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H-Y Hung,
C Browne,
K Guill,
N Coles,
M Eller,
A Garcia,
N Lepak,
S Melia-Hancock,
M Oropeza-Rosas,
S Salvo,
N Upadyayula,
E S Buckler,
S Flint-Garcia,
M D McMullen, T R Rocheford,
J B Holland
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ABSTRACT: Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.
Heredity 10/2011; 108(5):490-9. · 4.60 Impact Factor
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06/2010: pages 111 - 131; , ISBN: 9780470650240
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ABSTRACT: Maize is an important source of pro-vitamin A; beta-carotene, alpha-carotene and beta-cryptoxanthin, and the non-pro-vitamin A carotenoids including lutein and zeaxanthin. In the present study, a recombinant inbred (RI) population with 233 RI lines derived from a cross between By804 and B73 was employed to detect QTL for these nutritionally important components in maize grain. High Performance Liquid Chromatography was used to measure amounts of individual carotenoids over 2 years. A genetic linkage map was constructed with 201 molecular markers. In all, 31 putative QTL including 23 for individual and 8 for total carotenoids were detected on chromosome(s) 1, 3, 5, 6, 7, 8 and 10. The notable aspect of this study was that much of the phenotypic variation in contents of carotenoids could be explained by two loci (y1 and y9), and the QTL for carotenoids elucidated the interrelationships among these compounds at the molecular level. A gene targeted marker (Y1ssr) in the candidate gene phytoene synthase 1 (psy1) tightly linked to a major QTL explaining 6.6-27.2% phenotypic variation for levels of carotenoids was identified, which may prove useful to expedite breeding for higher level of carotenoids in maize grain. This functionally characterized gene (psy1) could also be exploited for further development of functional marker for carotenoids in maize. The QTL cluster located at y9 locus may also be used for pyramiding favorable alleles controlling contents of carotenoids from diverse maize germplasm.
Theoretical and Applied Genetics 02/2008; 116(2):223-33. · 3.30 Impact Factor
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ABSTRACT: Maize tassel inflorescence architecture is relevant to efficient production of F(1) seed and yield performance of F(1) hybrids. The objectives of this study were to identify genetic relationships among seven measured tassel inflorescence architecture traits and six calculated traits in a maize backcross population derived from two lines with differing tassel architectures, and identify Quantitative Trait Loci (QTL) involved in the inheritance of those tassel inflorescence architecture traits. A Principal Component (PC) analysis was performed to examine relationships among correlated traits. Traits with high loadings for PC1 were branch number and branch number density, for PC2 were spikelet density on central spike and primary branch, and for PC3 were lengths of tassel and central spike. We detected 45 QTL for individual architecture traits and eight QTL for the three PCs. For control of inflorescence architecture, important QTL were found in bins 7.02 and 9.02. The interval phi034-ramosa1 (ral) in bin 7.02 was associated with six individual architecture trait QTL and explained the largest amount of phenotypic variation (17.3%) for PC1. Interval bnlg344-phi027 in bin 9.02 explained the largest amount of phenotypic variation (14.6%) for PC2. Inflorescence architecture QTL were detected in regions with candidate genes fasciated ear2, thick tassel dwarf1, and ral. However, the vast majority of QTL mapped to regions without known candidate genes, indicating positional cloning efforts will be necessary to identify these genes.
Theoretical and Applied Genetics 12/2006; 113(8):1395-407. · 3.30 Impact Factor
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ABSTRACT: Maize (Zea mays L.) ear inflorescence architecture is directly relevant to grain yield components, and tassel architecture is relevant to hybrid seed production. The objectives of this study were to (1) determine heritabilities and correlations of a comprehensive set of tassel and ear inflorescence architecture traits in a set of (Illinois Low ProteinxB73) B73 S1 families, (2) identify chromosomal positions of QTL affecting tassel and ear architecture, and (3) identify possible candidate genes associated with these QTL. For tassel traits, the number of detected QTL ranged from one to five, and explained between 6.5 and 35.9% of phenotypic variation. For ear traits, the number of detected QTL ranged from one to nine and phenotypic variation explained by those QTL varied between 7.9 and 53.0%. We detected QTL for tassel architecture traits that required calculation of ratios from measured traits. Some of these calculated traits QTL were detected in regions that did not show QTL for the measured traits, suggesting that calculation of ratios may reveal developmentally relevant patterns of tassel architecture. We detected a QTL on chromosome 7 for tassel branch number near the gene ramosa1 (ra1), which is known to control tassel branch number, making ra1 a candidate gene for tassel branch number. We detected QTL for several traits on chromosomes 6, 8, and 9, where no inflorescence architecture genes have been mapped, thus providing initial information towards new gene discovery for control of inflorescence architecture.
Theoretical and Applied Genetics 03/2006; 112(4):592-606. · 3.30 Impact Factor
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ABSTRACT: Carotenoids are a class of fat-soluble antioxidant vitamin compounds present in maize ( Zea mays L.) that may provide health benefits to animals or humans. Four carotenoid compounds are predominant in maize grain: beta-carotene, beta-cryptoxanthin, zeaxanthin, and lutein. Although beta-carotene has the highest pro-vitamin A activity, it is present in a relatively low concentration in maize kernels. We set out to identify quantitative trait loci (QTL) affecting carotenoid accumulation in maize kernels. Two sets of segregating families were evaluated-a set of F2:3 lines derived from a cross of W64a x A632, and their testcross progeny with AE335. Molecular markers were evaluated on the F2:3 lines and a genetic linkage map created. High-performance liquid chromatography was performed to measure beta-carotene, beta-cryptoxanthin, zeaxanthin, and lutein on both sets of materials. Composite interval mapping identified chromosome regions with QTL for one or more individual carotenoids in the per se and testcross progenies. Notably QTL in the per se population map to regions with candidate genes, yellow 1 and viviparous 9, which may be responsible for quantitative variation in carotenoids. The yellow 1 gene maps to chromosome six and is associated with phytoene synthase, the enzyme catalyzing the first dedicated step in the carotenoid biosynthetic pathway. The viviparous 9 gene maps to chromosome seven and is associated with zeta-carotene desaturase, an enzyme catalyzing an early step in the carotenoid biosynthetic pathway. If the QTL identified in this study are confirmed, particularly those associated with candidates genes, they could be used in an efficient marker-assisted selection program to facilitate increasing levels of carotenoids in maize grain.
Theoretical and Applied Genetics 02/2004; 108(2):349-59. · 3.30 Impact Factor
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ABSTRACT: Carotenoids are a class of fat-soluble antioxidant vitamin compounds present in maize (Zea mays L.) that may provide health benefits to animals or humans. Four carotenoid compounds are predominant in maize grain: -carotene, -cryptoxanthin, zeaxanthin, and lutein. Although -carotene has the highest pro-vitamin A activity, it is present in a relatively low concentration in maize kernels. We set out to identify quantitative trait loci (QTL) affecting carotenoid accumulation in maize kernels. Two sets of segregating families were evaluated—a set of F2:3 lines derived from a cross of W64a x A632, and their testcross progeny with AE335. Molecular markers were evaluated on the F2:3 lines and a genetic linkage map created. High-performance liquid chromatography was performed to measure -carotene, -cryptoxanthin, zeaxanthin, and lutein on both sets of materials. Composite interval mapping identified chromosome regions with QTL for one or more individual carotenoids in the per se and testcross progenies. Notably QTL in the per se population map to regions with candidate genes, yellow1 and viviparous9, which may be responsible for quantitative variation in carotenoids. The yellow1 gene maps to chromosome six and is associated with phytoene synthase, the enzyme catalyzing the first dedicated step in the carotenoid biosynthetic pathway. The viviparous9 gene maps to chromosome seven and is associated with -carotene desaturase, an enzyme catalyzing an early step in the carotenoid biosynthetic pathway. If the QTL identified in this study are confirmed, particularly those associated with candidates genes, they could be used in an efficient marker-assisted selection program to facilitate increasing levels of carotenoids in maize grain.
Theoretical and Applied Genetics 12/2003; 108(2):349-359. · 3.30 Impact Factor
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ABSTRACT: Increased levels of oleic acid may enhance the nutritional and functional value of corn. Corn oil is primarily composed of palmitic, stearic, oleic, linoleic and linolenic fatty acids. Delta-12 desaturase in plants converts oleic acid (18:1) to linoleic acid (18:2) by inserting a double bond at the delta-12 position. Fatty acid desaturase-2 (fad2) encodes delta-12 desaturase that functions in the endoplasmic reticulum while fatty acid desaturase-6 (fad6) encodes delta-12 desaturase that functions in plastids. Complementary DNA (cDNA) clones from putative maize homologs for fad2 and fad6 were identified and the entire clones DNA sequenced. The maize fad2 cDNAs showed an amino-acid identity of 67-77% to fad2 of Glycine, Arabidopsis and Brassica species. Our cDNA sequence comparisons suggested that more than one fad2 gene is transcribed in maize embryos. Two different fad2 cDNAs from an embryo cDNA library map to separate chromosomal positions, providing evidence consistent with two different isoforms of fad2 expressed in the embryo. The fad2 cDNAs from multiple tissue sources clustered into three groups on a phenogram, and map to different positions on chromosomes 4, 5 and 10, which suggests at least three different isoforms of fad2 may be expressed in the maize plant. The two maize fad6 cDNAs share 81% amino-acid identity with the Arabidopsis fad6 and map to chromosome 1. Northern analysis revealed that fad2 is transcribed in embryos at 14, 21, 28 and 35 days after pollination, with the highest level observed at day 14. None of the fad2 or fad6 clones mapped to maize chromosome bins associated with QTLs for the ratio of oleic/linoleic acid, notably bin 6.04 which contains the linoleic1 locus and the largest reported QTL for the oleic/linoleic ratio. This suggests, but does not prove, that some of the QTLs for the oleic/linoleic acid ratio do not involve allelic variants of fad2 or fad6 but rather involve other genes that may influence flux through the enzymes encoded by fad2 or fad6.
Theoretical and Applied Genetics 06/2003; 106(7):1326-32. · 3.30 Impact Factor
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ABSTRACT: Treatments designed to influence abscisic acid (ABA) or gibberellin (GA) concentrations were applied to developing tassels of maize (Zea mays L.) plants in different environments or to anthers in culture to determine the effect on formation of embryo-like structures (ELS). Production of ELS was significantly affected in certain environments when ABA, GA3, ancymidol, or fluridone solutions were pipetted into whorls of field-grown plants approximately 3 days before tassel harvest. In 1996 anthers from 10 M ancymidol-treated plants were most responsive, producing 35 ELS/100 anthers and 50 M GA3-treated plants were least responsive, producing 12 ELS/100 anthers. In 1997 under hotter, drier conditions, anthers from 50 M GA3-treated plants were most responsive, producing 20 ELS/100 anthers and those from 50 M ABA-treated plants were least responsive, producing 2.4 ELS/100 anthers. Anthers from growth chamber plants were significantly more responsive when grown in a 16-h than a 12-h photoperiod. With the 16-h photoperiod the response was significantly greater with a 250 M ABA whorl treatment. With the 12-h photoperiod there was no significant effect from whorl treatments. Modification of the culture medium with added ABA, GA3, ancymidol, or fluridone was generally ineffective, except in 1997 when the response was significantly higher with 1 M ABA added to the culture medium. The results suggest that the maize anther culture response may be influenced by environmental conditions that interact with ABA and GA treatments to donor plants during tassel development.
Plant Cell Tissue and Organ Culture 12/2000; 64(1):69-72. · 3.09 Impact Factor
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ABSTRACT: The F2 generations from two maize crosses were used to compare the ability of RAPD and RFLP marker systems to create a genetic linkage map. Both RFLPs and RAPDs were shown to provide Mendelian-type markers. Most of the RFLPs (80%) could be placed with a good level of certainty (LOD>4) on the genetic linkage map. However, because of their dominant nature, only between 37% and 59% of the RAPDs could be placed with such a LOD score. The use of combined data from RFLPs and RAPDs increases the level of information provided by RAPDs and allows the creation of a combined RFLP/RAPD genetic linkage map. Thus, the RAPD technique was found to be a powerful method to provide improved probes coverage on a previously created RFLP map and to locate markers linked to chromosomal regions of interest.
Theoretical and Applied Genetics 08/1996; 93(4):606-612. · 3.30 Impact Factor
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ABSTRACT: Four maize (Zea mays L.) populations selected for grain yield (BS10, Iowa Two-ear Synthetic; BS11, formerly Pioneer Two-ear Composite; RBS10, Illinois strain of BS10; and RSSSC, Illinois strain of Iowa Stiff Stalk Synthetic) were assayed for molecular variation in the ribosomal DNA (rDNA) intergenic spacer (IGS) at initial and advanced cycles of selection. RSSSC and RBS10 underwent reciprocal recurrent selection with an inbred tester in a high-yield environment, whereas BS10 and BS11 were subjected to full-sib reciprocal recurrent selection. Maize rDNA, which encodes the ribosomal RNA genes, is highly repetitive and shows IGS length variation within and among individuals. Five different ribosomal spacer-length variants (rslvs) and a polymorphic SstI restriction site in the IGS were detected in the four populations. The five rslvs and the polymorphic restriction fragment were observed in 20 different combinations or hybridization fragment patterns (HP). RSSSC, RBS10, and BS11 showed significant changes in the overall rslv and HP frequencies between cycle 0 and the advanced cycle of selection, whereas BS10 did not. In general, two specific HPs were more frequent in the majority of the advanced cycles of the four populations. The frequency changes between initial and advanced cycles were more dramatic for HPs than rslvs. These results are consistent with earlier findings and further support the hypothesis that certain rDNA HPs and/or linked loci may be responding to selection for grain yield and may be associated with a selective advantage in US Corn Belt environments.
Theoretical and Applied Genetics 04/1996; 92(6):680-687. · 3.30 Impact Factor
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ABSTRACT: This study was conducted to ascertain the chromosomal location and magnitude of effect of quantitative trait loci (QTL) associated with the chemical and sensory properties of sweet corn (Zea mays L.) eating quality. Eighty-eight RFLPs, 3 cloned genes (sh1, sh2, and dhn1), and 2 morphological markers (a2 and se1) distributed throughout the sweet corn genome were scored in 214 F2:3 families derived from a cross between the inbreds W6786su1Se1 and IL731Asu1se1. Kernel properties associated with eating quality (kernel tenderness and starch, phytoglycogen, sucrose, and dimethyl sulfide concentrations) were quantified on F2:3 sib-pollinated ears harvested at 20 days after pollination. Sensory evaluation was conducted on a subset of 103 F2:3 families to determine intensity of attributes associated with sweet corn eating quality (corn aroma, grassy aroma, sweetness, starchiness, grassy flavor, crispness, tenderness, and juiciness) and overall liking. Single factor analysis of variance revealed significant QTL for all these traits, which accounted for from 3 to 42% of the total phenotypic variation. A proportion of the RFLP markers associated with human sensory response were also found to be associated with kernel characteristics. To our knowledge this is the first report of the identification of QTL associated with human flavor preferences in any food crop. Key words : sweet corn, RFLP, quantitative trait loci, eating quality, sensory evaluation.
Genome 03/1996; 39(1):40-50. · 1.65 Impact Factor
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ABSTRACT: In order to map the genes conditioning the induction of embryos during our anther culture process, we evaluated F2 plants from three different crosses for their anther culture ability and also performed RFLP analysis on these plants. The results showed that six chromosomal regions appear to be associated with the ability to induce embryo-like structures from maize microspores. These regions are located on chromosomes 1 (two regions), 3, 5, 7, and 8. Some of these chromosomes are identical to those found in previous studies and we have localized the regions more precisely. Notably, all chromosome regions identified, except one, are near viviparous mutant loci. Since the viviparous mutations are known to involve the plant hormone abscisic acid (ABA), these results suggest that ABA or its antagonist, gibberellic acid (GA3), might somehow be related to anther culture ability. We also propose some combinations of probes to screen for anther culture ability in the three genotypes studied.
Genome 11/1995; 38(5):968-75. · 1.65 Impact Factor
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ABSTRACT: A study was conducted to determine the number and chromosomal location of quantitative trait loci (QTL) influencing the concentration of five fatty acids in 200 F2S1 lines derived from an Illinois High Oil (IHO) by Illinois Low Oil (Early Maturity) (ILO(EM)) cross. Restriction fragment length polymorphism (RFLP) analysis was performed on the 200 S1 lines and concentrations of palmitic (16:0), stearic (18:0), oleic (18:1), linoleic (18:2), and linolenic (18:3) acids were determined in self-pollinated kernels harvested from plants grown in replicated field trials during 1992 and 1993. A series of 74 cDNA and genomic clones were used and these revealed 80 polymorphic loci spaced, on average, 24 cM apart throughout the maize genome. Analysis of variance detected significant (p < 0.05) associations between several RFLP loci and the concentration of each fatty acid. A total of 15 RFLP loci clustered in 12 chromosomal regions were associated with the concentration of 16:0, 17 loci clustered in 10 regions were associated with the concentration of 18:0, 12 loci clustered in eight regions were associated with the concentration of 18:1 and 18:2, and 17 loci clustered in eight regions were associated with the concentration of 18:3. Multiple linear regression models consisting of four RFLP loci explained 24 and 62% of the total phenotypic and genotypic variation (R2) among the 200 F2S1 lines for 16:0, five loci explained 51 and 71% of the variation for 18:0, three loci explained 67 and 79% of the variation for 18:1, two loci explained 67 and 81% of the variation for 18:2, and seven loci explained 52 and 78% of the variation for 18:3 in these 200 F2S1 lines. The ratio of 18:1 to 18:2 was tightly interrelated as the same QTL were associated with the concentrations of 18:1 and 18:2. A quantitative trait locus that explained 63% of the phenotypic variation in the ratio of 18:1 to 18:2 is tightly linked to umc65 on chromosome 6 in the region of the linoleic acid1 locus.
Genome 11/1995; 38(5):894-901. · 1.65 Impact Factor
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ABSTRACT: RFLP marker data from an F23 population derived from a cross between a sugary1 (su1) and a sugary enhancer1 (su1, sel) inbred were used to construct a genetic linkage map of maize. This map includes 93 segregating marker loci distributed throughout the maize genome, providing a saturated linkage map that is suitable for linkage analysis with quantitative trait loci (QTL). This population, which has been immortalized in the form of sibbed F23 families, was derived from each of the 214 F2 plants and along with probe data are available to the scientific community. QTL analysis for kernel sucrose (the primary form of sugar) concentration at 20 days after pollination (DAP) uncovered the segregation of seven major QTL influencing sucrose concentration; a locus linked to umc36a described the greatest proportion of the variation (24.7%). Since maltose concentration has previously been reported to be associated with the se1 phenotype, an analysis of probe associations with maltose concentration at 40 DAP was also conducted. The highly significant association of umc36a with maltose and sucrose concentrations provided evidence that this probe is linked to se1. Phenotypic evaluation for the se1 genotype in each F23 family enabled us to map the gene 12.1 cM distal to umc36a. In contrast to previous work where se1 was reported to be located on chromosome four, our data strongly suggest that the sugary enhancer1 locus maps on the the distal portion of the long arm of chromosome 2 in the maize genome.
Theoretical and Applied Genetics 07/1995; 91(3):489-494. · 3.30 Impact Factor
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ABSTRACT: RFLP analysis was performed with anther culture-derived callus lines developed from the maize F1 hybrids Pa91 x FR16 (PF), H99 x Pa91 (HP) and H99 x FR16 (HF). Relatively evenly spaced RFLP markers were selected to cover the maize genome with 52, 58 and 35 RFLP markers for the PF, HP and HF callus lines, respectively. The results from populations PF and HP combined with limited information from HF showed that six chromosomal regions on chromosomes 1, 2 (two regions), 3, 6 and 8 appear to be associated with the formation of embryo-like structures (ELSs) from microspores or the subsequent formation of regenerable callus from the ELSs. Regions at the end of the long arm of chromosome 2 and on the long arm of chromosome 8 appear to be associated with ELS formation, and the other regions appear to be associated with either ELS or regenerable callus formation or both. Certain regions that we have identified are the same as those found in other studies to be important for friable, embryogenic callus formation (chromosomes 1 and 3 and near the centromere of 2) and for ESL formation (chromosomes 1 and 3). This study has provided evidence for the genetic basis of the maize anther culture response and callus formation.
Theoretical and Applied Genetics 10/1992; 85(2):360-365. · 3.30 Impact Factor
