@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{tian_bradbury_brown_hung_sun_flint-garcia_rocheford_mcmullen_holland_buckler_2011, title={Genome-wide association study of leaf architecture in the maize nested association mapping population}, volume={43}, ISSN={["1546-1718"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79251561130&partnerID=MN8TOARS}, DOI={10.1038/ng.746}, abstractNote={US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.}, number={2}, journal={NATURE GENETICS}, author={Tian, Feng and Bradbury, Peter J. and Brown, Patrick J. and Hung, Hsiaoyi and Sun, Qi and Flint-Garcia, Sherry and Rocheford, Torbert R. and McMullen, Michael D. and Holland, James B. and Buckler, Edward S.}, year={2011}, month={Feb}, pages={159–U113} }
 @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{flint-garcia_mcmullen_darrah_2003, title={Genetic relationship of stalk strength and ear height in maize}, volume={43}, ISSN={["0011-183X"]}, DOI={10.2135/cropsci2003.0023}, abstractNote={Crop ScienceVolume 43, Issue 6 p. 2300-2301 Registrations Of Cultivar Registration of ‘Lamont’ Oat C.A. Erickson, Corresponding Author C.A. Erickson nsgcce@ars-grin.gov USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Corresponding author (nsgcce@ars-grin.gov)Search for more papers by this authorD.M. Wesenberg, D.M. Wesenberg USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Search for more papers by this authorD.E. Burrup, D.E. Burrup USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Search for more papers by this authorJ.C. Whitmore, J.C. Whitmore Univ. of Idaho Tetonia Res. & Ext. Ctr., 888 West Highway 33, Newdale, ID, 83436Search for more papers by this author C.A. Erickson, Corresponding Author C.A. Erickson nsgcce@ars-grin.gov USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Corresponding author (nsgcce@ars-grin.gov)Search for more papers by this authorD.M. Wesenberg, D.M. Wesenberg USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Search for more papers by this authorD.E. Burrup, D.E. Burrup USDA-ARS, Univ. of Idaho Aberdeen Res. & Ext. Ctr., USDA-ARS Natl. Small Grains Germplasm Res. Facility, 1691 S. 2700 W., Aberdeen, ID, 83210Search for more papers by this authorJ.C. Whitmore, J.C. Whitmore Univ. of Idaho Tetonia Res. & Ext. Ctr., 888 West Highway 33, Newdale, ID, 83436Search for more papers by this author First published: 01 November 2003 https://doi.org/10.2135/cropsci2003.2300Citations: 1 Registration by CSSA. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume43, Issue6November–December 2003Pages 2300-2301 RelatedInformation}, number={1}, journal={CROP SCIENCE}, author={Flint-Garcia, SA and McMullen, MD and Darrah, LL}, year={2003}, pages={23–31} }
 @article{flint-garcia_jampatong_darrah_mcmullen_2003, title={Quantitative trait locus analysis of stalk strength in four maize populations}, volume={43}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2003.0013}, abstractNote={Insensitivity of flowering to long daylengths is an important character in the adaptation of soybean [Glycine max (L.) Merrill] to higher latitudinal environments. The objective of this study was to identify and map the maturity genes for incandescent long daylength (ILD) insensitivity for two landraces, ‘Miharudaizu’ and ‘Sakamotowase’, which belong to different cultivar groups. Two F9 recombinant inbred line (RIL) families were developed by means of a repetitive heterozygote selection method from the F2 population of the cross between the two landraces. Linkage analyses with isozyme and simple sequence repeat (SSR) markers revealed that the maturity gene for ILD insensitivity from Miharudaizu was a recessive allele at the E4 locus on Molecular linkage group (MLG) I. The MLG I order of the E4 locus and four markers was determined as Satt239–Satt496–E4–Enp–Satt354. The maturity gene for ILD insensitivity from Sakamotowase was found to cosegregate with four tightly linked SSRs on MLG C2, and was determined as a recessive allele at the E1 locus. The genotypes at the E3 locus for both Miharudaizu and Sakamotowase were estimated as e3e3 on the basis of the responses of late-flowering near-isogenic lines to fluorescent long daylength (FLD). The results obtained in this study suggest that Miharudaizu has the genotype of E1E1e3e3e4e4 and Sakamotowase has the genotype of e1e1e3e3E4E4 Because the e1 allele cannot induce flowering in ILD in the presence of the E4 allele, an unknown gene may condition the ILD insensitivity of Sakamotowase, possibly while combined with the e1 allele.}, number={1}, journal={CROP SCIENCE}, author={Flint-Garcia, SA and Jampatong, C and Darrah, LL and McMullen, MD}, year={2003}, pages={13–22} }
 @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} }