High connectivity among argali sheep from Afghanistan and adjacent countries: Inferences from neutral and candidate gene microsatellites

We quantified population connectivity and genetic variation in the Marco Polo subspecies of argali mountain sheep (Ovis ammon polii) by genotyping 9 neutral and 8 candidate gene microsatellite loci in 172 individuals noninvasively sampled across five study areas in Afghanistan, China, and Tajikistan. Heterozygosity and allelic richness were generally high (mean H = 0.67, mean A = 6.1), but were significantly lower in the China study area (H = 0.61, P < 0.001; A = 4.9, P < 0.01). One marker in an immune system gene (TCRG4) showed an excess of rare alleles compared to neutral expectations. Another immune system gene (GLYCAM-1) showed excessive differentiation (high F _ST) between study areas. Estimates of genetic differentiation were similar (F _ST = 0.035 vs. 0.033) with and without the two loci deviating from neutrality, suggesting that selection is not a primary driver of overall molecular variation, and that candidate gene loci can be used for connectivity monitoring, as long as selection tests are conducted to avoid biased gene flow estimates. Adequate protection of argali and maintenance of inter-population connectivity will require monitoring and international cooperation because argali exhibit high gene flow across international borders.     

Genome-wide assessment reveals a significant association between ACSS3 and physical activity

Recent genetic studies have identified physical activity (PA)-susceptible loci in European ancestry subjects; however, due to considerable genetic differences, these findings are not likely extendable to East Asian populations. Therefore, the present study aimed to identify significantly associated PA-susceptible loci using genome-wide association studies (GWASs) with East Asian (EAS) subjects and to generalize the findings to European (EUR) ancestries. The mRNA levels of genes located near the genome-wide significantly associated single-nucleotide polymorphisms (SNP) were compared under PA and control conditions. Rs74937256, located in ACSS3 (chromosome 12), which primarily functions in skeletal muscle tissues, was identified as a genome-wide significant variant (P = 6.06 × 10⁻⁹) in EAS. Additionally, the rs2525840, also in ACSS3 satisfied the Bonferroni corrected significance (P = 3.77 × 10⁻⁵) in EUR. We found that rs74937256 is an expressed trait locus of ACSS3 (P = 10⁻⁴), and ACSS3 mRNA expression significantly differs after PA, based on PrediXcan (P = 7 × 10⁻⁸) and the gene expression omnibus database (P = 0.043).     

The population genetic structure of a common tropical damselfish on the Great Barrier Reef and eastern Papua New Guinea

Understanding patterns of connectivity in marine species is vital for the management and conservation of marine biodiversity. Here, the population genetic structure of a common and abundant tropical reef damselfish, Pomacentrus amboinensis, is reported. Using nine polymorphic microsatellite loci, the genetic structure at both small (i.e., around Lizard Island, Great Barrier Reef [GBR]) and large (GBR and Papua New Guinea [PNG]) spatial and temporal scales (2–1,600 km; 28 days– 6 years; n = 1,119) was analyzed. Temporal analyses found no evidence of genetic differentiation within or between Lizard Island recruitment pulses (R _ST = −0.001, P = 0.788), or corresponding established adult populations separated by 6 years of sampling (R _ST = 0.003, P = 0.116). The spatial analysis revealed that P. amboinensis populations are largely panmictic on the GBR and eastern PNG (R _ST = 0.001, P = 0.913), the only genetic discontinuity being between Kimbe Bay to the north of PNG and all populations south of PNG (R _ST = 0.077, P < 0.0001). Despite assumed high levels of self-recruitment based on previous tagging studies (15–60%), data presented here indicate that enough recruits are dispersing to impede the evolution of genetic structure over distances as great as 1,600 kms in this species. Data therefore indicate that the temporal genetic stability recorded here is maintained by high levels of gene flow.     

Genome-wide association study identifies 7q11.22 and 7q36.3 associated with noise-induced hearing loss among Chinese population

Noise-induced hearing loss (NIHL) seriously affects the life quality of humans and causes huge economic losses to society. To identify novel genetic loci involved in NIHL, we conducted a genome-wide association study (GWAS) for this symptom in Chinese populations. GWAS scan was performed in 89 NIHL subjects (cases) and 209 subjects with normal hearing who have been exposed to a similar noise environment (controls), followed by a replication study consisting of 53 cases and 360 controls. We identified that four candidate pathways were nominally significantly associated with NIHL, including the Erbb, Wnt, hedgehog and intraflagellar transport pathways. In addition, two novel index single-nucleotide polymorphisms, rs35075890 in the intron of AUTS2 gene at 7q11.22 (combined P = 1.3 × 10⁻⁶) and rs10081191 in the intron of PTPRN2 gene at 7q36.3 (combined P = 2.1 × 10⁻⁶), were significantly associated with NIHL. Furthermore, the expression quantitative trait loci analyses revealed that in brain tissues, the genotypes of rs35075890 are significantly associated with the expression levels of AUTS2, and the genotypes of rs10081191 are significantly associated with the expressions of PTPRN2 and WDR60. In conclusion, our findings highlight two novel loci at 7q11.22 and 7q36.3 conferring susceptibility to NIHL.     

Patterns of DNA sequence variation at candidate gene loci in black poplar (<Emphasis Type="Italic">Populus nigra</Emphasis> L.) as revealed by single nucleotide polymorphisms

Black poplar (Populus nigra L.) is an economically and ecologically important tree species and an ideal organism for studies of genetic variation. In the present work, we use a candidate gene approach to infer the patterns of DNA variation in natural populations of this species. A total of 312 single nucleotide polymorphisms (SNPs) are found among 8,056 bp sequenced from nine drought-adaptation and photosynthesis-related gene loci. The median SNP frequency is one site per 26 bp. The average nucleotide diversity is calculated to be θ_W = 0.01074 and π_T = 0.00702, higher values than those observed in P. tremula, P. trichocarpa and most conifer species. Tests of neutrality for each gene reveal a general excess of low-frequency mutations, a greater number of haplotypes than expected and an excess of high-frequency derived variants in P. nigra, which is consistent with previous findings that genetic hitchhiking has occurred in this species. Linkage disequilibrium is low, decaying rapidly from 0.45 to 0.20 or less within a distance of 300 bp, although the declines of r ² are variable among different loci. This is similar to the rate of decay reported in most other tree species. Our dataset is expected to enhance understanding of how evolutionary forces shape genetic variation, and it will contribute to molecular breeding in black poplar.     

Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar ‘Hartwig’ to three soybean cyst nematode populations

Soybean [Glycine max (L.) Merr.] cultivars varied in their resistance to different populations of the soybean cyst nematode (SCN), Heterodera glycines, called HG Types. The rhg1 locus on linkage group G was necessary for resistance to all HG types. However, the loci for resistance to H. glycines HG Type 1.3- (race 14) and HG Type 1.2.5- (race 2) of the soybean cyst nematode have varied in their reported locations. The aims were to compare the inheritance of resistance to three nematode HG Types in a population segregating for resistance to SCN and to identify the underlying quantitative trait loci (QTL). ‘Hartwig’, a soybean cultivar resistant to most SCN HG Types, was crossed with the susceptible cultivar ‘Flyer’. A total of 92 F5-derived recombinant inbred lines (RILs; or inbred lines) and 144 molecular markers were used for map development. The rhg1 associated QTL found in earlier studies were confirmed and shown to underlie resistance to all three HG Types in RILs (Satt309; HG Type 0, P = 0.0001 R ² = 22%; Satt275; HG Type 1.3, P = 0.001, R ² = 14%) and near isogeneic lines (NILs; or iso-lines; Satt309; HG Type 1.2.5-, P = 0.001 R ² = 24%). A new QTL underlying resistance to HG Type 1.2.5- was detected on LG D2 (Satt574; P = 0.001, R ² = 11%) among 14 RILs resistant to the other HG types. The locus was confirmed in a small NIL population consisting of 60 plants of ten genotypes (P = 0.04). This QTL (cqSCN-005) is located in an interval previously associated with resistance to both SDS leaf scorch from ‘Pyramid’ and ‘Ripley’ (cqSDS-001) and SCN HG Type 1.3- from Hartwig and Pyramid. The QTL detected will allow marker assisted selection for multigenic resistance to complex nematode populations in combination with sudden death syndrome resistance (SDS) and other agronomic traits.     

Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks

The evidence for adaptive phenotypic differentiation in mobile marine species remains scarce, partly due to the difficulty of obtaining quantitative genetic data to demonstrate the genetic basis of the observed phenotypic differentiation. Using a combination of phenotypic and molecular genetic approaches, we elucidated the relative roles of natural selection and genetic drift in explaining lateral plate number differentiation in threespine sticklebacks (Gasterosteus aculeatus) across the entire Baltic Sea basin (approximately 392 000 km²). We found that phenotypic differentiation (P_ST = 0.213) in plate number exceeded that in neutral markers (F_ST = 0.008), suggesting an adaptive basis for the observed differentiation. Because a close correspondence was found between plate phenotype and genotype at a quantitative trait loci (QTL; STN381) tightly linked to the gene (Ectodysplasin) underlying plate variation, the evidence for adaptive differentiation was confirmed by comparison of F_ST at the QTL (F_STQ = 0.089) with F_ST at neutral marker loci. Hence, the results provide a comprehensive demonstration of adaptive phenotypic differentiation in a high‐gene‐flow marine environment with direct, rather than inferred, verification for the genetic basis of this differentiation. In general, the results illustrate the utility of P_ST–F_ST–F_STQ comparisons in uncovering footprints of natural selection and evolution and add to the growing evidence for adaptive genetic differentiation in high‐gene‐flow marine environments, including that of the relatively young Baltic Sea.     

Genetic diversity and differentiation of <Emphasis Type="Italic">Fagus orientalis</Emphasis> Lipsky in Hyrcanian forests revealed by nuclear and chloroplast microsatellite markers

Oriental beech (Fagus orientalis Lipsky) is a widespread monoecious and wind-pollinated tree species. It is one of the major components of the Hyrcanian forests of Iran and it is of both ecological and economical importance. Twelve beech stands were surveyed at 9 chloroplast (cp) and 6 nuclear (n) polymorphic microsatellite loci (simple sequence repeats, SSR) to provide information on distribution of genetic diversity within and among populations and on gene conservation and silvicultural management of this species. High levels of genetic differentiation were detected for the chloroplast genome (F _ST = 0.80 and R _ST = 0.95), in sharp contrast to the nuclear genome (F _ST = 0.06, R _ST = 0.05). The analysis of molecular variance (AMOVA) showed that 48% of the total cpSSR variation was attributable to differences among regions and 30% to differences among populations within regions, suggesting multiple origins of beech populations in Hyrcanian forests. Nuclear SSRs confirmed the presence of significant differentiation among populations and among geographic regions, even if, as expected, this was less pronounced than that found with cpSSRs (based on AMOVA, differences among regions and among populations within regions each contribute 5% to total nSSR variance). A highly significant correlation between genetic (nSSRs) and geographic distances (R ² = 0.522) was estimated, thus showing an isolation by distance effect. The application of spatial analysis of molecular variance (SAMOVA) using both marker data allowed identification of genetically homogeneous groups of populations. Possible applications of these results for the certification of provenances and/or seed lots and for designing conservation programs are presented and discussed.     

The inheritance of resistance to Verticillium wilt caused by race 1 isolates of <Emphasis Type="Italic">Verticillium dahliae</Emphasis> in the lettuce cultivar La Brillante

Verticillium wilt of lettuce caused by Verticillium dahliae can cause severe economic damage to lettuce producers. Complete resistance to race 1 isolates is available in Lactuca sativa cultivar (cv.) La Brillante and understanding the genetic basis of this resistance will aid development of new resistant cultivars. F₁ and F₂ families from crosses between La Brillante and three iceberg cultivars as well as a recombinant inbred line population derived from L. sativa cv. Salinas 88 × La Brillante were evaluated for disease incidence and disease severity in replicated greenhouse and field experiments. One hundred and six molecular markers were used to generate a genetic map from Salinas 88 × La Brillante and for detection of quantitative trait loci. Segregation was consistent with a single dominant gene of major effect which we are naming Verticillium resistance 1 (Vr1). The gene described large portions of the phenotypic variance (R ² = 0.49–0.68) and was mapped to linkage group 9 coincident with an expressed sequence tag marker (QGD8I16.yg.ab1) that has sequence similarity with the Ve gene that confers resistance to V. dahliae race 1 in tomato. The simple inheritance of resistance indicates that breeding procedures designed for single genes will be applicable for developing resistant cultivars. QGD8I16.yg.ab1 is a good candidate for functional analysis and development of markers suitable for marker-assisted selection.     

A large-scale candidate gene association study of age at menarche and age at natural menopause

Recent genome-wide association (GWA) studies have identified several novel genetic loci associated with age at menarche and age at natural menopause. However, the stringent significance threshold used in GWA studies potentially led to false negatives and true associations may have been overlooked. Incorporating biologically relevant information, we examined whether common genetic polymorphisms in candidate genes of nine groups of biologically plausible pathways and related phenotypes are associated with age at menarche and age at natural menopause. A total of 18,862 genotyped and imputed single nucleotide polymorphisms (SNPs) in 278 genes were assessed for their associations with these two traits among a total of 24,341 women from the Nurses’ Health Study (NHS, N = 2,287) and the Women’s Genome Health Study (WGHS, N = 22,054). Linear regression was used to assess the marginal association of each SNP with each phenotype. We adjusted for multiple testing within each gene to identify statistically significant SNP associations at the gene level. To evaluate the overall evidence for an excess of statistically significant gene associations over the proportion expected by chance, we applied a one-sample test of proportion to each group of candidate genes. The steroid-hormone metabolism and biosynthesis pathway was found significantly associated with both age at menarche and age at natural menopause (P = 0.040 and 0.011, respectively). In addition, the group of genes associated with precocious or delayed puberty was found significantly associated with age at menarche (P = 0.013), and the group of genes involved in premature ovarian failure with age at menopause (P = 0.025).     

Are habitat fragmentation,local adaptation and isolation‐by‐distance driving population divergence in wild rice Oryza rufipogon?

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (m_h = 0.0002–0.0013, m_c = 0.007–0.029), indicating IBD and resulting in a high level of population divergence (F_ST = 0.343). High within‐population genetic variation (H_E = 0.377–0.515), relatively large effective population sizes (N_e = 96–158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene‐linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon.     

Asymmetric oceanographic processes mediate connectivity and population genetic structure,as revealed by RADseq,in a highly dispersive marine invertebrate (Parastichopus californicus)

Marine populations are typically characterized by weak genetic differentiation due to the potential for long‐distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (F_ST = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R² = .49) than geographic distance (IBD) (R² = .18), and directional processes played an important role in shaping fine‐scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.     

Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes,ploidies, gene pools,and cultivars

Switchgrass (Panicum virgatum L.) is an important crop for bioenergy feedstock development. Switchgrass has two main ecotypes: the lowland ecotype being exclusively tetraploid (2n = 4x = 36) and the upland ecotype being mainly tetraploid and octaploid (2n = 8x = 72). Because there is a significant difference in ploidy, morphology, growth pattern, and zone of adaptation between and within the upland and lowland ecotypes, it is important to discriminate switchgrass plants belonging to different genetic pools. We used 55 simple sequence repeats (SSR) loci and six chloroplast sequences to identify patterns of variation between and within 18 switchgrass cultivars representing seven lowland and 11 upland cultivars from different geographic regions and of varying ploidy levels. We report consistent discrimination of switchgrass cultivars into ecotype membership and demonstrate unambiguous molecular differentiation among switchgrass ploidy levels using genetic markers. Also, SSR and chloroplast markers identified genetic pools related to the geographic origin of the 18 cultivars with respect to ecotype, ploidy, and geographical, and cultivar sources. SSR loci were highly informative for cultivar fingerprinting and to classify plants of unknown origin. This classification system is the first step toward developing switchgrass complementary gene pools that can be expected to provide a significant heterotic increase in biomass yield.     

Spatial genetic structure of <Emphasis Type="Italic">Coccoloba cereifera</Emphasis> (Polygonaceae), a critically endangered microendemic species of Brazilian rupestrian fields

Coccoloba cereifera (Polygonaceae) is an extremely rare endemic shrub found exclusively in the rupestrian fields of Serra do Cipó, southeastern, Brazil. We assessed the genetic diversity and structure across the single occurrence area of C. cereifera. The genetic variation at 13 microsatellite loci was estimated from 139 individuals sampled in nine patches. The number of alleles per locus varied from two to ten; the expected and observed heterozygosity ranged from 0.324 to 0.566 and 0.337 to 0.529, respectively. Microsatellites detected low but statistically significant levels of differentiation among patches (F _ST = 0.123, R _ST = 0.105), whereas Mantel test results showed a weak but significant pattern of isolation by distance (r ² = 0.31, P < 0.002). Bayesian clustering indicated two subdivisions connected via admixture. Habitat heterogeneity across the drainage basin of the Rio Indequicé is likely limiting gene flow within patches of the geographically restricted population. While there is currently no evidence for a direct genetic risk to species survival, the apparent natural segregation occurring within the species could be exacerbated by future land use changes and the influx of alien species which could lead to demographic reductions in population size leading to a reduction in genetic diversity and an increase in population subdivision. We suggest that maintaining the integrity of the habitat within the small range of the species and continued monitoring of the effects of alien species would be the wisest use of management resources.     

Relationship between surfactant protein A polymorphisms and allergic rhinitis in a Chinese Han population

The development of allergic rhinitis is considered to be determined by the interaction between genetic and environmental factors. Surfactant protein A (SP-A), a member of the collectin family of proteins, plays an important role in immune regulation. The purpose of this study was to investigate the association between SP-A polymorphisms and allergic rhinitis. We conducted a case–control association study on a Chinese Han population, comprising 216 adult individuals with AR and 84 healthy controls. A total of 9 single-nucleotide polymorphisms (SNPs) mapped to the SP-A were genotyped using PCR-based molecular identification methods. The frequency of A allele at amino acid 223 in the patient group was significantly higher than that in the control group after correcting for multiple testing (P = 0.006). The 1A² allele haplotype in SFTPA2 was associated with decreased risk for allergic rhinitis, after applying Bonferroni corrections (P = 0.003). However, genetic variants of the SFTPA1 genes were not found to be associated with AR. In addition, no significant associations were established between any of the 9 SFTPA gene polymorphisms and the skin-prick test responses (P > 0.05). Further, no association was established between the 9 SNP loci and the levels of total serum immunoglobulin E (IgE) (P > 0.05). These results indicate that the gene polymorphism at the residue 223 in the carbohydrate recognition domain of SFTPA2 may be a genetic marker for the development of AR in the adult Chinese Han population.     

Temporal changes in genetic diversity of isolated populations of perch and roach

Genetic drift, together with natural selection and gene flow, affects genetic variation and is the major source of changes in allele frequencies in small and isolated populations. Temporal shifts in allele frequencies at five polymorphic loci were used to estimate the amount of genetic drift in an isolated population of perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.). Here, I used the populations from the Biotest basin at Forsmark, Sweden, to investigate genetic diversity between 1977 and 2000, during which time the population can be considered to be totally isolated from other populations. Microsatellite data reveal stable levels of gene diversity over time for both species. Estimates of genetic differentiation (F _ST) showed a significant divergence between 1977 and 2000 for both perch and roach. A positive correlation between genetic distance and time was found (Mantel test, perch: r = 0.724, P = 0.0112; roach: r = 0.59, P = 0.036). Estimates of effective population size (N _e) differed with a factor six between two different estimators (NeEstimator and TempoFS) applying the temporal method. Ratios of N _e/N ranged between 10⁻² and 10⁻³, values normally found in marine species. Despite low N _e the populations have not lost their evolutionary potential due to drift. But two decades of isolation have lead to isolation by time for populations of perch and roach, respectively.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

Genetic variants and underlying mechanisms influencing variance heterogeneity in maize

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance‐heterogeneity genome‐wide association study to examine the contribution of variance heterogeneity to oil‐related quantitative traits. We identified 79 unique variance‐controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance‐heterogeneity genes for 21 oil‐related traits using the Levene test (P < 1.0 × 10^?5). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean‐effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two‐hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high‐oil maize (Zea mays L.).