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 AJPS  Vol.12 No.7 , July 2021
Mapping Qtls for Grain Yield and Yield Components in Kenyan Maize (Zea mays L.) Under Low Phosphorus Using Single Nucleotide Polymorphism (SNPS)
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Abstract: Selection for tolerance to low phosphorus (P) using morphological traits alone is slow and often confounded by environmental effects. This study identified some Quantitative Trait Loci (QTLs) associated with grain yield (GYLD), Plant (PHT) and Ear heights (EHT) under low P in maize using single nucleotide polymorphic markers. 228 F2:3 individuals derived from a cross between two contrasting maize inbred lines together with 239 SNPs were mapped onto ten linkage groups (LGs) spanning 2255 centiMorgans (cM) with an average inter-marker distance of 9.44 cM. Majority of the SNP markers (63%) followed the Mendelian segregation and were fairly distributed in all the LGs. Mean performance for all the traits in the F3 population was higher than the parental values, which suggested transgressive segregation for all traits. Low to moderate broad sense heritability (0.35 - 0.50) in the F3 population for GYLD, PHT and EHT indicated that tolerance to low P is controlled by complex multi genetic factors. A full multi-QTL model analysis suggested six QTLs (2 QTLs each for GYLD, PHT and EHT) located on chromosomes 1, 3, 4 and 8. The two QTLs for GYLD increased maize yield under low P soils by 173 kg/ha while the 2 QTLs for PHT increased plant growth by 18.14 cm. The % phenotypic variance explained by these QTLs under low P environments had a wide range (0.242% - 53.34%) and was much lower for GYLD compared to plant growth. Both additive and dominance gene actions contributed differentially to the observed phenotypic variance for tolerance to low P soils with dominance contributing more genetic effects compared additive effects for majority of the QTLs. The findings of this study will provide some basis for marker-assisted selection for yield improvement and further guide breeding strategies under low P soils of western Kenya.
Cite this paper: Ouma, E. and Samuel, G. (2021) Mapping Qtls for Grain Yield and Yield Components in Kenyan Maize (Zea mays L.) Under Low Phosphorus Using Single Nucleotide Polymorphism (SNPS). American Journal of Plant Sciences, 12, 1106-1123. doi: 10.4236/ajps.2021.127077.
References

[1]   White, P.J. and Hammond, J.P. (2008) Phosphorus Nutrition of Terrestrial Plants. In: White, P.J. and Hammond, J.P., Eds., The Ecophysiology of Plant Phosphorus Interactions, Vol. 7, Springer, Dordrecht, 51-81.
https://doi.org/10.1007/978-1-4020-8435-5_4

[2]   Ozturk, L., Eker, S., Torum, B. and Cakmak, I. (2005) Variation in Phosphorus Efficiency among 73 Bread and Durum Wheat Genotypes Grown in a Phosphorus-Deficient Calcareous Soil. Plant and Soil, 269, 69-80.
https://doi.org/10.1007/s11104-004-0469-z

[3]   Lynch, J.P. (2011) Root Phenes for Enhanced Soil Exploration and Phosphorus Acquisition: Tools for Future Crops. Plant Physiology, 156, 1041-1049.
https://doi.org/10.1104/pp.111.175414

[4]   Tilman, D., Cassman, K.G., Matson, P.A., Naylor, R. and Polasky, S. (2002) Agricultural Sustainability and Intensive Production Practices. Nature, 418, 671-677.
https://doi.org/10.1038/nature01014

[5]   Cordell, D. and White, S. (2013) Sustainable Measures: Strategies and Technologies for Achieving Phosphorus Security. Agronomy, 3, 86-116.
https://www.mdpi.com/2073-4395/3/1/86
https://doi.org/10.3390/agronomy3010086


[6]   Obersteiner, M., Penielas, J, Clais, P., Van der Velde, M. and Janssen, I.A. (2013) The Phosphorus Trielema. Nature Geoscience, 6, 897-898.
https://doi.org/10.1038/ngeo1990

[7]   Ouma, E.O. (2016) Inheritance of Maize Phosphorus Efficiency in Acid Soils of Western Kenya. International Journal of Information Research and Review, 3, 2091-2097.
http://repository.rongovarsity.ac.ke/handle/123456789/2257

[8]   Parentoni, S.N., Souza, J.R., Alves, V.M.C., Gama, E.E.G., Coelho, A.M., Oliveira, A.C., Guimaraes, P.E.O., Guimaraes, C.T., Vasconcelos, M.J.V., Pacheco, C.A.P., Magalhaes, J.V., Meirelles, W.F., Guimaraes, L.J.M., Silva, A.R., Mendes, F.F. and Schaffert, R.E. (2010) Inheritance and Breeding Strategies for Phosphorus Efficiency in Tropical Maize (Zea mays L.). Maydica, 55, 1-15.
https://www.researchgate.net/publication/285752925

[9]   Yu, X., Zhang, M., Yu, Z., Yang, D., Li, J., Wu, G. and Li, J. (2020) An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology. Agronomy, 10, Article No. 114.
https://doi.org/10.3390/agronomy10010114

[10]   Ouma, E., Ligeyo, D., Matonyei, T., Were, B., Agalo, J., Emily, T., Onkware, A., Gudu, S., Kisinyo, P., Okalebo, J. and Othieno, C. (2012) Development of Maize Single cross Hybrids for Tolerance to Low Phosphorus. African Journal of Plant Science, 6, 394-402. http://www.academicjournals.org/AJPS

[11]   Maron, L.G., Guimaraes, C.T., Kirst, M., Alberte, P.S., Birchlere, J.A., Bradbury, P.J., Buckler, E.S., Coluccio, A.E., Danilova, T.V., Kudrna, D., Magalhaes, J.V., Pineros, M.A., Schatzh, M.C., Wing, R.A. and Kochian, L.V. (2014) Aluminum Tolerance in Maize Is Associated with Higher MATE1 Gene Copy Number. Proceedings of the National Academy of Sciences of the United States of America, 110, 5241-5246.
https://www.pnas.org/cgi/doi/10.1073/pnas.1220766110
https://doi.org/10.1073/pnas.1220766110


[12]   Guimraes, C.T., Christiano, C.S., Maria, M.P., Maron L.G., Jurandir V.M. Renato, C.C.V., Lauro, J.M.G., Ubiraci, G.P.L., Carlos, F.S.T., Roberto, W.N., Silvia, N.J.B., Leon, V.K., Vera, M.C.A. and Sydney, P.N. (2014) Genetic Dissection of Al Tolerance QTLs in the Maize Genome by High Density SNP Scan. BMC Genomics, 15, Article No. 153.
https://doi.org/10.1186/1471-2164-15-153

[13]   Yuan, Y., Gao, M., Zhang, M., Zheng, H., Zhou, X., Guo, Y., Zhao, Y., Kong, F. and Li, S. (2017) Mapping for Phosphorus Efficiency and Morphological Traits at Seedling and Maturity Stages in Wheat. Frontiers in Plant Science, 8, Article No. 614.
https://doi.org/10.3389/fpls.2017.00614

[14]   Su, C., Wang, W., Gong, S., Zuo, J., Li, S. and Xu, S. (2017) High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology. Frontiers in Plant Science, 8, Article No. 706.
https://doi.org/10.3389/fpls.2017.00706

[15]   Jarne, P. and Lagoda, P. (1996) Microsatellites, from Molecules to Populations and Back. Trends in Ecology and Evolution, 11, 424-429.
https://doi.org/10.1016/0169-5347(96)10049-5

[16]   Hamblin, M.T, Warburton, M.L. and Buckler E.S. (2007) Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness. PLoS ONE, 2, e1367.
https://doi.org/10.1371/journal.pone.0001367

[17]   Jones, E.S., Sullivan, H., Bhattramakki, D. and Smith, J.S.C. (2007) A Comparison of Simple Sequence Repeat and Single Nucleotide Polymorphism Marker Technologies for the Genotypic Analysis of Maize (Zea mays L.). Theoretical and Applied Genetics, 115, 361-371.
https://doi.org/10.1007/s00122-007-0570-9

[18]   Ganal, M.W., Durstewitz, G., Polley, A., Bérard, A., Buckler, E.S., et al. (2011) A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome. PLoS ONE, 6, e28334.
https://pubmed.ncbi.nlm.nih.gov/22174790
https://doi.org/10.1371/journal.pone.0028334

[19]   Rafalski, A. (2002) Applications of Single Nucleotide Polymorphisms in Crop Genetics. Current Opinion in Plant Biology, 5, 94-100.
https://doi.org/10.1016/S1369-5266(02)00240-6

[20]   Zhu, Y.L., Song, Q.J., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K. and Grimm, D.R. (2003) Single-Nucleotide Polymorphisms in Soybean. Genetics, 163, 1123-1134.
https://doi.org/10.1093/genetics/163.3.1123

[21]   Dreisigacker, S., Sehgal, D., Reyes Jaimez, A.E., Luna Garrido, B., Munoz Zavala, S., Núnez Ríos, C., Mollins, J. and Mall, S. (Eds.) (2016) CIMMYT Wheat Molecular Genetics: Laboratory Protocols and Applications to Wheat Breeding. International Maize and Wheat Improvement Center (CIMMYT), Mexico, D.F.
https://www.researchgate.net

[22]   Wissuwa, M. and Ae, N. (2001) Further Characterization of Two QTLs that Increase Phosphorus Uptake of Rice (Oryza sativa L.) under Phosphorus Deficiency. Plant Soil, 237, 275-286.
https://link.springer.com/article/10.1023/A:1013385620875
https://doi.org/10.1023/A:1013385620875

[23]   Chin, H.J., Lu, X., Haefele, S.M., Gamuyao, R., Ismail, A.M., Wissuwa, M. and Heuer, S. (2010) Development and Application of Gene-Based Markers for the Major rice QTL Phosphate uptake 1 (Pup1). Theoretical and Applied Genetics, 120, 1073-1086.
https://doi.org/10.1007/s00122-009-1235-7

[24]   Gamuyao, R., Chin, J.H., Pariasca-Tanaka, J., Pesaresi, P., Catausan, S., Dalid, C., Slamet-Loedin, I., Tecson-Mendoza, E.M., Wissuwa, M. and Heuer, S. (2012) The Protein Kinase Pstol1 from Traditional Rice Confers Tolerance of Phosphorus Deficiency. Nature, 488, 535-539.
https://www.nature.com/articles/nature11346
https://doi.org/10.1038/nature11346


[25]   Hufnagel, B., Sylvia, M.S., Lidianne, A., Claudia, T.G., Willmar, L., Gabriel, C.A., Barbara, N., Brandon, G.L., Jon, E.S., Maria, M.P., Beatriz, A.B., Eva, W., Frederick, W.R., Joao, H.V., Randy, T.C., Alexandre, F., Rodrigo, G., Antonio, A.F., Robert, E.S., Leon, V.K. and Jurandir, V.M. (2014) Duplicate and Conquer: Multiple Homologs of Phosphorus-Starvation Tolerance1 Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus. Soils Plant Physiology, 166, 659-677.
https://doi.org/10.1104/pp.114.243949

[26]   Bernardino, K.C., Pastina, M.M., Menezes, C.B., et al. (2019) The Genetic Architecture of Phosphorus Efficiency in Sorghum Involves Pleiotropic QTL for Root Morphology and Grain Yield under Low Phosphorus Availability in the Soil. BMC Plant Biology, 19, Article No. 87.
https://doi.org/10.1186/s12870-019-1689-y

[27]   Chen, J., Xu, L., Cai, Y. and Xu, J. (2009) Identification of QTLs for Phosphorus Utilization Efficiency in Maize (Zea mays L.) across P Levels. Euphytica, 167, 245-252.
https://doi.org/10.1007/s10681-009-9883-x

[28]   Chen, J., Cai, Y., Xu, L., Wang, J., Zhang, W., Wang, G., Xu, D., Chen, T., Lu, X., Sun, H., Huang, A., Liang, Y., Dai, G., Qin, H., Huang, Z., Zhu, Z., Yang, Z., Xu, J. and Kuang, S. (2011) Identification of QTLs for Biomass Production in Maize (Zea mays L.) under Different Phosphorus Levels at Two Sites. Frontiers of Agriculture in China, 5, 152-161.
https://doi.org/10.1007/s11703-011-1077-3

[29]   Maia, C., do Vale, J.C., Fritsche-Neto, R., Cavatte, P.C. and Miranda, G.V. (2011) Difference between Breeding for Nutrient Use Efficiency and Nutrient Stress Tolerance. Crop Breeding and Applied Biotechnology, 11, 270-275.
https://doi.org/10.1590/S1984-70332011000300010

[30]   de Sousa, S.M., Randy, T., Clark, R.T., Mendes, F.F., Oliveira, A.C., Vasconcelos, M.J.V., Parentoni, S.N., Kochian, L.V., Guimaraes, C.T. and Magalhaes, J.V. (2012) A Role for Root Morphology and Related Candidate Genes in P Acquisition Efficiency in Maize. Functional Plant Biology, 39, 925-935.
https://doi.org/10.1071/FP12022

[31]   Azevedo, G.C., Cheavegatti-Gianotto, A., Negri, B.F., Hufnagel, B., da Costa e Silva, L., Magalhaes, J.V., et al. (2015) Multiple Interval QTL Mapping and Searching for PSTOL1 Homologs Associated with Root Morphology, Biomass Accumulation and phosphorus Content in Maize Seedlings under Low-P. BMC Plant Biology, 15, Article No. 172.
https://doi.org/10.1186/s12870-015-0561-y

[32]   Mendes, F.F., Guimaraes, L.J.M., Souza, J.C., Guimaraes, P.E.O., Magalhaes, J.V., Garcia, A.A.F., et al. (2015) Genetic Architecture of Phosphorus Use Efficiency in Tropical Maize Cultivated in a Low-P Soil. Crop Science, 54, 1530-1538.
https://doi.org/10.2135/cropsci2013.11.0755

[33]   Hoisington, D., Khairallah, M. and Gonzalez-de-Lion, D. (1994) Laboratory Protocols: CIMMYT Applied Molecular Genetics Laboratory. 2nd Edition, International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF.

[34]   Gaur, R., Azam, S., Jeena, G., Choudhary, S., Jain, M., Yadav, G., Tyagi, A.K., Chattopadhyay, D. and Bhatia, S. (2012) High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.). DNA Research, 19, 357-373.
https://doi.org/10.1093/dnares/dss018

[35]   Semagn, K., Cosmos, M., Bindiganavile, S., Dan, M., Yoseph, B., Stephen, M., Prasanna, B. and Warburton, M. (2012) Molecular Characterization of Diverse CIMMYT Maize Inbred Lines from Eastern and Southern Africa Using Single Nucleotide Polymorphic Markers. BMC Genomics, 13, Article No. 113.
https://doi.org/10.1186/1471-2164-13-113

[36]   Deng, Y., Chen, K., Teng, W., Zhan, A., Tong, Y., Feng, G., et al. (2014) Is the Inherent Potential of Maize Roots Efficient for Soil Phosphorus Acquisition? PLoS ONE, 9, e90287.
https://doi.org/10.1371/journal.pone.0090287

[37]   Li, M., Guo, X., Zhang, M., Wang, X., Zhang, G., Tian, Y. and Wang, Z. (2010) Mapping QTLs for Grain Yield and Yield Components under High and Low Phosphorus Treatments in Maize (Zea mays L.). Plant Science, 178, 454-462.
https://doi.org/10.1016/j.plantsci.2010.02.019

[38]   Kosambi, D.D. (1944) The Estimation of Map Distances from Recombination Values. Annals of Eugenics, 12, 172-175.
https://doi.org/10.1111/j.1469-1809.1943.tb02321.x

[39]   VSN International (2015) GenStat for Windows. 18th Edition. VSN International, Hemel Hempstead. Genstat.co.uk
https://find-and-update.company-information.service.gov.uk/company/04027977

[40]   Kearsey, M.J. and Pooni, H.S. (1998) The Genetically Analysis of Quantitative Traits. Chapman and Hall, London. http://dx.doi.org/10.1007/978-1-4899-4441-2

[41]   Ribaut, J.M., Hoisington, D.A., Deutsch, J.A., Jiang, C. and Gonzalez-de-Leon, D. (1996) Identification of Quantitative Trait Loci under Drought Conditions in Tropical Maize. I. Flowering Parameters and the Anthesis-Silking Interval. Theoretical and Applied Genetics, 92, 905-914.
https://doi.org/10.1007/BF00221905

[42]   Jansen, R.C. and Stam, P. (1994) High Resolution of Quantitative Traits into Multiple Loci via Interval Mapping. Genetics, 136, 1447-1455.
https://doi.org/10.1093/genetics/136.4.1447

[43]   Zeng, Z.B. (1994) Precision Mapping of Quantitative Trait Loci. Genetics, 136, 1457-1468.
https://doi.org/10.1093/genetics/136.4.1457

[44]   Lander, E.S. and Botstein, D. (1989) Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps. Genetics, 121, 185-199
https://www.genetics.org/content/genetics/121/1/185.full.pdf
https://doi.org/10.1093/genetics/121.1.185


[45]   Utz, H.F. and Melchinger, A.E. (1996) PLABQTL: A Program for Compolocation Interval Mapping of QTL. Journal of Quantitative Trait Loci, 2, 1-9. http://probe.nalusda.gov:8000/otherdocs/jqtl

[46]   Liu, B. (1998) Statistical Genomics: Linkage, Mapping and QTL Analysis. CRC Press, Boca Raton.
https://www.amazon.com/Statistical-Genomics

[47]   Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L., Thomas, W.T.B., Flavell, A.J. and Marshall, D. (2010) Flapjack-Graphical Genotype Visualization. Bioinformatics, 26, 3133-3134.
https://doi.org/10.1093/bioinformatics/btq580

[48]   Wang, A.-Y., Li, Y. and Zhang, C.-Q. (2012) QTL Mapping for Stay-Green in Maize (Zea mays). Canadian Journal of Plant Science, 92, 249-256.
https://doi.org/10.4141/cjps2011-108

[49]   Choudhary, S., Gaur, R., Gupta, S. and Bhatia, S. (2012) EST-Derived Genic Molecular Markers: Development and Utilization for Generating an Advanced Transcript Map of Chickpea. Theoretical and Applied Genetics, 124, 1449-1462.
https://doi.org/10.1007/s00122-012-1800-3

[50]   Ouma, E.O. (2021) Evaluating Heritability and Relationships among Phosphorus Efficiency Traits in Maize under Low P Soils of Western Kenya. Current Journal of Applied Science and Technology, 40, 83-96.
https://doi.org/10.9734/cjast/2021/v40i1131373

[51]   Weber, V.S., Melchinger, A.E., Magorokosho, C., Makumbi, D., BAnziger, M. and Atlin, G.N. (2012) Efficiency of Managed-Stress Screening of Elite Maize Hybrids under Drought and Low Nitrogen for Yield under Rain Fed Conditions in Southern Africa. Crop Science, 52, 1011-1020.
https://doi.org/10.2135/cropsci2011.09.0486

[52]   Edmeades, G.O., Bolanos, J., Chapman, S.C., Lafitte, H.R. and Banziger, M. (1999) Selection Improves Drought Tolerance in Tropical Maize Populations. Crop Science, 39, 1306-1315.
https://doi.org/10.2135/cropsci1999.3951306x

[53]   Mohan, Y.C., Singh, K. and Rao, N.V. (2002) Path Coefficient Analysis for Oil and Grain Yield in Maize Genotypes. National Journal of Plant Improvement, 4, 75-76.
https://www.researchgate.net/publication/326246902

[54]   Rafiq, C.M., Rafique, M. and Hussain, A. (2010) Studies on Heritability, Path Analysis in Maize (Zea mays L.) Journal of Agricultural Research, 48, 1-35.
https://apply.jar.punjab.gov.pk/upload/1374660174

[55]   Aminu, D. and Izge, A.U. (2012) Heritability and Correlation Estimates in Maize under Drought Conditions in Northern Guinea and Sudan Savannas of Nigeria. World Journal of Agricultural Sciences, 8, 598-602.
https://link.citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1

 
 
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