Papers by Candice Gardner
Crop Science, 2016
M aize (Zea mays L.) is the most important food crop in the world in terms of total production, w... more M aize (Zea mays L.) is the most important food crop in the world in terms of total production, with over one billion metric tonnes (1,007,473,000) produced in 2014 (USDA FAS, 2015). Maize yields in the United States have increased more than fivefold from less than 1885 kg ha-1 (30 bushels acre-1) using open pollinated landraces to greater than 10,040 kg ha-1 (160 bushels acre-1) (Fig. 1) as a result of public and private investments in hybrids and use of improved agronomic practices (Smith et al., 2014a; USDA NASS, 2015). Most recent estimates of the proportion of yield gain attributable to breeding (genetic gain) during the era of single-cross maize hybrids in the United States (1963-present) range from 74% to 66-77% when grown in rainfed and well-watered conditions, respectively (Smith et al., 2014a). Maize is just one example of the numerous contributions plant breeders make globally in marshalling useful genetic diversity from a broader pool of available diversity in the service of agriculture and society (
Genome Biology, 2013
Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was u... more Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions: The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.
Genetics, 2014
Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pe... more Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7300 inbreds representing most publically available maize inbreds in the United States and families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome-wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of maize height was estimated to be >90%. Mapping NAM family-nested QTL revealed the largest explained 2.1 ± 0.9% of hei...
Journal of Applied Glycoscience, 2003
... 論文検索. 著者検索. 論文検索. Structures of Amylopectin and Starch Granules : How Are They Synthesized? J... more ... 論文検索. 著者検索. 論文検索. Structures of Amylopectin and Starch Granules : How Are They Synthesized? JANE Jay-lin; Center for Crops Utilization Research and Department of Food Science and Human Nutrition, Iowa State University. AO Zihau; ...
Plant Breeding, 2015
ABSTRACT
BMC plant biology, Jan 30, 2014
BackgroundResistance to Fusarium ear rot of maize is a quantitative and complex trait. Marker-tra... more BackgroundResistance to Fusarium ear rot of maize is a quantitative and complex trait. Marker-trait associations to date have had small additive effects and were inconsistent between previous studies, likely due to the combined effects of genetic heterogeneity and low power of detection of many small effect variants. The complexity of inheritance of resistance hinders the use marker-assisted selection for ear rot resistance.ResultsWe conducted a genome-wide association study (GWAS) for Fusarium ear rot resistance in a panel of 1687 diverse inbred lines from the USDA maize gene bank with 200,978 SNPs while controlling for background genetic relationships with a mixed model and identified seven single nucleotide polymorphisms (SNPs) in six genes associated with disease resistance in either the complete inbred panel (1687 lines with highly unbalanced phenotype data) or in a filtered inbred panel (734 lines with balanced phenotype data). Different sets of SNPs were detected as associate...
Journal of ASTM International, 2010
Page 1. Sathaporn Srichuwong, 1 Jelena Gutesa, 1 Michael Blanco, 2 Susan A. Duvick, 2 Candice Gar... more Page 1. Sathaporn Srichuwong, 1 Jelena Gutesa, 1 Michael Blanco, 2 Susan A. Duvick, 2 Candice Gardner, 2 and Jay-Lin Jane 3 ... Sample Code Inventory Pedigree GEM Code Country Race A 05GEM06031 DKB844:S1601-073-001-BBBBB GEMS-0115 Mexico Tropical hybrid ...
Journal of Cereal Science, 2012
of near infrared spectroscopy for analyzing corn kernel damage and viability of soybean and corn ... more of near infrared spectroscopy for analyzing corn kernel damage and viability of soybean and corn kernels" (2012). Publications from USDA-ARS / UNL Faculty. Paper 828.
AIDS Research and Human Retroviruses, 2006
The genotypes and biological phenotypes of HIV-1 isolates obtained from 40 perinatally infected c... more The genotypes and biological phenotypes of HIV-1 isolates obtained from 40 perinatally infected children in South Africa were analyzed. This included 15 infants who had HIV-related symptoms, most of whom died within 2 years of birth (rapid progressors), and 25 children who survived between 4 and 9 years with varying signs of disease (slow progressors). Heteroduplex mobility assays and sequence analysis confirmed that within the env and gag regions, all isolates were HIV-1 subtype C. Viral isolates from 14 of the 15 rapid progressors used the CCR5 coreceptor, whereas 1 (02ZARP1) used both the CXCR4 and CCR5 coreceptors. Among the 25 slow progressors, 22 isolates used CCR5 only, 2 used CXCR4 only, and 1 used both CCR5 and CXCR4. Two of the slow-progressing children who harbored CXCR4-using viruses had AIDS. All four CXCR4-using viruses had genotypic changes in the V3 region previously shown to be associated with CXCR4 usage. This cross-sectional study shows that HIV-1 subtype C viruse...
BMC genomics, Jan 5, 2015
BackgroundPlants rely on the root system for anchorage to the ground, as well the acquisition and... more BackgroundPlants rely on the root system for anchorage to the ground, as well the acquisition and absorption of nutrients critical to sustaining productivity. Genome wide association analysis enables to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.ResultsUtilizing both a general linear model and mixed linear model genome wide association study to account for population structure, 268 marker trait associations (p¿¿¿5.3x10-7) were identified. Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions with previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is...
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Papers by Candice Gardner