2013. The genetic architecture of maize domestication and range expansion

2013. The genetic architecture of maize domestication and range expansion

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Abstract

The genetic architecture of the evolution of extreme morphological divergence is one of the fundamental questions of evolutionary biology. Maize (Zea Mays ssp. mays) and its wild ancestor, teosinte (Zea mays ssp. parviglumis) provide an ideal model for examining this question in part because of their extreme phenotypic divergence in plant architecture, ear morphology, and environmental range. In order to examine the genetic changes underlying this divergence, we use a population of maize-teosinte BC2S3 RILs. Using these RILs allows us to examine genetic architecture on multiple levels. First, whole genome QTL mapping is used to explore the diversity of genetic architectures which control domestication traits. These genetic architectures range from nearly Mendelian to polygenic. For two near Mendelian traits, glume architecture and barren ear base, the largest QTL contained a single gene in the 1.5 LOD confidence interval. The most polygenic trait was ear diameter, for which we found 35 QTL of varying effect sizes. As part of this project we extended the capabilities of the statistical program R/qtl to apply to a wider variety of experimental crosses. In order to examine the causes of extreme morphological divergence on the single gene level, we fine-mapped a single gene, ZmCCT which controls an approximately 9 day difference in flowering time between the homozygous maize and teosinte classes. We demonstrate that the causative difference is cis-regulatory, as under long day lengths ZmCCT alleles from diverse teosintes were consistently expressed at a higher level than the corresponding temperate maize alleles. Taken together these results provide examples of the variety of ways in which complex traits evolve .

2013. Quantitative genetic analysis of 16 maize populations adapted to the northern US corn belt

2013. Quantitative genetic analysis of 16 maize populations adapted to the northern US corn belt

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ABSTRACT

Genetic diversity is essential for genome sequencing and a key contributor to increase frequency of favorable alleles for maize improvement. The objectives of this study were to determine the genetic components, assess the genetic diversity, and propose the heterotic grouping of a large sample of short-season maize populations based on multiple traits. Sixteen maize populations were included in a diallel mating design that followed Gardner-Eberhart Analysis (GEAN) II to estimate variety (v,) and heterosis (hy) genetic effects. The general combining ability (g;) estimates were also determined and used to classify the populations based on their genetic diversity. Data were generated in partially balanced single lattice experiments  across North Dakota (ND) locations in 2010,2011, and 2012. Combined analyses of variance showed significant differences among genotypes. Heterosis effects explained the most among dial lei entries sum of squares for grain yield, while v,- effects had greater influence on grain quality traits. The g, effects agreed with the genetic effect that had larger contribution to the total among diallel entries sum of squares for various traits. Three groups were formed based on the genetic distances (GD) of the g, estimates. Four heterotic groups were established based on s,j estimates for grain yield. Close correspondence was observed between the groups formed using GD and stj. The heterotic grouping among populations agreed with their genetic background information and heterotic group’s specific and general combining ability (HSGCA) estimates. The EARLYGEM 21 populations having exotic background were assigned to a unique heterotic group. The heterotic groups established among these populations will increase breeding efficiency to improve and develop genetically broad-based populations. Inter-population recurrent selection programs can be employed for population crosses with high grain yield and above average grain quality formed by parental populations belonging to different heterotic groups. Intra-population recurrent selection programs can also be established for the parental populations identified with desirable grain quality traits. These populations will serve as unique germplasm sources of short-season diverse inbred lines to produce the next generation of diverse northern U.S. hybrids. New heterotic patterns have been established as a source of new commercially viable single-cross and population hybrids  .

2012. Genetic analysis of cell expansion during maize leaf development

2012. Genetic analysis of cell expansion during maize leaf development

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ABTRACT

The growth and development of plants requires a finely tuned and exquisitely controlled sequence of events, including cell division and expansion. Efforts in the Sylvester lab have focused on understanding the mechanisms of cell expansion during maize leaf development. In this dissertation, the role of several proteins in cell expansion is investigated. First, evidence is presented that Z/77RAB2A1, a small guanosine-triphosphatase (GTPase) of the Ras superfamily, is localized to the Golgi in growing leaf cells. The localization pattern of this protein primarily to the Golgi and only secondarily to the ER, suggests a diversified, or altered, function from that observed in other eukaryotes and dicots. The research here shows that ZmRab2Al is differentially expressed in cells primarily undergoing cytokinesis and cell expansion, but is not highly expressed in fully differentiated, non-expanding tissue. Disruption of ZmRab2Al by transposon insertion correlates with an overexpansion phenotype in leaf epidermal cells. This report represents the first association of a RAB, or any portion of the vesicle transport machinery, with anisotropic cell expansion. The results presented here suggest a diversified function for the RAB2-family protein trafficking pathway in monocot cells when compared to either dicots or to animals.

A major goal of the research was to determine the subcellular localization of ZmRAB2Al, a critical step for determining its function. To accomplish this goal, an efficient method for transient transformation of maize leaf tissue was developed. This method is amenable to expressing genes that are encoded either by their cDNAs or in their intact genomic context (i.e., with regulatory sequences and introns present). The technique can also be used for expressing constructs that have been cloned into GATEWAY plasmids and so could be used for semi-high throughput expression studies, particularly due to the potential for simultaneous transient expression of multiple genes. This technique will simplify subcellular localization studies, and will also likely be useful for a wider variety of techniques, such as functional studies with rationally-designed, dominant-negative alleles or mislocalization studies with plant chromobodies. This technique is expected to be a major breakthrough for maize functional genetics.

Finally, the wartyl-0 allele was cloned using positional cloning techniques and shown shown here to encode ZmCSLD1, a member of the CELLULOSE SYNTHASE-LIKE superfamily predicted to be involved in the biosynthesis of cell wall material. Two other amino acid substitutions in this protein that result in mutant phenotypes, in the warty 1-bumpy and wartyl-rough liueate alleles, were also identified. In the absence of a crystal structure for any plant cellulose synthase protein, this work contributes to the understanding of amino acids that are essential for normal function in this protein. These alleles should also prove useful as material for further genetic screens, such as enhancer and suppressor screens that will identify additional key factors involved in cell wall biosynthesis and deposition.
 

The research presented here demonstrates that ZmRAB2Al and ZwCLSDl contribute to normal cell expansion in maize. These findings, along with the establishment of a novel method for transient gene expression in maize leaf tissue, provide insight into mechanisms of cell expansion and offer new tools that increase the experimental and engineering potential of maize as a major crop plant .

2010. Marker assisted selection and breeding for desirable thinner pericarp thickness and ear traits in fresh market waxy corn germplasm

2010. Marker assisted selection and breeding for desirable thinner pericarp thickness and ear traits in fresh market waxy corn germplasm

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ABSTRACT

Kernel pericarp thickness and ear architectural traits arc important selection criteria in fresh waxy com breeding programs as they are associated with consumer sensory and visual preferences. An F2:3 mapping population from the cross between South Korean inbreds BH20 and BH30 was developed in order to estimate genetic relationships among pericarp thickness traits and car architectural traits, and to identify QTL regions for these traits through univariate and multivariate approaches. High correlations among pericarp thickness traits were detected and QTL regions associated with multiple pericarp thickness traits were identified. Through incorporating principal component analysis (PCA) of pericarp thickness traits and car traits with QTL analysis, we detected PC-QTL regions that appear to have pleiotropic effects on multiple traits, particularly the pericarp traits on different parts of the kernel. The pericarp thickness QTL information was used to perform marker assisted selection to pyramid favorable QTL, as well as validate pericarp QTL. The MAS population was designed to try and maintain favorable ear traits by making crosses between lines chosen for favorable ear and pericarp thickness phenotypes and lines chosen for favorable QTL alleles for pericarp thickness traits. A few ear traits showed weak but favorable associations with pericarp thickness traits. Evaluation of the MAS population revealed that most selected QTL markers were significant for at least one pericarp thickness trait. Comparing groups of lines in the MAS population sorted by: phenotypes for thinner pericarp; favorable QTL alleles for pericarp thickness; and unfavorable alleles for pericarp thickness from MAS population, we found that in some cases that marker based selection might be effective for reducing pericarp thickness. Pyramiding significant favorable marker alleles showed reduction of pericarp thickness on all kernel regions. Since tcstcross performance (TP) is ultimately more important than per se line performance (LP), a testcross population was generated for groups of selected lines from MAS population. This was done to enable assessment of the effect of groups of lines and different testers, and to compare LP with TP. Group 1 with most favorable alleles showed significantly thinner pericarp than group 2 with fewest favorable alleles in testcross evaluation, regardless of tester. The TP with tester BH1030, which was the thinner pericarp testcross hybrid showed thinner pericarp than TP with tester Bl 11020. We found evidences that suggested the tester had dominance effects on reducing pericarp thickness in testcross population. In summary, pericarp thickness QTL information was useful for marker assisted selection of favorable loci within Korean germplasm, and therefore offers the potential to be useful for introgression of these favorable loci into more adapted U.S. germplasm. Weak but favorable relationships among pericarp thickness and some ear traits could be used collectively to improve overall features through independent selection in a fresh waxy com breeding program  .

2010. Genome wide association mapping and detection of copy-number variations in maize

2010. Genome wide association mapping and detection of copy-number variations in maize

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ABSTRACT

The identification of genes responsible for phenotypes represents a central genetic problem. Specific methods and experimental designs are needed in order to elucidate complex phenotypes. These methodologies usually depend on the development of a suitable population of individuals and appropriate techniques to investigate DNA polymorphisms in that population. Two independent projects are presented here to improve the investigation of gene-phenotype associations and also the investigation of DNA polymorphisms in plant genetics. In the first, genome-wide association mapping of SNPs with oleic acid content in maize kernel is presented, including a comprehensive introduction and analysis of this methodology in comparison to classical QTL mapping. This is one of the first reports in the field implementing novel methods, detecting a gene responsible for a QTL, validating the locus, and showing common pitfalls that can occur in such projects. In the second, structural variations were detected among 13 maize inbred lines demonstrating that this kind of DNA polymorphism is a common feature in the maize genome and probably associated with plant phenotypes. Together these two projects provide an important contribution to the field of plant genetics laying the ground for future investigations and also their application in plant breeding  .

2009. The genetic architecture of maize photoperiod sensitivity as defined by recombinant inbred line backcross, and heterogeneous inbred family populations.

2009. The genetic architecture of maize photoperiod sensitivity as defined by recombinant inbred line backcross, and heterogeneous inbred family populations.

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ABSTRACT

Tropical maize germplasm has frequently been cited as a potential source of enhanced genetic diversity that could be used to increase corn productivity. One obstacle to utilizing tropical maize germplasm in temperate breeding programs is photoperiod sensitivity, which is very common in tropical adapted maize lines. An investigation of the quantitative trait loci (QTL) contributing to maize photoperiod sensitivity may increase the facility with which maize breeders can adapt tropical maize germplasm to temperate latitudes.

The photoperiod sensitive phase of maize was studied in a diverse set of inbreds. From a factorial mating of two temperate and two tropical inbreds, four populations of recombinant inbred lines (RIL) were developed for the purpose of mapping the QTL underlying photoperiod sensitivity in tropical maize. Plants were grown in both long- and short-day environments and a number of traits were measured in each environment. These traits include flowering time, plant height, leaf number, and ear structure traits. The trait differences between long- and short-day environments were reported as the photoperiodic responses of the RILs. Utilizing the data of both individual and combined mapping populations, QTL were identified using iterative QTL mapping (iQTLm). The positions and effects of these QTL were compared between populations and with flowering time, plant height, and leaf number QTL from other mapping studies. We detected four regions in the genome that produced large photoperiodic effects and named these Zea mays Photoperiodic Response 1-4 (ZmPRl, ZmPR2, ZmPR3, and ZmPR4). Similar QTL positions have been detected by other researchers studying photoperiod sensitivity and flowering time in maize. In addition to a major QTL on chromosome 3, QTL affecting the tasseled ear phenotype of maize were also found in the ZmPR3 and ZmPR4 QTL regions, implicating these QTL as also having effects on floral morphology. The four ZmPR loci are the most promising targets of marker-assisted selection against photoperiod sensitivity in maize.

Verification of the four ZmPR QTL was undertaken in four BC2F3:4 mapping populations, each having B73 as the recurrent parent. The CML254 backcross population had the same parentage as one of the RIL populations originally used to identify the ZmPR loci. We verified the presence of three of the four ZmPR loci in this population. We also found that the other three mapping populations, derived from CML247, Ki3, and Kil 1 showed significant flowering time and plant height associations at some of the ZmPR loci. Winter nurseries were used to verify that the ZmPR4 QTL, which was the strongest photoperiodic flowering time QTL detected in previous mapping studies, was indeed a photoperiodic and not flowering time per se QTL. An Ft population derived from a Kil 4 x CML254 cross was used to identify functional allelic differences among these two tropical lines at the ZmPR loci. Alleles of Ki 14 and CML254 were functionally distinct at ZmPR4 and ZmPR2.

The utility of QTL mapping for applied breeding programs is often limited by the transferability of QTL across populations and by the lack of precision in QTL mapping. One solution to these obstacles is to fine-map and clone the gene or genes underlying the QTL. I developed several heterogeneous inbred families (HIFs) from four RIL populations in order to facilitate fine-mapping. I observed several traits in these HIFs in phytotron, greenhouse, and field environments. I report the manner with which the HIFs were derived, as well as some observations and notes about future fine-mapping directions with these HIFs  .

2009. Regulation of aleurone cell fate determinants in Zea mays

2009. Regulation of aleurone cell fate determinants in Zea mays

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INTRODUCTION

 
Human nutrition is provided by a limited number of plant species. About 90% of mankind’s food supply is derived from approximately 17 species, of which cereal grains supply the greatest percentage. Wheat, maize and rice together comprise at least 75% of the world’s grain production (Cordain 1999) The primary nutritious part of the cereal grain is the seed endosperm. Despite detailed knowledge of events that occur in angiosperm fertilization and endosperm formation, very little is known about the regulatory networks controlling the complex developmental and metabolic processes of cereal grain formation.

In cereal plants, double fertilization initiates the process of seed formation, in which one sperm nucleus fertilizes the egg cell in the embryo sac resulting in a diploid zygote, a second sperm nucleus fuses with two polar nuclei of the central cell to initiate the development of the triploid endosperm (Dumas and Mogensen 1993). The diploid zygote and the primary triploid nucleus enter separate developmental patterns to give rise to the embryo and the nutritive endosperm. The pathway leading to the formation of the endosperm from the triploid nucleus is a four stage process. (1) syncytial stage, where the primary triploid nucleus in the central cell undergoes a period of mitotic nuclear divisions without cytokinesis resulting in a large syncytium; (2) cellularization, a period during which cytokinesis separates the nuclei into discrete cells involving both anticlinal and periclinal divisions; (3) growth and differentiation, which results in distinct tissues namely starchy endosperm, basal transfer layer and aleurone and (4) maturation, an important process characterized by accumulation of storage reserves and the development of desiccation tolerance and dormancy (Becraft 2001, Olsen 2001)  .

2009. Identification and fine-mapping genomic regions associated with plant regeneration response in maize (Zea mays L.)

2009. Identification and fine-mapping genomic regions associated with plant regeneration response in maize (Zea mays L.)

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ABSTRACT

Maize (Zea mays L.) is an important model organism for scientific advances in crop improvement and answering basic genetic and biological questions. Genetic engineering is an invaluable research tool for exploiting extensive genetic resources available to maize researchers for scientific advancement. Utilization of genetic engineering leads to advances in maize production and basic knowledge of plant genetic and biological systems. Application of genetic engineering in the study of maize is hindered, however, by the requirement for tissue culture as part of the genetic engineering process. Only a few genotypes of maize demonstrate high culture and regeneration response suitable for genetic engineering. The genotype-dependent tissue culture response of maize greatly impedes progress in functional genomics studies, and adds years to genetics research and crop improvement efforts. The goal of this research is to identify and characterize maize genes significantly associated to tissue culture response. Identification and characterization of genes associated with tissue culture response will likely lead to the development of new maize culture and transformation systems that are genotype-independent.

Two inbred maize lines, A188 (high Type-II culturability and regenerability; poor agronomic performance), and B73 (poor culturability/regenerability; excellent agronomic performance), formed the basis of the mapping populations used in this research. Results show chromosome 3 (3.07) has a QTL associated with plant regeneration response in a 3.58 cM PHM13673.53-umc2050 marker interval. SSR marker umc2050 accounts for 20.0% of the total variation, and the marker interval contains ~1.9 Mb of genomic sequence. Further analysis revealed an additional significant plant regeneration QTL on chromosome 4 (4.10) and a putative plant regeneration QTL on chromosome 2 (2.08). Future evaluation of the chromosome 3 (3.07) 1.9 Mb sequence interval, chromosomes 2 (2.08), and 4 (4.10) will likely yield genetic factors responsible for enhancing plant regeneration response in recalcitrant lines. Additionally, lines derived from the A188xB73 mapping population, which are ~95 - 99% B73, could be suitable for use in tissue culture and transformation experiments. Lastly, identification and characterization of genetic factors regulating plant regeneration response will increase the likelihood of developing a line-independent maize tissue culture and transformation system  .

2008. Genetic mapping and analysis of traits related to improvement of popcorn

2008. Genetic mapping and analysis of traits related to improvement of popcorn

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ABSTRACT

 
Popcorn and dent maize are distinct gene pools and are maintained and utilized as such in maize breeding programs. Popcorn is inferior to dent maize in traits related to crop productivity. Dent maize is a potential source of favorable alleles to improve the productivity of popcorn, but its utility is hindered by dent alleles with negative effects on popping expansion volume (PEV), an important quality trait of popcorn. If the genetic architecture of popping expansion and other important traits is known in dent x popcorn populations, the negative effects of dent germplasm on PEV may be minimized by marker-assisted selection (MAS). Use of DNA markers in breeding programs requires that quantitative trait loci (QTL) associated with target traits be identified. QTL for PEV, kernel weight (KW), growing degree units to anthesis (GDU), and plant height were mapped in F2 plants and their F2:3 families in a dent (B104) x popcorn (BP3) population. Seven QTL associated with 82% of the phenotypic variance were detected for PEV on chromosomes 1 (bins 1.05 and 1.07), 2, 3, 5, 8, and 9. The BP3 allele increased PEV at six of the QTL on chromosomes 1, 2, 3, 5, and 9. The dent parent, B104 contributed the allele that increased PEV at the QTL on chromosome 8. Epistasis was detected for PEV between QTL on chromosomes 2 and 5 such that the magnitude of the additive effect on chromosome 5 was larger when the genotype on chromosome 2 was a BP3 homozygote than when it was B104 homozygote. For kernel weight, six QTL explaining 66% of the phenotypic variance were on chromosomes 1 (bins 1.03 and 1.05), 6, 7, 8, and 9. The B104 allele increased KW at all QTL. QTL for PEV and KW were less than 10 cM apart on chromosomes 1 and 9. Association of PEV and KW QTL may be the cause of the significant phenotypic (rp) and genotypic (rg) correlation detected between the two traits (rp = -0.55 ± 0.04; rg = -0.68 ± 0.05). The test of linkage vs. pleiotropy for PEV and KW QTL on chromosomes 1 and 9 suggested pleiotropy. For GDU, QTL were detected on chromosomes 1, 2, 3,4, 6, and 8. QTL for plant height were detected on chromosomes 1,2, 8, and 9. GDU and plant height QTL accounted for 68 and 48% of the phenotypic variance, respectively. QTL for both traits were in regions (bins) where QTL affecting flowering time and plant height were detected in dent maize populations, suggesting that some of the same genetic factors may be affecting these traits in both dent and popcorn gene pools. In addition, GDU and plant height QTL were in regions where genes and other genetic factors affecting both traits have been mapped in maize. Because QTL in this study were mapped a reference population relevant to popcorn breeding objectives, they can be used to augment phenotypic selection and ensure retention of favorable alleles in a breeding program to improve productivity of BP3 with B104 alleles .

2006. Finemapping, cloning, verification, and fitness evaluation of a QTL, Rcg1, which confers resistance to Colletotrichum graminicola in maize

2006. Finemapping, cloning, verification, and fitness evaluation of a QTL, Rcg1, which confers resistance to Colletotrichum graminicola in maize

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ABSTRACT

Colletotrichum graminicola (Cg) causes anthracnose stalk rot and anthracnose leaf blight of maize and other graminaceous hosts (Bergstrom and Nicholson, 1999). Anthracnose has been found to occur in the United States since 1855 and occurs in the Americas, Europe, Africa, Asia, and Australia. Over 37.5 million acres are infested annually in the United States with average yield losses of 6.6%. Previously, a QTL region on chromosome 4 was reported to carry resistance to Cg in the maize line DE811ASR (Jung et al. 1994). DE811ASR was further backcrossed to DE811 (susceptible maize line) to develop DE811 Rcgl which was used to develop a BC7 segregating population for mapping. Utilizing 4784 genotyped BC7 individuals, 856 BC7 individuals were selected as recombinants within the region of interest. The selfed progeny of those 856 individuals were phenotyped to obtain family means, and a high-resolution genetic-linkage map was constructed to further resolve the previously described QTL. Initial markers identified two physical contigs within the region of interest. Using public and private physical and genetic integrated maps, the gap between the contigs was closed, and a complete tiling path through the region was constructed. Additional PCR-based fragment length polymorphic markers were created from BAC end sequences, overgoes and ESTs present on the BAC clones. Subsequent analysis of phenotypic data integrated with the BC7 genetic-linkage map resolved the QTL location to an approximate 3 cM region (~400kb physical distance based on the B73 and Mo 17 physical maps) with a peak LOD score of approximately 55. This 400kb region was sequenced using the corresponding BACs from a library made from the resistant parent, and a candidate gene for resistance to Cg was discovered in the region. Four independent Mu insertion events were identified in putative susceptible mutants derived from a targeted Mu-transposon population containing the resistance gene. Sequence data confirmed the presence of the Mu element within the candidate gene causing these plants to be susceptible to Cg.

The effects of Cg on maize growth and development can be very substantial; estimates of yield loss range from zero to over 40%. A multi-year multilocation trial was conducted to evaluate the agronomic and disease performance of DE81 IRcgl isohybrids compared to DE811 isohybrids when inoculated with Cg. Isogenic hybrids created by crossing each isogenic line, DE811 and DE81 IRcgl, to a diverse set of inbred lines, H99, Mo 17, B73, LH132, and DE4 were evaluated in a randomized complete block design over three locations in 2004 and four locations in 2005 across Delaware with three replications per location. A more detailed split-split plot design was conducted in 2005 to determine if any fitness costs were associated with the isogenic line DE81 \Rcgl when inoculated with Cg, wounded (inoculated with water), or not inoculated. The isogenic hybrids were created by crossing DE811 and DE81 \Rcgl with Mo 17 and B73 and planted in six locations across the U.S. with three replicates at each location. The data indicate that the near isogenic line DE81 \Rcgl does not cause significant negative effects in hybrid combinations for most agronomic traits compared to hybrids made with the recurrent parent, DE811. The results suggest that there was no apparent fitness cost associated with Rcgl in uninoculated or wounded treatments. The presence of Rcgl reduced the overall economic impact incurred by infection in inoculated plots by almost three-fold in comparison to isohybrids that lacked the gene. The resistance appears to act on delaying the onset of the disease until later in the season when the pathogens effects have less impact on plant yield. These results in addition to the asexual life cycle and limited variability of Cg, suggest that Rcgl may be a very durable disease resistance. These data also indicate the importance of diversity and germplasm conservation and evaluation. The low frequency of Rcgl in modem maize hybrids indicates that this resistance may have been lost without a sustained effort to maintain and evaluate diverse germplasm .

2005. Identification of quantitative trait loci (QTL) affecting endoreduplication and characterization of cyclin dependent kinase inhibitors in developing maize (Zea mays L.) endosperm

2005. Identification of quantitative trait loci (QTL) affecting endoreduplication and characterization of cyclin dependent kinase inhibitors in developing maize (Zea mays L.) endosperm

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ABSTRACT

Endoreduplication is a process of genome duplication without mitosis. This cell cycle results in an increase in nuclear DNA content, hence gene copy number. Although endoreduplication is common among plants and animals, the molecular mechanisms involved with this process are not fully understood. Elucidating the mechanisms that control this type of cell cycle could provide a better understanding of endosperm development, and ultimately could provide new insights for manipulating the genetic components involved with grain yield. Two strategies were used in this study to determine the genetic components involved with endoreduplication. One, based on QTL analysis to investigate the number, location and interaction of loci involved with endoreduplication. The other strategy involved identifying cell cycle candidate genes, more specifically cyclin dependent kinase inhibitors (CKIs), and characterizing them in regard to endoreduplication.

In an effort to map genes influencing endoreduplication, four backcross populations were created from crosses between a high (Sgl 8) and a low (Mo 17) endoreduplication inbred and their Fi (Sgl8 x Mo 17) progeny. These populations were used to detect quantitative trait loci with different modes of inheritance that influence endoreduplication. In all, fourteen quantitative trait loci were identified that affect the degree of endoreduplication in maize endosperm. Six QTLs were mapped using a statistical model that considers the triploid mode of inheritance in the endosperm. Two QTLs were mapped using a statistical model that considers parent-of-origin effect inheritance. Six QTLs were mapped using a model that considers genetic interaction between embryo and endosperm.

Previous studies with maize endosperm showed that accumulation of a cyclin-dependent kinase (CDK) inhibitor is coincident with the onset of endoreduplication, but the identity of this inhibitor is unknown, nor is it clear whether it affects M- or S-phase CDKs. We therefore tried to determine if cyclin-dependent kinase inhibitor (CKI) activity is required for the occurrence of endoreduplication in maize endosperm. The expression of two maize CKI genes, Zeama;CKI; 1 and Zeama;CKI;2, were characterized in developing endosperm, and their functional activities were investigated. The accumulation of Zeama;CKI;l RNA is not developmentally regulated, and its expression encompasses the period in which endoreduplication takes place during maize endosperm development. In contrast, Zeama;CKI;2 gene expression appears to be developmentally regulated in the endosperm, since its protein level decreases after 13 days after pollination (DAP). Both proteins were able to inhibit the maize Cdc2/CDK kinase activity associated with pl3Sucl, through in vitro assays. They were also able to specifically inhibit cyclin Al;3/ and cyclin D5;l/-associated CDK activities, but not cyclin B1;3/CDK, at least in vitro. Although Zeama;CKI;l was found to be associated with the endosperm CKI activity, it did not account for all of the CDK inhibitor present in this fraction. Over-expression of ZeamaCKIl in maize embryonic calli that ectopically expressed the wheat dwarf virus RepA protein, which counteracts retinoblastoma-related protein (RBR) function in the cell cycle, led to an additional round of DNA replication without nuclear division. However, a role for Zeama;CKI;l in endoreduplication could not be demonstrated in maize endosperm  .

2002. Molecular mechanisms controlling cell division and differentiation during maize development

2002. Molecular mechanisms controlling cell division and differentiation during maize development

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Abstract

Elaborate genetic mechanisms are involved in controlling cell division and differentiation during plant development. The maize Extra cell Layers 1 (Xcll) mutation provides insight into these developmental pathways since it causes aberrant oblique, periclina! divisions to occur in the protoderm layer. These periclinal divisions occur at the expense of normal anticlinal divisions in the protoderm and cause the production of extra cell layers with epidermal characteristics, indicating that cells are differentiating according to lineage instead of position. Mutant kernels have several aleurone layers instead of one, indicating that Xcll alters cell division orientation in cells that divide predominantly in the anticlinal plane. Dosage analysis of Xcll reveals that the mutant phenotype is caused by overproduction of a normal gene product. This allows cells that have already received differentiation signals to continue to divide in aberrant planes and suggests that the timing of cell division determines differentiation. Cells that divide early and in the absence of differentiation signals use positional information, while cells that divide late after perceiving differentiation signals use lineage information instead of position.

Double mutant analyses indicate that XCL1 may interact with several other genetic pathways during normal shoot development. Among these are TANGLED 1, a microtubule-binding protein, and CRINKLY4, a receptor kinase involved in epidermal differentiation. XCL1 also displays genetic interactions with KNOTTED I-like homeobox (KNOX) proteins involved in maintaining pools of undifferentiated cells in the shoot apical meristem. The double mutant interactions of Xcll with dominant KNOX mutants such as Knotted1, Gnarlyl, and Rough sheathl indicate that XCL1 may play a role in linking KNOX proteins with auxin-mediated developmental pathways. Thus, XCL1 is an important regulator of both cell division orientation and differentiation signal transduction pathways during plant development  .

2000. Empirical evaluation of marker-assisted selection for improving quantitative traits in sweet corn

2000. Empirical evaluation of marker-assisted selection for improving quantitative traits in sweet corn

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INTRODUCTION

This thesis consists of two related experiments concerning the application of marker-assisted selection (MAS) in plant breeding programs. The first was conducted to compare progress over one cycle of selection in sweet com populations using MAS and phenotypic selection (PS). Single trait selection was conducted for seedling emergence, kernel sucrose content, and cooked kernel tenderness. Multiple trait selection was applied to simultaneously improve emergence/tendemess, emergence/hedonic, and emergence/sucrose/tendemess. From each base population (38 sulSel, 48 sulsel, and 117 sh2 F2:3 families), 20% of families were selected to generate Ci composites for single and multiple traits. In each population, 50% of the families were randomly selected to serve as control (Co). Selection progress was evaluated using the following criteria: selection gain (percent increase of Q over Co), divergence between high and low Ci composites, realized heritability, and cost efficiency.

Results indicated that, although using relatively small base population size particularly in sulSel and sulsel, MAS showed higher selection gains compared to PS. In single trait selection, MAS increased seedling emergence by 8.3% and 14.9% while PS provided 1.5% and 3.1% gains compared to C0 performance in the sulSel and sulsel Ci composites, respectively. In the sh2 population, while the MAS selected composites had higher emergence, the difference was not significantly greater than PS. Selection gains were significantly higher with MAS than PS for kernel sucrose concentration and cooked kernel tenderness. MAS and PS showed comparable selection gains among low-direction composite selections. Additional comparisons were conducted on combinations of three traits under selection where selection efficiency was reduced with increasing numbers of traits in both PS and MAS. The application of MAS resulted in greater cost-efficiency with eating quality traits which are difficult and expensive to measure using phenotypic evaluations. MAS also appeared to be appropriate for seedling emergence since the enhanced selection gain compensated for the lower costs of phenotypic evaluation.

In the second study, three chromosomal regions carrying QTL previously found to improve seedling emergence in a shrunken2 population were introgressed using marker-assisted backcrossing into three sweet com elite inbreds. Comparisons of field seedling emergence were made among 50 different BC2F1 families and Fi hybrids (controls) generated from crosses between the original inbreds. Significant effects associated with the beneficial QTL alleles were observed. Across the three populations, BC2F1 genotypes heterozygous for the beneficial QTL alleles linked to umcl39, bnl9.08, and php200689 displayed an average of 48.6%, 35.6%, and 36.2% increase in seedling emergence, respectively, over the Fi controls.

Results generated from this study suggest that incorporating DNA markers in breeding programs can expedite selection progress and therefore increase the economic return. Also, data suggest that beneficial QTL identified in one population can exert similar effects in other genetic backgrounds .

1993. Identification of quantitative trait loci (QTL) in maize on the basis of F3 and testcross progeny performance

1993. Identification of quantitative trait loci (QTL) in maize on the basis of F3 and testcross progeny performance

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INTRODUCTION

The phenotypic expression of a quantitative trait is due to the combined genetic effects of several to many genes, each contributing a small amount to total phenotype, plus environmental effects (Falconer, 1981). Quantitative genetic theory is based on the idea that genes controlling quantitative characters are subject to the same laws of inheritance as those controlling qualitative characters. In practice, however, quantitative traits are usually described in biometrical terms and gene effects are not considered individually. One way to study a quantitative trait at the gene level is to identify associations between phenotypic expression of the trait and the genotypes of scorable markers, resulting from linkage between the marker loci and quantitative trait loci (QTL).

Until recently, the ability to identify marker-QTL linkages has been hindered by the lack of marker systems that could provide plentiful informative markers in germplasm of interest (Sax, 1923, Thoday, 1961). This limitation has been largely overcome by the development of molecular marker systems, such as RFLPs, which can detect polymorphisms at the DNA sequence level. Such markers have been used to construct linkage maps in many major crop species (Tanksley et al., 1989; Melchinger, 1990) permitting QTL mapping throughout all or much of the genome. QTL analysis has also benefited from advances in statistical techniques for detecting associations between marker genotypes and phenotypic effects. Maximum likelihood and least squares methods have been developed to conduct searches for QTL in intervals between linked markers (Lander and Botstein, 1989; Knapp et al., 1990; Haley and Knott, 1992).

While these advances have greatly improved the ability to estimate the positions and effects of QTL, the actual expression of QTL effects remains dependent on characteristics of the population and how it is evaluated phenotypically. QTL analysis, like biometrical analysis of quantitative traits, is subject to factors, such as, the germplasm evaluated (Abler et al., 1991; Beavis, et al., 1991) whether individuals or their progenies are evaluated (Cowen, 1988; Soller and Beckman, 1990), and environmental conditions (Patterson et al., 1991)  .

1991. Molecular-marker-mediated dissection of quantitative inheritance in maize (Zea mays L)

1991. Molecular-marker-mediated dissection of quantitative inheritance in maize (Zea mays L)

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Abstract

 
RAGOT, MICHEL. Molecular-Marker-Mediated Dissection of Quantitative Inheritance in Maize (Zea mays L.): Characterization of Favorable Exotic Factors and Comparisons of Statistical Methodologies and Marker Technologies. (Under the direction of Charles W. Stuber and Paul H. Sisco.)

Exotic maize germplasm, shown to be useful for developing improved temperate cultivars, has remained little used partly because of many inherent shortcomings. Molecular markers allow the identification of genetic factors underlying the expression of agronomic traits and can also facilitate their introgression from donor (exotic) into recipient (US) germplasm. However, cost and time involved in molecular marker analyses are still limiting factors for most breeding applications.

Five F2 populations, developed from South American and US germplasm, were used to detect favorable factors of exotic origin at agronomic trait loci, using isozymes and RFLPs. A number of traits of agronomic importance, including grain yield, were measured on F2 individuals and / or F3 families grown in several environments, and analyzed using several statistical methodologies, whose relative merits were evaluated. Many QTLs were identified, mostly with small effects. Major QTLs for grain yield and number of ears per plant were located on chromosomes 3 and 6. Favorable exotic factors were found for both traits on these chromosomes. Single-factor analyses and interval mapping yielded very similar results in terms of QTL detection. However, interval mapping allowed more precise location of QTLs than single-factor analyses. Selective genotyping failed to detect QTLs with minor effects but allowed the identification of QTLs possibly epistatic to major QTLs. Stability of QTLs across environments was high. Differences among locations often could be attributed to the chosen significance thresholds.

Three molecular marker technologies, RFLPs based on chemiluminescence, RFLPs based on radioactivity, and RAPDs, were compared in terms of cost and time efficiencies using simulations of maize genotyping projects. RAPDs were the most cost-efficient strategy when small sample sizes were to be analyzed. RFLPs were the least expensive methods for large numbers of individuals. Relative time efficiencies were comparable to cost efficiencies, except that RFLPs based on radioactivity always required more time than RFLPs based on chemiluminescence. The choice of a molecular marker strategy should be determined by the type and amount of information sought, the availability of markers or previous information for the species, and the ability to integrate the generated information into a general database .