Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt

Hanaa Mahdy Abouzied; Walid Mohamed El-Orabey; Mohamed Abd El-Halim Abou-Zeid

doi:doi:10.11648/j.ijgg.20180604.11

| Peer-Reviewed

Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt

Hanaa Mahdy Abouzied, Walid Mohamed El-Orabey, Mohamed Abd El-Halim Abou-Zeid

Published in International Journal of Genetics and Genomics (Volume 6, Issue 4)

Received: 12 November 2018 Accepted: 4 December 2018 Published: 23 January 2019

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.

Published in	International Journal of Genetics and Genomics (Volume 6, Issue 4)
DOI	10.11648/j.ijgg.20180604.11
Page(s)	37-43
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2019. Published by Science Publishing Group

Keywords

Wheat, Leaf Rust, QTL Mapping, GBS by Sequencing

References

[1]	Roelfs AP, Singh RP, Saari EE. (1992). Rust diseases of wheat: concepts and methods of disease management. CIMMYT, Mexico.
[2]	Saari EE, Prescott JM. (1985). World distribution in relation to economic losses. In: Roelfs AP, Bushnell WR (eds) The cereal rusts, vol 2. Academic Press, Orlando, pp 259–298 Samborski DJ (1985) Wheat leaf rust. In: Roelfs AP, Bushnell WR (eds) The cereal rusts, vol 2. Academic Press, Orlando, pp 39–59.
[3]	Samborski DJ. (1985). Wheat leaf rust. In: Roelfs AP, Bushnell WR (eds) The cereal rusts, vol 2. Academic Press, Orlando, pp 39–59.
[4]	Nazim MS, El-Shehidi AA, Abdou YA, El-Daoudi YH. (1983). Yield loss caused by leaf rust on four wheat cultivars under epiphytotic levels. In: 4th Conference. Microbiology., Cairo, pp 17–27.
[5]	El-Orabey WM. (2018). Virulence of some Puccinia triticina races to the effective wheat leaf rust resistant genes Lr 9 and Lr 19 under Egyptian field conditions. Physiological and Molecular Plant Pathology, 102: 163-172.
[6]	El-Orabey WM, Nagwa I Abd El-Malik, Ashmawy MA and Abou-Zeid MA. (2017). Reduction in grain yield caused by leaf rust infection in seven Egyptian wheat cultivars. Minufiya J. Plant Protection, 2: 71-81.
[7]	Shahin SI and El-Orabey WM. (2016). Assessment of grain yield losses caused by Puccinia triticina in some Egyptian wheat genotypes. Minufiya J. Agric. Res., 41 (1): 29-37.
[8]	Hussain W, Baenziger SP, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A and Poland J. (2017). Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat. Scientific Reports 7: (16394), 1-15.
[9]	Sharma S, Sharma R, Chaudhary HK. (2012). Vernlization response of winter x spring wheat derived doubled-haploids, African Journal of Agricultural Research, 7: 6465-6473.
[10]	Shoran J, Kant L, Singh R. (2003). Winter and Spring Wheat: An Analysis of Combining Ability. Cereal Research Communications, 31 (3/4), 347-354.
[11]	Elshire RJ. et al. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLOS ONE 6, e19379.
[12]	Poland JA, Brown P J, Sorrells M E, Jannink J L and Rostoks N. (2012). Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7, e32253.
[13]	Poland JA and Rife T W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome J. 5, 92.
[14]	Chen Z, Wang B, Dong X, Liu H, Ren L, Chen J, Hauck A, Song W, Lai J. (2014). An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population. BMC Genomics 15, 433.
[15]	Davey JW, Hohenlohe PA, Etter PD, Boone JQ. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499–510.
[16]	Kumar S, Banks T W and Cloutier S. (2012). SNP discovery through Next-Generation Sequencing and its applications. International journal of Plant Genomics, 15.
[17]	Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, Zhang A. (2010). Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat. Journal of Integrative Plant Biolology. 52, 996–1007.
[18]	El-Orabey WM, Omara, RI, and Abou-Zeid MA. (2018). Diversity and virulence dynamics within Puccinia triticina populations in Egypt. J. Plant Prot. and Path., Mansoura Univ., 9 (11): 735-745.
[19]	Kolmer, JA, Long DL and Hughes ME. (2005). Physiologic specialization of Puccinia triticina on wheat in the United States in 2003. Plant Dis., 89: 1201-1206.
[20]	Stakman EC, Stewart DM, Loegering WQ. (1962). Identification of Physiologic Races of Puccinia graminis var. tritici. Washington, USA: United States Department of Agriculture, Agricultural Research Service E-617 (revised), 1-53.
[21]	McVey, DV, Nazim M, Leonard KJ and Long DL. (2004). Patterns of virulence diversity in Puccinia triticina on wheat in Egypt and the United States in 1998-2000. Plant Disease, 88: 271-279.
[22]	Sallam ME, El-Orabey WM and Omara RI. (2016). Seedling and adult plant resistance to leaf rust in some Egyptian wheat genotypes. African Journal of Agricultural Research, 11 (4): 247-258.
[23]	Marais GF, McCallum B, Marais AS. (2006). Leaf rust and stripe rust resistance genes derived from Aegilops sharonensis. Euphytica 2006; 149: 373–380.
[24]	Marais GF, Badenhorst PE, Eksteen A, et al. (2010). Reduction of Aegilops sharonensis chromatin associated with resistance genes Lr 56 and Yr 38 in wheat. Euphytica; 171: 15–22.
[25]	Spielmeyer W, Hyles J, Joaquim P, Azanza F, Bonnett D, Ellis ME, Moore C, Richards RA. (2007). A QTL on chromosome 6A in bread wheat (Triticum aestivum) is associated with longer coleoptiles, greater seedling vigor and final plant height. Theoretical and Applied Genetics. 115 (1): 59-66.
[26]	Yang Z, Bai Z, Li X, Wang P, Wu Q, Yang L, et al. (2012) SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theoretical and Applied Genetics. 125: 1057–1068.
[27]	Su Z, Hao C, Wang L, Dong Y, Zhang X. (2011). Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics. 122 (1): 211-23. doi: 10.1007/s00122-010-1437-z.
[28]	Simmonds J, Scott P, Brinton J, Mestre TC, Bush M, del Blanco A, Dubcovsky J, Uauy C. (2016). A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grain. Theoretical and Applied Genetics. 129 (6): 1099-112. doi: 10.1007/s00122-016-2686-2.
[29]	Mains EB, Leighty CE, Johnston CO. (1926). Inheritance of resistance to leaf rust Puccinia triticina Eriks., in crosses in common wheat Triticum vulgare Vill. Journal of Agricultural Research. 2: 931–971.
[30]	Aktar-Uz-Zaman MD, Tuhina-Khatun MST, Hanafi MM & Sahebi M. (2017) Genetic analysis of rust resistance genes in global wheat cultivars: an overview, Biotechnology & Biotechnological Equipment. 31: 3, 431-445.
[31]	McIntosh RA, Wellings CR and Park RF. (1995). Wheat rusts: an atlas of resistance genes. Dordrecht: Kluwer Academic Publishers.
[32]	McIntosh RA, Devos KM, Dubcovsky J et al., Catalogue of gene symbols for wheat. (2007); Available from supplement: http://www.shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2007.pdf.
[33]	McCallum BD, Hiebert C, Huerta-Espino J, Cloutier S. (2012). Wheat leaf rust. In: Sharma I, editor. Disease resistance in wheat. Wallingford: CAB International. p. 33–62.
[34]	Samsapour D, Maleki Zanjani B, Pallavi JK, et al. (2010). Identification of molecular markers linked to adult plant leaf rust resistance gene Lr 48 in wheat and detection of Lr 48 in the Thatcher near-isogenic line with gene Lr25. Euphytica. 174 (3): 337–342.
[35]	Nanda GS, Afzali AB and Singh G. (1990). Genetic analysis of the role of intermitting in an intervarietal cross of bread wheat. Indian Journal of Genetics. 50: 210-215.
[36]	Nanda GS, Sohu VS. (1998). Breeding methodologies for wheat improvement. In: Nayar et al. (ed.) Wheat pathology, genetics and breeding for resistance, 1999. Advance course 14-17 Sept. 1998, DWR, Regional Station, Flowerdale, Shimla, India, pp. 51-60.
[37]	Kant L, Mani VP and Gupta HS. (2001). Winter X spring wheat hybridization - A promising avenue for yield enhancement. Plant Breeding. 120: 255-258.
[38]	Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T and Dubcovsky J. (2003). Positional cloning of the wheat vernalization gene VRN1. Proceedings of the National Academy of Sciences 100 (10): 6263-6268.

Cite This Article

Plain Text BibTeX RIS

APA Style

Hanaa Mahdy Abouzied, Walid Mohamed El-Orabey, Mohamed Abd El-Halim Abou-Zeid. (2019). Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. International Journal of Genetics and Genomics, 6(4), 37-43. https://doi.org/10.11648/j.ijgg.20180604.11

Copy | Download

ACS Style

Hanaa Mahdy Abouzied; Walid Mohamed El-Orabey; Mohamed Abd El-Halim Abou-Zeid. Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. Int. J. Genet. Genomics 2019, 6(4), 37-43. doi: 10.11648/j.ijgg.20180604.11

Copy | Download

AMA Style

Hanaa Mahdy Abouzied, Walid Mohamed El-Orabey, Mohamed Abd El-Halim Abou-Zeid. Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. Int J Genet Genomics. 2019;6(4):37-43. doi: 10.11648/j.ijgg.20180604.11

Copy | Download

@article{10.11648/j.ijgg.20180604.11,
  author = {Hanaa Mahdy Abouzied and Walid Mohamed El-Orabey and Mohamed Abd El-Halim Abou-Zeid},
  title = {Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt},
  journal = {International Journal of Genetics and Genomics},
  volume = {6},
  number = {4},
  pages = {37-43},
  doi = {10.11648/j.ijgg.20180604.11},
  url = {https://doi.org/10.11648/j.ijgg.20180604.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20180604.11},
  abstract = {Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt
AU  - Hanaa Mahdy Abouzied
AU  - Walid Mohamed El-Orabey
AU  - Mohamed Abd El-Halim Abou-Zeid
Y1  - 2019/01/23
PY  - 2019
N1  - https://doi.org/10.11648/j.ijgg.20180604.11
DO  - 10.11648/j.ijgg.20180604.11
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 37
EP  - 43
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20180604.11
AB  - Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.
VL  - 6
IS  - 4
ER  -

Copy | Download

Author Information

Hanaa Mahdy Abouzied

Department of Crop Science, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
Walid Mohamed El-Orabey

Department of Wheat Diseases Research, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
Mohamed Abd El-Halim Abou-Zeid

Department of Wheat Diseases Research, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Hanaa Mahdy Abouzied, Walid Mohamed El-Orabey, Mohamed Abd El-Halim Abou-Zeid. (2019). Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. International Journal of Genetics and Genomics, 6(4), 37-43. https://doi.org/10.11648/j.ijgg.20180604.11

Copy | Download

ACS Style

Hanaa Mahdy Abouzied; Walid Mohamed El-Orabey; Mohamed Abd El-Halim Abou-Zeid. Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. Int. J. Genet. Genomics 2019, 6(4), 37-43. doi: 10.11648/j.ijgg.20180604.11

Copy | Download

AMA Style

Hanaa Mahdy Abouzied, Walid Mohamed El-Orabey, Mohamed Abd El-Halim Abou-Zeid. Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt. Int J Genet Genomics. 2019;6(4):37-43. doi: 10.11648/j.ijgg.20180604.11

Copy | Download

@article{10.11648/j.ijgg.20180604.11,
  author = {Hanaa Mahdy Abouzied and Walid Mohamed El-Orabey and Mohamed Abd El-Halim Abou-Zeid},
  title = {Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt},
  journal = {International Journal of Genetics and Genomics},
  volume = {6},
  number = {4},
  pages = {37-43},
  doi = {10.11648/j.ijgg.20180604.11},
  url = {https://doi.org/10.11648/j.ijgg.20180604.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20180604.11},
  abstract = {Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt
AU  - Hanaa Mahdy Abouzied
AU  - Walid Mohamed El-Orabey
AU  - Mohamed Abd El-Halim Abou-Zeid
Y1  - 2019/01/23
PY  - 2019
N1  - https://doi.org/10.11648/j.ijgg.20180604.11
DO  - 10.11648/j.ijgg.20180604.11
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 37
EP  - 43
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20180604.11
AB  - Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.
VL  - 6
IS  - 4
ER  -

Copy | Download