Single-nucleotide polymorphisms in the 5′ UTR of UDP-glucose dehydrogenase (PtUGDH) associate with wood properties in Populus tomentosa

Association studies have emerged as a powerful tool for identification of markers associated with quantitative traits in forest trees. The cytosolic enzyme uridine 5′ diphosphate-glucose dehydrogenase (UGDH) converts UDP-glucose to UDP-glucuronate and affects cell wall formation in higher plants. Here, we used association genetics to identify UDP-glucose dehydrogenase (PtUGDH) allelic variation that associates with wood quality traits in Populus tomentosa. We isolated a 1,828 bp PtUGDH cDNA encoding a polypeptide of 481 amino acids. Expression analysis revealed that PtUGDH was expressed predominantly in young root, developing xylem from vascular tissues, and young leaves, suggesting that UGDH functions in cell wall formation. We identified 59 single-nucleotide polymorphisms (SNPs; π _T ?=?0.00475) by resequencing the PtUGDH locus of 40 individuals and genotyped the 22 most common SNPs (minor allele frequency >10 %) in a discovery population (n?=?426). Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r ²?<?0.1, within 300 bp). Association studies indicated that three SNPs (false discovery rate, Q?<?0.05) and 12 haplotypes (Q?<?0.05) were significantly associated with wood properties. The three significant SNPs are all in the 5′ untranslated regions of PtUGDH, and the phenotypic variance explained by each SNP ranged from 5.37 to 11.97 %. We validated one association in a validation population (n?=?1,200) and validated another association by examining its effect on gene expression. The present study provided molecular markers associated with fiber length and holocellulose content, markers that have potential applications in marker-assisted breeding.     

Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection

Association mapping based on the linkage disequilibrium provides a promising tool to identify genes responsible for quantitative variations underlying complex traits. Presented here is a maize association mapping panel consisting of 155 inbred lines with mainly temperate germplasm, which was phenotyped for 34 traits and genotyped using 82 SSRs and 1,536 SNPs. Abundant phenotypic and genetic diversities were observed within the panel based on the phenotypic and genotypic analysis. A model-based analysis using 82 SSRs assigned all inbred lines to two groups with eight subgroups. The relative kinship matrix was calculated using 884 SNPs with minor allele frequency ≥20% indicating that no or weak relationships were identified for most individual pairs. Three traits (total tocopherol content in maize kernel, plant height and kernel length) and 1,414 SNPs with missing data <20% were used to evaluate the performance of four models for association mapping analysis. For all traits, the model controlling relative kinship (K) performed better than the model controlling population structure (Q), and similarly to the model controlling both population structure and relative kinship (Q + K) in this panel. Our results suggest this maize panel can be used for association mapping analysis targeting multiple agronomic and quality traits with optimal association model.     

Genotypic variation in wood properties and growth traits of triploid hybrid clones of Populus tomentosa at three clonal trials

To better understand the genetic control of growth traits (tree height, dbh, and stem volume) and wood properties (basic wood density and fiber length) in triploid hybrid clones of Populus tomentosa, genetic relationships among selected wood properties with growth traits were examined in 5-year-old clonal field trials located in Yanzhou, Gaotang, and Xiangfen, northern China. In total, 180 trees from 10 clones were sampled from the three sites. The site had a moderate effect on basic wood density (BWD), stem wood dry weight (DWT), and tree growth and had a highly significant effect on fiber length (FL) (P?<?0.001). Clonal effects were also significant (P?<?0.05) for all studied traits (except for diameter at breast height (DBH) and stem volume (SV)). Clone × site interaction was significant for all the studied traits except for FL. The estimated repeatability of clonal means for FL (0.91) was higher than for BWD (0.71), DWT (0.62), tree height (0.62), DBH (0.61), and SV (0.55). Intersite genetic correlation estimates indicated that wood properties were more stable than growth traits. Phenotypic correlation estimates between SV and BWD ranged from ?0.29 to ?0.10.     

Genetic variation of wood chemical traits and association with underlying genes in Eucalyptus urophylla

We developed a quantitative and association genetic study with Eucalyptus urophylla using a progeny trial. Based on a sample of 831 trees distributed in 84 half-sib families whose wood was phenotyped by near-infrared spectroscopy, the results showed that traits related to lignin, cellulose, and wood extractives presented significant additive genetic variability with moderate to high narrow sense heritability (h ²?=?0.28 to 0.93). Genetic correlations varied with high standard error and showed low to moderate values. Using three cellulose synthase genes (EuCesA1, EuCesA2, and EuCesA3) and three candidate genes involved in the lignin pathway (EuC4H1, EuC4H2, and EuCAD2), an association study was performed for each of the gene action models (co-dominant, recessive, and dominant) using two methods. Firstly, single-marker association tests were done and 539 tests (49 single nucleotide polymorphisms (SNPs)?×?11 traits) were analyzed. After Bonferroni correction with a significance level of P?=?0.00102, only four SNPs presented significant association with syringyl and syringyl-to-guaiacyl ratio with an adjusted coefficient of determination varying between 2.6 and 4.4 %. Secondly, a model selection method, the backward approach, was implemented. Similar SNPs were detected by both the backward selection and the individual marker approaches. However, the latter detected new associations with other traits, genes, and SNPs and improved the quality of the model as shown by the BIC criteria and the higher adjusted determination coefficient (1.5 to 8.3 %). Our results reveal that cellulose genes can be associated with lignin traits (syringyl-to-guaiacyl ratio) and stress the possible pleiotropic effect of some genes.     

Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa

Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.     

Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle

Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10^?6) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.     

Is there an optimum level of diversity in utilization of genetic resources?

Key message

Capitalizing upon the genomic characteristics of long-term random mating populations, sampling from pre-selected landraces is a promising approach for broadening the genetic base of elite germplasm for quantitative traits.

Abstract

Genome-enabled strategies for harnessing untapped allelic variation of landraces are currently evolving. The success of such approaches depends on the choice of source material. Thus, the analysis of different strategies for sampling allelic variation from landraces and their impact on population diversity and linkage disequilibrium (LD) is required to ensure the efficient utilization of diversity. We investigated the impact of different sampling strategies on diversity parameters and LD based on high-density genotypic data of 35 European maize landraces each represented by more than 20 individuals. On average, five landraces already captured ~95% of the molecular diversity of the entire dataset. Within landraces, absence of pronounced population structure, consistency of linkage phases and moderate to low LD levels were found. When combining data of up to 10 landraces, LD decay distances decreased to a few kilobases. Genotyping 24 individuals per landrace with 5k SNPs was sufficient for obtaining representative estimates of diversity and LD levels to allow an informed pre-selection of landraces. Integrating results from European with Central and South American landraces revealed that European landraces represent a unique and diverse spectrum of allelic variation. Sampling strategies for harnessing allelic variation from landraces depend on the study objectives. If the focus lies on the improvement of elite germplasm for quantitative traits, we recommend sampling from pre-selected landraces, as it yields a wide range of diversity, allows optimal marker imputation, control for population structure and avoids the confounding effects of strong adaptive alleles.

     

Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing methods, a new allelic variant corresponding to the A → G mutation (aspartic to glycine amino acid replacement) of the bovine CACNA2D1 gene was detected. Two alleles and three genotypes (AA, AG, and GG) were defined. Genetic character indicated that the A526745G locus showed moderate polymorphism and was in Hardy–Weinberg equilibrium. Gene-specific SNP marker association analysis showed that the A526745G mutant was significantly associated with carcass weight, dressing percentage, meat percentage, and backfat thickness. The results add new evidence that CACNA2D1 is an important candidate gene for the selection of carcass and meat quality traits in the cattle industry.     

Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan

We examined the genetic background of nonalcoholic fatty liver disease (NAFLD) in the Japanese population, by performing a genome-wide association study (GWAS). For GWAS, 392 Japanese NAFLD subjects and 934 control individuals were analyzed. For replication studies, 172 NAFLD and 1,012 control subjects were monitored. After quality control, 261,540 single-nucleotide polymorphisms (SNPs) in autosomal chromosomes were analyzed using a trend test. Association analysis was also performed using multiple logistic regression analysis using genotypes, age, gender and body mass index (BMI) as independent variables. Multiple linear regression analyses were performed to evaluate allelic effect of significant SNPs on biochemical traits and histological parameters adjusted by age, gender, and BMI. Rs738409 in the PNPLA3 gene was most strongly associated with NAFLD after adjustment (P = 6.8 × 10^?14, OR = 2.05). Rs2896019, and rs381062 in the PNPLA3 gene, rs738491, rs3761472, and rs2143571 in the SAMM50 gene, rs6006473, rs5764455, and rs6006611 in the PARVB gene had also significant P values (<2.0 × 10^?10) and high odds ratios (1.84–2.02). These SNPs were found to be in the same linkage disequilibrium block and were associated with decreased serum triglycerides and increased aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in NAFLD patients. These SNPs were associated with steatosis grade and NAFLD activity score (NAS). Rs738409, rs2896019, rs738491, rs6006473, rs5764455, and rs6006611 were associated with fibrosis. Polymorphisms in the SAMM50 and PARVB genes in addition to those in the PNPLA3 gene were observed to be associated with the development and progression of NAFLD.     

Time‐specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus

In perennial woody plants, the coordinated increase of stem height and diameter during juvenile growth improves competitiveness (i.e. access to light); however, the factors underlying variation in stem growth remain unknown in trees. Here, we used linkage‐linkage disequilibrium (linkage‐LD) mapping to decipher the genetic architecture underlying three growth traits during juvenile stem growth. We used two Populus populations: a linkage mapping population comprising a full‐sib family of 1,200 progeny and an association mapping panel comprising 435 unrelated individuals from nearly the entire natural range of Populus tomentosa. We mapped 311 quantitative trait loci (QTL) for three growth traits at 12 timepoints to 42 regions in 17 linkage groups. Of these, 28 regions encompassing 233 QTL were annotated as 27 segmental homology regions (SHRs). Using SNPs identified by whole‐genome re‐sequencing of the 435‐member association mapping panel, we identified significant SNPs (P ≤ 9.4 × 10^?7) within 27 SHRs that affect stem growth at nine timepoints with diverse additive and dominance patterns, and these SNPs exhibited complex allelic epistasis over the juvenile growth period. Nineteen genes linked to potential causative alleles that have time‐specific or pleiotropic effects, and mostly overlapped with significant signatures of selection within SHRs between climatic regions represented by the association mapping panel. Five genes with potential time‐specific effects showed species‐specific temporal expression profiles during the juvenile stages of stem growth in five representative Populus species. Our observations revealed the importance of considering temporal genetic basis of complex traits, which will facilitate the molecular design of tree ideotypes.     

Novel SNPs in the bovine ADIPOQ and PPARGC1A genes are associated with carcass traits in Hanwoo (Korean cattle)

Adiponectin (ADIPOQ) modulates several biological processes including energy homeostasis, glucose and lipid metabolism. The bovine ADIPOQ gene was located near the QTL affecting marbling, ribeye muscle area and fat thickness on BTA1. The gene encoding peroxisome proliferator-activated receptor-γ coactivator-1α (PPARGC1A) was located within the QTL region of the traits on BTA6. Moreover, its protein product has various biological functions such as cellular energy homeostasis, including adaptive thermogenesis, adipogenesis and gluconeogenesis. Therefore, the ADIPOQ and PPARGC1A genes are a positional and functional candidate gene for carcass traits in beef cattle. The objectives of this study were to identify polymorphisms in the bovine ADIPOQ and PPARGC1A genes, to evaluate their associations with carcass traits in Hanwoo (Korean cattle) population. We identified nine SNPs in the ADIPOQ gene. Two SNPs (DQ156119: g.1436T > C and DQ156119: g.1454A > G) in the promoter region were recognized as new SNPs identified in Hanwoo. Association analysis indicated that the g.1454A > G SNP genotype was significantly associated with effects on LMA (P = 0.004) and BF (P = 0.021). The ADIPOQ haplotype was also found to have significant effect on the LMA. In the PPARGC1A gene, we identified 11 SNPs in the two unexplored regions (intron 3 and 5). Among them, seven SNPs were located in intron 3 and four SNPs were located in intron 5. Of these 11 putative novel SNPs, two SNPs (AY839822: g.292C > T and AY839823: g.1064C > T) with minor allele frequency (MAF) > 0.20 were examined for associations with carcass traits. The association analysis revealed that both SNPs in PPARGC1A gene were significantly associated with LMA (P < 0.05). These findings suggest that the SNPs of bovine ADIPOQ and PPARGC1A genes may be a useful molecular marker for selection of carcass traits in Hanwoo.     

Association of HSL gene E1-c.276C>T and E8-c.51C>T mutation with economical traits of Chinese Simmental cattle

Hormone-sensitive lipase (HSL) is responsible for the decomposition of triglycerides in adipose tissue to release free fatty acids, and it is a key rate-limiting enzyme in the regulation of adipose tissue deposition and decomposition. The objective of this study was to evaluate the association between novel SNPs in the coding region of bovine HSL gene and carcass and meat quality traits of Chinese Simmental-cross steers. Two novel SNPs were genotyped and the 47 traits of carcass and meat quality traits were measured in the population studied. Statistical analysis revealed that the SNPs of HSL gene were associated with the carcass and meat quality traits. The individuals with TT genotypes of E1-276C>T showed significant higher dressing percentage, net meat rate, hind legs circumference, fat coverage rate, mesenteric fat and kidney fat (p < 0.05). E8-51C>T (P17S) also showed a significant association with the pH of beef and fatty acids content in Chinese Simmental cattle (p < 0.01). Our findings indicated that polymorphisms in HSL might be one of important genetic factors that influence carcass yield and meat quality in beef cattle, and it may be a useful marker for meat quality traits in future marker-assisted selection programs in beef cattle breeding and production.     

Association of Porcine IGF Binding Protein-5 Gene with Meat Quality

IGFBP-5 is a member of the IGF families. Using PCR-SSCP, genotypic and allelic frequencies were analyzed in 18 pig breeds (n = 600). The association between haplotypes and production performance was analyzed in a Jinhua × Pietrain population family (n = 212, total 24 traits). Two SNPs (T199C and G485A) within the gene were analyzed. The breeds had different genotypic and allelic frequencies. Typically, the Chinese native pig breeds carried a higher allele C and G frequency (over 50%) than those of the European pigs, and only Guangdong Large White and wild boar were at Hardy–Weinberg equilibrium. The pigs carrying the CG haplotype had higher hue, loin, and thigh pH1 values than pigs with the TA haplotype, and pigs with the TA haplotype had the lowest loin pH2 value and highest color-a value among the haplotypes. It is proposed that the IGFBP-5 gene is associated with the variation in meat quality, especially in pH value together with other QTLs on chromosome 15.     

Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield

Wood is an important biological resource which contributes to nutrient and hydrology cycles through ecosystems, and provides structural support at the plant level. Thousands of genes are involved in wood development, yet their effects on phenotype are not well understood. We have exploited the low genomic linkage disequilibrium (LD) and abundant phenotypic variation of forest trees to explore allelic diversity underlying wood traits in an association study. Candidate gene allelic diversity was modelled against quantitative variation to identify SNPs influencing wood properties, growth and disease resistance across three populations of Corymbia citriodora subsp. variegata, a forest tree of eastern Australia. Nine single nucleotide polymorphism (SNP) associations from six genes were identified in a discovery population (833 individuals). Associations were subsequently tested in two smaller populations (130-160 individuals), 'validating' our findings in three cases for actin 7 (ACT7) and COP1 interacting protein 7 (CIP7). The results imply a functional role for these genes in mediating wood chemical composition and growth, respectively. A flip in the effect of ACT7 on pulp yield between populations suggests gene by environment interactions are at play. Existing evidence of gene function lends strength to the observed associations, and in the case of CIP7 supports a role in cortical photosynthesis.     

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals’ growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction–restriction fragment length polymorphism (forced PCR–RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.