Abstract
Key message
Combining biparental and multiparental connected population analyses was useful for the identification of 11 QTLs in two new genetic backgrounds of carrot resistance to Alternaria dauci and for breeding recommendations.
Abstract
Leaf blight due to the fungus Alternaria dauci is the major carrot foliar disease worldwide. Some resistance QTLs have been previously identified in one population, but the evaluation of additional genetic backgrounds with higher level of resistance would give opportunities for breeders to combine them by pyramiding. For this purpose, two segregating populations were evaluated twice across 4 years in the same environment (1) to compare the efficiency of the single vs. the connected populations approach for characterizing the new sources of carrot resistance to Alternaria dauci; (2) to evaluate the stability of QTLs over the years; and (3) to give recommendations to breeders for marker-assisted selection. Single and connected analyses were complementary; their combination allowed the detection of 11 QTLs. Connected analyses allowed the identification of common and specific QTLs among the two populations and the most favorable allele at each QTL. Important contrasts between allelic effects were observed with four and five most favorable alleles coming from the two resistant parental lines, whereas two other favorable alleles came from the susceptible parental line. While four QTLs were consistent across years, seven were detected within a single year. The heritabilities for both populations PC2 and PC3 were high (75 and 78 %, respectively), suggesting that the resistance of carrot to A. dauci was little affected by these environmental conditions, but the instability of QTL over years may be due to changing environmental conditions. The complementarity between these parental lines in terms of interesting allelic combinations is also discussed.
Similar content being viewed by others
References
Azzimonti G, Marcel TC, Robert O, Paillard S, Lannou C, Goyeau H (2014) Diversity, specificity and impact on field epidemic of QTLs involved in components of quantitative resistance in the wheat leaf rust pathosystem. Mol Breed 34:549–567
Benichou S, Dongo A, Eddine Henni D, Peltier D, Simoneau P (2009) Isolation and characterization of microsatellite markers from the phytopathogenic fungus Alternaria dauci. Mol Ecol Resour 9:390–392
Billotte N, Jourjon MF, Marseillac N, Berger A, Flori A, Asmady H, Adon B, Singh R, Nouy B, Potier F, Cheah SC, Rohde W, Ritter E, Courtois B, Charrier A, Mangin B (2010) QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.). TAG 120:1673–1687
Blanc G, Charcosset A, Mangin B, Gallais A, Moreau L (2006) Connected populations for detecting QTL and testing for epistasis, an application in maize. TAG 113:206–224
Boedo C, Berruyer R, Lecomte M, Bersihand S, Briard M, Le Clerc V, Simoneau P, Poupard P (2010) Evaluation of different methods for the characterization of carrot resistance to the alternaria leaf blight pathogen (Alternaria dauci) revealed two qualitatively different resistances. Plant Pathol 59:368–375
Boedo C, Benichou S, Berruyer R, Bersihand S, Lecomte M, Dongo A, Simoneau P, Briard M, Le Clerc V, Poupard P (2012) Evaluating aggressiveness and host range of Alternaria dauci in a controlled environment. Plant Pathol 61:63–75
Boiteux LS, Della Vecchia PT, Reifschneider FJB (1993) Heritability estimate for resistance to Alternaria dauci in carrot. Plant Breed 110:165–167
Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2007) Analysis of mixed models for S language environments. ASReml-R reference manual, Technical report, Queensland Department of Primary Industries
Cavagnaro PF, Chung SM, Manin S, Yildiz M, Ali A, Alessandro MS, Lorizzo M, Senalik DA, Simon PW (2011) Microsatellite isolation and marker development in carrot-genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genom 12:386
Charcosset A, Mangin B, Moreau L, Combes L, Jourjon MF, Gallais A (2001) Heterosis in maize investigated using connected RIL populations. Quant Genet Breed Methods Way Ahead 96:89–98
Chung CL, Longfellow J, Walsh E, Kerdieh Z, Van Esbroeck G, Balint-Kurti P, Nelson R (2010) Resistance loci affecting distinct stages of fungal pathogenesis: use of introgression lines for QTL mapping and characterization in the maize—Setosphaeria turcica pathosystem. BMC Plant Biol 10:103
Espinoza L, Huguet T, Julier B (2012) Multi-population QTL detection for aerial morphogenetic traits in the model legume Medicago truncatula. TAG 124:739–754
Farrar JJ, Pryor BM, Davis RM (2004) Alternaria diseases of carrot. Plant Dis 88:776–784
Haggard JE, Johnson EB, St. Clair DA (2014) Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11. G3: Genes|Genomes|Genetics. doi:10.1534/g3.114.014654
Jourjon MF, Jasson S, Marcel J, Ngom B, Mangin B (2005) MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics 21:128–130
Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer program for constructing genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Le Clerc V, Pawelec A, Birolleau-Touchard C, Suel A, Briard M (2009) Genetic architecture of factors underlying partial resistance to Alternaria leaf blight in carrot. TAG 118:1251–1259
Le Clerc V, Suel A, Marques Pawelec A, Huet S, Lecomte M, Poupard P, Briard M (2015) Is there variety X isolate interaction in the polygenic quantitative resistance of carrot to Alternaria dauci? Euphytica 202:235–243
Lecomte M, Hamama L, Voisine L, Gatto J, Hélesbeux JJ et al (2014) Partial resistance of carrot to Alternaria dauci correlates with in vitro cultured carrot cell resistance to fungal exudates. PLoS ONE 9(7):e101008. doi:10.1371/journal.pone.0101008
Li X, Quigg RJ, Zhou J, Xu S, Masinde G, Mohan S, Baylink DJ (2006) A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population. Genet Mol Biol 29:166–173
Liu W, Reif JC, Ranc N, Della Porta G, Würschum T (2012) Comparison of biometrical approaches for QTL detection in multiple segregating families. TAG 125:987–998
Marcel TC, Gorguet B, Truong Ta M, Kohutova Z, Vels A, Niks RE (2007) Isolate specificity of quantitative trait loci for partial resistance of barley to Puccinia hordei confirmed in mapping populations and near-isogenic lines. New Phytol 178:743–755
Nanson A (1970) L’héritabilité et le gain d’origine génétique dans quelques types d’experiences. Silvae Genet 19:113–121
Negeri AT, Coles ND, Holland JB, Balint-Kurti PJ (2011) Mapping QTL controlling southern leaf blight resistance by joint analysis of three related recombinant inbred line populations. Crop Sci 51:1571–1579
Pauly L, Flajoulot S, Garon J, Julier B, Béguier V, Barre P (2012) Detection of favorable alleles for plant height and crown rust tolerance in three connected populations of perennial ryegrass (Lolium perenne L.). TAG 124:1139–1153
Pawelec A, Dubourg C, Briard M (2006) Evaluation of carrot resistance to alternaria leaf blight in controlled environments. Plant Pathol 55:68–72
Rogers PM, Stevenson WR (2010) Aggressiveness and fungicide sensitivity of Alternaria dauci from cultivated carrot. Plant Dis 94:405–412
Schiex T, Gaspin C (1997) CARTHAGENE: constructing and joining maximum likelihood genetic maps. Proc Int Conf Intell Syst Mol Biol 5:258–267
Simon PW, Strandberg JO (1998) Diallel analysis of resistance in carrot to Alternaria leaf blight. JASHS 123:412–415
Steinhoff J, Liu W, Maurer HP, Würschum T, Friedrich HLC, Ranc N, Reif JC (2011) Multiple-line cross quantitative trait locus mapping in European elite maize. Crop Sci 51:2505–2516
Strandberg JO (1977) Spore production and dispersal of Alternaria dauci. Phytopathology 67:1262–1266
Truong HTH, Kim KT, Kim DW, Kim S, Chae Y, Park JH, Oh DG, Cho MC (2012) Identification of isolate-specific resistance QTLs to phytophtora root using an intraspecific recombinant inbred line population of pepper (Capsicum annuum). Plant Pathol 61:48–56
van Ooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. TAG 84:803–811
Vieira VJ, Dias Casali VW, Milagres JC, Cardoso AA, Regazzi AJ (1991) Heritability and genetic gain for resistance to leaf blight in carrot (Daucus carota L.) populations evaluated at different times after sowing. Revista Brazilian de Genetica 14:501–508
Würschum T (2012) Mapping QTL for agronomic traits in breeding populations. TAG 125:201–210
Acknowledgments
We are grateful to our colleagues from INEM (Remi Gardet and Jacky Granger, Agrocampus Ouest-IRHS, Angers) involved in tunnel experiments, and our colleagues involved in field testing in the Landes region [B. Peyre, L. Oger and M. Lovera (Vilmorin & Cie); P. Berthy and C. Poisblaud (HMClause)], Stéphan Plas (Invénio) for providing meteorological data and finding field for evaluations in 2014, Cédric Loi (Vilmorin & Cie, Chappes) for adjusting values, Sylvain Jasson and Brigitte Mangin (INRA, UBIA, Toulouse) for their helpful advice and interesting discussion on QTL detection with MCQTL, Laurent Crespel for his valuable contribution to the writing of the manuscript and Gail Wagman and Peter Balint-Kurti for reviewing the English. This work was financed by the French General Board for Companies (‘Création Variétale Potagère’ FCE project, 2007–2010) and by the Permanent Technical Committee of Selection (CTPS, Ministry of Agriculture).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Communicated by M. J. Havey.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Le Clerc, V., Marques, S., Suel, A. et al. QTL mapping of carrot resistance to leaf blight with connected populations: stability across years and consequences for breeding. Theor Appl Genet 128, 2177–2187 (2015). https://doi.org/10.1007/s00122-015-2576-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-015-2576-z