Genetic mapping of green curd gene Gr in cauliflower
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Gr5.1 is the major locus for cauliflower green curd color and mapped to an interval of 236 Kbp with four most likely candidate genes.
Cauliflower with colored curd enhances not only the visual appeal but also the nutritional value of the crop. Green cauliflower results from ectopic development of chloroplasts in the normal white curd. However, the underlying genetic basis is unknown. In this study, we employed QTL-seq analysis to identify the loci that were associated with green curd phenotype in cauliflower. A F2 population was generated following a cross between a white curd (Stovepipe) and a green curd (ACX800) cauliflower plants. By whole-genome resequencing and SNP analysis of green and white F2 bulks, two QTLs were detected on chromosomes 5 (Gr5.1) and 7 (Gr7.1). Validation by traditional genetic mapping with CAPS markers suggested that Gr5.1 represented a major QTL, whereas Gr7.1 had a minor effect. Subsequent high-resolution mapping of Gr5.1 in the second large F2 population with additional CAPS markers narrowed down the target region to a genetic and physical distance of 0.3 cM and 236 Kbp, respectively. This region contained 35 genes with four of them representing the best candidates for the green curd phenotype in cauliflower. They are LOC106295953, LOC106343833, LOC106345143, and LOC106295954, which encode UMP kinase, DEAD-box RNA helicase 51-like, glutathione S-transferase T3-like, and protein MKS1, respectively. These findings lay a solid foundation for the isolation of the Gr gene and provide a potential for marker-assisted selection of the green curd trait in cauliflower breeding. The eventual isolation of Gr will also facilitate better understanding of chloroplast biogenesis and development in plants.
We thank Mr. Evan Rees for field phenotyping, preparation of bulked DNA samples for QTL-seq analysis, and critical comments on this manuscript. HT acknowledges the graduate training scholarship from the China Scholarship Council (CSC). This work was supported by the Agriculture and Food Research Initiative competitive award Grant No. 2016-67013-24612 from the USDA National Institute of Food and Agriculture, the USDA-ARS base fund, and the United States–Israel Binational Agricultural Research and Development Fund (Grant No. US-4918-16CR).
Author contribution statement
HT performed most of the experiments. XW performed bioinformatic data analysis. ZF, HL, YT, and MM aided research design, assisted data analysis and interpretation, and/or edited the manuscript. HT and LL wrote the manuscript with contribution from all coauthors.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This research complies with the current laws of the USA.
- Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NH, Zhu S, Qiu JL, Micheelsen P, Rocher A, Petersen M, Newman MA, Bjorn Nielsen H, Hirt H, Somssich I, Mattsson O, Mundy J (2005) The MAP kinase substrate MKS1 is a regulator of plant defense responses. EMBO J 24:2579–2589PubMedPubMedCentralGoogle Scholar
- Chayut N, Yuan H, Ohali S, Meir A, Sa’ar U, Tzuri G, Zheng Y, Mazourek M, Gepstein S, Zhou X, Portnoy V, Lewinsohn E, Schaffer AA, Katzir N, Fei Z, Welsch R, Li L, Burger J, Tadmor Y (2017) Distinct mechanisms of the ORANGE protein in controlling carotenoid flux. Plant Physiol 173:376–389PubMedGoogle Scholar
- Crisp P, Angell S (1985) Genetic control of green curd colour in cauliflower. Ann Appl Biol 107:601–603Google Scholar
- Crisp P, Walkey DGA, Bellman E, Roberts E (1975) A mutation affecting curd colour in cauliflower (Brassica oleracea L. var. Botrytis DC). Euphytica 24:173–176Google Scholar
- Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi Kumar V, Tripathi S, Gowda CL, Sharma S, Singh S, Tyagi AK, Parida SK (2015) Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res 22:193–203PubMedPubMedCentralGoogle Scholar
- Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21Google Scholar
- Kasajima I, Ide Y, Ohkama-Ohtsu N, Hayashi H, Yoneyama T, Fujiwara T (2004) A protocol for rapid DNA extraction from Arabidopsis thaliana for PCR analysis. Plant Mol Biol Rep 22:49–52Google Scholar
- Kosambi DD (2016) The estimation of map distances from recombination values. Springer, Berlin, pp 125–130Google Scholar
- Labate JA, Robertson LD, Baldo AM, Börkman T (2006) Inflorescence identity gene alleles are poor predictors of inflorescence type in broccoli and cauliflower. J Am Soc Hortic Sci 131:667–673Google Scholar
- Lee GA, Koh HJ, Chung HK, Dixit A, Chung JW, Ma KH, Lee SY, Lee JR, Lee GS, Gwag JG, Kim TS, Park YJ (2009) Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice. Mol Breeding 24:93–101Google Scholar
- Link G, Tiller K, Baginsky S (1997) Glutathione, a regulator of chloroplast transcription. In: Hatzios KK (ed) Regulation of enzymatic systems detoxifying xenobiotics in plants. Kluwer, Dordrecht, pp 125–137Google Scholar
- Lu S, Van Eck J, Zhou X, Lopez AB, O’Halloran DM, Cosman KM, Conlin BJ, Paolillo DJ, Garvin DF, Vrebalov J, Kochian LV, Kupper H, Earle ED, Cao J, Li L (2006) The cauliflower Or gene encodes a DnaJ cysteine-rich domain-containing protein that mediates high levels of beta-carotene accumulation. Plant Cell 18:3594–3605PubMedPubMedCentralGoogle Scholar
- Manchali S, Murthy KNC, Patil BS (2012) Crucial facts about health benefits of popular cruciferous vegetables. J Funct Foods 4:94–106Google Scholar
- Masumoto H, Takagi H, Mukainari Y, Terauchi R, Fukunaga K (2016) Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq. Mol Breeding 36:59Google Scholar
- Noctor G, Mhamdi A, Chaouch S, Han Y, Neukermans J, Marquez-Garcia B, Queval G, Foyer CH (2012) Glutathione in plants: an integrated overview. Plant, Cell Environ 35:454–484Google Scholar
- Pandey MK, Khan AW, Singh VK, Vishwakarma MK, Shasidhar Y, Kumar V, Garg V, Bhat RS, Chitikineni A, Janila P, Guo B, Varshney RK (2017) QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnol J 15:927–941PubMedPubMedCentralGoogle Scholar
- Qiu JL, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Palma K, Suarez-Rodriguez MC, Sandbech-Clausen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M (2008) Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus. EMBO J 27:2214–2221PubMedPubMedCentralGoogle Scholar
- Sappl PG, Carroll AJ, Clifton R, Lister R, Whelan J, Harvey Millar A, Singh KB (2009) The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress. Plant J 58:53–68PubMedGoogle Scholar
- Singh VK, Khan AW, Jaganathan D, Thudi M, Roorkiwal M, Takagi H, Garg V, Kumar V, Chitikineni A, Gaur PM, Sutton T, Terauchi R, Varshney RK (2016a) QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea. Plant Biotechnol J 14:2110–2119PubMedPubMedCentralGoogle Scholar
- Singh VK, Khan AW, Saxena RK, Kumar V, Kale SM, Sinha P, Chitikineni A, Pazhamala LT, Garg V, Sharma M, Sameer Kumar CV, Parupalli S, Vechalapu S, Patil S, Muniswamy S, Ghanta A, Yamini KN, Dharmaraj PS, Varshney RK (2016b) Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnol J 14:1183–1194PubMedGoogle Scholar
- Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183PubMedPubMedCentralGoogle Scholar
- Van Ooijen JW (2006) JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
- Welsch R, Zhou X, Yuan H, Alvarez D, Sun T, Schlossarek D, Yang Y, Shen G, Zhang H, Rodriguez-Concepcion M, Thannhauser TW, Li L (2018) Clp protease and OR directly control the proteostasis of phytoene synthase, the crucial enzyme for carotenoid biosynthesis in Arabidopsis. Mol Plant 11:149–162PubMedGoogle Scholar
- Yuan H, Owsiany K, Sheeja TE, Zhou X, Rodriguez C, Li Y, Welsch R, Chayut N, Yang Y, Thannhauser TW, Parthasarathy MV, Xu Q, Deng X, Fei Z, Schaffer A, Katzir N, Burger J, Tadmor Y, Li L (2015) A single amino acid substitution in an ORANGE protein promotes carotenoid overaccumulation in Arabidopsis. Plant Physiol 169:421–431PubMedPubMedCentralGoogle Scholar