Abstract
As an important commodity trait in melons, the rind is the most direct standard of evaluation for consumers. In this study, we obtained an F2 melon population derived from self-crossing an F1 generation from a cross between X010 (green rind with stripes) and M1-113 (white rind without stripes) and performed genetic analysis and mapping. Genetic analysis revealed that a single dominant gene (st3) controlled the striped rind trait in melons. According to bulked segregant analysis, two DNA bulks were constructed (20 striped and 20 solid-colored rind plants). Next-generation sequencing was used on two parental lines (X010 and M1-113) and two DNA bulks. The st3 gene was identified on chromosome 4 within 2.7 Mbp region. Fourty cleaved amplified polymorphic sequences (CAPS) markers were developed, and sixteen CAPS markers with polymorphisms on chromosome 4 were used for constructing a genetic linkage map, and identifying recombinants in a large F2 population with six new CAPS markers. The location of the st3 gene was narrowed to 172.8 kbp on chromosome 4 between markers M-4-28 (825,401 bp) and M-4-27 (998,261 bp). This study provides a theoretical basis for the fine mapping, cloning and functional characterization of st3.
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References
Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using Mut Map. Nat Biotechnol 30:174–178. https://doi.org/10.1038/nbt.2095
Baloch AM, Baloch AW, Liu S, Gao P, Baloch MJ, Wang XZ, Davis AR, Ali M, Luan FS (2016) Linkage map construction and QTL analysis of fruit traits in melon (Cucumis melo L.) based on CAPS markers. Pak J Bot 48(4):1579–1584
Burger Y, Sa’ar U, Paris HS, Lewinsohn E, Katzir N, Tadmor Y, Schaffer AA (2006) Genetic variability for valuable fruit quality traits in Cucumis melo. Isr J Plant Sci 54(3):233–242. https://doi.org/10.1560/IJPS_54_3_233
Burger Y, Paris HS, Cohen R, Katzir N, Tadmor Y, Lewinsohn E, Schaffer AA (2010) Genetic diversity of Cucumis melo. Hortic Rev 36:165–198
Cohen S, Itkin M, Yeselson Y et al (2014) The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nat Commun 5(1):4026. https://doi.org/10.1038/ncomms5026
Cuevas HE, Staub JE, Simon PW, Zalapa JE, McCreight JD (2008) Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.). Theor Appl Genet 117(8):1345–1359. https://doi.org/10.1007/s00122-008-0868-2
Cuevas HE, Staub JE, Simon PW, Zalapa JE (2009) A consensus linkage map identi es genomic regions controlling fruit maturity and beta-carotene-associated flesh color in melon (Cucumis melo L.). Theor Appl Genet 119:741–756. https://doi.org/10.1007/s00122-009-1085-3
Danin-Poleg Y, Tadmor Y, Tzuri G, Reis N, Hirschbery J, Katzir N (2002) Construction of a genetic map of melon with molecular markers for horticultural traits, and localization of genes associated with ZYMV resistance. Euphytica 125(3):373–384
Díaz A, Zarouri B, Fergany M, Eduardo I, Alvarez JM, Pico B, Moreno AJ (2014) Mapping and introgression of QTL involved in fruit shape transgressive segregation into ‘Piel de Sapo’ Melon (Cucumis melo L.). PLoS ONE 9(8):1–12(e104188)
Dou JL, Zhao SJ, Lu XQ, He N, Zhang L, Ali A, Kuang HH, Liu WG (2018) Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.). Theor Appl Genet 4:947–958. https://doi.org/10.1007/s00122-018-3050-5
Duan JF (2016) Genetic analysis of fruit appearance characteristics and prelimininary mapping of the genes related to fruit skin color in melon. Dissertation, Hua Zhong Agricultural University (in Chinese)
Eyberg DA, Summers WL, Hall CV (1980) The inheritance of rind color patterns in watermelon Citrullus lanatus (Thunb.), Matsum. and Nakai. HortScience 15:420
FAO (2017) Statistics Division of Food and Agriculture Organization of the United Nations. FAOSTAT. http://faostat.fao.org/. Accessed 30 May 2017
Feder A, Burger J, Gao S, Lewinsohn E, Katzir N, Schaffer AA, Meir A, Davidovich-Rikanati R, Portnoy V, Gal-On A, Fei ZJ, Kashi Y, Tadmor Y (2015) A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo. Plant Physiol 169(3):1714–1726. https://doi.org/10.1104/pp.15.01008
Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, Fei ZJ, Xu YM, Mao LY, Jiao C (2018) Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. Plant J 94(1):169–191. https://doi.org/10.1111/tpj.13838
Gama RNCS, Santos CAF, Dias RCS, Alves JCSF, Nogueira TO (2015) Microsatellite markers linked to the locus of the watermelon fruit stripe pattern. Genet Mol Res 14(1):269–276. https://doi.org/10.4238/2015.January.16.11
Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S (2010) A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theor Appl Genet 121(3):511–533. https://doi.org/10.1007/s00122-010-1327-4
Kang SI, Rahim MA, Afrin KS, Jung HJ, Kim HT, Park JI, Nou IS (2018) Expression of anthocyanin biosynthesis-related genes reflects the peel color in purple tomato. Hortic Environ Biotechnol 59(3):435–445. https://doi.org/10.1007/s13580-018-0046-7
Kim H, Han D, Kang J, Choi Y, Levi A, Lee GP, Park Y (2015) Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus L.). Hortic Environ Biotechnol 56(3):341–349. https://doi.org/10.1007/s13580-015-0017-1
Kumar R, Wehner TC (2011) Discovery of second gene for solid dark green versus light green rind pattern in watermelon. J Hered 102(4):489–493. https://doi.org/10.1093/jhered/esr025
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAM tools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Li B, Zhao YL, Zhu QL, Zhang ZP, Fan C, Amanullah S, Gao P, Luan FS (2017) Mapping of powdery mildew resistance genes in melon (Cucumis melo L.) by bulked segregant analysis. Sci Hortic 220:160–167. https://doi.org/10.1016/j.scienta.2017.04.001
Lida A, Kazuoka T, Torikai S, Kikuchi H, Oeda K (2000) A zinc finger protein RHL41 mediates the light acclimatization response in Arabidopsis. Plant J 24(2):191–203
López-Sesé AI, Staub JE, Gómez-Guillamón ML (2003) Genetic analysis of Spanish melon (Cucumis melo L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions. Theor Appl Genet 108(1):41–52. https://doi.org/10.1007/s00122-003-1404-z
Lou L (2009) Inheritance of fruit characteristics in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai]. Dissertation, North Carolina State University
Lou L, Wehner TC (2016) Qualitative inheritance of external fruit traits in watermelon. HortScience 51(5):487–496
Lu HF, Lin T, Klein J, Wang SH, Qi JJ, Zhou Q, Sun JJ, Zhang ZH, Weng YQ, Huang SW (2014) QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theor Appl Genet 127(7):1491–1499. https://doi.org/10.1007/s00122-014-2313-z
Luan F, Delannay I, Staub JE (2008) Chinese melon (Cucumis melo L.) diversity analyses provide strategies for germplasm curation genetic improvement, and evidentiary support of domestication patterns. Euphytica 164(2):445–461. https://doi.org/10.1007/s10681-008-9699-0
Meng L, Li H, Zhang LY, Wang JK (2015) QTL Ici mapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3(3):269–283. https://doi.org/10.1016/j.cj.2015.01.001
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in septic genomic regions by using segregating populations. Proc Natl Acad Sci 88(21):9828–9832. https://doi.org/10.1073/pnas.88.21.9828
Monforte AJ, Oliver M, Gonzalo MJ, Alvarez JM, Dolcet-Sanjuan R, Arus P (2004) Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.). Theor Appl Genet 108(4):750–758. https://doi.org/10.1007/s00122-003-1483-x
Montero-Pau J, Blanca J, Esteras C, Martínez-Pérez EM, Gómez P, Monforte AJ, Cañizares J, Picó B (2017) An SNP-based sa turated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing. BMC Genom 18(1):94. https://doi.org/10.1186/s12864-016-3439-y
Porter DR (1937) Inheritance of certain fruit and seed characters in watermelons. Hilgardia 10(12):489–509. https://doi.org/10.3733/hilg.v10n12p489
Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A (2018) An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Sci Rep. https://doi.org/10.1038/s41598-018-26416-2
Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10(6):297–304. https://doi.org/10.1016/j.tplants.2005.04.008
Song M, Wei Q, Wang J, Fu W, Qin X, Lu X (2018) Fine mapping of CsVYL, conferring virescent leaf through the regulation of chloroplast development in cucumber. Plant Sci 9:432. https://doi.org/10.3389/fpls.2018.00432
Su XM, Yang WC, Huang ZJ, Wang XX, Guo YM, Du YC, Gao JC (2018) Analysis and fine mapping of a gene controlling the folded-leaf phenotype of a mutant tomato line. Euphytica 214(6):97. https://doi.org/10.1007/s10681-018-2148-9
Tadmor Y, Burger J, Yaakov I, Feder A, Libhaber SE, Portnoy V, Meir A, Tzuri G, Saar U, Rogachev I (2010) Genetics of flavonoid, carotenoid, and chlorophyll pigments in melon fruit rinds. J Agric Food Chem 58(19):10722–10728. https://doi.org/10.1021/jf1021797
Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32(1):5e-5. https://doi.org/10.1093/nar/gnh006
Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-perfor-mance genomics data visualization and exploration. Brief Bioinform 14:178–192. https://doi.org/10.1093/bib/bbs017
Watanabe K, Saito T, Hirota S, Takahashi B, Fujishita N (1991) Carotenoid pigments in orange, light orange, green and white flesh colored fruits of melon (Cucumis melo L.). J Jpn Soc Food Sci Technol 38(2):153–159. https://doi.org/10.3136/nskkk1962.38.153
Yang GH, Fan R, Yang XF, Hou JL, Yuan SC, Cao M, Wang XL, Li JS (2014) Construction of a highly dense genetic map using SNP and mapping of three qualitative traits in Cucumis melo. Acta Hortic Sin 41(5):898–906 (in Chinese)
Yang HB, Sungwoo P, Younghoon P, Gungpyo L, Kang SC, Yongkwon K (2015) Linkage analysis of the three loci determining rind color and stripe pattern in watermelon. Hortic Sci Technol 33(4):559–565. https://doi.org/10.7235/hort.2015.14070
Zhang ZP, Zhang YN, Sun L, Qiu G, Sun YJ, Zhu ZC, Luan FS, Wang XZ (2017) Construction of a genetic map for Citrullus lanatus based on CAPS markers and mapping of three qualitative traits. Sci Hortic 233:532–538. https://doi.org/10.1016/j.scienta.2017.10.029
Zhao ZG, Yan HF, Zheng R, Saeed KM, Fu X, Tao Z, Zhang ZY (2018) Anthocyanins characterization and antioxidant activities of sugarcane (Saccharum officinarum L.) rind extracts. Ind Crops Prod 133:38–45. https://doi.org/10.1016/j.indcrop.2018.01.015
Zheng WJ, Yan W, Wang LL, Ma Z, Zhao JM, Wang P, Zhang LX, Liu Zh, Lu XC (2016) Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. Theor Appl Genet 129(5):1035–1044. https://doi.org/10.1007/s00122-016-2681-7
Acknowledgments
Authors highly acknowledged the funding granted by “The National Nature Science Foundation of China” (Grant No. 31672177), the “Academic Backbone” Project of Northeast Agricultural University (Grant No. 16XG06), the “Young Talents” Project of Northeast Agricultural University (Grant No. 14QC09), Heilongjiang Province Collegial Young Innovative Talent Training Program (Grant No. UNPYSCT-2016136), and “The National Nature Science Foundation of China” (Grant No. 31372028).
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Liu, L., Sun, T., Liu, X. et al. Genetic analysis and mapping of a striped rind gene (st3) in melon (Cucumis melo L.). Euphytica 215, 20 (2019). https://doi.org/10.1007/s10681-019-2353-1
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DOI: https://doi.org/10.1007/s10681-019-2353-1