Cải thiện hiệu quả giống khoai tây bằng cách sử dụng di truyền phân tử và di truyền định lượng

Theoretical and Applied Genetics - Tập 127 - Trang 2279-2292 - 2014
Anthony T. Slater1,2, Noel O. I. Cogan1, Benjamin J. Hayes1,2, Lee Schultz1, M. Finlay B. Dale3, Glenn J. Bryan3, John W. Forster1,2
1Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Melbourne, Australia
2La Trobe University, Melbourne, Australia
3James Hutton Institute, Dundee, Scotland, UK

Tóm tắt

Khoai tây có tính đa hợp gen cao và việc lai giống các phẩm chất ưu việt là một thách thức, nhưng việc sử dụng kết hợp giữa lựa chọn dấu hiệu phân tử (MAS) và giá trị giống ước tính (EBVs) có thể tăng tốc độ gia tăng di truyền. Khoai tây được trồng có tính đa hợp gen cao do bản chất giao phối giữa các giống, và gặp phải tình trạng suy thoái do tự thụ phấn nghiêm trọng. Các giống khoai tây hiện đại cũng thể hiện kiểu di truyền tetrasomic. Do sự đa dạng di truyền này, số lượng lớn các đặc điểm mục tiêu và những yêu cầu cụ thể của các giống thương mại, việc lai giống khoai tây gặp nhiều khó khăn. Chiến lược lai giống thông thường áp dụng lựa chọn lặp lại theo kiểu hình qua một số thế hệ, một quy trình có thể mất hơn 10 năm. Gần đây, những tiến bộ lớn trong di truyền và sinh học phân tử đã cung cấp cho các nhà lai tạo những công cụ phân tử để tăng tốc độ gia tăng cho một số đặc điểm. Lựa chọn hỗ trợ dấu hiệu (MAS) có thể được sử dụng hiệu quả để xác định các gen chính và vị trí đặc điểm định lượng có ảnh hưởng lớn. Cũng có một số đặc điểm phức tạp được quan tâm, chẳng hạn như năng suất, chịu ảnh hưởng bởi nhiều gen có ảnh hưởng nhỏ, trong khi việc triển khai MAS sẽ gặp khó khăn. Kiểm tra con cháu và việc sử dụng phả hệ trong phân tích có thể cung cấp nhận diện hiệu quả các yếu tố di truyền ưu việt mà hỗ trợ những đặc điểm phức tạp này. Gần đây, đã có nhiều nghiên cứu cho thấy các giá trị giống ước tính (EBVs) có thể được phát triển cho các đặc điểm khoai tây phức tạp. Việc sử dụng kết hợp giữa MAS và EBVs cho các đặc điểm đơn giản cũng như phức tạp có thể dẫn đến việc giảm đáng kể thời gian của chu kỳ giống để xác định các nguồn giống ưu việt.

Từ khóa

#Khoai tây #di truyền phân tử #di truyền định lượng #lựa chọn hỗ trợ dấu hiệu #giá trị giống ước tính

Tài liệu tham khảo

Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560 Andolfo G, Sanseverino W, Rombauts S, Van de Peer Y, Bradeen JM, Carputo D, Frusciante L, Ercolano MR (2013) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol 197:223–237 Anithakumari AM, Dolstra O, Vosman B, Visser RGF, van der Linden CG (2011) In vitro screening and QTL analysis for drought tolerance in diploid potato. Euphytica 181:357–369 Bakker E, Achenbach U, Bakker J, Vliet J, Peleman J, Segers B, Heijden S, Linde P, Graveland R, Hutten R, Eck H, Coppoolse E, Vossen E, Bakker J, Goverse A (2004) A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis. Theor Appl Genet 109:146–152 Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Ml Muskens, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A (2011) A genome-wide genetic map of NB-LRR disease resistance loci in potato. Theor Appl Genet 123:493–508 Baldwin SJ, Dodds KG, Auvray B, Genet RA, Macknight RC, Jacobs JME (2011) Association mapping of cold-induced sweetening in potato using historical phenotypic data. Ann Appl Biol 158:248–256 Ballvora A, Hesselbach J, Niewöhner J, Leister D, Salamini F, Gebhardt C (1995) Marker enrichment and high-resolution map of the segment of potato chromosome VII harbouring the nematode resistance gene Gro1. Mol Gen Genet 249:82–90 Barone A (2004) Molecular marker-assisted selection for potato breeding. Am J Potato Res 81:111–117 Barone A, Ritter E, Schachtschabel U, Debener T, Salamini F, Gebhardt C (1990) Localization by restriction fragment length polymorphism mapping in potato of a major dominant gene conferring resistance to the potato cyst nematode Globodera rostochiensis. Mol Gen Genet 224:177–182 Barrell PJ, Meiyalaghan S, Jacobs JME, Conner AJ (2013) Applications of biotechnology and genomics in potato improvement. Plant Biotechnol J 11:907–920 Bendahmane A, Kanyuka K, Baulcombe D (1997) High-resolution genetical and physical mapping of the Rx gene for extreme resistance to potato virus X in tetraploid potato. Theor Appl Genet 95:153–162 Biryukova V, Zhuravlev A, Abrosimova S, Kostina L, Khromova L, Shmyglya I, Morozova N, Kirsanova S (2008) Use of molecular markers of potato golden nematode resistance genes H1 and GRO1. Russ Agric Sci 34:365–368 Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103 Bradshaw J (2007a) The canon of potato science: four tetrasomic inheritance. Potato Res 50:219–222 Bradshaw JE (2007b) Potato-breeding strategy. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor MA, Ross HA (eds) Potato biology and biotechnology: advances and perspectives. Elsevier, Amsterdam, pp 157–177 Bradshaw JE, Mackay GR (1994) Breeding strategies for clonally propagated potatoes. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. Cab International, Wallingford, pp 467–497 Bradshaw JE, Dale MFB, Mackay GR (2003) Use of mid-parent values and progeny tests to increase the efficiency of potato breeding for combined processing quality and disease and pest resistance. Theor Appl Genet 107:36–42 Bradshaw JE, Bryan GJ, Ramsay G (2006) Genetic resources (including wild and cultivated Solanum species) and progress in their utilisation in potato breeding. Potato Res 49:49–65 Bradshaw JE, Hackett CA, Pande B, Waugh R, Bryan GJ (2008) QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet 116:193–211 Bradshaw JE, Dale MFB, Mackay GR (2009) Improving the yield, processing quality and disease and pest resistance of potatoes by genotypic recurrent selection. Euphytica 170:215–227 Brigneti G, Garcia-Mas J, Baulcombe DC (1997) Molecular mapping of the potato virus Y resistance gene Ry sto in potato. Theor Appl Genet 94:198–203 Brown CR (1993) Outcrossing rate in cultivated autotetraploid potato. Am Potato J 70:725–734 Celis-Gamboa C, Struik PC, Jacobsen E, Visser RGF (2003) Temporal dynamics of tuber formation and related processes in a crossing population of potato (Solanum tuberosum). Ann Appl Biol 143:175–186 Chen X, Salamini F, Gebhardt C (2001) A potato molecular-function map for carbohydrate metabolism and transport. Theor Appl Genet 102:284–295 Cockerham G (1970) Genetical studies on resistance to potato viruses X and Y. Heredity 25:309–348 Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B 363:557–572 Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196 Colton LM, Groza HI, Wielgus SM, Jiang J (2006) Marker-assisted selection for the broad-spectrum potato late blight resistance conferred by gene RB derived from a wild potato species. Crop Sci 46:589–594 Dale MFB, Mackay GR (1994) Inheritance of table and processing quality. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, UK, pp 285–315 Dalla Rizza M, Vilaró F, Torres D, Maeso D (2006) Detection of PVY extreme resistance genes in potato germplasm from the Uruguayan breeding program. Am J Potato Res 83:297–304 de Jong H (1981) Inheritance of russeting in cultivated diploid potatoes. Potato Res 24:309–313 De Jong WS, De Jong DM, Bodis M (2003) A fluorogenic 5’ nuclease (TaqMan) assay to assess dosage of a marker tightly linked to red skin color in autotetraploid potato. Theor Appl Genet 107:1384–1390 De Koeyer D, Douglass K, Murphy A, Whitney S, Nolan L, Song Y, de Jong W (2010) Application of high-resolution DNA melting for genotyping and variant scanning of diploid and autotetraploid potato. Mol Breed 25:67–90 De Koeyer D, Chen H, Gustafson V (2011) Molecular breeding for potato improvement. In: Bradeen J, Kole C (eds) Genetics, genomics and breeding of potato. Science Publishers, Enfield, New Hampshire, pp 41–67 D’Hoop BB, Paulo MJ, Mank RA, Van Eck HJ, Van Eeuwijk FA (2008) Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica 161:47–60 D’hoop B, Keizer PC, Paulo MJ, Visser RF, Eeuwijk F, Eck H (2014) Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis. Theor Appl Genet 127:731–748 Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C, Jiang J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 101:1001–1007 Donnelly DJ, Prasher SO, Patel RM (2007) Towards the development of salt-tolerant potato. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor M, Ross H (eds) Potato biology and biotechnology, advances and perspectives. Elsevier, Amsterdam, pp 415–437 Dreher K, Khairallah M, Ribaut J-M, Morris M (2003) Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT. Mol Breed 11:221–234 Falconer DS, Mackay TFC (1996) Introduction to Quantitative Genetics, 4th edn. Pearson, Prentice Hall, Harlow, England Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7:e36347 Finkers-Tomczak A, Bakker E, de Boer J, van der Vossen E, Achenbach U, Golas T, Suryaningrat S, Smant G, Bakker J, Goverse A (2011) Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). Theor Appl Genet 122:595–608 Flis B, Hennig J, Strzelczyk-Zyta D, Gebhardt C, Marczewski W (2005) The Ry-f sto gene from Solanum stoloniferum for extreme resistant to Potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122718 in PVY resistant potato cultivars. Mol Breed 15:95–101 Gebhardt C (2013) Bridging the gap between genome analysis and precision breeding in potato. Trends Genet 29:248–256 Gebhardt C, Valkonen JPT (2001) Organization of genes controlling disease resistance in the potato genome. Ann Rev Phytopathol 39:79–102 Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75 Gebhardt C, Ritter E, Barone A, Debener T, Walkemeier B, Schachtschabel U, Kaufmann H, Thompson RD, Bonierbale MW, Ganal MW, Tanksley SD, Salamini F (1991) RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor Appl Genet 83:49–57 Gebhardt C, Mugniery D, Ritter E, Salamini F, Bonnel E (1993) Identification of RFLP markers closely linked to the H1 gene conferring resistance to Globodera rostochiensis in potato. Theor Appl Genet 85:541–544 Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13:93–102 Gebhardt C, Lörz H, Wenzel G (2005) Potato genetics: Molecular maps and more. Molecular marker systems in plant breeding and crop improvement, Springer Berlin Heidelberg, pp 215–227 Gebhardt C, Bellin D, Henselewski H, Lehmann W, Schwarzfischer J, Valkonen J (2006) Marker-assisted combination of major genes for pathogen resistance in potato. Theor Appl Genet 112:1458–1464 Grube RC, Radwanski ER, Jahn M (2000) Comparative genetics of disease resistance within the solanaceae. Genetics 155:873–887 Hackett CA, Luo ZW (2003) TetraploidMap: construction of a linkage map in autotetraploid species. J Hered 94:358–359 Hackett CA, Milne I, Bradshaw JE, Luo Z (2007) TetraploidMap for Windows: Linkage map construction and QTL mapping in autotetraploid species. J Hered 98:727–729 Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8:e63939 Hämäläinen JH, Watanabe KN, Valkonen JPT, Arihara A, Plaisted RL, Pehu E, Miller L, Slack SA (1997) Mapping and marker-assisted selection for a gene for extreme resistance to potato virus Y. Theor Appl Genet 94:192–197 Hämäläinen JH, Sorri VA, Watanabe KN, Gebhardt C, Valkonen JPT (1998) Molecular examination of a chromosome region that controls resistance to potato Y and A potyviruses in potato. Theor Appl Genet 96:1036–1043 Hamilton J, Hansey C, Whitty B, Stoffel K, Massa A, Van Deynze A, De Jong W, Douches D, Buell CR (2011) Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genom 12:302 Hanneman REJ (1989) The potato germplasm resource. Am J Potato Res 66:655–667 Hawkes JG (1990) The potato; evolution, biodiversity and genetic resources. Belhaven Press, London Hawkes JG (1994) Origins of cultivated potatoes and species relationships. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. Cab International, Wallingford, pp 3–42 Hayes BJ, Cogan NOI, Pembleton LW, Goddard ME, Wang J, Spangenberg GC, Forster JW (2013) Prospects for genomic selection in forage plant species. Plant Breed 132:133–143 Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12 Heldák J, Bežo M, Štefúnová V, Galliková A (2007) Selection of DNA markers for detection of extreme resistance to potato virus Y in tetraploid potato (Solanum tuberosum L.) F1 progenies. Czech J Genet Plant Breed 43:125–134 Henderson CR (1984) Applications of Linear Models in Animal Breeding. University of Guelph, Guelph Howard HW (1970) The Genetics of the Potato. Logos Press, London Jacobs JME, Eck HJ, Horsman K, Arens PFP, Verkerk-Bakker B, Jacobsen E, Pereira A, Stiekema WJ (1996) Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei. Mol Breed 2:51–60 Jacobs M, Vosman B, Vleeshouwers V, Visser R, Henken B, van den Berg R (2010) A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map. Theor Appl Genet 120:785–796 Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177 Jansky S (2009) Breeding, genetics and cultivar development. In: Singh J, Kaur L (eds) Advances in potato chemistry and technology. Academic Press, New York, pp 27–62 Jupe F, Pritchard L, Etherington G, MacKenzie K, Cock P, Wright F, Sharma SK, Bolser D, Bryan G, Jones J, Hein I (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genom 13:75 Jupe F, Witek K, Verweij W, Śliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JDG (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J 76:530–544 Kasai K, Morikawa Y, Sorri VA, Valkonen JP, Gebhardt C, Watanabe KN (2000) Development of SCAR markers to the PVY resistance gene Ry adg based on a common feature of plant disease resistance genes. Genome 43:1–8 Kawchuk L, Lynch D, Yada R, Bizimungu B, Lynn J (2008) Marker assisted selection of potato clones that process with light chip color. Am J Potato Res 85:227–231 Kearsey MJ, Pooni HS (1998) The genetical analysis of quantitative traits. Stanley Thornes Ltd, Cheltenham Kloosterman B, Abelenda JA, Gomez MdMC, Oortwijn M, de Boer JM, Kowitwanich K, Horvath BM, van Eck HJ, Smaczniak C, Prat S, Visser RGF, Bachem CWB (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495:246–250 Kuchel H, Ye G, Fox R, Jefferies S (2005) Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy. Mol Breed 16:67–78 Leister D, Ballvora A, Salamini F, Gebhardt C (1996) A PCR-based approach for isolating pathogen resistance genes from potato with potential for wide application in plants. Nat Genet 14:421–429 Li X-Q, De Jong H, De Jong DM, De Jong WS (2005) Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes. Theor Appl Genet 110:1068–1073 Li L, Paulo M-J, Strahwald J, Lübeck J, Hofferbert H-R, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, Gebhardt C (2008a) Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet 116:1167–1181 Li XQ, Griffiths R, De Koeyer D, Rothwell C, Gustafson V, Regan S, Flinn B (2008b) Functional genomic resources for potato. Can J Plant Sci 88:573–581 Luo ZW, Zhang RM, Kearsey MJ (2004) Theoretical basis for genetic linkage analysis in autotetraploid species. Proc Natl Acad Sci USA 101:7040–7045 Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ (2006) Constructing genetic linkage maps under a tetrasomic model. Genetics 172:2635–2645 Marczewski W, Flis B, Syller J, Schäfer-Pregl R, Gebhardt C (2001) A major quantitative trait locus for resistance to Potato leafroll virus is located in a resistance hotspot on potato chromosome XI and is tightly linked to N-gene-like markers. Mol Plant-Microbe Interact 14:1420–1425 Marczewski W, Hennig J, Gebhardt C (2002) The Potato virus S resistance gene Ns maps to potato chromosome VIII. Theor Appl Genet 105:564–567 Marczewski W, Flis B, Syller J, Strzelczyk-Zyta D, Hennig J, Gebhardt C (2004) Two allelic or tightly linked genetic factors at the PLRV.4 locus on potato chromosome XI control resistance to potato leafroll virus accumulation. Theor Appl Genet 109:1604–1609 Marczewski W, Strzelczyk-Żyta D, Hennig J, Witek K, Gebhardt C (2006) Potato chromosomes IX and XI carry genes for resistance to potato virus M. Theor Appl Genet 112:1232–1238 Maris B (1986) The effect of seed tuber weight on characters in the first and the second clonal generation of potato populations. Euphytica 35:465–482 Maris B (1988) Correlations within and between characters between and within generations as a measure for the early generation selection in potato breeding. Euphytica 37:205–224 Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829 Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245 Milbourne D, Bradshaw JE, Hackett CA (2008) Molecular mapping and breeding in polyploid crop plants. In: Kole C, Abbott AG (eds) Principles and practices of plant genomics. Science Publishers, Enfield, pp 355–394 Moloney C, Griffin D, Jones P, Bryan G, McLean K, Bradshaw J, Milbourne D (2010) Development of diagnostic markers for use in breeding potatoes resistant to Globodera pallida pathotype Pa2/3 using germplasm derived from Solanum tuberosum ssp. andigena CPC 2802. Theor Appl Genet 120:679–689 Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977 Morris M, Dreher K, Ribaut J-M, Khairallah M (2003) Money matters (II): costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection. Mol Breed 11:235–247 Naess SK, Bradeen JM, Wielgus SM, Haberlach GT, McGrath JM, Helgeson JP (2000) Resistance to late blight in Solanum bulbocastanum is mapped to chromosome 8. Theor Appl Genet 101:697–704 Ortega F, Lopez-Vizcon C (2012) Application of molecular marker-assisted selection (MAS) for disease resistance in a practical potato breeding programme. Potato Res 55:1–13 Ortiz R, Huaman Z (1994) Inheritance of morphological and tuber characteristics. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, UK, pp 263–283 Ottoman R, Hane D, Brown C, Yilma S, James S, Mosley A, Crosslin J, Vales M (2009) Validation and implementation of marker-assisted selection (MAS) for PVY resistance (Ry adg gene) in a tetraploid potato breeding program. Am J Potato Res 86:304–314 Oud JSN, Schneiders H, Kool AJ, van Grinsven MQJM (1995) Breeding of transgenic orange Petunia hybrida varieties. Euphytica 84:175–181 Ovchinnikova A, Krylova E, Gavrilenko T, Smekalova T, Zhuk M, Knapp S, Spooner DM (2011) Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae). Bot J Linn Soc 165:107–155 Paal J, Henselewski H, Muth J, Meksem K, Menéndez CM, Salamini F, Ballvora A, Gebhardt C (2004) Molecular cloning of the potato Gro1-4 gene conferring resistance to pathotype Ro1 of the root cyst nematode Globodera rostochiensis, based on a candidate gene approach. Plant J 38:285–297 Pavek JJ, Corsini DL (1994) Inheritance of resistance to warm-growing-season fungal diseases. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, pp 403–409 Peters SA, Bargsten JW, Szinay D, van de Belt J, Visser RGF, Bai Y, de Jong H (2012) Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper. Plant J 71:602–614 Phillips MS (1994) Inheritance of resistance to nematodes. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, pp 319–337 Pineda O, Bonierbale MW, Plaisted RL, Brodie BB, Tanksley SD (1993) Identification of RFLP markers linked to the H1 gene conferring resistance to the potato cyst nematode Globodera rostochiensis. Genome 36:152–156 Plaisted R, Hoopes R (1989) The past record and future prospects for the use of exotic potato germplasm. Am J Potato Res 66:603–627 Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195 Quirin EA, Mann H, Meyer RS, Traini A, Chiusano ML, Litt A, Bradeen JM (2012) Evolutionary meta-analysis of solanaceous resistance gene and Solanum resistance gene analog sequences and a practical framework for cross-species comparisons. Mol Plant-Microbe Interact 25:603–612 Ribaut J-M, Hoisington D (1998) Marker-assisted selection: new tools and strategies. Trends Plant Sci 3:236–239 Ross H (1986) Potato breeding—problems and perspectives. In: Parey P (ed) Advances in Plant Breeding, Verlag Berlin Sattarzadeh A, Achenbach U, Lübeck J, Strahwald J, Tacke E, Hofferbert H-R, Rothsteyn T, Gebhardt C (2006) Single nucleotide polymorphism (SNP) genotyping as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida pathotype Pa2/3. Mol Breed 18:301–312 Schmidt MA, Martin GS, Artelt BJ, Parrott WA (2004) Increased transgene expression by breeding and selection in white clover. Crop Sci 44:963–967 Schultz L, Cogan NOI, Forster JW, Slater AT (2010) Evaluation and optimisation of the TG689 marker linked to PCN resistance. Potato Res 53:247–248 Schultz L, Cogan NOI, McLean K, Dale MFB, Bryan GJ, Forster JW, Slater AT (2012) Evaluation and implementation of a potential diagnostic molecular marker for H1-conferred potato cyst nematode resistance in potato (Solanum tuberosum L.). Plant Breed 131:315–321 Simko I, Costanzo S, Haynes KG, Christ BJ, Jones RW (2004) Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor Appl Genet 108:217–224 Simko I, Jansky S, Stephenson S, Spooner DM (2007) Genetics of resistance to pests and diseases. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor MA, Ross HA (eds) Potato biology and biotechnology: advances and perspectives. Elsevier, Amsterdam, pp 117–155 Simmonds NW (1964) The genetics of seed and tuber dormancy in the cultivated potatoes. Heredity 19:489–504 Slater AT, Cogan NOI, Forster JW (2013) Cost analysis of the application of marker-assisted selection in potato breeding. Mol Breed 32:299–310 Slater AT, Wilson GM, Cogan NOI, Forster JW, Hayes BJ (2014) Improving the analysis of low heritability complex traits for enhanced genetic gain in potato. Theor Appl Genet 127:809–820 Song YS, Schwarzfischer A (2008) Development of STS markers for selection of extreme resistance (Ry sto ) to PVY and maternal pedigree analysis of extremely resistant cultivars. Am J Potato Res 85:159–170 Song YS, Hepting L, Schweizer G, Hartl L, Wenzel G, Schwarzfischer A (2005) Mapping of extreme resistance to PVY (Ry sto ) on chromosome XII using anther-culture-derived primary dihaploid potato lines. Theor Appl Genet 111:879–887 Sorri VA, Watanabe KN, Valkonen JPT (1999) Predicted kinase-3a motif of a resistance gene analogue as a unique marker for virus resistance. Theor Appl Genet 99:164–170 Spooner DM, Bamberg JB (1994) Potato genetic resources: Sources of resistance and systematics. Am Potato J 71:325–337 Spooner DM, Hijmans RJ (2001) Potato systematics and germplasm collecting, 1989–2000. Am J Potato Res 78:237–268 Spooner DM, Nunez J, Trujillo G, del Rosario HM, Guzman F, Ghislain M (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci USA 104:19398–19403 Spooner DM, Ames M, Fajardo D, Rodriguez F (2009) Species boundaries and interrelationships of Solanum sect. Petota (wild and cultivated potatoes) are drastically altered as a result of PBI-funded research. Botany & Mycology 2009 Annual Meeting Stein J, Quarin CL, Martinez EJ, Pessino SC, Ortiz JPA (2004) Tetraploid races of Paspalum notatum show polysomic inheritance and preferential chromosome pairing around the apospory-controlling locus. Theor Appl Genet 109:186–191 Swaminathan MS, Howard HW (1953) The cytology and genetics of the potato (Solanum tuberosum) and related species. Bibliogr Genet 16:1–192 Swiezynski KM (1994) Inheritance of resistance to viruses. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, pp 339–363 Tameling W, Takken F (2008) Resistance proteins: scouts of the plant innate immune system. Eur J Plant Pathol 121:243–255 Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160 Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641 Toxopeus HJ, Huijsman CA (1953) Breeding for resistance to potato root eelworm. Euphytica 2:180–186 Uitdewilligen JGAML, Wolters A-MA, D’hoop BB, Borm TJA, Visser RGF, van Eck HJ (2013) A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 8:e62355 Umaerus V, Umaerus M (1994) Inheritance of resistance to late blight. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, UK, pp 365–401 Valkonen JPT, Wiegmann K, Hämäläinen JH, Marczewski W, Watanabe KN (2008) Evidence for utility of the same PCR-based markers for selection of extreme resistance to Potato virus Y controlled by Ry sto of Solanum stoloniferum derived from different sources. Ann Appl Biol 152:121–130 Van Eck HJ (2007) Genetics of morphological and tuber traits. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor MA, Ross HA (eds) Potato biology and biotechnology: advances and perspectives. Elsevier, Amsterdam, pp 91–115 Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, De Jong W, Van Koert P, Lefebvre V, Milbourne D, Ritter E, Rouppe Van Der Voort JNAM, Rousselle-Bourgeois F, Van Vliet J, Waugh R, Visser RGF, Bakker J, Van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087 Van Sanford D, Anderson J, Campbell K, Costa J, Cregan P, Griffey C, Hayes P, Ward R (2001) Discovery and deployment of molecular markers linked to fusarium head blight resistance: An integrated system for wheat and barley. Crop Sci 41:638–644 Van Vleck LD, Westell RA, Schneider JC (1986) Genetic change in milk yield estimated from simultaneous genetic evaluation of bulls and cows. J Dairy Sci 69:2963–2965 Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630 Vos J, Haverkort AJ (2007) Water availability and potato crop performance. In: Vreugdenhil D, Bradshaw J, Gebhardt C, Govers F, MacKerron DKL, Taylor M, Ross H (eds) Potato biology and biotechnology, advances and perspectives. Elsevier, Amsterdam, pp 333–351 Wallace AJ, Callow RS (1995) Meiotic variation in an intergenomic autopolyploid series. II. Pairing behaviour. Genome 38:133–139 Wastie RL (1991) Resistance to powdery scab of seedling progenies of Solanum tuberosum. Potato Res 34:249–252 Wastie RL (1994) Inheritance of fungal diseases of tubers. In: Bradshaw JE, Mackay GR (eds) Potato Genetics. CAB International, Wallingford, pp 411–427 Wastie RL, Caligari PDS, Stewart HE, Mackay GR (1988) Assessing the resistance to gangrene of progenies of potato (Solanum tuberosum L.) from parents differing in susceptibility. Potato Res 31:355–365 Whitworth J, Novy R, Hall D, Crosslin J, Brown C (2009) Characterization of broad spectrum potato virus Y resistance in a Solanum tuberosum ssp. andigena-derived population and select breeding clones using molecular markers, grafting, and field inoculations. Am J Potato Res 86:286–296 Witek K, Strzelczyk-Żyta D, Hennig J, Marczewski W (2006) A multiplex PCR approach to simultaneously genotype potato towards the resistance alleles Ry-f sto and Ns. Mol Breed 18:273–275 Xu Y, Lu Y, Xie C, Gao S, Wan J, Prasanna B (2012) Whole-genome strategies for marker-assisted plant breeding. Mol Breed 29:833–854 Yu K, Park SJ, Poysa V (2000) Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics. Plant Breed 119:411–415 Zhang L-H, Mojtahedi H, Kuang H, Baker B, Brown CR (2007) Marker-assisted selection of columbia root-knot nematode resistance introgressed from Solanum bulbocastanum. Crop Sci 47:2021–2026 Zhang Y, Jung C, De Jong W (2009) Genetic analysis of pigmented tuber flesh in potato. Theor Appl Genet 119:143–150