wide association study (GWAS) was undertaken to identify genomic regions that control days to flowering (DTF) and maturity (DTM) using a soybean association mapping panel genotyped for single nucleotide polymorphism (SNP) markers. Complementarily, yield-related traits were also assessed to discuss the implications for breeding strategies. To detect either stable or specific associations, the soybean cultivars (N = 141) were field-evaluated across eight tropical environments of Brazil. Seventy-two and forty associations were significant at the genome-wide level relating respectively to DTM and DTF, in two or more environments. Haplotype-based GWAS identified three haplotypes (Gm12_Hap12; Gm19_Hap42 and Gm20_Hap32) significantly co-associated with DTF, DTM and yield-related traits in single and multiple environments. These results indicate that these genomic regions may contain genes that have pleiotropic effects on time to flowering, maturity and yield-related traits, which are tightly linked with multiple other genes with high rates of linkage disequilibrium.

A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean cultivars (N = 169) were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes) identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12). The haplotype block 42 on Chr19 (Gm19_Hap42) was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.

Validation of PDE9A Gene Identified in GWAS Showing Strong Association with Milk Production Traits in Chinese Holstein

Phosphodiesterase9A (PDE9A) is a cyclic guanosine monophosphate (cGMP)-specific enzyme widely expressed among the tissues, which is important in activating cGMP-dependent signaling pathways. In our previous genome-wide association study, a single nucleotide polymorphism (SNP) (BTA-55340-no-rs(b)) located in the intron 14 of PDE9A, was found to be significantly associated with protein yield. In addition, we found that PDE9A was highly expressed in mammary gland by analyzing its mRNA expression in different tissues. The objectives of this study were to identify genetic polymorphisms of PDE9A and to determine the effects of these variants on milk production traits in dairy cattle. DNA sequencing identified 11 single nucleotide polymorphisms (SNPs) and six SNPs in 5' regulatory region were genotyped to test for the subsequent association analyses. After Bonferroni correction for multiple testing, all these identified SNPs were statistically significant for one or more milk production traits (p < 0.0001~0.0077). Interestingly, haplotype-based association analysis revealed similar effects on milk production traits (p < 0.01). In follow-up RNA expression analyses, two SNPs (c.-1376 G>A, c.-724 A>G) were involved in the regulation of gene expression. Consequently, our findings provide confirmatory evidences for associations of PDE9A variants with milk production traits and these identified SNPs may serve as genetic markers to accelerate Chinese Holstein breeding program.

Prospecting major genes in dairy buffaloes

BACKGROUND

Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different.

RESULTS

The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits.

CONCLUSIONS

Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production.

Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins

BACKGROUND

The sensitivity of genome-wide association studies for the detection of quantitative trait loci (QTL) depends on the density of markers examined and the statistical models used. This study compares the performance of three marker densities to refine six previously detected QTL regions for mastitis traits: 54 k markers of a medium-density SNP (single nucleotide polymorphism) chip (MD), imputed 777 k markers of a high-density SNP chip (HD), and imputed whole-genome sequencing data (SEQ). Each dataset contained data for 4496 Danish Holstein cattle. Comparisons were performed using a linear mixed model (LM) and a Bayesian variable selection model (BVS).

RESULTS

After quality control, 587, 7825, and 78 856 SNPs in the six targeted regions remained for MD, HD, and SEQ data, respectively. In general, the association patterns between SNPs and traits were similar for the three marker densities when tested using the same statistical model. With the LM model, 120 (MD), 967 (HD), and 7209 (SEQ) SNPs were significantly associated with mastitis, whereas with the BVS model, 43 (MD), 131 (HD), and 1052 (SEQ) significant SNPs (Bayes factor > 3.2) were observed. A total of 26 (MD), 75 (HD), and 465 (SEQ) significant SNPs were identified by both models. In addition, one, 16, and 33 QTL peaks for MD, HD, and SEQ data were detected according to the QTL intensity profile of SNP bins by post-analysis of the BVS model.

CONCLUSIONS

The power to detect significant associations increased with increasing marker density. The BVS model resulted in clearer boundaries between linked QTL than the LM model. Using SEQ data, the six targeted regions were refined to 33 candidate QTL regions for udder health. The comparison between these candidate QTL regions and known genes suggested that NPFFR2, SLC4A4, DCK, LIFR, and EDN3 may be considered as candidate genes for mastitis susceptibility.