Quantitative trait loci (QTL) mapping of blush skin and flowering time in a European pear (Pyrus communis) progeny of ‘Flamingo’ × ‘Abate Fetel’
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Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored phenotypically over three seasons and flowering time was scored over two seasons. A total of 160 loci from 137 simple sequence repeat (SSR) markers were scored in the progeny and used to construct parental genetic linkage maps. Quantitative trait loci (QTL) analysis revealed two QTLs for blush skin, a major QTL on linkage group (LG) 5 in ‘Flamingo’, and a major QTL on LG9 in ‘Abate Fetel’. Two SSR markers, NB101a and SAmsCO865954, were closely linked with the major QTL on LG5 in ‘Flamingo’, with alleles 139 bp and 462 bp in coupling, respectively. These markers were present in approximately 90% of the seedlings scored as good blush (class 4) based on the average data set. These two markers were used to genotype other pear accessions to validate the QTL on LG5 with the view of marker-assisted selection. Two candidate genes, MYB86 and UDP-glucosyl transferase, were associated with the QTL on LG5 and MYB21 and MYB39 were associated with the QTL on LG9. QTL analysis for flowering time revealed a major QTL located on LG9 in both parents. Marker GD142 with allele 161 bp from ‘Flamingo’ was present in approximately 88% of the seedlings that flowered earlier than either parent, based on the average data set. The QTLs and linked markers will facilitate marker-assisted selection for the improvement of these complex traits.
KeywordsEuropean pear Blush skin Flowering time Candidate genes SSRs QTLs
SM Ntladi thanks the National Research Foundation (NRF) for a Professional Development Programme (PDP) PhD studentship. Other costs were funded by the NRF Technology and Human Resource for Industry Programme (THRIP) (grants TP2011062500004 and TP1407249871) and the Agricultural Research Council (ARC). Mardé Booyse is thanked for statistical analysis of the phenotypic data. Justin Lashbrooke and Fabrizio Costa are thanked for analysis of anthocyanin-related genes. Kashief Soeker is acknowledged for screening of the associated markers in 25 pear accessions.
Data archiving statement
PCR multiplexes made up of pear and apple SSR primer pairs used to genotype the ‘Flamingo’ × ‘Abate Fetel’ pear progeny for mapping are provided in Table S1.
Blush skin data sets used to detect QTLs in the ‘Flamingo’ × ‘Abate Fetel’ progeny are provided in Table S2.
Flowering time data sets (Julian date of 80% full bloom) used to detect QTLs in the ‘Flamingo’ × ‘Abate Fetel’ progeny are provided in Table S3.
Information on markers not used for mapping in the progeny of ‘Flamingo’ × ‘Abate Fetel’ is provided in Table S4.
Genotypic data for the SSR markers in the pear progeny of ‘Flamingo’ × ‘Abate Fetel’ are provided in Table S5.
Position of the QTLs for blush skin detected on LG5 in ‘Flamingo’ and LG9 in ‘Abate Fetel’ in the pear progeny of ‘Flamingo’ × ‘Abate Fetel’ based on grouping of classes is provided in Fig. S1.
- Allard A, Bink MC, Martinez S, Kelner JJ, Legave JM, di Guardo M, Di Pierro EA, Laurens F, van de Weg EW, Costes E (2016) Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population. J Exp Bot 67:2875–2888CrossRefPubMedCentralPubMedGoogle Scholar
- Bouvier L, Bourcy M, Boulay M, Tellier M, Gueif P, Denance C, Durel CE, Lespinasse Y (2012) A new pear scab resistance gene Rvp1 from the European pear cultivar ‘Navara’ maps in a genomic region syntenic to an apple scab resistance gene cluster on linkage group 2. Tree Genet Genomes 8:53–60CrossRefGoogle Scholar
- Celton J-M, Martinez S, Jammes M-J, Bechti A, Salvi S, Legave J-M, Costes E (2011) Deciphering the genetic determinism of bud phenology in apple progenies: a new insight into chilling and heat requirement effects on flowering dates and positional candidate genes. New Phytol 192:378–392CrossRefGoogle Scholar
- Di Guardo M, Bink MCAM, Guerra W, Letschka T, Lozano L, Busatto N, Poles L, Tadiello A, Bianco L, Visser RGF, van de Weg E, Costa F (2017) Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association. J Exp Bot 68:1451–1466CrossRefPubMedCentralPubMedGoogle Scholar
- Dirlewanger E, Quero-García J, Le Dantec L, Lambert P, Ruiz D, Dondini L, Illa E, Quilot-Turion B, Audergon J-M, Tartarini S, Letourmy P, Arús P (2012) Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry. Heredity 109:280–292CrossRefPubMedCentralPubMedGoogle Scholar
- Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
- Dussi MC, Sugar D, Wrolstad RE (1995) Characterizing and quantifying anthocyanins in red pears and the effect of light quality on fruit color. J Am Soc Hortic Sci 120:785–789Google Scholar
- Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Longmans Green, HarlowGoogle Scholar
- Francis FJ (1970) Anthocyanins in pear. HortScience 5:42Google Scholar
- Hauagge R, Cummins JN (1991) Genetics of length of dormancy period in Malus vegetative buds. J Am Soc Hortic Sci 116:121–126Google Scholar
- Hemmat M, Weeden NF, Brown SK (2003) Mapping and evaluation of Malus x domestica microsatellites in apple and pear. J Am Soc Hortic Sci 128:515–520Google Scholar
- Hjeltnes SH, Vercammen J, Gomand A, Måge F, Røen D (2015) High potential in new Norwegian bred pear cultivars. Proc XII International Pear Symposium. Acta Horti 1094: 111–116Google Scholar
- Human T, von Mollendorff L (2009) Cultivar Info: Cheeky™. Cultivar Information Sheet. ARC Infruitec-Nietvoorbij, Stellenbosch, South AfricaGoogle Scholar
- Illa E, Sargent DJ, Girona EL, Bushakra J, Cestaro A, Crowhurst R, Pindo M, Cabrera A, Van der Knaap E, Iezzoni A, Gardiner S, Velasco R, Arús P, Chagné D, Troggio M (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol 11:9CrossRefPubMedCentralPubMedGoogle Scholar
- Knäbel M, Friend AP, Palmer JW, Diack R, Wiedow C, Alspach P, Deng C, Gardiner SE, Tustin DS, Schaffer R, Foster T, Chagné D (2015) Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci. BMC Plant Biol 15:230CrossRefPubMedCentralPubMedGoogle Scholar
- Kunihisa M, Moriya S, Abe K, Okada K, Haji T, Hayashi T, Kim H, Nishitani C, Terakami S, Yamamoto T (2014) Identification of QTLs for fruit quality traits in Japanese apples: QTLs for early ripening are tightly related to preharvest fruit drop. Breed Sci 64:240–251CrossRefPubMedCentralPubMedGoogle Scholar
- Maliepaard C, Alston FH, Van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, Van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, Den Nijs APM, Periam N, Rikkerink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, Verhaegh JJ, Vrielink-van Ginkel M, King GJ (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73CrossRefGoogle Scholar
- Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won KH, Durel C, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 8:e77022CrossRefPubMedCentralPubMedGoogle Scholar
- Montanari S, Perchepied L, Renault D, Frijters L, Velasco R, Horner M, Gardiner SE, Chagné D, Bus VGM, Durel C-E, Malnoy M (2016) A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds. Mol Breed 36:47CrossRefGoogle Scholar
- Ramkumar G, Srinivasarao K, Madhan Mohan K, Sudarshan I, Sivaranjani AKP, Gopalakrishna K, Neeraja CN, Balachandran SM, Sundaram RM, Prasad MS, Shobha Rani N, Rama Prasad AM, Viraktamath BC, Madhav MS (2011) Development and validation of functional marker targeting an indel in the major rice blast disease resistance gene Pi54 (Pik h). Mol Breed 27:129–135CrossRefGoogle Scholar
- LeRoux PMF, Christen D, Duffy B, Tartarini S, Dondini L, Yamamoto T, Nishitani C, Terakami S, Lespinasse Y, Kellerhals M, Patocchi A (2012) Redefinition of the map position and validation of a major quantitative trait locus for fire blight resistance of the pear cultivar ‘Harrow Sweet’ (Pyrus communis L.). Plant Breed 131:656–664CrossRefGoogle Scholar
- Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
- Song S, Qi T, Huang H, Ren Q, Wu D, Chang C, Peng W, Liu Y, Peng J, Xie D (2011) The Jasmonate-ZIM domain proteins interact with the R2R3-MYB transcription factors MYB21 and MYB24 to affect jasmonate-regulated stamen development in Arabidopsis. Plant Cell 23:1000–1013CrossRefPubMedCentralPubMedGoogle Scholar
- Steyn WJ, Holcroft DM, Wand SJE, Jacobs G (2004a) Anthocyanin degradation in detached pome fruit with reference to preharvest red color loss and pigmentation patterns of blushed and fully red pear. J Am Soc Hortic Sci 129:13–19Google Scholar
- Steyn WJ, Holcroft DM, Wand SJE, Jacobs G (2004b) Regulation of pear color development in relation to activity of flavonoid enzymes. J Am Soc Hortic Sci 129:6–12Google Scholar
- Terakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y, Takada N, Saito T, Yamamoto T (2014) Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai). Tree Genet Genomes 10:853–863CrossRefGoogle Scholar
- Van Ooijen JW (2006) JoinMap ® 4 Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
- Van Ooijen JW (2009) MapQTL ® 6 Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, WageningenGoogle Scholar
- Wang C, Tian Y, Buck EJ, Gardiner SE, Dai H, Jai Y (2011) Genetic mapping of PcDw determining pear dwarf trait. J Am Soc Hortic 136:48–53Google Scholar
- Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban S, Wang H, Chen N, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408CrossRefPubMedCentralPubMedGoogle Scholar
- Xie R, Zheng L, He S, Zheng Y, Yi S, Deng L (2011) Anthocyanin biosynthesis in fruit tree crops: genes and their regulation. Afr J Biotechnol 10:19890–19897Google Scholar
- Zielinski QB, Reimer FC, Quakenbush VL (1965) Breeding behaviour of fruit characteristics in pears, Pyrus communis L. J Am Soc Hortic Sci 86:81–87Google Scholar