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Special Issue:
植物抗病遗传合辑Plant Disease-resistance Genetics
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| Genome-wide association analysis for stripe rust resistance in spring wheat (Triticum aestivum L.) germplasm |
Sher MUHAMMAD1*, Muhammad SAJJAD2*, Sultan Habibullah KHAN3, Muhammad SHAHID1, Muhammad ZUBAIR1, Faisal Saeed AWAN3, Azeem Iqbal KHAN4, Muhammad Salman MUBARAK3, Ayesha TAHIR2, Muhammad UMER2, Rumana KEYANI2, Muhammad Inam AFZAL2, Irfan MANZOOR1, Javed Iqbal WATTOO5, Aziz-ur REHMAN6 |
1 Department of Bioinformatics and Biotechnology, GC University, Faisalabad 38090, Pakistan
2 Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
3 Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan
4 Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
5 Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Pakistan
6 Wheat Research Institute, Ayub Agricultural Research Institute (AARI), Faisalabad 38950, Pakistan |
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Abstract Stripe rust is a continuous threat to wheat crop all over the world. It causes considerable yield losses in wheat crop every year. Continuous deployment of adult plant resistance (APR) genes in newly developing wheat cultivars is the most judicious strategy to combat this disease. Herein, we dissected the genetics underpinning stripe rust resistance in Pakistani wheat germplasm. An association panel of 94 spring wheat genotypes was phenotyped for two years to score the infestation of stripe rust on each accession and was scanned with 203 polymorphic SSRs. Based on D´ measure, linkage disequilibrium (LD) exhibited between loci distant up to 45 cM. Marker-trait associations (MTAs) were determined using mixed linear model (MLM). Total 31 quantitative trait loci (QTLs) were observed on all 21 wheat chromosomes. Twelve QTLs were newly discovered as well as 19 QTLs and 35 previously reported Yr genes were validated in Pakistani wheat germplasm. The major QTLs were QYr.uaf.2AL and QYr.uaf.3BS (PVE, 11.9%). Dissection of genes from the newly observed QTLs can provide new APR genes to improve genetic resources for APR resistance in wheat crop.
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Received: 08 August 2019
Accepted:
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| Fund: The authors acknowledge Higher Education Commission (HEC), Islamabad, Pakistan for providing for funding (21-179/SRGP/R&D/HEC/2014) and the International Research Support Initiative Program (IRSIP) Scholarship for this research work. |
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Corresponding Authors:
Correspondence Muhammad Sajjad, Tel: +92-334-6609080, E-mail: muhammad.sajjad@comsats.edu.pk; Sultan Habibullah KHAN, Tel: +92-333-9917733, E-mail: sultan@uaf.edu.pk
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| About author: * These authors contributed equally to this study. |
Cite this article:
Sher MUHAMMAD, Muhammad SAJJAD, Sultan Habibullah KHAN, Muhammad SHAHID, Muhammad ZUBAIR, Faisal Saeed AWAN, Azeem Iqbal KHAN, Muhammad Salman MUBARAK, Ayesha TAHIR, Muhammad Umer, Rumana KEYANI, Muhammad Inam AFZAL, Irfan MANZOOR, Javed Iqbal WATTOO, Aziz-ur REHMAN.
2020.
Genome-wide association analysis for stripe rust resistance in spring wheat (Triticum aestivum L.) germplasm. Journal of Integrative Agriculture, 19(8): 2035-2043.
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Ain Q U, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia X, He Z, Quraishi U M. 2015. Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan. Frontier in Plant Sciences, 6, 743.
Arief V N. 2010. Methodology development to integrate phenotypic and genotypic data from a plant breeding program through association analysis with a case study using data from the CIMMYT International Spring Wheat field trials. Ph D thesis, School of Agriculture and Food Sciences, The University of Queensland, Australia.
Bansal U K, Forrest K L, Hayden M J, Miah H, Singh D, Bariana H S. 2011. Characterisation of a new stripe rust resistance gene Yr47 and its genetic association with the leaf rust resistance gene Lr52. Theoretical and Applied Genetics, 122, 1461–1466.
Basnet B R, Singh R P, Ibrahim A M H, Herrera-Foessel S A, Huerta-Espino J, Lan C, Rudd J C. 2014. Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3. Molecular Breeding, 33, 385–399.
Beddow J M, Pardey P G, Chai Y, Hurley T M, Kriticos D J, Braun H J, Park R F, Cuddy W S, Yonow T. 2015. Research investment implications of shifts in the global geography of wheat stripe rust. Nature Plants, 1, 15132.
Borner A, Roder M S, Unger O, Meinel A. 2000.The detection and molecular mapping of a major gene for non-specific adult-plant disease resistance against stripe rust (Puccinia striiformis) in wheat.Theoretical and Applied Genetics, 100, 1095–1099.
Breseghello F, Sorrells M E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172, 1165–1177.
Chao S, Zhang W, Dubcovsky J, Sorrells M. 2007. Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Science, 47, 1018–1030.
Cheng P, Xu L S, Wang M N, See D R, Chen X M. 2014. Molecular mapping of genes Yr64 and Yr65 for stripe rust resistance in hexaploid derivatives of durum wheat accessions PI 331260 and PI 480016. Theoretical and Applied Genetics, 127, 2267–2277.
Crossa J, Burgueno J, Dreisickacker S, Vargas M, Herrera-Foessel S A, Lillemo M, Singh R P, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch J H, Ortiz R. 2007. Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics, 177, 1889–1913.
Dadkhodaie N, Karaoglou H, Wellings C, Park R. 2011. Mapping genes Lr53 and Yr35 on the short arm of chromosome 6B of common wheat with microsatellite markers and studies of their association with Lr36. Theoretical and Applied Genetics, 122, 479–487.
Devlin B, Risch N. 1995. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics, 29, 311–322.
Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin, 19, 11–15.
Eriksen L, Afshari F, Christiansen M J, McIntosh R A, Jahoor A, Wellings C R. 2004. Yr32 for resistance to stripe (yellow) rust present in the wheat cultivar Carstens V. Theoretical and Applied Genetics, 108, 567–575.
Gulnaz S, Zulkiffal M, Sajjad M, Ahmed J, Musa M, Abdullah M, Ahsan A, Rehman A U. 2019. Identifying Pakistani wheat landraces as genetic resources for yield potential, heat tolerance and rust resistance. International Journal of Agriculture and Biology, 21, 520–526.
Helguera M, Khan I A, Kolmer J, Lijavetzky D, Zhong-qi L, Dubcovsky J. 2003. PCR assays for the Lr37-Yr17-Sr38 cluster of rust resistance genes and their use to develop isogenic hard red spring wheat lines. Crop Science, 43, 1839–1847.
Herrera-Foessel S A, Lagudah E S, Huerta-Espino J, Hayden M J, Bariana H S, Singh D, Singh R P. 2011. New slow-rusting leaf rust and stripe rust resistance genes Lr67 and Yr46 in wheat are pleiotropic or closely linked. Theoretical and Applied Genetics, 122, 239–249
Herrera-Foessel S A, Singh R P, Lan C X, Huerta-Espina J, Calvo-Salazar V, Bansal U K, Bariana H S, Lagudah E S. 2015. Yr60, a gene conferring moderate resistance to stripe rust in wheat. Plant Disease, 99, 508–511.
Hickey L T, Lawson W, Platz G J, Dieters M, Arief V N, German S, Fletcher S, Park R F, Singh D, Pereyra S, Franckowiak J. 2011. Mapping Rph20: A gene conferring adult plant resistance to Puccinia hordei in barley. Theoretical and Applied Genetics, 123, 55–68.
Lagudah E, Krattinger S, Herrera-Foessel S A, Singh R, Huerta-Espino J, Spielmeyer W, Brown-Guedira G, Selter L, Keller B. 2009. Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens. Theoretical and Applied Genetics, 119, 889–898.
Lan C, Singh R P, Huerta-Espino J, Calvo-Salazar V, Herrera-Foessel S A. 2014. QTL characterization of resistance to leaf rust and stripe rust in the spring wheat line Francolin-1. Molecular Breeding, 34, 789–803.
Li Q, Chen X M, Wang M N, Jing J X. 2011. Yr45, a new wheat gene for stripe rust resistance on the long arm of chromosome 3D. Theoretical and Applied Genetics, 122, 189–197.
Lin F, Chen X M. 2007. Genetics and molecular mapping of genes for race-specific all-stage resistance and non-race-specific high-temperature adult-plant resistance to stripe rust in spring wheat cultivar Alpowa. Theoretical and Applied Genetics, 114, 1277–1287.
Liu C, Yang Z J, Li G R, Zeng Z X, Zhang Y, Zhou J P, Liu Z H, Ren Z L. 2008. Isolation of a new repetitive DNA sequence from Secale africanum enables targeting of Secale chromatin in wheat background. Euphytica, 159, 249–258.
Liu W, Maccaferri M, Chen X, Laghetti G, Pignone D, Pumphrey M, Tuberosa R. 2017. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum). Theoretical and Applied Genetics,130, 2249–2270.
Lowe I, Jankuloski L, Chao S M, Chen X M, See D, Dubcovsky J. 2011. Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theoretical and Applied Genetics, 123, 143–157.
Luo X Y. 2009. Residues from pesticides and countermeasures.Chinese Agricultural Science Bulletin, 18, 344–347. (in Chinease)
Maccaferri M, Ricci A, Salvi S, Milner S G, Noli E, Martelli P L, Casadio R, Akhunov E, Scalabrin S, Vendramin V. 2015. A high-density, SNP based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal, 13, 648–663.
Maccaferri M, Sanguineti M C, Mantovani P, Demontis A, Massi A, Ammar K, Kolmer J A, Czembor J H, Ezrati S, Tuberosa R. 2010. Association mapping of leaf rust response in durum wheat. Molecular Breeding, 26, 189–228.
Maccaferri M, Sanguineti M C, Noli E, Tuberosa R. 2005. Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Molecular Breeding, 15, 271–290.
Muhammad S, Ahmad A, Awan F S, Khan A I, Qasim M, Rehman A, Javed M A, Manzoor I, Sajjad M. 2018. Genome wide association analysis for leaf rust resistance in spring wheat (Triticum aestivum) germplasm. International Journal of Agriculture and Biology, 20, 2387–2394.
Mulki M A, Jighly A, Ye G, Emebiri L C, Moody D, Ansari O, Ogbonnaya F C. 2013. Association mapping for soilborne pathogen resistance in synthetic hexaploid wheat. Molecular Breeding, 31, 299–311.
Murphy L R, Santra D, Kidwell K, Yan G, Chen X, Campbell K G. 2009. Linkage maps of wheat stripe rust resistance genes Yr5 and Yr15 for use in marker-assisted selection. Crop Science, 49, 1786–1790.
Nsabiyera V, Bariana H S, Qureshi N, Wong D, Hayden M J, Bansal U K. 2018. Characterization and mapping of adult plant stripe rust resistance in wheat accession Aus27284. Theoretical and Applied Genetics, 131, 1–9.
Peterson R F, Campbell A B, Hannah A E. 1948. A diagrammatic scale for estimating rust intensity on leaves and stems of cereals. Canadian Journal of Research, 26, 496–500.
Qi A Y, Zhang P P, Zhou Y, Yao Z J, Li Z F, Liu D Q, 2016.Mapping of QTL conferring leaf rust resistance in Chinese wheat lines W014204 and Fuyu 3 at adult plant stage. Journal of Integrative Agriculture, 15, 18–28.
Randhawa M, Bansal U K, Valárik M, Klocová B, Dole?el J, Bariana H. 2014. Molecular mapping of stripe rust resistance gene Yr51 in chromosome 4AL of wheat. Theoretical and Applied Genetics, 127, 317–324.
Rehman A, Sajjad M, Khan S H, Ahmad N. 2013. Prospects of wheat breeding for durable resistance against brown, yellow and black rust fungi. International Journal of Agriculture and Biology, 15, 1209?1220.
Reif J C, Gowda M, Maurer H P, Longin C F H, Korzun V, Ebmeyer E, Bothe R, Pietsch C, Würschum T. 2011. Association mapping for quality traits in soft winter wheat.Theoretical and Applied Genetics, 122, 961–970.
Ren R S, Wang M N, Chen X M, Zhang Z J. 2012. Characterization and molecular mapping of Yr52 for high-temperature adult-plant resistance to stripe rust in spring wheat germplasm PI 183527. Theoretical and Applied Genetics, 125, 847–857.
Rosewarne G M, Singh R P, Huerta-Espino J, Herrera-Foessel S A, Forrest K L, Hayden M J, Rebetzke G J. 2013. Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet×Pastor wheat population. Theoretical and Applied Genetics, 124, 1283–1294.
Sajjad M, Khan S H, Ahmad M Q, Rasheed A, Mujeeb-Kazi A, Khan I A. 2014. Association mapping identifies QTLS on wheat chromosome 3A for yield related traits. Cereal Reseach Communications, 42, 177–188.
Sajjad M, Khan S H, Kazi A M. 2012. Low down on association mapping in hexaploid wheat (Triticum aestivum L.). Journal of Crop Science and Biotechnology, 15, 147–158.
Sajjad M, Khan S H, Shahzad M. 2018. Patterns of allelic diversity in spring wheat populations by SSR markers. Cytology and Genetics, 52, 155–160.
Shahzad M, Khan S H, Khan A S, Sajjad M, Rehman A, Khan A I. 2016. Identification of QTLs on chromosome 1B for grain quality traits in bread wheat (Triticum aestivum L.). Cytology and Genetics, 50, 89–95.
Singh R, Datta D, Priyamvada, Singh S, Tiwari R. 2009. A diagnostic PCR based assay for stripe rust resistance gene Yr10 in wheat. Acta Phytopathologica et Entomologica Hungarica, 44, 11–18.
Somers D J, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C. 2007. Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome, 50, 557?567.
Somers D J, Isaac P, Edwards K. 2004. A high density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 109, 1105–1114.
Suenaga K, Singh R P, Huerta-Espino J, William H M. 2003. Microsatellite markers for genes Lr34/Yr18 and other quantitative trait loci for leaf rust and stripe rust resistance in bread wheat. Phytopathology, 93, 881–890.
Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B. 2007. Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties.Theoretical and Applied Genetics, 115, 697–708.
Uauy C, Brevis J C, Chen X, Khan I, Jackson L, Chicaiza O, Distelfeld A, Fahima T, Dubcovsky J. 2005. High-temperature adult-plant (HTAP) stripe rust resistance gene Yr36 from Triticum turgidum ssp. dicoccoides is closely linked to the grain protein content locus Gpc-B1. Theoretical and Applied Genetics, 112, 97.
Yu L X, Lorenz A, Rutkoski J, Singh R P, Bhavani S, Huerta-Espino J, Sorrells M E. 2011. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theoretical and Applied Genetics, 123, 1257–1268.
Zhao Y, Wang H, Chen W, Li Y. 2014. Genetic structure, linkage disequilibrium and association mapping of verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS ONE, 9, e86308.
Zheng J, Yan Z, Zhao L, Li S, Zhang Z, Garry R, Yang W, Pu Z. 2014. Molecular mapping of a stripe rust resistance gene in wheat line 51. Journal of Genetics, 93, 443–450.
Zhou X L, Han D J, Gou H L, Wang Q L, Zeng Q D, Yuan F P, Zhan G M, Huang L L, Kang Z S. 2014. Molecular mapping of a stripe rust resistance gene in wheat cultivar Wuhan 2. Euphytica, 196, 251–259.
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