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A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits

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Abstract

In the present study, a detailed deletion map for wheat chromosomes 5A and 5B is reported, as well as an integrated genetic linkage map of chromosome 5A enriched with single nucleotide polymorphism (SNP) markers, useful both for comparison studies with other existing maps and for mapping major genes and quantitative trait loci (QTLs). Physical mapping of 5,011 SNP markers was obtained using Chinese Spring bin deletion lines for the homoeologous chromosomes of group 5; 509 SNPs were also genetically mapped in a recombinant inbred line population segregating for chromosome 5A only, obtained by crossing the cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides. The whole 5A genetic map, containing 572 markers, covered a total length of 248.7 cM distributed among three linkage groups of 83.5, 117.8 and 47.4, respectively. The majority of SNP markers physically mapped on 5A were mapped to a unique bin, while a small percentage was assigned a double location, suggesting the presence of a segment of 5A short arm which may have undergone a duplication followed by an insertion into the long arm of the same chromosome. A QTL analysis for yield components was performed, identifying a major QTL in the sub-telomeric region of chromosome 5A, corresponding to the 5AL15-0.67-0.78 bin; the chromosome segment was 23.5 cM long and included 111 markers. Candidate genes for yield components on chromosome 5A were identified through a syntenic genomic approach by comparison with genomes of model species. Putative function analysis revealed genes involved in basic metabolism and in stress condition responses, including heat shock proteins, chaperones, serine/threonine protein kinases and membrane transporters, located in the region of the QTL. This information represents an important step for map-based and candidate gene-based cloning of yield QTLs.

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References

  • Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507–517

    CAS  PubMed Central  PubMed  Google Scholar 

  • Akhunov E, Sehgal S, Liang H, Wang S, Akhunova A et al (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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Altintas S, Toklu F, Kafkas S, Kilian B, Brandolini A, Ozkan H (2008) Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant Breed 127:9–14

    CAS  Google Scholar 

  • Autrique E, Nachit M, Monneveux P, Tanksley SD, Sorrells ME (1996) Genetic diversity in durum wheat based on RFLP, morphophysiological traits and coefficient of parentage. Crop Sci 36:735–742

    Google Scholar 

  • Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, Lopez da Silva M, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA 110(20):8057–8062

    CAS  PubMed Central  PubMed  Google Scholar 

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307. doi:10.1093/oxfordjournalsjhereda023003

    CAS  Google Scholar 

  • Eversole K, Graner A, Stein N (2009) Wheat and barley genome sequencing. Plant Genet Genom 7:713–742. doi:10.1007/978-0-387-77489-3_24

    Google Scholar 

  • Fleury D, Luo MC, Dvorak J, Ramsay L, Gill BS et al (2010) Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilopstauschii chromosome 3DS. BMC Genom 11:382. doi:10.1186/1471-2164-11-382

    Google Scholar 

  • Förster S, Schumann E, Baumann M, Weber WE, Pillen K (2013) Copy number variation of chromosome 5A and its association with Q gene expression, morphological aberrations, and agronomic performance of winter wheat cultivars. Theor Appl Genet 126:3049–3063

    Google Scholar 

  • Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, Wilson RE, McLean R (2009) Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genomics 281:181–191

    CAS  PubMed  Google Scholar 

  • Gadaleta A, Giancaspro A, Giove SL, Zacheo S, Mangini G, Simeone R, Signorile A, Blanco A (2009) Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat. Theor Appl Genet 118:1015–1025

    CAS  PubMed  Google Scholar 

  • Gadaleta A, Giancaspro A, Giove SL, Zacheo S, Incerti O, Simeone R, Colasuonno P, Nigro D, Valè G, Cattivelli L, Stanca M, Blanco A (2012) Development of a deletion and genetic linkage map for the 5A and 5B chromosomes of wheat (Triticum aestivum). Genome 55(6):417–427

    CAS  PubMed  Google Scholar 

  • Gegas VC, Nazari A, Griffiths S, Simmonds J, Fish L et al (2010) A genetic framework for grain size and shape variation in wheat. Plant Cell 22:1046–1056

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gil-Humanes J, Pistón F, Martín A, Barro F (2009) Comparative genomic analysis and expression of the APETALA2-like genes from barley, wheat, and barley-wheat amphiploids. BMC Plant Biol 9:66

    PubMed Central  PubMed  Google Scholar 

  • Incirli A, Akkaya MS (2001) Assessment of genetic relationships in durum wheat cultivars using AFLP markers. Genet Resour Crop Evol 48:233–238

    Google Scholar 

  • International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):286, 287, 1251788-1–1251788-11

  • Joehanes R, Nelson JC (2008) QGene 40, an extensible Java QTL-analysis platform. Bioinformatics 24(23):2788–2789

    CAS  PubMed  Google Scholar 

  • Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, Bhamidimarri S, Gonzalez-Hernandez JL, Maan SS, Kianian SF (2006) High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 173:1089–1099

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR (1993) CTRI, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72:427–441

    CAS  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breed 19:163–177. doi:10.1007/s10681-010-0128-9

    Google Scholar 

  • Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175:361–374

    PubMed Central  PubMed  Google Scholar 

  • Maccaferri M, Sanguineti MC, Corneti S, Araus Ortega JL, Ben Salem M, Bort J, DeAmbrogio E, Garcia del Moral LF, Demontis A, El-Ahmed A et al (2008) Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf) across a wide range of water availability. Genetics 178:489–511

    PubMed Central  PubMed  Google Scholar 

  • Mao XG, Zhang HY, Tian SJ, Chang XP, Xie HM, Jing RL (2010) TaSnRK24, a SNF1-type serine-threonine protein kinase of wheat (Triticum aestivum L.) confers enhanced multi-stress tolerance in Arabidopsis. J Exp Bot 61:683–696

    CAS  PubMed Central  PubMed  Google Scholar 

  • Marone D, Laidò G, Gadaleta A, Colasuonno P, Ficco DB et al (2012) A high-density consensus map of A and B wheat genomes. Theor Appl Genet 125:1619–1638. doi:10.1007/s00122-012-1939-y

    PubMed Central  PubMed  Google Scholar 

  • Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Gen Devel 15(6):589–594

    CAS  Google Scholar 

  • MSTAT-C (1983) A microcomputer program for the design, management and analysis of agronomic research experiments. Michigan State University, East Lansing

    Google Scholar 

  • Peng J, Korol AB, Fahima T, Röder MS, Ronin YI, Li YC, Nevo E (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: Genome-wide coverage, massive negative interference, and putative quasi-linkage. Genome Res 10:1509–1531

    CAS  PubMed Central  PubMed  Google Scholar 

  • Qi LL, Echalier B, Friebe B, Gill B (2004) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics 3:39–55

    Google Scholar 

  • Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo M-C, Peng J (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 14(4):7061–7088

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rustgi S, Shafqat MN, Kumar N, Baenziger PS, Ali ML, Dweikat I, Campbell BT, Gill KS (2013) Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3a: bridging gaps between QTLs and underlying genes. PLoS ONE 8(7):e70526. doi:10.1371/journalpone0070526

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. Agr Exp Stn Res Bull Univ Missouri 572:1–58

    Google Scholar 

  • Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome Manipulations and Plant Genetics. Oliver and Boyd, Edinburgh, pp 20–45

    Google Scholar 

  • Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat. In: Ramanujam S (ed) Proceedings of the 5th international wheat genetics symposium, Indian society of genetics and plant breeding, New Delhi, pp 389–407

  • Semagn K, Bjornstad A, Skinnes A, Marøy AG, Tarkegne Y et al (2006) Distribution of DArT, AFLP and SSR markers in a genetic linkage map of a double haploid hexaploid wheat population. Genome 49:545–555

    CAS  PubMed  Google Scholar 

  • Shi J, Li R, Qiu D, Jiang C, Long Y, Morgan C, BancroftI I, Zhao J, Meng J (2009) Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus. Genetics 182:851–861

    CAS  PubMed Central  PubMed  Google Scholar 

  • Shoaib A, Arabi MIE (2006) Genetic diversity among Syrian cultivated and landraces wheat revealed by AFLP markers. Genet Resour Crop Evol 53:901–906

    CAS  Google Scholar 

  • Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555

    CAS  PubMed Central  PubMed  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L). Theor Appl Genet 109:1105–1114. doi:10.1007/s00122-004-1740-7

    CAS  PubMed  Google Scholar 

  • Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, Qi L et al (2004) Microsatellite-based deletion bin system for the establishment of genetic–physical map relationships in wheat (Triticum aestivum L). Funct Integr Genomics 4:12–25

    CAS  PubMed  Google Scholar 

  • Thuillet AC, Bataillon T, Poirier S, Santoni S, David JL (2005) Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 169:1589–1599

    CAS  PubMed Central  PubMed  Google Scholar 

  • Trebbi D, Maccaferri M, Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, Vossen EAG, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123:555–569

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3, software in the calculation of genetic linkage maps. Plant research international, Wageningen. http://www.Kyazmanl/index,php/mcJoinMap. Accessed Nov 2001

  • Wang S, Wong D, Forrest K, Allen A, Chao S, Huang E, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Stephen S, Luo M-C, Dvorak J, Mather D, Appels R, Dulferos R, Brown-Guedira G, Akhunova A, Feuillet C, Salse J, Morgante M, Pozniak C, Wieseke R, Plieske 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 the high-density 90,000 SNP array. Plant Biotechnol J 12(6):787–796. doi:10.1111/pbi.12183

    CAS  PubMed  Google Scholar 

  • Wu XS, Chang XP, Jing RL (2012) Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS ONE 7(2):e31249

    CAS  PubMed Central  PubMed  Google Scholar 

  • Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92:230–244

    CAS  PubMed  Google Scholar 

  • Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153

    CAS  PubMed  Google Scholar 

  • Zhang Z, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Gill BS, Rasmussen JB, Barbe V, Faris JD, Chalhoub B (2011) Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108:18737–18742

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou C, Dong W, Han L, Wei J, Jia L, Tan Y, Zhi D, Wang Z-Y, Xia G (2012) Construction of whole genome radiation hybrid panels and map of chromosome 5A of wheat using asymmetric somatic hybridization. PLoS ONE 7(7):e40214

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Acknowledgments

The research project was supported by grants from Ministero dell’Istruzione, dell’Università e della Ricerca, projects ‘PON01_01145 ISCOCEM’, ‘PRIN-2010–2011’ and Ministero delle Politiche Agricole e Forestali project ‘Mappa 5A’.

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Authors and Affiliations

  1. Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126, Bari, Italy

    A. Gadaleta, A. Giancaspro, D. Nigro, S. L. Giove, Ornella Incerti, R. Simeone, L. Piarulli, P. Colasuonno & A. Blanco

  2. Consiglio per la Ricerca e la sperimentazione in Agricoltura, Genomics Research Centre, Via S. Protaso 302, 29017, Fiorenzuola D’Arda, PC, Italy

    G. Valè & L. Cattivelli

  3. Consiglio per la Ricerca e la sperimentazione in Agricoltura, Rice Research Unit, S.S. 11 to Torino, Km 2,5, 13100, Vercelli, Italy

    G. Valè

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  1. A. Gadaleta
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  2. A. Giancaspro
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  3. D. Nigro
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  4. S. L. Giove
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Correspondence to A. Gadaleta.

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Gadaleta, A., Giancaspro, A., Nigro, D. et al. A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits. Mol Breeding 34, 1599–1611 (2014). https://doi.org/10.1007/s11032-014-0185-1

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