Multilocus functional characterization of indigenous and exotic inbreds for dgat1-2, fatb, ge2 and wri1a genes affecting kernel oil and fatty acid profile in maize.

Demand for maize oil is progressively increasing due to its diverse industrial applications, aside from its primary role in human nutrition and animal feed. Oil content and composition are two crucial determinants of maize oil in the international market. As kernel oil in maize is a complex quantitative trait, improving this trait presents a challenge for plant breeders and biotechnologists. Here, we characterized a set of 292 diverse maize inbreds of both indigenous and exotic origin by exploiting functional polymorphism of the dgat1-2, fatb, ge2, and wri1a genes governing kernel oil in maize. Genotyping using gene-based functional markers revealed a lower frequencies of dgat1-2 (0.15) and fatb (0.12) mutant alleles and a higher frequencies of wild-type alleles (Dgat1-2: 0.85; fatB: 0.88). The favorable wri1a allele was conserved across genotypes, while its wild-type allele (WRI1a) was not detected. In contrast, none of the genotypes possessed the ge2 favorable allele. The frequency of favorable alleles of both dgat1-2 and fatb decreased to 0.03 when considered together. Furthermore, pairwise protein-protein interactions among target gene products were conducted to understand the effect of one protein on another and their responses to kernel oil through functional enrichments. Thus, the identified maize genotypes with dgat1-2, fatb, and wri1a favourable alleles, along with insights gained through the protein-protein association network, serve as prominent and unique genetic resources for high-oil maize breeding programs. This is the first comprehensive report on the functional characterization of diverse genotypes at the molecular and protein levels.

Genetic basis of maize kernel oil-related traits revealed by high-density SNP markers in a recombinant inbred line population.

BACKGROUND: Maize (Zea mays ssp. mays) is the most abundantly cultivated and highly valued food commodity in the world. Oil from maize kernels is highly nutritious and important for the diet and health of humans, and it can be used as a source of bioenergy. A better understanding of genetic basis for maize kernel oil can help improve the oil content and quality when applied in breeding. RESULTS: In this study, a KUI3/SC55 recombinant inbred line (RIL) population, consisting of 180 individuals was constructed from a cross between inbred lines KUI3 and SC55. We phenotyped 19 oil-related traits and subsequently dissected the genetic architecture of oil-related traits in maize kernels based on a high-density genetic map. In total, 62 quantitative trait loci (QTLs), with 2 to 5 QTLs per trait, were detected in the KUI3/SC55 RIL population. Each QTL accounted for 6.7% (qSTOL1) to 31.02% (qBELI6) of phenotypic variation and the total phenotypic variation explained (PVE) of all detected QTLs for each trait ranged from 12.5% (OIL) to 52.5% (C16:0/C16:1). Of all these identified QTLs, only 5 were major QTLs located in three genomic regions on chromosome 6 and 9. In addition, two pairs of epistatic QTLs with additive effects were detected and they explained 3.3 and 2.4% of the phenotypic variation, respectively. Colocalization with a previous GWAS on oil-related traits, identified 19 genes. Of these genes, two important candidate genes, GRMZM2G101515 and GRMZM2G022558, were further verified to be associated with C20:0/C22:0 and C18:0/C20:0, respectively, according to a gene-based association analysis. The first gene encodes a kinase-related protein with unknown function, while the second gene encodes fatty acid elongase 2 (fae2) and directly participates in the biosynthesis of very long chain fatty acids in Arabidopsis. CONCLUSIONS: Our results provide insights on the genetic basis of oil-related traits and a theoretical basis for improving maize quality by marker-assisted selection.

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.).

Genomic Prediction using Existing Historical Data Contributing to Selection in Biparental Populations: A Study of Kernel Oil in Maize.

Maize ( L.) kernel oil provides high-quality nutrition for animal feed and human health. A certain number of maize breeding programs seek to enhance oil concentration and composition. Genomic selection (GS), which entails selection based on genomic estimated breeding values (GEBVs), has proven to be efficient in breeding programs. Here, we estimate the robustness of predictions for the oil traits of maize kernels in biparental recombination inbred lines (RILs) using a GS model built based on an association population. Most statistical models, including ridge regression-best linear unbiased prediction (RR-BLUP), showed high prediction accuracy in the training population through a cross validation procedure. The training population size was more important than marker density and a statistical model for prediction performance. Using the optimized GS model, prediction of the biparental RIL population showed medium-high prediction accuracy (0.68) compared with prediction using only oil associated markers ( = 0.43). The potential to apply the GS model to another RIL population that is genetically less related to the training population was also examined, showing promising prediction accuracy in the top selected lines. Our results proved that genomic prediction using existing data is robust for the prediction of polygenic traits with moderate to high heritability.

A truncated FatB resulting from a single nucleotide insertion is responsible for reducing saturated fatty acids in maize seed oil.

KEY MESSAGE: We identified a G-nucleotide insertion in a maize FatB responsible for reducing saturated fatty acids through QTL mapping and map-based cloning and developed an allele-specific DNA marker for molecular breeding. Vegetable oils with reduced saturated fatty acids have signficant health benefits. SRS72NE, a Dow AgroSciences proprietory maize inbred line, was found to contain signficantly reduced levels of palmitic acid and total saturated fatty acids in seed oil when compared to other common inbreds. Using F2 and F3 populations derived from a cross between SRS72NE and a normal inbred SLN74, we have demonstrated that the reduced saturated fatty acid phenotype in SRS72NE is controlled by a single QTL on chromosome 9 that explains 79.1 % of palmitic acid and 79.6 % total saturated fatty acid variations. The QTL was mapped to an interval of 105 kb that contains one single gene, a type B fatty acyl-ACP thioesterase (ZmFatB; GRMZM5G829544). ZmFatB alleles from SRS72NE and common inbreds were cloned and sequenced. SRS72NE fatb allele contains a single nucleotide (G) insertion in the 6th exon, which creates a premature stop codon 22 base pairs down stream. As a result, ZmFatB protein from SRS72NE is predicted to contain eight altered and 90 deleted amino acids at its C-terminus. Because the affected region is part of the conserved acyl-ACP thioesterase catalytic domain, the truncated ZmFatB in SRS72NE is likely non-functional. We also show that fatb RNA level in SRS72NE is reduced by 4.4-fold when compared to the normal allele SNL74. A high throughput DNA assay capable of differentiating the normal and reduced saturate fatty acid alleles has been developed and can be used for accelerated molecular breeding.

QTL verification of grain protein content and its correlation with oil content by using connected RIL populations of high-oil maize.

Maize with high grain protein and oil contents offers great advantages for human food and animal feed. In this study, grain protein contents of 282 and 263 F7:8 recombinant inbred lines (RILs) of 2 crosses were evaluated in 4 environments within and between populations. The RILs were developed from crosses between an inbred high-oil maize line and 2 normal dent inbred maize lines. A total of 16 single-population QTLs and 19 joint-population QTLs were identified for protein content, and 21 QTLs were detected for protein-oil in each of the 4 environments tested and in combination. Most of the QTLs for protein content were greatly influenced by variation among populations and environments. Seven QTLs showed generational consistency compared with QTLs detected in the 2 F2:3 populations. However, 7 and 6 QTLs were detected in only the RIL and F2:3 populations, respectively. Protein and protein-oil QTLs with the same parental effects were detected at bins 3.03-3.05, 5.04-5.06, 6.03-6.05, 8.03-8.04, and 8.04-8.06, demonstrating that tightly linked and/or pleiotropic QTLs are controlling both traits at these bins. Four single-population QTLs and 11 joint-population QTLs identified at bins 3.02-3.03, 3.05, 7.01, 8.02, 8.03, 8.04-8.05, 8.05, 9.03, and 9.05 with intervals <5 cM could be used in marker-assisted selection. Along with the previously detected QTLs qPRO1-8-1 and qPRO1-5-1 at bins 8.03-8.04 and 5.02-5.04, the QTLs detected herein could be used to develop near isogenic lines and chromosome segment substitution lines in future studies.

High susceptibility of heterozygous (+/fa) lean Zucker rats to 7,12-dimethylbenz(a)anthracene-induced mammary carcinogenesis.

Susceptibility to 7,12-dimethylbenz(a)anthracene (DMBA)-induced mammary carcinogenesis was investigated in lean Zucker (+/fa) rats carrying one mutated leptin receptor gene and wild-type controls (+/+). Rats with both genotypes were given a single DMBA administration and divided into two groups, one group was fed on basal diet mixed with 10% corn oil and the other was fed on basal diet alone. The minimum latency period of palpable carcinomas in +/fa rats of both groups was 8 weeks following DMBA treatment, in contrast to the 11-12 weeks in +/+. The incidence and multiplicity of carcinomas increased or showed a tendency for increase in the early stages in +/fa rats of both groups as compared to the +/+ counterparts. The volumes of carcinomas showed a tendency to increase in the corn oil diet groups of both genotypes. The major histopathological phenotype of carcinomas in all groups was well-differentiated without distinct atypia (multiplicity, 0.69-1.09/rat), but moderately/poorly differentiated carcinomas with atypia were also found, predominantly in +/fa rats (0.09-0.21). These latter tumors were characterized by elevated ERK activity but not estrogen receptor expression. Serum leptin concentrations in +/fa rats at 7 weeks of age were higher than those in +/+ and were elevated by the corn oil diet; however, no obvious change was detected in other serum parameters examined. In conclusion, +/fa rats proved more susceptible to DMBA-induced mammary carcinogenesis than +/+ controls, and hyperleptinemia was suggested to contribute to tumor growth as well as to susceptibility to tumorigenesis and more aggressive phenotypes in Zucker lean rats.

Verification of QTL for grain starch content and its genetic correlation with oil content using two connected RIL populations in high-oil maize.

Grain oil content is negatively correlated with starch content in maize in general. In this study, 282 and 263 recombinant inbred lines (RIL) developed from two crosses between one high-oil maize inbred and two normal dent maize inbreds were evaluated for grain starch content and its correlation with oil content under four environments. Single-trait QTL for starch content in single-population and joint-population analysis, and multiple-trait QTL for both starch and oil content were detected, and compared with the result obtained in the two related F(2∶3) populations. Totally, 20 single-population QTL for grain starch content were detected. No QTL was simultaneously detected across all ten cases. QTL at bins 5.03 and 9.03 were all detected in both populations and in 4 and 5 cases, respectively. Only 2 of the 16 joint-population QTL had significant effects in both populations. Three single-population QTL and 8 joint-population QTL at bins 1.03, 1.04-1.05, 3.05, 8.04-8.05, 9.03, and 9.05 could be considered as fine-mapped. Common QTL across F(2∶3) and RIL generations were observed at bins 5.04, 8.04 and 8.05 in population 1 (Pop.1), and at bin 5.03 in population 2 (Pop.2). QTL at bins 3.02-3.03, 3.05, 8.04-8.05 and 9.03 should be focused in high-starch maize breeding. In multiple-trait QTL analysis, 17 starch-oil QTL were detected, 10 in Pop.1 and 7 in Pop.2. And 22 single-trait QTL failed to show significance in multiple-trait analysis, 13 QTL for starch content and 9 QTL for oil content. However, QTL at bins 1.03, 6.03-6.04 and 8.03-8.04 might increase grain starch content and/or grain oil content without reduction in another trait. Further research should be conducted to validate the effect of these QTL in the simultaneous improvement of grain starch and oil content in maize.

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels.

Maize kernel oil is a valuable source of nutrition. Here we extensively examine the genetic architecture of maize oil biosynthesis in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines, including 'high-oil' lines. We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition (P < 1.8 × 10(-6)), which we subsequently examined using expression quantitative trait loci (QTL) mapping, linkage mapping and coexpression analysis. More than half of the identified loci localized in mapped QTL intervals, and one-third of the candidate genes were annotated as enzymes in the oil metabolic pathway. The 26 loci associated with oil concentration could explain up to 83% of the phenotypic variation using a simple additive model. Our results provide insights into the genetic basis of oil biosynthesis in maize kernels and may facilitate marker-based breeding for oil quantity and quality.

Identifying quantitative trait loci and determining closely related stalk traits for rind penetrometer resistance in a high-oil maize population.

Stalk lodging in maize causes annual yield losses between 5 and 20% worldwide. Many studies have indicated that maize stalk strength significantly negatively correlates with lodging observed in the field. Rind penetrometer resistance (RPR) measurements can be used to effectively evaluate maize stalk strength, but little is known about the genetic basis of this parameter. The objective of this study was to explore a genetic model and detect quantitative trait loci (QTL) of RPR and determine relationships between RPR and other stalk traits, especially cell wall chemical components. RPR is quantitative trait in nature, and both additive and non-additive effects may be important to consider for the improvement of RPR. Nine additive-effect QTLs covering nine chromosomes, except chromosome 5, and one pair of epistatic QTLs were detected for RPR. CeSA11 involved in cellulose synthesis and colorless2 involved in lignin synthesis were identified as possible candidate genes for RPR. Internode diameter (InD), fresh weight of internode (FreW), dry weight of internode (DryW), fresh weight and dry weight as well as cell wall components per unit volume significantly positively correlated with RPR. The internode water content (InW) significantly negatively correlated with RPR. Notably, these traits significantly correlated with RPR, and the QTLs of these traits co-localized with those of RPR. The corresponding results obtained from correlation analysis and QTL mapping suggested the presence of pleitropism or linkage between genes and indicated that these different approaches may be used for cross authentication of relationships between different traits.

Influence of dent corn genetic backgrounds on QTL detection for plant-height traits and their relationships in high-oil maize.

QTL mapping for plant-height traits has not been hitherto reported in high-oil maize. A high-oil maize inbred 'GY220' was crossed with two dent maize inbreds ('8984' and '8622') to generate two connected F2:3 populations. Four plant-height traits were evaluated in 284 and 265 F2:3 families. Single-trait QTL mapping and multiple-trait joint QTL mapping was used to detect QTLs for the traits and the genetic relationship between plant height (PH) and two other plant-height traits. A total of 28 QTLs and 12 pairs of digenic interactions among detected QTLs for four traits were detected in the two F2:3 families. Only one marker was shared between the two populations. Joint analysis of PH with ear height (EH) and PH with top height (TH) detected 32 additional QTLs. Our results showed that QTL detection for PH was dependent on the genetic background of dent corn inbreds. Multiple-trait joint QTL analysis could increase the number of detected QTLs.

The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel.

In one of the longest-running experiments in biology, researchers at the University of Illinois have selected for altered composition of the maize kernel since 1896. Here we use an association study to infer the genetic basis of dramatic changes that occurred in response to selection for changes in oil concentration. The study population was produced by a cross between the high- and low-selection lines at generation 70, followed by 10 generations of random mating and the derivation of 500 lines by selfing. These lines were genotyped for 488 genetic markers and the oil concentration was evaluated in replicated field trials. Three methods of analysis were tested in simulations for ability to detect quantitative trait loci (QTL). The most effective method was model selection in multiple regression. This method detected approximately 50 QTL accounting for approximately 50% of the genetic variance, suggesting that >50 QTL are involved. The QTL effect estimates are small and largely additive. About 20% of the QTL have negative effects (i.e., not predicted by the parental difference), which is consistent with hitchhiking and small population size during selection. The large number of QTL detected accounts for the smooth and sustained response to selection throughout the twentieth century.

Nutritional value of a genetically improved high-lysine, high-oil corn for young pigs.

Two experiments were conducted to compare the nutritional adequacy of a genetically improved high-lysine, high-oil corn (HLHOC; .408% lysine, 6.21% fat, as-fed basis) and a high-oil corn (HOC; .289% lysine, 5.97% fat, as-fed basis) for young growing pigs. Experiment 1 used four non-littermate barrows (initially 20.0 kg BW) fitted with ileal T-cannulas in a crossover-designed digestion study. The .75% total lysine diets contained 8.5% casein and an equal amount of lysine (.25%) from the test corn. Apparent ileal digestibilities of amino acids, GE, DM, and CP were similar (P > .10) between diets. Apparent ileal lysine digestibilities were 65 and 71% for the HOC and HLHOC, respectively, assuming the lysine in casein to be 100% digestible. Experiment 2 used 100 barrows reared in a segregated early-weaning environment (initially 8.3 kg BW and 27 d of age) to evaluate five corn-soybean meal-based diets in a 2 x 2 factorial arrangement with main effects being corn type and dietary lysine (.80 or 1.15% digestible lysine). The fifth diet consisted of the .80% digestible lysine HOC diet supplemented with .23% additional L-lysine x HCl (.975% digestible lysine) to verify that lysine was the limiting amino acid in the low-lysine diets. Increasing digestible lysine from .80 to 1.15% increased (P < .001) ADG and gain/feed (G/F) regardless of corn variety. Combined ADG and G/F were .347 kg and .641 and .443 kg and .790 for the .80 and 1.15% digestible lysine diets, respectively. Within lysine level, corn type did not affect ADG, ADFI, or G/F (P > .10). The results of these studies indicate that the lysine in HLHOC is as available as the lysine in HOC and that HLHOC can be used successfully in swine diets.