Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.
Anchoring
Chromosome 2A
Diploid wheat
Genetic map
Linkage map
Physical map
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
received:
05
11
2019
accepted:
30
01
2020
pubmed:
9
2
2020
medline:
11
11
2020
entrez:
9
2
2020
Statut:
ppublish
Résumé
Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.
Identifiants
pubmed: 32034627
doi: 10.1007/s11033-020-05295-9
pii: 10.1007/s11033-020-05295-9
doi:
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1991-2003Subventions
Organisme : Department of Biotechnology, New Delhi
ID : BT/IWGSC/03/TF/2008
Organisme : European Regional Development Fund
ID : CZ.02.1.01/0.0/0.0/16_019/0000827
Références
Hawkesford MJ, Araus JL, Park R, Calderini D, Miralles D, Shen T, Zhang J, Parry MAJ (2013) Prospects of doubling global wheat yields. Food Energy Secur 2:34–48
doi: 10.1002/fes3.15
Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46
doi: 10.1038/nrg2626
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100
doi: 10.1016/S1369-5266(02)00240-6
Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploidy wheat with the illumina golden gate assay. Theor Appl Genet 119:507–517
doi: 10.1007/s00122-009-1059-5
pubmed: 2715469
pmcid: 2715469
Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG, Humphreys DG, Harrison NR, Fellers JP, McCallum BD, McCartney CA (2017) Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr 16. BMC Plant Biol 17:45
doi: 10.1186/s12870-017-0993-7
pubmed: 5311853
pmcid: 5311853
Wu J, Wang Q, Kang Z, Liu S, Li H, Mu J, Dai M, Han D, Zeng Q, Chen X (2017) Development and validation of KASP-SNP markers for QTL underlying resistance to stripe rust in common wheat cultivar P10057. Plant Dis 101:2079–2087
doi: 10.1094/PDIS-04-17-0468-RE
Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, Leveugle M, Duarte J, Rivière N, Eversole K, LeGouis J, Davassi A, Balfourier F, Le Paslier MC, Berard A, Brunel D, Feuillet C, Poncet C, Soudielle P, Paux E (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE 13:e0186329
doi: 10.1371/journal.pone.0186329
pubmed: 5749704
pmcid: 5749704
Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, Mahdy E, Bakheit B, El-Wafaa AA, Poland J, Baenziger PS (2018) Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Front Plant Sci 9:380
doi: 10.3389/fpls.2018.00380
pubmed: 5881291
pmcid: 5881291
Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30:1071–1088
doi: 10.1016/j.biotechadv.2011.09.015
Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J 7:733–742
doi: 10.1111/j.1467-7652.2012.00713.x
Akhunov E, Sehgal S, Liang H, Wang S, Akhunova AR, Kaur G, Li W, Forrest KL, See D, Šimková H, Ma Y, Hayden MJ, Luo M, Faris JD, Doležel J, Gill BS (2013) Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol 161:252–265
doi: 10.1104/pp.112.205161
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796
doi: 10.1111/pbi.12183
pubmed: 4265271
pmcid: 4265271
International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:e1251788
doi: 10.1126/science.1251788
International Wheat Genome Sequencing Consortium (2018) Shifting the limits in wheat research and breeding through a fully annotated and anchored reference genome sequence. Science 361:eaar7191
doi: 10.1126/science.aar7191
Singh K, Ghai M, Garg M, Chhuneja P, Kaur P, Schnurbusch T, Keller B, Dhaliwal HS (2007) An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum × T monococcum RIL population. Theor Appl Genet 115:301–312
doi: 10.1007/s00122-007-0543-z
Dubcovsky J, Luo MC, Zhong GY, Brandsteitter R, Desai A, Kilian A, Kleinhofs A, Dvorak J (1996) Genetic map of diploid wheat, Triticum monococcum L. and its comparison with maps of Hordeum vulgare L. Genetics 143:983–999
pubmed: 1207354
pmcid: 1207354
Boyko EV, Gill KS, Mickelson-Young L, Nasuda S, Raupp WJ, Ziegle JN, Singh S, Hassawi DS, Fritz AK, Namuth D, Lapitan NLV, Gill BS (1999) A high-density genetic map of Aegilops tauschii, the D genome progenitor of bread wheat. Theor Appl Genet 99:16–26
doi: 10.1007/s001220051204
Luo M, Deal KR, Yang Z, Dvorak J (2005) Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes Theor. Appl Genet 111:1098–1106
doi: 10.1007/s00122-005-0035-y
Chhuneja P, Kaur S, Garg T, Ghai M, Kaur S, Prashar M, Bains NS, Goel RK, Keller B, Dhaliwal HS, Singh K (2008) Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor Appl Genet 116:313–324
doi: 10.1007/s00122-007-0668-0
Tiwari VK, Rawat N, Chhuneja P, Singh N, Aggarwal R, Randhawa GS, Dhaliwal HS, Keller B, Singh K (2009) Mapping of quantitative trait loci for grain iron and zinc concentration in A genome diploid wheat. J Heredity 100:771–776
doi: 10.1093/jhered/esp030
Singh K, Chhuneja P, Singh I, Sharma SK, Garg T, Garg M, Keller B (2010) Molecular mapping of cereal cyst nematode resistance in Triticum monococcum L and its transfer to the genetic background of cultivated wheat. Euphytica 176:213–222
doi: 10.1007/s10681-010-0227-7
Chhuneja P, Kumar K, Stirnweis D, Hurni S, Keller B, Dhaliwal HS, Singh K (2012) Identification and mapping of two powdery mildew resistance genes in Triticum boeoticum L. Theor Appl Genet 124:1051–1058
doi: 10.1007/s00122-011-1768-4
Chhuneja P, Yadav B, Stirnweis D, Hurni S, Kaur S, Elkot AFA, Keller B, Wicker T, Sehgal S, Gill BS, Singh K (2015) Fine mapping of powdery mildew resistance genes PmTb7A1 and PmTb7A2 in Triticum boeoticum (Boiss) using the shotgun sequence assembly of chromosome 7AL. Theor Appl Genet 128:2099–2111
doi: 10.1007/s00122-015-2570-5
Elkot AFA, Chhuneja P, Kaur S, Saluja M, Keller B, Singh K (2015) Marker assisted transfer of two powdery mildew resistance genes PmTb7A1. PLoS ONE 10:e0128297
doi: 10.1371/journal.pone.0128297
pubmed: 4466026
pmcid: 4466026
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA apacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018
doi: 10.1073/pnas.81.24.8014
Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat In S Ramanujams, ed. Proc 5th Int Wheat Genetics Symp, p 389–407 New Delhi, Indian Agricultural Research Institute
Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104:1362–1372
doi: 10.1007/s00122-002-0888-2
Šimková H, Svensson JT, Condamine P, Hřibová E, Suchánková P, Bhat PR, Bartoš J, Šafář J, Close TJ, Doležel J (2008) Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genom 9:294
doi: 10.1186/1471-2164-9-294
Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7:561–562
doi: 10.1016/S1360-1385(02)02372-5
Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210
doi: 10.1111/j.1467-7652.2009.00477.x
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg LA (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
doi: 10.1016/0888-7543(87)90010-3
Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic maps with MAPMAKER/EXP version 30: a tutorial and reference manual Whitehead Inst Biomed Res Tech Rpt, 3rd edn Whitehead Institute for Biomedical Research, Cambridge, p 97
Haldane JBS (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. J Genet 8:299–309
doi: 10.1007/BF02983270
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
doi: 10.1093/jhered/93.1.77
pubmed: 12011185
pmcid: 12011185
Krzywinski M, Schien JE, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetics for comparative genomics. Genome Res 19:1639–1645
doi: 10.1101/gr.092759.109
pubmed: 19541911
pmcid: 19541911
Kaur P, Yadav IS, Yadav B, Mahato A, Gupta OP, Doležel J, Singh NK, Khurana JP, Singh K (2019) In silico annotation of 458 genes identified from comparative analysis of Full length cDNAs and NextGen sequence of chromosome 2A of hexaploid wheat. J Plant Biochem Biotechnol 28:25–34
doi: 10.1007/s13562-018-0460-z
Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier MHN, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023
pubmed: 9691054
pmcid: 9691054
Johnson BL, Dhaliwal HS (1976) Reproductive isolation of Triticum boeoticum and Triticum urartu and the origin of the tetraploid wheat. Am J Bot 63:1088–1094
doi: 10.1002/j.1537-2197.1976.tb13193.x
Doležel J, Vrána J, Šafář J, Bartoš J, Kubaláková M, Šimková H (2012) Chromosomes in the flow to simplify genome analysis. Funct Integr Genom 12:397–416
doi: 10.1007/s10142-012-0293-0
Akpinar BA, Lucas S, Budak H (2017) A large-scale chromosome-specific SNP discovery guideline. Funct Integr Genom 17(1):97–105
doi: 10.1007/s10142-016-0536-6
Dobrovolskaya O, Boeuf C, Salse J, Pont C, Sourdille P, Bernard M, Salina E (2011) Microsatellite mapping of Ae. speltoides and map-based comparative analysis of the S, G, and B genomes of Triticeae species. Theor Appl Genet 123:1145–1157
doi: 10.1007/s00122-011-1655-z
Molnár I, Vrána J, Burešová V, Cápal P, Farkas A, Darko E, Cseh A, Kubaláková M, Molnár-Láng M, Doležel J (2016) Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp) into chromosomes and exploring their synteny with wheat. The Plant J 88:452–467
doi: 10.1111/tpj.13266
Lucas SJ, Salantur A, Yazar S, Budak H (2017) High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genom 17(6):667–685
doi: 10.1007/s10142-017-0563-y
Sharma P, Bawa P, Yadav B, Kaur P, Jindal S, Yadav I, Kaur S, Singh K, Chhuneja P (2019) Physical mapping of an adult plant stripe rust resistance gene from Triticum monococcum. J Plant Biochem Biotech. https://doi.org/10.1007/s13562-019-00511-5
doi: 10.1007/s13562-019-00511-5