Tuber shape and eye depth variation in a diploid family of Andean potatoes

BMC Genetics

Merideth Bonierbale²  Rene Gomez²  Susan Thomson¹  Sathiyamoorthy Meiyalaghan¹  Elisa Salas²  Awais Khan²  Hannele Lindqvist-Kreuze² 

[1] The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand;International Potato Center (CIP), Av. La Molina 1895, Apartado 1558, Lima 12, Peru

关键词: Quantitative trait loci (QTL);    Morphological descriptors;    Eye depth;    Tuber shape;   

Others  :  1216018
DOI  :  10.1186/s12863-015-0213-0

 received in 2015-02-11, accepted in 2015-05-04,  发布年份 2015

【 摘 要 】

Background

Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation.

Results

Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified.

Conclusions

Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation.

【 授权许可】

   
2015 Lindqvist-Kreuze et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Bradshaw JE. Quantitative genetics theory for tetrasomic inheritance. In: Potato genetics. Bradshaw JE, Mackay GR, editors. CAB International, Wallingford, UK; 1994: p.71-107.
• [2]De Haan S: Potato diversity at height: multiple dimensions of farmer-driven in-situ conservation in the Andes. PhD thesis. The Netherlands: Wageningen University; 2009.
• [3]De Jong H, Burns V. Inheritance of tuber shape in cultivated diploid potatoes. Am J Potato Res. 1993; 70:267-84.
• [4]De Maine MJ, Fleming MLMH. The hybridisation of somatically chromosome-doubled dihaploid potatoes with tetraploid cultivars and the use of doubled dihaploids in genetic analysis of Solanum tuberosum. Ann Appl Biol. 1991; 119:339-47.
• [5]Jong H, Rowe PR. Genetic markers in inbred clones of cultivated diploid potatoes. Potato Res. 1972; 15:200-8.
• [6]Taylor LM. Variation patterns of parthenogenetic plants derived from “unreduced” embryo-sacs of Solanum tuberosum subspecies andigena (Juz. et Buk.) Hawkes. Theor Appl Genet. 1978; 52:241-9.
• [7]Okwuagwu CO: Phenotypic evaluation and cytological analysis of 24-chromosome hybrids for analytical breeding in potato. PhD thesis. Madison, WI: University of Wisconsin; 1981.
• [8]Masson MF: Mapping, combining abilities, heritabilities and heterosis with 4x X 2x crosses in potato. PhD thesis. Madison, WI: University of Wisconsin; 1985.
• [9]van-Eck HJ, Jacobs J, Stam P, Ton J, Stiekema WJ, Jacobsen E: Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs. Genetics 1994, 137:303–309.
• [10]Li X-Q, De Jong H, De Jong DM, De Jong WS. Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes. Theor Appl Genet. 2005; 110:1068-73.
• [11]Prashar A, Hornyik C, Young V, McLean K, Sharma S, Dale MF et al.. Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth. Theor Appl Genet. 2014; 127:2159-71.
• [12]Śliwka J, Wasilewicz-Flis I, Jakuczun H, Gebhardt C. Tagging quantitative trait loci for dormancy, tuber shape, regularity of tuber shape, eye depth and flesh colour in diploid potato originated from six Solanum species. Plant Breed. 2008; 127:49-55.
• [13]Cuesta Subía X: Potato quality traits: variation and genetics in Ecuadorian potato landraces. PhD thesis. The Netherlands: Wageningen University; 2013.
• [14]Von Rathlef H, Siebeneick H. Über Einige Kreuzungen Eruanischer Sorten von Solanum andigenum Juz. et Buk. Mit Richters Jubel und Die Genetik von Schalenfarbe, Knollenfarbe, Fleischfarbe, Blütenfarbe und Knollenform Bei Der Kartoffel (On some crosses of Peruvian sorts of Solanum andigenum Juz. et Buk. with Richters Jubel and the genetics of colour of skin, tuber, flesh and flower colour and of tuber shape in the potato). Genetica. 1934; 16:153-76.
• [15]Maris B. The modifiability of characters important in potato breeding. Euphytica. 1966; 15:18-31.
• [16]Ortiz R, Huaman Z: Inheritance of morphological and tuber characteristics. In: Potato genetics. Edited by Bradshaw JE, Mackay GR. Wallingford, UK: CAB International; 1994: 263–283.
• [17]Bonierbale M, Amoros W, Simon R: P4: towards public precision phenotyping of potato (P4). In: The 7th Solanaceae Conference: September 5–9 2010; Dundee, Scotland.
• [18]Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS et al.: Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3 2013, 3:2031–2047.
• [19]Paz MM, Veilleux RE. Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breed. 1999; 118:53-7.
• [20]Spooner DM, Nunez J, Trujillo G, Herrera MD, Guzman F, Ghislain M. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci U S A. 2007; 104:19398-403.
• [21]Ovchinnikova A, Krylova E, Gavrilenko T, Smekalova T, Zhuk M, Knapp S et al.. Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae). Bot J Linn Soc. 2011; 165:107-55.
• [22]Khan A, Bonierbale M, Amoros W, Lindqvist-Kreuze H, Munive S, Salas E, et al. DMDD, a bi-parental resource population, holds great potential as a genetic discovery platform for complex traits in potato. China. 2013;2013.
• [23]Khan MA, Saravia D, Munive S, Lozano F, Farfan E, Eyzaguirre R, et al. Multiple QTLs linked toa agro-morphological and physiological traits related to drought tolerance in potato. Plant Mol Biol Rep. 2014;1–13.
• [24]Bradshaw J, Hackett C, Pande B, Waugh R, Bryan G. QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet. 2008; 116:193-211.
• [25]D’hoop B, Paulo M, Mank R, van Eck H, van Eeuwijk F. Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica. 2008; 161:47-60.
• [26]D’hoop B, Keizer PC, Paulo MJ, Visser RF, van Eeuwijk F, van Eck H. Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis. Theor Appl Genet. 2014; 127:731-48.
• [27]Gopal J, Kumar V, Pandey SK, Kumar R, Pande PC, Singh SV. Morphological descriptors for DUS testing of potato varieties. Potato J. 2007; 34:59-60.
• [28]Genome sequence and analysis of the tuber crop potato. Nature. 2011; 475:189-95.
• [29]Gehring WJ, Affolter M, Burglin T. Homeodomain proteins. Annu Rev Biochem. 1994; 63:487-526.
• [30]Bürglin TR. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 1997; 25:4173-80.
• [31]Banerjee AK, Lin T, Hannapel DJ. Untranslated regions of a mobile transcript mediate RNA metabolism. Plant Physiol. 2009; 151:1831-43.
• [32]Chen H, Rosin FM, Prat S, Hannapel DJ. Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation. Plant Physiol. 2003; 132:1391-404.
• [33]Rosin FM, Hart JK, Horner HT, Davies PJ, Hannapel DJ. Overexpression of a knotted-like homeobox gene of potato alters vegetative development by decreasing gibberellin accumulation. Plant Physiol. 2003; 132:106-17.
• [34]Chen H, Banerjee AK, Hannapel DJ. The tandem complex of BEL and KNOX partners is required for transcriptional repression of ga20ox1. Plant J. 2004; 38:276-84.
• [35]Roumeliotis E, Kloosterman B, Oortwijn M, Lange T, Visser RGF, Bachem CWB. Down regulation of StGA3ox genes in potato results in altered GA content and affect plant and tuber growth characteristics. J Plant Physiol. 2013; 170:1228-34.
• [36]Sharma P, Lin T, Grandellis C, Yu M, Hannapel DJ. The BEL1-like family of transcription factors in potato. J Exp Bot. 2014; 65:709-23.
• [37]Cosgrove DJ. Loosening of plant cell walls by expansins. Nature. 2000; 407:321-6.
• [38]Jung J, O’Donoghue EM, Dijkwel PP, Brummell DA. Expression of multiple expansin genes is associated with cell expansion in potato organs. Plant Sci. 2010; 179:77-85.
• [39]Lamport DTA, Kieliszewski MJ, Chen Y, Cannon MC. Role of the extensin superfamily in primary cell wall architecture. Plant Physiol. 2011; 156:11-9.
• [40]Showalter AM. Structure and function of plant cell wall proteins. Plant Cell. 1993; 5:9-23.
• [41]Neubauer JD, Lulai EC, Thompson AL, Suttle JC, Bolton MD. Wounding coordinately induces cell wall protein, cell cycle and pectin methyl esterase genes involved in tuber closing layer and wound periderm development. J Plant Physiol. 2012; 169:586-95.
• [42]Orfila C, Degan F, Jørgensen B, Scheller H, Ray P, Ulvskov P. Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties. Planta. 2012; 236:185-96.
• [43]Oxenbøll Sørensen S, Pauly M, Bush M, Skjøt M, McCann MC, Borkhardt B et al.. Pectin engineering: modification of potato pectin by in vivo expression of an endo-1,4-β-d-galactanase. Proc Natl Acad Sci U S A. 2000; 97:7639-44.
• [44]Ross HA, Wright KM, McDougall GJ, Roberts AG, Chapman SN, Morris WL et al.. Potato tuber pectin structure is influenced by pectin methyl esterase activity and impacts on cooked potato texture. J Exp Bot. 2010; 62:371-81.
• [45]Licausi F, Giorgi F, Zenoni S, Osti F, Pezzotti M, Perata P. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics. 2010; 11:719. BioMed Central Full Text
• [46]Nakano T, Suzuki K, Fujimura T, Shinshi H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 2006; 140:411-32.
• [47]Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T et al.. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol. 2011; 52:344-60.
• [48]Patterson HD, Williams ER. A new class of resolvable incomplete block designs. Biometrika. 1976; 63:83-92.
• [49]R: A language and environment for statistical computing [http://www.R-project.org]
• [50]Van Ooijen JW. JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Wageningen, The Netherlands, Kyazma BV; 2006.
• [51]Van Ooijen JW. MapQTL 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Wageningen, The Netherlands, Kyazma BV; 2009.