Single Nucleotide Polymorphisms in HSP17.8 and Their Association with Agronomic Traits in Barley

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Xia, Yanshi ^a,b   Li, Ronghua ^a   Ning, Zhengxiang ^b   Bai, Guihua ^c   Siddique, Kadambot H M ^d   Yan, Guijun ^d   Baum, Michael ^e   Varshney, Rajeev K ^f   Guo, Peiguo ^a  

^a GUANGZHOU UNIVERSITY   (China)

^b SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^c United States Department of Agriculture Agricultural Research Service   (United States)

^d UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^e INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS ICARDA   (Syrian Arab Republic)

^f INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; SMALL HEAT SHOCK PROTEIN; SMALL HEAT SHOCK PROTEIN 17.8; UNCLASSIFIED DRUG;

AGRONOMIC TRAIT; ARTICLE; BARLEY; CONTROLLED STUDY; CULTIVATED SPECIES; DROUGHT TOLERANCE; GENE AMPLIFICATION; GENE EXPRESSION; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GRAIN YIELD; HAPLOTYPE; HSP17.8 GENE; LEAF AREA; LEAF COLOR; MIDDLE EAST; MISSENSE MUTATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT HEIGHT; PLANT PARAMETERS; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SPIKE LENGTH; THOUSAND KERNEL WEIGHT; WILD SPECIES;

GENE FREQUENCY; GENETIC VARIATION; GENOTYPE; GEOGRAPHY; HAPLOTYPES; HEAT-SHOCK PROTEINS, SMALL; HORDEUM; OPEN READING FRAMES; PHENOTYPE; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SPECIES SPECIFICITY;

EID: 84873908815     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0056816     Document Type: Article

References (70)

1. Sun W, Montagu MV, Verbruggen N, (2002) Small heat shock proteins and stress tolerance in plants. Biochim Biophys Acta 1577: 1-9.
2. Hu W, Hu G, Han B, (2009) Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Sci 176: 583-590.
3. Kim DH, Xu ZY, Na YJ, Yoo YJ, Lee J, et al. (2011) Small heat shock protein HSP17.8 functions as an AKR2A cofactor in the targeting of chloroplast outer membrane proteins in Arabidopsis. Plant Physiol 157: 132-146.
4. Sato Y, Yokoya S, (2008) Enhanced tolerance to drought stress in transgenic rice plants overexpressing a small heat-shock protein, sHSP17.7. Plant Cell Rep 27: 329-334.
5. Song NH, Ahn YJ, (2011) DcHSP17.7, a small heat shock protein in carrot, is tissue-specifically expressed under salt stress and confers tolerance to salinity. New Biotechnol 28: 6.
6. Timperio AM, Egidi MG, Zolla L, (2008) Proteomics applied on plant abiotic stresses: role of heat shock proteins (HSP). J Proteom 71: 391-411.
7. Waters ER, Lee GJ, Vierling E, (1996) Evolution, structure and function of the small heat shock proteins in plants. J Exp Bot 47: 325-338.
8. Liu X, Huang W, Li M, Wu Q, (2005) Purification and characterization of two small heat shock proteins from Anabaena sp. PCC 7120. IUBMB Life 57: 449-454.
9. Kant P, Gordon M, Kant S, Zolla G, Davydov O, et al. (2008) Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses. Plant Cell Environ 31: 697-714.
10. Shou H, Bordallo P, Fan JB, Yeakley JM, Bibikova M, et al. (2004) Expression of an active tobacco mitogen-activated protein kinase kinase kinase enhances freezing tolerance in transgenic maize. PNAS 101: 3298-3303.
11. Grigorova B, Vaseva II, Demirevska K, Feller U, (2011) Expression of selected heat shock proteins after individually applied and combined drought and heat stress. Acta Physiol Plant 33: 2041-2049.
12. Guo P, Baum M, Grando S, Ceccarelli S, Bai G, et al. (2009) Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage. J Exp Bot 12: 3531-3544.
13. Witkin SS, Linhares IM (2010) Heat shock proteins, genital tract infections and reproductive outcome. Prokaryotic and Eukaryotic Heat Shock Proteins in Infectious Disease, Heat Shock Proteins 4:241-256.
14. Comai L, Young K, Till BJ, Reynolds SH, Greene EA, et al. (2004) Efficient discovery of DNA polymorphisms in natural populations by EcoTILLING. Plant J 37: 778-786.
15. Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, et al. (2006) Use of EcoTILLING as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15: 1367-1378.
16. Nieto C, Piron F, Dalmais M, Marco CF, Moriones E, et al. (2007) EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility. BMC Plant Biology 7: 34.
17. Till BJ, Zerr T, Comai L, Henikoff S, (2006) A protocol for TILLING and EcoTILLING in plants and animals. Nat Protoc 5: 2465-2477.
18. Wang N, Shi L, Tian F, Ning H, Wu X, et al. (2010) Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents. BMC Plant Biology 10: 137.
19. Yu J, Buckler ES, (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155-160.
20. Zhu C, Gore M, Buckler ES, Yu J, (2008) Status and prospects of association mapping in plants. The Plant Genome 1: 5-20.
21. Wu D, Qiu L, Xu L, Ye L, Chen M, et al. (2011) Genetic variation of HvCBF genes and their association with salinity tolerance in Tibetan annual wild barley. PLoS one 6(7): e22938 Doi:10.1371/journal.Pone.0022938.
22. Xia Y, Ning Z, Bai G, Li R, Yan G, et al. (2012) Allelic Variations of a Light Harvesting Chlorophyll A/B-Binding Protein Gene (Lhcb1) Associated with Agronomic Traits in Barley. PLoS ONE 7(5): e37573 doi:10.1371/journal.pone.0037573.
23. Varshney RK, Baum M, Guo P, Grando S, Ceccarelli S, et al. (2010) Features of SNP and SSR diversity in a set of ICARDA barley germplasm collection. Mol Breeding 26: 229-242.
24. Gupta R, Guhey A, Jadhav A, Ahad I, (2011) Physiological boost to improve the yield of rice germplasm under different water regimes. Research Journal of Agricultural Science 2: 87-90.
25. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RH, et al. (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 12: 2700-2707.
26. Guo P, Bai G, Li R, Carver B, Baum M, (2007) Molecular characterization of atlas 66-derived wheat near-isogenic lines contrasting in aluminum (Al) tolerance. Agr Sci China 5: 522-528.
27. Wang GX, Tan MK, Rakshit SR, Saitoh H, Terauchi R, et al. (2007) Discovery of single-nucleotide mutations in acetolactate synthase genes by Ecotilling. Pestic Biochem Phys 88: 143-148.
28. Raghavan C, Naredo MEB, Wang HH, Atienza G, Liu B, et al. (2007) Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol Breeding 19: 87-101.
29. Guo PG, Li RH (2010) A method for isolation of CEL I enzyme from celery. Chinese Patent, ZL200910038725.9, 2010-9-29.
30. Zerr T, Henikoff S, (2005) Automated band mapping in electrophoretic gel image using background information. Nucleic Acids Res 33: 2806-2812.
31. Ng PC, Henikoff S, (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
32. Taylor NE, Greene EA, (2003) PARSESNP: a tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 31: 3808-3811.
33. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
34. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
35. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
36. Cseri A, Cserháti M, von Korff M, Nagy B, Horváth GV, et al. (2011) Allele mining and haplotype discovery in barley candidate genes for drought tolerance. Euphytica 181: 341-356.
37. Chung JD, Lin TP, Cheng YP, Hwang SY, (2010) Geographical variation and differential selection modes of paralogs of chloroplast small heat shock protein genes in Machilus kusanoi (Lauraceae). Bot Stud 51: 27-36.
38. Russell J, Booth A, Fuller J, Harrower B, Hedley P, et al. (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47: 389-398.
39. Chen G, Yang S, Li W, Li W, Wei Y, et al. (2009) Variations of single nucleotide polymorphism (SNP) of Hordoindoline a gene (hina) and its relationships with kernel hardness in 92 North American barley varieties (Hordeum vulgare L.). Agr Sci China 12: 1440-1447.
40. Zeng X, Wei Y, Jiang Q, Qi P, Zheng Y, (2009) SNP analysis and haplotype identification in chymotrypsin inhibitor-2 (CI-2) gene of barley. Agr Sci China 8: 8-14.
41. Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudies S, et al. (2005) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 6: R54.
42. Bundock PC, Henry RJ, (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109: 543-551.
43. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, et al. (2009) Single nucleotide polymorphism discover in barley using autoSNPdb. Plant Biotechnol J 7: 326-333.
44. Kilian B, Ozkan H, Kohl J, von Haeseler A, Barale F, et al. (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics 276: 230-241.
45. Tanksley SD, McCouch SR, (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277: 1063-1066.
46. Malysheva-Otto LV, Ganal MW, Röder MS, (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics 7: 6.
47. Nevo E (1992) Origin, evolution, population genetics and resources for breeding of wild barley, Hordeum spontaneum in the Fertile Crescent. In: Shewry PR(ed) Barley: genetics, biochemistry, molecular biology and biotechnology. C.A.B. International, Wallingford, Oxford, pp19-43.
48. Ceccarelli S, Grando S, van Leur JAG, (1995) Barley landraces of the fertile crescent offer new breeding options for stress environments. Diversity 11: 112-113.
49. Ellis RP, Forster BP, Robinson D, Handley LL, Gordon DC, et al. (2000) Wild barley: a source of genes for crop improvement in the 21st century? J Exp Bot 51: 9-17.
50. Abdellaoui R, M'Hamed HC, Naceur MB, Bettaïeb-Kaab L, Hanida JB, (2007) Morpho-physiological and molecular characterization of some Tunisian barley ecotypes. Asian Journal of Plant Sciences 6: 261-268.
51. Peter-Schmid MKI, Boller B, Kölliker R, (2008) Habitat and management affect genetic structure of Festuca pratensis but not Lolium multiflorum ecotype populations. Plant Breeding 127: 510-517.
52. Inostroza L, del Pozo A, Matus I, Castillo D, Hayes P, et al. (2009) Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol Breeding 23: 365-376.
53. Lakew B, Eglinton J, Henry RJ, Baum M, Grando S, et al. (2011) The potential contribution of wild barley (Hordeum vulgare ssp. spontaneum) germplasm to drought tolerance of cultivated barley (H. vulgare ssp. vulgare). Field Crops Research 120: 161-168.
54. Schmalenbach I, Léon J, Pillen K, (2008) Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet 18: 483-497.
55. Guo PG, Baum M, Li RH, Grando S, Varshney RK, et al. (2007) Transcriptional analysis of barley genes in response to drought stress at the reproductive growth stage using affymetrix Barley 1 genechip. J Guangzhou Univ (Nat Sci Ed) 5: 32-36.
56. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, et al. (2007) A 1000 loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 114: 823-839.
57. Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS, (2006) Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley. Genome 49: 454-466.
58. Teulat B, Merah O, Souyris I, This D, (2001) QTLs for agronomic traits from a Mediterranean barley progeny grown in several environments. Theor Appl Genet 103: 774-787.
59. Schmalenbach I, Léon J, Pillen K, (2009) Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet 118: 483-497.
60. Sun D, Ren W, Sun G, Peng J, (2011) Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm. Euphytica 178: 31-43.
61. Guo P, Baum M, Varshney RK, Graner A, Grando S, et al. (2008) QTLs for chlorophyll and chlorophyll fluorescence parameters in barley under post-flowering drought. Euphytica 163: 203-214.
62. Mohammed KAH (2004) Improving crop varieties of spring barley for drought and heat tolerance with AB-QTL analysis. PhD Thesis, Bonn University, Germany.
63. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, et al. (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
64. Szalma SJ, Buckler ES, Snook ME, McMullen MD, (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110: 1324-1333.
65. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, et al. (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721-726.
66. Varshney RK, Paulo MJ, Grando S, van Eeuwijk FA, Keizer LCP, et al. (2012) Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Research 126: 171-180.
67. Yu S, Liao F, Wang F, Wen W, Li J, et al. (2012) Identification of rice transcription factors associated with drought tolerance using the ecotilling method. PLoS ONE 7(2): e30765.
68. Thornton KR, Jensen JD, Becquet C, Andolfatto P, (2007) Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-348.
69. Breseghello F, Sorrells ME, (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
70. Peng JH, Bai Y, Haley SD, Lapitan NLV, (2009) Microsatellite-based molecular diversity of bread wheat germplasm and association mapping of wheat resistance to the Russian wheat aphid. Genetica 135: 95-122.