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Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (06): 795-802.doi: 10.3724/SP.J.1006.2016.00795

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Analysis of TaNBS Resistance Genes and Development of Chromosome 2AL-specific NBS-SSR Markers in Wheat

QIAO Lin-Yi1,2,CHANG Jian-Zhong4,GUO Hui-Juan2,GAO Jian-Gang5,ZHENG Jun3,*,CHANG Zhi-Jian1,2,*   

  1. 1 Graduate School of Shanxi University, Taiyuan 030006, China; 2 Institute of Crop Science, Shanxi Academy of Agricultural Sciences / Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Taiyuan 030031, China; 3Institute of Wheat Research, Shanxi Academy of Agricultural Sciences, Linfen 041000, China; 4 Institute of Dryland Farming, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, China; 5 Hybrid Technology Engineering Research Center of Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
  • Received:2015-10-20 Revised:2016-03-14 Online:2016-06-12 Published:2016-03-21
  • Contact: 畅志坚, E-mail: wrczj@126.com; 郑军, E-mail: zhengjsxaas@126.com E-mail:qiaoly1988@126.com
  • Supported by:

    This study was supported by the National Natural Science Foundation of China (31171839,31401385), Shanxi Province Science Foundation for Youths (2015021145), Shanxi Province Technologies R&D Program (20150311001-1,20150311001-5), the Technologies R&D Program of the Shanxi Academy of Agricultural Sciences (15YGG01), and the Youth Foundation of Beijing Academy of Agricultural and Forestry Sciences (QNJJ201428).

Abstract:

Nucleotide binding site (NBS)-encoding genes are the most important resistance genes (R genes) in plant kingdom. In this study, 2406 full-length NBS protein sequences, of which single protein varies from 48 aa to 2272 aa, were identified from wheat (Triticum aestivum L.) genome using bioinformatic method. These TaNBSs were divided into four categories, including N, CN, NL and CNL, according to whether the NBS domains connect CC or LRR domains at both ends. Diagnosis results showed that 1203 of all the scaffolds with TaNBS contained 2177 simple sequence repeats (SSR) loci, 73.5% of which were dinucleotide repeat sites. Based on the NBS-SSR loci on chromosome 2AL in wheat, we developed 51 molecular markers , and 39 of them (76.5%) were confirmed as chromosome specific markers using Chinese Spring nulli-tetrasomic and ditelosomic lines. Furthermore, 24 2AL-specific NBS-SSR markers showed polymorphism between resistant material Khapli carried Pm4a on chromosome 2AL and susceptible material Chancellor. Finally, three 2AL-specific NBS-SSR markers, Sxaas_2AL22, Sxaas_2AL39, and Sxaas_2AL46, were probably linked to Pm4a gene based on genetic linkage test using Pm4a-NILs (Khapli/8*Cc). These chromosome specific 2AL-NBS-SSR markers can be used to locate novel R genes or screen the candidate sequences for known R genes on chromosome 2AL.

Key words: Wheat, Disease resistance, NBS-encoding genes, SSR markers, Chromosome 2AL

[1]Li H J, Wang X M. Thinopyrum ponticum and Th. intermedium: the promising source of resistance to fungal and viral diseases of wheat. J Genet Genomics, 2009, 36: 557–565
[2]Line R F, Chen X M. Success in breeding for and managing durable resistance to wheat rusts. Plant Dis, 1995, 79: 125−1255
[3]Ott A, Trautschold B, Sandhu D. Using microsatellites to understand the physical distribution of recombination on soybean chromosomes. PLoS One, 2011, 6: e22306
[4]Yahiaoui N, Srichumpa P, Dudler R, Keller B. Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J, 2004, 37: 528–538
[5]Tommasini L, Yahiaoui N, Srichumpa P, Keller B. Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theor Appl Genet, 2006, 114: 165–175
[6]Srichumpa P, Brunner S, Keller B, Yahiaoui N. Allelic series of four powdery mildew resistance genes at the Pm3 locus in hexaploid bread wheat. Plant Physiol, 2005, 139: 885–895
[7]Liu W, Frick M, Huel R, Nykiforuk C L, Wang X, Gaudet D A, Eudes F, Conner R L, Kuzyk A, Chen Q, Kang Z, Laroche A. The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC-NBS-LRR sequence in wheat. Mol Plant, 2014, 7: 1740–1755
[8]Cloutier S, McCallum B D, Loutre C, Banks T W, Wicker T, Feuillet C, Keller B, Jordan M C. Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. Plant Mol Biol, 2007, 65: 93–106
[9]Sela H, Spiridon L N, Petrescu A J, Akerman M, Mandel-Gutfreund Y, Nevo E, Loutre C, Keller B, Schulman A H, Fahima T. Ancient diversity of splicing motifs and protein surfaces in the wild emmer wheat (Triticum dicoccoides) LR10 coiled coil (CC) and leucine-rich repeat (LRR) domains. Mol Plant Pathol, 2012, 13: 276–287
[10]Huang L, Brooks S A, Li W, Fellers J P, Trick H N, Gill B S. Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics, 2003, 164: 655–664
[11]Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, McIntosh R, Dodds P, Dvorak J, Lagudah E. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science, 2013, 341: 786–788
[12]Saintenac C, Zhang W, Salcedo A, Rouse M N, Trick H N, Akhunov E, Dubcovsky J. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science, 2013, 341: 783–786
[13]Cao A, Xing L, Wang X, Yang X, Wang W, Sun Y, Qian C, Ni J, Chen Y, Liu D, Wang X, Chen P. Serine/threonine kinase gene Stpk-V, a key member of powdery mildew resistance gene Pm21, confers powdery mildew resistance in wheat. Proc Natl Acad Sci USA, 2011, 108: 7727–7732
[14]Krattinger S G, Lagudah E S, Spielmeyer W, Singh R P, Espino J H, McFadden H, Bossolini E, Selter L L, Keller B. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science, 2009, 323: 1360–1363
[15]Meyers B C, Kozik A, Griego A, Kuang H, Michelmore R W. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 2003, 15: 809–834
[16]Bourne H R, Sanders D, McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature, 1991, 349: 117–127
[17]Belkhadir Y, Subramaniam R, Dangl J L. Plant disease resistance protein signaling: NBS-LRR proteins and their partners. Curr Opin Plant Biol, 2004, 7: 391–399
[18]史静东, 张小娟, 黄丽丽, 韩德俊, 康振生. 小麦 NBS-LRR类抗病基因类似片段分离和定位. 中国农业科学, 2013, 46: 2022–2031
Shi J D, Zhang X J, Huang L L, Han D J, Kang Z S. Isolation and mapping of NBS-LRR resistance gene homology sequences from wheat. Sci Agric Sin, 2013, 46: 2022–2031 (in Chinese with English abstract)
[19]Rachel B, Manuel S, Matthias P, Gary L A B, Rosalinda D A, Alexandra M A, Neil M, Melissa K, Arnaud K, Dan B, Suzanne K, Darren W, Martin T, Ian B, Gu Y, Huo N X, Luo M C, Sunish S, Bikram G, Sharyar K, Olin A, Paul K, Jan D, Richard M, Anthony H, Klaus F M, Keith J E, Michael W B, Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012, 491: 705–710
[20]Bouktila D, Khalfallah Y, Habachi Y, Mezghani M, Makni M, Makni H. Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat. Mol Genet Genomics, 2015, 290: 257–271
[21]International Wheat Genome Sequencing Consortium (IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 2014, 345: 1251788
[22]Shang J, Tao Y, Chen X, Zou Y, Lei C, Wang J, Li X, Zhao X, Zhang M, Lu Z, Xu J, Cheng Z, Wan J, Zhu L. Identification of a new rice blast resistance gene, Pid3, by genome wide comparison of paired nucleotide-binding site leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics, 2009, 182: 1303–1311
[23]Kang Y J, Kim K H, Shim S, Yoon M Y, Sun S, Kim M Y, Van K, Lee S H. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol, 2012, 12: 139
[24]Paterson A H, Bowers J E, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti A K, Chapman J, Feltus F A, Gowik U, Grigoriev I V, Lyons E, Maher C A, Martis M, Narechania A, Otillar R P, Penning B W, Salamov A A, Wang Y, Zhang L, Carpita N C, Freeling M, Gingle A R, Hash C T, Keller B, Klein P, Kresovich S, McCann M C, Ming R, Peterson D G, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer K F, Messing J, Rokhsar D S. The Sorghum bicolor genome and the diversifcation of grasses. Nature, 2009, 457: 551–556
[25]Cheng Y, Li X, Jiang H, Ma W, Miao W, Yamada T, Zhang M. Systematic analysis and comparison of nucleotide-binding site disease resistance genes in maize. FEBS J, 2012, 279: 2431–2443
[26]Ma Q H, Zhen W B, Liu Y C. Jacalin domain in wheat jasmonate-regulated protein Ta-JA1 confers agglutinating activity and pathogen resistance. Biochimie, 2013, 95: 359–365
[27]Guo J, Bai P, Yang Q, Liu F, Wang X, Huang L, Kang Z. Wheat zinc finger protein TaLSD1, a negative regulator of programmed cell death, is involved in wheat resistance against stripe rust fungus. Plant Physiol Biochem, 2013, 71: 164–172
[28]Deslandes L, Olivier J, Theulieres F, Hirsch J, Feng D X, Bittner-Eddy P D, Beynon J, Marco Y. Resistance to Ralstonias olanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. Proc Natl Acad Sci USA, 2002, 99: 2404–2409
[29]Ma Z Q, Wei J B, Cheng S H. PCR-based markers for the powdery mildew resistance gene Pm4a in wheat. TheorAppl Genet, 2004, 109: 140–145
[30]Yi Y J, Liu H Y, Huang X Q, An L Z, Wang F, Wang X L. Development of molecular markers linked to the wheat powdery mildew resistance gene Pm4b and marker validation for molecular breeding. Plant Breed, 2008, 127: 116–120
[31]Hao Y, Liu A, Wang Y, Feng D, Gao J, Li X, Liu S, Wang H. Pm23: a new allele of Pm4 located on chromosome 2AL in wheat. Theor Appl Genet, 2008, 117: 1205–1212
[32]Michael Schmolke M, Mohler V, Hartl L, Zeller F J, Hsam S K. A new powdery mildew resistance allele at the Pm4 wheat locus transferred from einkorn (Triticum monococcum). Mol Breed, 2012, 29: 449–456
[33]Mohler V, Bauer C, Schweizer G, Kempf H, Hartl L. Pm50: a new powdery mildew resistance gene in common wheat derived from cultivated emmer. J Appl Genet, 2013, 54: 259–263
[34]Bariana H S, McIntosh R A. Cytogenetic studies in wheat: XV. Location of rust resistance genes in VPM1 and their genetic linkage with other disease resistance genes in chromosome 2A. Genome, 1993, 36: 476–482
[35]Eriksen L, Afshari F, Christiansen M J, McIntosh R A, Jahoor A, Wellings C R. Yr32 for resistance to stripe (yellow) rust present in the wheat cultivar Carstens V. TheorAppl Genet, 2004, 108: 567–575
[36]Friebe B, Zeller F J, Mukai Y, Forster B P, Bartos P, McIntosh R A. Characterization of rust-resistant wheat-Agropyron intermedium derivatives by C-banding, in situ hybridization and isozyme analysis. Theor Appl Genet, 1992, 83: 775–782
[37]Chen S, Rouse M N, Zhang W, Jin Y, Akhunov E, Wei Y, Dubcovsky J. Fine mapping and characterization of Sr21, a temperature-sensitive diploid wheat resistance gene effective against the Puccinia graminis f. sp. tritici Ug99 race group. Theor Appl Genet, 2015, 128: 645–656

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