World Journal of Agricultural Research
ISSN (Print): 2333-0643 ISSN (Online): 2333-0678 Website: Editor-in-chief: Rener Luciano de Souza Ferraz
Open Access
Journal Browser
World Journal of Agricultural Research. 2017, 5(3), 126-134
DOI: 10.12691/wjar-5-3-2
Open AccessArticle

Identification of Major QTLs in an Advanced Backcross Lines Associated with Waterlogging Tolerance at Maize Seedling Stage

Khalid A. Osman1, 2, Bin Tang1, Fazhan Qiu1 and Ahmed M. El Naim3,

1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China

2Agricultural Research Corporation, P.O Box 126 Wed Medani, Sudan

3Department of Crop Sciences, Faculty of Natural Resources and Environmental Studies, University of Kordofan, Elobied, Sudan

Pub. Date: April 28, 2017

Cite this paper:
Khalid A. Osman, Bin Tang, Fazhan Qiu and Ahmed M. El Naim. Identification of Major QTLs in an Advanced Backcross Lines Associated with Waterlogging Tolerance at Maize Seedling Stage. World Journal of Agricultural Research. 2017; 5(3):126-134. doi: 10.12691/wjar-5-3-2


Waterlogging strongly affects agronomic performance and yield of maize. In order to investigate the genetic basis of maize seedling response, remapping of the majors quantitative trait loci (QTL) associated with waterlogging tolerance (WT) related traits were subjected, including plant height, root length, shoot fresh weight, root fresh weight, root dry weight, shoot dry weight, total dry weight, during maize seedling stage by using advanced backcross QTL (AB-QTL) analysis approach in a mixed linear model and inclusive composite interval mapping method under waterlogging and control conditions. A 266 BC2F2 population derived from a cross between a waterlogging-tolerant line ‘HZ32’ and a susceptible line ‘K12’ was used. A new linkage map constructed, consisting of 167 polymorphic SSR markers, spanned 1797.6 cM in length across a maize genome, with an average distance of 10.8 cM between adjacent markers. A total of 44 and 25 putative QTLs were detected under waterlogging treatment and control conditions, respectively. These QTLs were distributed over all 10 chromosomes, and had LOD scores ranging from 2.58 to 14.74, explaining 3.46 to 24.37% phenotypic variation in the individual traits. Out of which, thirty one major QTLs individually accounted for more than 10% of the phenotypic variation; they were governed traits associated with RL, PH, SDW, RDW, TDW and RFW were mapped in the different genomic region on chromosomes 1, 2, 3, 4, 6, 7 and 9. The results reveal that the former major QTL mapped by AB-QTL, could be selected in backcross population for fine mapping of waterlogging tolerance. The results also may provide new insight into the molecular basis of the waterlogging response of seedlings stage and useful markers for MAS and further genetic studies on maize waterlogging tolerance.

AB-QTL mapping Maize (Zea Mays) SSR marker MAS waterlogging stress

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


[1]  Rathore TR, Warsi MZ. Production of maize under excess soil moisture (waterlogging) conditions. In: Proceedings of the 2nd Asian Regional Maize Workshop PACARD. Laos Banos, Phillipines, Feb 23-27, 1998. p.23.
[2]  Ghassemi F, Jakeman AJ, Nix HA. Salinisation of Land and Water Resources, Human Causes, Extent, Management and Case Studies. University of New South Wales Press, Sydney, 1995. pp. 1-526.
[3]  Ahmed F, Rafii MY, Ismail MR, Juraimi AS, Rahim HA, Asfaliza R, Latif MA. Waterlogging Tolerance of Crops: Breeding, Mechanism of Tolerance, Molecular Approaches, and Future Prospects. BioMed Research International, 2013.
[4]  Qiu FZ, Zheng YL, Zhang ZL, Xu SZ. “Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize”. Ann Bot-London, 2007, 6:1067-1081.
[5]  Zaidi PH, Rafique S, Rai P, Singh N, Srinivasan G. “Tolerance to excess moisture in maize (Zea mays L.): susceptible crop stages and identification of tolerant genotypes”, Field Crop Res, 90:189-202. 2004.
[6]  Mustroph A, Boamfa EI, Laarhoven LJJ, Harren FJM, Pors Y, Grimm B. “Organ specific analysis of the anaerobic primary metabolism in rice and wheat seedlings II: Light exposure reduces needs for fermentation and extends survival during anaerobiosis”. Planta 225:139-152. 2006.
[7]  Zhou L, Wang J, Yi Q, Wang Y, Zhu Y, Zhang Z. “Quantitative trait loci for seedling vigor in rice under field conditions”. Field Crops Res., 100:294-301. 2007.
[8]  Li HM, Liang H, Tang ZX, Zhang HQ, Yan BJ, Ren ZL. “QTL Analysis for grain pentosans and hardness index in a Chinese 1RS.1BL × non-1RS.1BL wheat cross”. Plant Mol Biol Report, 2012.
[9]  Liu J, Li J, Chen F, Zhang F, Ren T, Zhuang Z, Mi G. “Mapping QTLs for root traits under different nitrate levels at the seedling stage in maize (Zea mays L.) ”. Plant Soil, 305:253-265. 2008.
[10]  Liu YZ, Tang B, Zheng YL, Ma KJ, Xu SZ, Qiu FZ. “Screening methods for waterlogging tolerance at Maize (Zea mays L.) seedling stage. Agric Sci China, 9: 362-369. 2010.
[11]  Mano Y, Omori F, Takeda K. “Construction of intraspecific linkage maps, detection of a chromosome inversion, and mapping of QTL for constitutive root aerenchyma formation in the teosinte “Zea nicaraguensis”. Mol Breeding, 29: 137-146. 2012.
[12]  Mano Y, Muraki M, Fujimori M, Takamizo T, Kindiger B. “AFLP–SSR maps of maize × teosinte and maize × maize: comparison of map length and segregation distortion”. Plant Breeding, 124: 432-439. 2005.
[13]  Mano Y, Muraki M, Fujimori M, Takamizo T. “Identification of QTL controlling flooding tolerance in reducing soil conditions in maize (Zea mays L.) Seedlings”. Plant Production Science, 9: 176-181. 2006.
[14]  Fukao T, Harris T, Bailey-Serres J. “Evolutionary analysis of the sub1 gene cluster that confers submergence tolerance to domesticated rice”. Ann Bot, 2009, 103:143-150.
[15]  Tanksley SD, Nelson JC. “Advanced backcross QTL analysis: a method for simultaneous discovery and transfer of valuable QTL from unadapted germplasm into elite breeding lines”. Theor Appl Genet, 92: 191-203. 1996.
[16]  Li H, Ye G, Wang J. “A modified algorithm for the improvement of composite interval mapping”. Genetics, 2007, 175, 361-374.
[17]  Liu RH, Meng JL. “Map Draw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data”. Yi Chuan, 25, 317-321. 2003.
[18]  Lander ES, Green P, Abrahamson J, Barlow A, “Daly MJ, Lincoln SE, Newberg LA. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations”. Genomics, 1:174-181. 1987.
[19]  Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT. “Mapping QTLs for root traits in a recombinant inbred population from two indicia ecotypes in rice”. Theoretical and Applied Genetics, 101: 756-766. 2000.
[20]  Marathi B, Guleria S, Mohapatra T, Parsad R, Mariappan N, Kurungara VK, Atwal SS, Prabhu KV, Singh NK, Singh AK. “QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.)”. BMC Plant Biol, 2012, 12:137.
[21]  Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S, van Beuningen L, Issac P, Edwards K, Phillips RL. “Towards positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize”. Plant Mol Biol., 48: 601-613. 2002.
[22]  Liao CT, Lin CH. “Physiological adaptation of crop plants to flooding stress”. Proceedings of the National Science Council ROC (B), 25:148-157. 2001.
[23]  Toojinda T, Siangliw M, Tragoonrung S, Vanavichit A. “Molecular genetics of submergence tolerance in rice: QTL analysis of key traits”. Ann Bot., 91:243-253. 2003.
[24]  Zhang X, Tang B, Yu F, Liu L, Wang M, Xue Y, Zhang Z, Yan J, Bing Y, zheng Y, Qiu F. Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings. Plant Molecular Biology Report, 2012.
[25]  Subbaiah CC, Sachs MM. “Molecular and cellular adaptations of maize to flooding stress”. Annals of Botany, 91: 119-127. 2003.
[26]  Rahman H, Pekic S, Lazic-Jancic V, Quarrie SA, Shah SM, Pervez A, Shah MM. “Molecular mapping of quantitative trait loci for drought tolerance in maize plants”. Genetics and Molecular Research, 10: 889-901. 2011.
[27]  Zhu J, Mickelson SM, Kaeppler SM, Lynch JP. “Detection of quantitative trait loci for seminal root traits in maize (Zea mays L.) seedlings grown under differential phosphorus levels”. Theor Appl Genet., 113: 1-10. 2006.
[28]  Hund A, Fracheboud Y, Soldati A, Frascaroli E, Salvi S, Stamp P. “QTL controlling root and shoot traits of maize seedlings under cold stress”. Theoretical and Applied Genetics, 109, 618-629. 2004.
[29]  Bernacchi D, Beck Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D, Tanksley S. “Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium”. Theor Appl Genet., 97: 170-180. 1998.
[30]  Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Collnayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PA, Mao M, Stoughton RB, Friend SH. “Genetics of gene expression surveyed in maize, mouse and man”. Nature, 422:297-302. 2003.
[31]  Cai W, Morishima H. “QTL clusters reflect character associations in wild and cultivated rice”. Theoretical and Applied Genetics, 104:1217-1228. 2002.
[32]  Rae AM, Street NR, Robinson KM, Harris N, Taylor G: “Five QTL hotspots for yield in short rotation coppice bioenergy poplar: The poplar biomass loci”. BMC Pl Bio. 9:23. 2009.
[33]  Yano M, Sasaki T: “Genetic and molecular dissection of quantitative traits in rice”. Pl Mol Bio, 35:145-153. 1997.
[34]  Tang B, Xu SZ, Zou XL, Zheng YL, Qiu FZ. “Changes of Antioxidative Enzymes and Lipid Peroxidation in Leaves and Roots of Waterlogging-Tolerant and Waterlogging-Sensitive Maize Genotypes at Seedling Stage”. Agricultural Sciences in China, 9:651-661. 2010.
[35]  Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW. “Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics”. Proceeding of the National Academy of Sciences United States of America, 81: 8014-8018. 1984.