Conner RL, Davidson JGN. Resistance in wheat to black point caused by Alternaria alternata and Cochliobolus sativus. Can J Plant Pathol. 1988;68:351–9.
Sissons M, Sissons S, Egan N. The black point status of selected tetraploid species and Australian durum wheat and breeding lines. Crop Sci. 2010;50:1279–86.
Dexter JE, Matsuo RR. Effect of smudge and black point, mildewed kernels, and ergot on durum wheat quality. Cereal Chem. 1982;59:63–9.
Li QY, Qin Z, Jiang YM, Shen CC, Duan ZB, Niu JS. Screening wheat genotypes for resistance to black point and the effects of diseased kernels on seed germination. J Plant Dis Protect. 2014;121:79–88.
Logrieco A, Bottalico A, Mulé G, Moretti A, Perrone G. Epidemiology of toxigenic fungi and their associated mycotoxins for some Mediterranean crops. Eur J Plant Pathol. 2003;109:645–67.
Desjardins AE, Busman M, Proctor RH, Stessman R. Wheat kernel black point and fumonisin contamination by Fusarium proliferatum. Food Addit Contam. 2007;24:1131–7.
Busman M, Desjardins AE, Proctor RH. Analysis of fumonisin contamination and the presence of Fusarium in wheat with kernel black point disease in the United States. Food Addit Contam. 2012;29:1092–100.
Palacios SA, Susca A, Haidukowski M, Stea G, Cendoya E, Ramírez ML, Chulze SN, Farnochi MC, Moretti A, Torres AM. Genetic variability and fumonisin production by Fusarium proliferatum isolated from durum wheat grains in Argentina. Int J Food Microbiol. 2015;201:35–41.
Maloy OC, Spetch KL. Black point of irrigated wheat in Central Washington. Plant Dis. 1988;72:1031–3.
Fernandez MR, Wang H, Singh AK. Impact of seed discoloration on emergence and early plant growth of durum wheat at different soil gravimetric water contents. Can J Plant Pathol. 2014;36:509–16.
Southwell RJ, Brown JF, Wong PT. Effect of inoculum density, stage of plant growth and dew period on the incidence of black point caused by Alternaria alternata in durum wheat. Ann Appl Biol. 1980;96:29–35.
Kumar J, Schäfer P, Hückelhoven R, Langen G, Baltruschat H, Stein E, Nagarajan S, Kogel KH. Bipolaris sorokiniana, a cereal pathogen of global concern: cytological and molecular approaches towards better control. Mol Plant Pathol. 2002;3:85–195.
Williamson PM. Black point of wheat: in vitro production of symptoms, enzymes involved, and association with Alternaria alternata. Aust J Agri Res. 1997;48:13–9.
Hudec K. Pathogenicity of fungi associated with wheat and barley seedling emergence and fungicide efficacy of seed treatment. Biologia. 2007;62:287–91.
March TJ, Able J, Schultz C, Able AJA. Novel late embryogenesis abundant protein and peroxidase associated with black point in barley grains. Proteomics. 2007;7:3800–8.
Mak Y, Willows RD, Roberts TH, Wrigley CW, Sharp PJ, Copeland LES. Black point is associated with reduced levels of stress, disease and defence related proteins in wheat grain. Mol Plant Pathol. 2006;7:177–89.
Anderson JV, Morris CF. An improved whole-seed assay for screening wheat germplasm for polyphenol oxidase activity. Crop Sci. 2001;41:1697–705.
Fuerst EP, Okubara PA, Anderson JV, Morris CF. Polyphenol oxidase as a biochemical seed defense mechanism. Front Plant Sci. 2014;5:689.
Porta H, Rocha-Sosa M. Plant lipoxygenases. Physiological and molecular features. Plant Physiol. 2002;130:15–21.
Tomás-Barberán FA, Espín JC. Phenolic compounds and related enzymes as determinants of quality in fruits and vegetables. J Sci Food Agr. 2001;81:853–76.
Regnier T, Macheix JJ. Changes in wall bound phenolic acids, phenylalanine and tyrosine ammonia-lyases, and peroxidases in developing durum wheat grains (Triticum turgidum L. Var. durum). J Agric Food Chem 1996;44: 1727–1730.
Lehmensiek A, Campbell AW, Williamson PM, Michalowitz M, Sutherland MW, Daggard GQTL. For black point resistance in wheat and the identification of potential markers for use in breeding programs. Plant Breed. 2004;123:410–6.
Liu JD, He ZH, Wu L, Bai B, Wen WE, Xie CJ, Xia XC. Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.). Theor Appl Genet 2016;129:2179–2190.
March TJ, Able JA, Willsmore K, Schultz CJ, Able AJ. Comparative mapping of a QTL controlling black point formation in barley. Funct Plant Biol. 2008;35:427–37.
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dulferos R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using the high-density 90,000 SNP array. Plant Biotech J. 2014;12:787–96.
Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J. High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J. 2015;14:1195–206.
Flint-Garcia SA, Thornsberry JM, Buckler ES. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 2003;54:357–74.
Breseghello F, Sorrells ME. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics. 2006;172:1165–77.
Zhu CS, Gore M, Buckler ES, Status YJM. Prospects of association mapping in plants. Plant Genome. 2008;1:5–20.
Zegeye H, Rasheed A, Makdis F, Badebo A, Ogbonnaya FC. Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat. PLoS One. 2014;9:e105593.
Pasam RK, Bansal U, Daetwyler HD, Forrest KL, Wong D, Petkowski J, Willey N. Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches. Theor Appl Genet. 2017;130:777–93.
Marcotuli I, Houston K, Waugh R, Fincher GB, Burton RA, Blanco A, Gadaleta A. Genome-wide association mapping for arabinoxylan content in a collection of tetraploid wheats. PLoS One. 2015;10:e0132787.
Rasheed A, Xia XC, Ogbonnaya F, Mahmood T, Zhang Z, Mujeeb-Kazi A, He ZH. Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis. BMC Plant Biol. 2014;14:128.
Ain QU, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia XC, He ZH, Quraishi UM. Genome-wide association for grain yield under rain-fed conditions in historical wheat cultivars from Pakistan. Front Plant Sci. 2015;6:743.
Sun CW, Zhang FY, Yan XF, Zhang XF, Dong ZD, Cui DQ, Chen F. Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the yellow and Huai Valley of China. Plant Biotechnol J. 2017; doi:10.1111/pbi.12690.
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ESTASSEL. Software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5.
Liu X, Huang M, Fan B, Buckler ES, Zhang Z. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet. 2016;12(2):e1005767.
Kahl SM, Ulrich A, Kirichenko AA, Müller ME. Phenotypic and phylogenetic segregation of Alternaria infectoria from small-spored Alternaria species isolated from wheat in Germany and Russia. J Appl Microbiol. 2015;119:1637–50.
Chen XJ, Min DH, Tauqeer AY, Genetic HYG. Diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One. 2012;7:e44510.
Lopes M, Dreisigacker S, Peña R, Sukumaran S, Reynolds M. Genetic characterization of the wheat association mapping initiative (WAMI) panel for dissection of complex traits in spring wheat. Theor Appl Genet. 2014;128:453–64.
Botstein D, Wlllte RL, Skolinck M. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32:314–9.
Chao S, Zhang W, Dubcovsky J, Sorrells M. Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci. 2007;47:1018–30.
Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet. 2000;67:170–81.
Yu J, Buckler ES. Genetic association mapping and genome organization of maize. Curr Opin Biotechnol. 2006;17:155–60.
Cormier F, Gouis JL, Dubreuil P, Lafarge S, Praud S. A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.). Theor Appl Genet 2014;127:2679–2693.
Hao CY, Wang LF, Ge HM, Dong YC, Zhang XY. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS One. 2011;6:e17279.
Sukumaran S, Dreisigacker S, Lopes M, Chavez P, Reynolds MP. Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor Appl Genet. 2015;128:353–63.
Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED. Population and genome specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 2010;11:727.
Edae EA, Byrne PF, Haley SD, Lopes MS, Reynolds MP. Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theor Appl Genet. 2014;127:791–807.
Chen GF, Zhang H, Deng ZY, Wu RG., Li DM, Wang MY, Tian JC. Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population. Euphytica 2016;212:173-185.
Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, Würschum T, Mapping QTL. With main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet. 2011;123:283–2927.
Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC. Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet. 2011;123:1121–31.
Poznial CJ, Clarke JM, Clarke FR. Potential for detection of marker-trait associations in durum wheat using unbalanced, historical phenotypic datasets. Mol Breed. 2012;30:1537–50.
Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D’Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 2011;9:1086–1099.
Zhai SN, He ZH, Wen WE, Jin H, Liu JD, Zhang Y, Liu ZY, Xia XC. Genome-wide linkage mapping of flour color-related traits and polyphenol oxidase activity in common wheat. Theor Appl Genet. 2016;129:377–94.
Sun DJ, He ZH, Xia XC, Zhang LP, Morris CF, Appels R, Ma WJ, Wang HA, Novel STS. Marker for polyphenol oxidase activity in bread wheat. Mol Breed. 2005;16:209–18.
Wei JX, Geng HW, Zhang Y, Liu JD, Wen WE, Xia XC, Chen XM, He ZH. Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL. Theor Appl Genet. 2015;128:2067–76.
Kumar S, Kawałek A, van der Klei IJ. Peroxisomal quality control mechanisms. Curr Opin Microbiol. 2014;22:30–7.
Sun TP, Gubler F. Molecular mechanism of gibberellin signaling in plants. Annu Rev Plant Biol. 2004;55:197–223.
Frigerio M, Alabadí D, Pérez-Gómez J, García-Cárcel L, Phillips AL, Hedden P, Blázquez MA. Transcriptional regulation of gibberellin metabolism genes by auxin signaling in Arabidopsis. Plant Physiol. 2006;142:553–63.
Kim HS, Delaney TP. Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell. 2002;14:1469–82.
Xiong L, Yang Y. Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase. Plant Cell. 2003;15:745–59.
Li FH, FL F, Sha LN, He L, Li WC. Differential expression of serine/threonine protein phosphatase type-2C under drought stress in maize. Plant Mol Biol Rep. 2009;27:29–37.
Hameed U, Pan YB, Iqbal J. Genetic analysis of resistance gene analogues from a sugarcane cultivar resistant to red rot disease. J Phytopathol. 2015;163:755–63.
Semagn K, Babu R, Hearne S, Olsen M. Single nucleotide polymorphism genotyping using Kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 2014;33:1–14.
Rasheed A, Hao YF, Xia XC, Khan A, Yb X, Varshney RK, He ZH. Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Mol Plant. 2017;10:1047–64.
Long YM, Chao WS, Ma GJ, SS X, Qi LL. An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theor Appl Genet. 2016;130:597–607.
Veldboom LR, Lee M. Genetic mapping of quantitative trait loci in maize in stress and non-stress environments: I. Grain yield and yield components. Crop Sci. 1996;36:1310–9.
Doyle JJ, Doyle JL. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bull. 1987;19:11–5.
Liu K, Muse SV. PowerMarker. An integrated analysis environment for genetic marker analysis. Bioinformatics. 2005;21:2128–9.
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14:2611–20.
Holm SA. Simple sequentially rejective multiple test procedure. Scand J Stat. 1979;6:65–70.
Houston K, Russell J, Schreiber M, Halpin C, Oakey H, Washington JM, Booth A, Shirley N, Burton RA, Fincher GB, Waugh R. A Genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2- row spring and winter barleys. BMC Genomics 2014;15:907.
Gurung S, Mamidi S, Bonman JM, Xiong M, Brown-Guedira G, Adhikari TB. Genome-wide association study reveals novel quantitative trait loci associated with resistance to multiple leaf spot diseases of spring wheat. PLoS One. 2014;9:e108179.
Bellucci A, Torp AM, Bruun S, Magid J, Andersen SB, Rasmussen SK. Association mapping in scandinavian winter wheat for yield, plant height, and traits important for second-generation bioethanol production. Front Plant Sci. 2015;6:1046.
Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–5.