@article{cook_mcmullen_holland_tian_bradbury_ross-ibarra_buckler_flint-garcia_2012, title={Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels}, volume={158}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84856582669&partnerID=MN8TOARS}, DOI={10.1104/pp.111.185033}, abstractNote={Abstract
               The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS associations were detected, including several oil and starch associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested association mapping were verified in a 282 inbred association panel using both GWAS and candidate gene association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Cook, Jason P. and McMullen, Michael D. and Holland, James B. and Tian, Feng and Bradbury, Peter and Ross-Ibarra, Jeffrey and Buckler, Edward S. and Flint-Garcia, Sherry A.}, year={2012}, month={Feb}, pages={824–834} }
 @article{hung_browne_guill_coles_eller_garcia_lepak_melia-hancock_oropeza-rosas_salvo_et al._2012, title={The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population}, volume={108}, ISSN={["1365-2540"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84859947989&partnerID=MN8TOARS}, DOI={10.1038/hdy.2011.103}, abstractNote={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.}, number={5}, journal={HEREDITY}, author={Hung, H-Y and Browne, C. and Guill, K. and Coles, N. and Eller, M. and Garcia, A. and Lepak, N. and Melia-Hancock, S. and Oropeza-Rosas, M. and Salvo, S. and et al.}, year={2012}, month={May}, pages={490–499} }
 @article{wilson_whitt_ibanez_rocheford_goodman_buckler_2004, title={Dissection of maize kernel composition and starch production by candidate gene association}, volume={16}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.104.025700}, abstractNote={Cereal starch production forms the basis of subsistence for much of the world's human and domesticated animal populations. Starch concentration and composition in the maize (Zea mays ssp mays) kernel are complex traits controlled by many genes. In this study, an association approach was used to evaluate six maize candidate genes involved in kernel starch biosynthesis: amylose extender1 (ae1), brittle endosperm2 (bt2), shrunken1 (sh1), sh2, sugary1, and waxy1. Major kernel composition traits, such as protein, oil, and starch concentration, were assessed as well as important starch composition quality traits, including pasting properties and amylose levels. Overall, bt2, sh1, and sh2 showed significant associations for kernel composition traits, whereas ae1 and sh2 showed significant associations for starch pasting properties. ae1 and sh1 both associated with amylose levels. Additionally, haplotype analysis of sh2 suggested this gene is involved in starch viscosity properties and amylose content. Despite starch concentration being only moderately heritable for this particular panel of diverse maize inbreds, high resolution was achieved when evaluating these starch candidate genes, and diverse alleles for breeding and further molecular analysis were identified.}, number={10}, journal={PLANT CELL}, author={Wilson, LM and Whitt, SR and Ibanez, AM and Rocheford, TR and Goodman, MM and Buckler, ES}, year={2004}, month={Oct}, pages={2719–2733} }
 @article{du_buckler_muse_2003, title={Development of a maize molecular evolutionary genomic database}, volume={4}, ISSN={["1531-6912"]}, DOI={10.1002/cfg.282}, abstractNote={PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on ‘Maize Evolutionary Genomics’. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web.}, number={2}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Du, CG and Buckler, E and Muse, S}, year={2003}, month={Apr}, pages={246–249} }
 @article{jaenicke-despres_buckler_smith_gilbert_cooper_doebley_paabo_2003, title={Early allelic selection in maize as revealed by ancient DNA}, volume={302}, ISSN={["0036-8075"]}, DOI={10.1126/science.1089056}, abstractNote={Maize was domesticated from teosinte, a wild grass, by ∼ 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.}, number={5648}, journal={SCIENCE}, author={Jaenicke-Despres, V and Buckler, ES and Smith, BD and Gilbert, MTP and Cooper, A and Doebley, J and Paabo, S}, year={2003}, month={Nov}, pages={1206–1208} }
 @article{liu_goodman_muse_smith_buckler_doebley_2003, title={Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites}, volume={165}, number={4}, journal={Genetics}, author={Liu, K. J. and Goodman, M. and Muse, S. and Smith, J. S. and Buckler, E. and Doebley, J.}, year={2003}, pages={2117–2128} }
 @misc{flint-garcia_thornsberry_buckler_2003, title={Structure of linkage disequilibrium in plants}, volume={54}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.arplant.54.031902.134907}, abstractNote={ Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed. }, journal={ANNUAL REVIEW OF PLANT BIOLOGY}, author={Flint-Garcia, SA and Thornsberry, JM and Buckler, ES}, year={2003}, pages={357–374} }
 @article{matsuoka_vigouroux_goodman_sanchez_buckler_doebley_2002, title={A single domestication for maize shown by multilocus microsatellite genotyping}, volume={99}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.052125199}, abstractNote={There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.}, number={9}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Matsuoka, Y and Vigouroux, Y and Goodman, MM and Sanchez, GJ and Buckler, E and Doebley, J}, year={2002}, month={Apr}, pages={6080–6084} }
 @article{buckler_doebley_gaut_goodman_kresovich_muse_weir_2002, title={Evolutionary genomics of maize}, number={76}, journal={Maize Genetics Cooperation Newsletter}, author={Buckler, E. and Doebley, J. and Gaut, B. and Goodman, M. and Kresovich, S. and Muse, S. and Weir, B.}, year={2002}, pages={86} }
 @article{whitt_wilson_tenaillon_gaut_buckler_2002, title={Genetic diversity and selection in the maize starch pathway}, volume={99}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.202476999}, abstractNote={
            Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (
            Zea mays
            ssp.
            mays
            ) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like
            c1
            and
            tb1
            . However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives.
          }, number={20}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Whitt, SR and Wilson, LM and Tenaillon, MI and Gaut, BS and Buckler, ES}, year={2002}, month={Oct}, pages={12959–12962} }
 @misc{buckler_thornsberry_2002, title={Plant molecular diversity and applications to genomics}, volume={5}, ISSN={["1879-0356"]}, DOI={10.1016/S1369-5266(02)00238-8}, abstractNote={Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Buckler, ES and Thornsberry, JM}, year={2002}, month={Apr}, pages={107–111} }
 @article{rauh_basten_buckler_2002, title={Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis thaliana}, volume={104}, ISSN={["0040-5752"]}, DOI={10.1007/s00122-001-0815-y}, abstractNote={Nitrogen absorption and assimilation is variable among plants as a result of two factors: the source of nitrogen available and the genetic variation among species within the resulting nitrogen pathways. Several genes involved in nitrogen cycling have been identified, yet little is known about the genes that control quantitative responses to different nitrogen sources. With quantitative trait loci (QTL) mapping in Arabidopsis thaliana recombinant inbred lines (Columbia x Landsberg erecta) we have identified chromosomal regions controlling aerial mass, root mass, and root length when plants are grown in nitrate, ammonium, ammonium nitrate, or low nitrogen treatments. A total of 16 QTL ( P < 0.01) were identified among the nitrogen treatments. Most of the QTL were specific to a single treatment. The percentage additive genetic effects of significant QTL were as high as 17%. Five significant QTL corresponded to the locations of candidate genes associated with nitrogen assimilation, while a few QTL corresponded with candidate genes in the developmental pathways. Most QTL were not shared across treatments, suggesting that there is no optimal genotype for all nitrogen sources.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Rauh, BL and Basten, C and Buckler, ES}, year={2002}, month={Apr}, pages={743–750} }
 @article{thornsberry_goodman_doebley_kresovich_nielsen_buckler_2001, title={Dwarf8 polymorphisms associate with variation in flowering time}, volume={28}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/90135}, DOI={10.1038/90135}, abstractNote={Historically, association tests have been used extensively in medical genetics, but have had virtually no application in plant genetics. One obstacle to their application is the structured populations often found in crop plants, which may lead to nonfunctional, spurious associations. In this study, statistical methods to account for population structure were extended for use with quantitative variation and applied to our evaluation of maize flowering time. Mutagenesis and quantitative trait locus (QTL) studies suggested that the maize gene Dwarf8 might affect the quantitative variation of maize flowering time and plant height. The wheat orthologs of this gene contributed to the increased yields seen in the 'Green Revolution' varieties. We used association approaches to evaluate Dwarf8 sequence polymorphisms from 92 maize inbred lines. Population structure was estimated using a Bayesian analysis of 141 simple sequence repeat (SSR) loci. Our results indicate that a suite of polymorphisms associate with differences in flowering time, which include a deletion that may alter a key domain in the coding region. The distribution of nonsynonymous polymorphisms suggests that Dwarf8 has been a target of selection.}, number={3}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Thornsberry, Jeffry M. and Goodman, Major M. and Doebley, John and Kresovich, Stephen and Nielsen, Dahlia and Buckler, Edward S.}, year={2001}, month={Jul}, pages={286–289} }
 @article{bennetzen_buckler_chandler_doebley_dorweiler_gaut_freeling_hake_kellogg_poethig_et al._2001, title={Genetic evidence and the origin of maize (Biology, archaeology)}, volume={12}, ISSN={["2325-5080"]}, DOI={10.2307/971759}, abstractNote={The origin of maize has been a topic of interest to both biologists and archaeologists. During the twentieth century, the view point that maize is a domesticated form of teosinte received convincing support from biological data and is now broadly accepted among biologists familiar with the issues and data. There is no support of any kind for an alternative view that maize is a hybrid of the grassesZea diploperennisandTripsacum.}, number={1}, journal={LATIN AMERICAN ANTIQUITY}, author={Bennetzen, J and Buckler, E and Chandler, V and Doebley, J and Dorweiler, J and Gaut, B and Freeling, M and Hake, S and Kellogg, E and Poethig, RS and et al.}, year={2001}, month={Mar}, pages={84–86} }
 @article{buckler_thornsberry_kresovich_2001, title={Molecular diversity, structure and domestication of grasses}, volume={77}, number={3}, journal={Genetical Research}, author={Buckler, E. S. and Thornsberry, J. M. and Kresovich, S.}, year={2001}, pages={213–218} }
 @article{remington_thornsberry_matsuoka_wilson_whitt_doeblay_kresovich_goodman_buckler_2001, title={Structure of linkage disequilibrium and phenotypic associations in the maize genome}, volume={98}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.201394398}, abstractNote={
            Association studies based on linkage disequilibrium (LD) can
 provide high resolution for identifying genes that may contribute to
 phenotypic variation. We report patterns of local and genome-wide LD in
 102 maize inbred lines representing much of the worldwide genetic
 diversity used in maize breeding, and address its implications for
 association studies in maize. In a survey of six genes, we found that
 intragenic LD generally declined rapidly with distance
 (
            r
            2
            < 0.1 within 1500 bp), but rates
 of decline were highly variable among genes. This rapid decline
 probably reflects large effective population sizes in maize during its
 evolution and high levels of recombination within genes. A set of 47
 simple sequence repeat (SSR) loci showed stronger evidence of
 genome-wide LD than did single-nucleotide polymorphisms (SNPs) in
 candidate genes. LD was greatly reduced but not eliminated by grouping
 lines into three empirically determined subpopulations. SSR data also
 supplied evidence that divergent artificial selection on flowering time
 may have played a role in generating population structure. Provided the
 effects of population structure are effectively controlled, this
 research suggests that association studies show great promise for
 identifying the genetic basis of important traits in maize with very
 high resolution.
          }, number={20}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Remington, DL and Thornsberry, JM and Matsuoka, Y and Wilson, LM and Whitt, SR and Doeblay, J and Kresovich, S and Goodman, MM and Buckler, ES}, year={2001}, month={Sep}, pages={11479–11484} }
 @article{buckler_phelps-durr_buckler_dawe_doebley_holtsford_1999, title={Meiotic drive of chromosomal knobs reshaped the maize genome}, volume={153}, number={1}, journal={Genetics}, author={Buckler, E. S. and Phelps-Durr, T. L. and Buckler, C. S. K. and Dawe, R. K. and Doebley, J. F. and Holtsford, T. P.}, year={1999}, pages={415–426} }
 @article{buckler_pearsall_holtsford_1998, title={Climate, plant ecology, and central Mexican archaic subsistence}, volume={39}, ISSN={["1537-5382"]}, DOI={10.1086/204705}, abstractNote={Les moyens de subsistance humaine sont lies, entre autre, a trois modes d'approvisionnement en ressources vegetales : la collecte (recolte des plantes sauvages), la culture (manipulation de la repartition des plantes) et la domestication (modification genetique des plantes). Afin de comprendre l'apparition du processus de domestication au Mexique, les auteurs etudient les pratiques de collecte et de culture entre 11.000 et 4000 BP. Le materiel le plus probant est celui provenant des fouilles des vallees semi-arides d'Oaxaca et Tehuacan}, number={1}, journal={CURRENT ANTHROPOLOGY}, author={Buckler, ES and Pearsall, DM and Holtsford, TP}, year={1998}, month={Feb}, pages={152–164} }