Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (17): 3375-3385.doi: 10.3864/j.issn.0578-1752.2017.17.012

• HORTICULTURE • Previous Articles     Next Articles

Genome-Wide Association Studies for Flowering Time in Brassica rapa

GAO BaoZhen1, LIU Bo1, LI ShiKai2, LIANG JianLi1, CHENG Feng1, WANG XiaoWu1, WU Jian1   

  1. 1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081; 2Institute of horticultural crops, Yunnan Academy of Agricultural Sciences, Kunming 650205
  • Received:2017-01-20 Online:2017-09-01 Published:2017-09-01

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Abstract: 【Objective】To identify the genetic loci or candidate genes for flowering time regulation in Brassica rapa for improvement of pre-mature bolting resistance of B. rapa. 【Method】 In this study, 116 B. rapa germplasm accessions were selected to evaluate flowering time variations in greenhouse and open-field, respectively. Total genomic DNA was extracted with 1.2x re-sequenced depth. Filtering, mapping with reference by Pooled Mapping was conducted to obtain a genomic high quality SNP set. Then the population structure and linkage disequilibrium (LD) were analyzed using SNP set after condition filtering. In total 2000 SNP points were selected from all SNPs randomly to conduct phylogenetic tree analysis using PhyML software with maximum likelihood method. all high quality SNPs were used to conduct genomic linkage disequilibrium analysis with Haploview software. Genome-wide association study (GWAS) for flowering time variations was then conducted based on software TASSEL, GAPIT and R. According to the position of strong association signals and LD block, the candidate signals for flowering time were identified. Eventually, flowering time candidate genes in B. rapa were predicted by gene colinearity relationship between A. thaliana and B. rapa, and gene function annotation.【Result】The 116 B. rapa accessions showed extensive variations in flowering time. Significant variation was also observed between greenhouse and open-field environments. The distribution of flowering time under open-field was partial normal, while the flowering time distributed evenly under greenhouse. Phenotypes of flowering time were significantly correlated between different environments, indicating that genetic effect played a crucial role in regulation of flowering time. A total of 1.03 million SNPs covering genome-wide were generated by biotechnology analysis. Population structure showed that accessions from each sub-group were clustered, and had a close relationship with geographic origin in phylogenetic tree. The linkage disequilibrium decay across genome-wide was 2.3 kb, demonstrating that there were frequent recombinations and variants in 116 B. rapa accessions. A total of 54 strong signals (P＞4) were detected using mixed linear model and 87 (P＞5) using general linear model under two different environments. Thirty-three strong signals (27 loci under greenhouse, 19 loci under open-field) were saved after considering LD block (r2＞0.33), including 13 co-identified SNPs. Based on genome colinearity between A. thaliana and B. rapa, and gene function annotation, 14 candidate genes were predicted. Three candidate genes, FUL, PHYB, FPF1, were co-identified under greenhouse and open-field environments. FT1, a key gene involved in flowering time regulation was also identified under open-field condition.【Conclusion】 Correlation analysis of flowering time under different environments indicated that genetic control is a decisive effect on flowering time. A total of 33 significant associated SNPs controlling flowering time were identified by GWAS. By combining LD block, genome colinearity between A. thaliana and B. rapa, and gene annotation, 14 flowering time candidate genes were predicted.

Key words: Brassica rapa, flowering time, linkage disequilibrium, genome-wide association study, candidate gene

[1]    ROUX F, TOUZET P, CUGUEN J, LE C V. How to be early flowering: an evolutionary perspective. Trends in Plant Science,2006, 11(8): 375-381.
[2]    ALONSO-BLANCO C, KOORMNEEF M. What has natural variation taught us about plant development, physiology, and adaptation? The Plant Cell,2009, 21(7): 1877-1896.
[3]    KIM D H, DOYLE M R, SUNG S, AMASINO R M. Vernalization: winter and the timing of flowering in plants. Annual Review of Cell and Developmental Biology,2009, 25(1): 277-299.
[4]    FORNARA F, DE M A, COUPLAND G. Snaphot: Control of flowering in Arabidopsis. Cell,2010, 141(3): 1-2.
[5]    WAHL V, PONNU J, SCHLERETH A, ARRIVAULT S, LANGENECKER T, FRANKE A, FEIL R, LUNG JE, STITT M, SCHMID M. Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science,2013, 339(6120): 704-707.
[6]   SHRESTHA R, GOMEZ-ARIZA J, BRAMBILLA V, FORMARA F. Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals. Annals of Botany,2014, 114(7): 1445.
[7]    WANG X, WANG H, WANG J, SUN R, WU J, LIU S, BAI Y, MUN J H, BANCROFT I, CHENG F, et al. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics, 2011, 43(10): 1035-1039.
[8]    LOU P, XIE Q, XU X, EDWARDS C E, BROCK M T, WEINIG C, MCCLUNG C R. Genetic architecture of the circadian clock and flowering time in Brassica rapa. Theoretical and Applied Genetics,2011, 123(3): 397-409.
[9]    WU J, WEI K, CHENG F, LI S, WANG Q, ZHAO J, BONNERMA G, WANG X. A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa. BMC Plant Biology,2012, 12(1): 1-9.
[10]   XIAO D, ZHAO J J, HOU X L, BASNET R K, CARPIO D P D, ZHANG N W, JOHAN B, KE L, FENG C, Wang X W. The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks. Journal of Experimental Botany,2013, 64(14): 4503-4516.
[11]   KITAMOTO N, YUI S, NISHIKAWA K, TAKAHATA Y, YOKOI S. A naturally occurring long insertion in the first intron in the Brassica rapa FLC2 gene causes delayed bolting. Euphytica,2014, 196(2): 213-223.
[12]   ATWELL S, HUANG Y S, VILHJALMSSON B J, WILLEMS G, HORTON M, LI Y, MENG D, PLATT A, TARONE A M, HU T T, et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature,2010, 465(7298): 627-631.
[13]   BRACHI B, MORRIS G P, BOREVITZ J O. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biology,2011, 12(10): 1-8.
[14]   WANG M, YAN J, ZHAO J, SONG W, ZHANG X, XIAO Y, ZHENG Y. Genome-wide association study (GWAS) of resistance to head smut in maize. Plant Science, 2012, 196(11): 125-131.
[15]   ARANZANA M J, KIM S, ZHAO K, BAKKER E, HORTON M, JAKOB K, LISTER C, MOLITOR J, SHINDO C, TANG C. Genome- wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genetics,2005, 1(5): e60.
[16] HUANG X, WEI X, SANG T, ZHAO Q, FENG Q, ZHAO Y, LI C, ZHU C, LU T, ZHANG Z. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 2010, 42(11): 961-967.
[17]   ZHANG J, SONG Q, CREGAN P B, NELSON R L, WANG X, WU  J, JIANG G L. Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm. BMC Genomics,2015, 16(1): 1-11.
[18]   FU L X, CAI C C, CUI Y N, WU J, LIANG J L, CHENG F, WANG X W. Pooled mapping: an efficient method of calling variations for population samples with low-depth resequencing data. Molecular Breeding,2016, 36(4): 1-12.
[19]   GUINDON S, GASCUEL O. PhyML-A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology,2003, 52(5): 696-704.
[20]   YANG J, LEE S H, GODDARD M E, VISSCHER P M. GCTA: A tool for genome-wide complex trait analysis. American Journal of Human Genetics,2011, 88(1): 76-82.
[21]   BARRETT J C, FRY B, MALLER J, DALY M J. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics,2005, 21(2): 263-265.
[22]   BRADBURY P J, ZHANG Z, KROON D E, CASSTEVENS T M, RAMDOSS Y, BUCKLER E S. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics,2007, 23(19): 2633-2635.
[23]   ZHANG Z, ERSOZ E, LAI C Q, TODHUNTER R J, TIWARI H K, GORE M A, BRADBURY P J, YU J, ARNETT D K, ORDOVAS J M. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics,2010, 42(4): 355-360.
[24]   BRACHI B, FAURE N, HORTON M, FLAHAUW E, VAZQUEZ A, NORDBORG M, BERGELSON J, CUGUEN J, ROUX F. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genetics,2010, 6(5): e1000940.
[25]   付丽霞. 芸薹属蔬菜低深度测序SNP分型及其应用[D]. 北京: 中国农业科学院, 2016.
FU L X. SNP genotyping using low-depth resequencing data and its application in Brassica vegetables [D]. Beijing: Chinese Academy of Agricultural Science, 2016. (in Chinese)
[26]   CHENG F, FANG L, WANG X W. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Frontiers in Plant Science, 2012, 3: 198.
[27]   MELZER S, LENS F, GENNEN J, VANNESTE S, ROHDE A, BEECKMAN T. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana. Nature Genetics, 2008, 40(12): 1489-1492.
[28]   TEPER-BAMNOLKER P, SAMACH A. The flowering integrator FT regulates SEPALLATA3 and FRUITFULL accumulation in Arabidopsis leaves. The Plant Cell, 2005, 17(10): 2661-2675.
[29]   FERRáNDIZ C, GU Q, MARTIENSSEN R, YANOFSKY M F. Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development, 2000, 127(4): 725-734.
[30]   SHIMADA S, OGAWA T, KITAGAWA S, SUZUKI T, IKARI C, SHITSUKAWA N, MURAI K. A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULL-like gene, VRN1, is upstream of FLOWERING LOCUS T. The Plant Journal, 2009, 58(4): 668-681.
[31]   ENDO M, NAKAMURA S, ARAKI T, MOCHIZUKI N, NAGATANI A. Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles. The Plant Cell, 2005, 17(7): 1941-1952.
[32] VALVERDE F, MOURADOV A, SOPPE W, RAVENSCROFT D, SAMACH A, COUPLAND G. Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science, 2004, 303(5660): 1003-1006.
[33]   CERDAN P D, CHORY J. Regulation of flowering time by light quality. Nature, 2003, 423(6942): 881-885.
[34]   REED J W, NAGPAL P, POOLE D S, FURUYA M, CHORY J. Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. The Plant Cell, 1993, 5(2): 147-157.
[35]   CASSON S A, FRANKLIN K A, GRAY J E, GRIERSON C S, WHITELAM G C, HETHRINGTON A M. Phytochrome B and PIF4 regulate stomatal development in response to light quantity. Current. Biology, 2009, 19: 229-234.
[36]   LEIVAR P, MONTE E, Al-SADY B, CARLE C, STORER A, ALONSO J M, ECKER J R, QUAIL P H. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. The Plant Cell, 2008, 20: 337-352.
[37]   RAUSENBERGER J, HUSSONG A, KIRCHER S, KIRCHENBAUER D, TIMMER J, NAGY F, SCHAFER E, FLECK C. An integrative model for phytochrome B mediated photomorphogenesis: From protein dynamics to physiology. PLoS ONE, 2010, 5: e10721.
[38]   SWEERE U, EICHENBERG K, LOHRMANN J, MIRA-RODADO V, BAURLE I, KUDLA J, NAGY F, SCHAFER E, HARTER K. Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling. Science, 2001, 294: 1108-1111.
[39]   CAGNOLA J I, PLOSCHUK E, BENECH-ARNOLD T, FINLAYSON S A, CASAL J J. Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato. Plant Physiology, 2012, 160: 1110-1119.
[40]   ADAMSE P, JASPERS P, KENDRICK R E, KOORNNEEF M. Photomorphogenetic responses of a long hypocotyl mutant of Cucumis sativus L.. Journal of Plant Physiology, 1987, 127(5): 481-491.
[41]   DEVLIN P F, ROOD S B, SOMERS D E, QUAIL P H, WHITELAM G C. Photophysiology of the elongated internode (ein) mutant of Brassica rapa ein mutant lacks a detectable phytochrome B-like polypeptide. Plant Physiology, 1992, 100(3): 1442-1447.
[42]   PROCKO C, CRENSHAW C M, LJUNG K, NOEL J P, CHORY J. Cotyledon-generated auxin is required for shade-induced hypocotyl growth in Brassica rapa. Plant Physiology, 2014, 165(3): 1285-1301.
[43]   FINLAYSON S A, Lee I J, MORGAN P W. Phytochrome B and the regulation of circadian ethylene production in sorghum. Plant Physiology, 1998, 116: 17-25.
[44]   FRANKLIN KA, WHITELAM G C. Phytochromes and shade- avoidance responses in plants. Annals of Botany, 2005, 96: 169-175.
[45]   ROBSON P R H, WHITELAM G C, SMITH H. Selected components of the shade-avoidance syndrome are displayed in a normal manner in mutants of Arabidopsis thaliana and Brassica rapa deficient in phytochrome B. Plant Physiology, 1993, 102(4): 1179-1184.
[46]   KANIA T, RUSSENBERGER D, PENG S, APEL K, MELZER S. FPF1 promotes flowering in Arabidopsis. The Plant Cell, 1997, 9(8): 1327-1338.
[47]   MELZER S, KAMPMANN G, CHANDLER J. FPF1 modulates the competence to flowering in Arabidopsis. The Plant Journal, 1999, 18(4): 395-405.
[48]   XU M L, JIANG J F, GE L, XU Y Y, CHEN H, ZHAO Y, BI Y R, WEN J Q, CHONG K. FPF1 transgene leads to altered flowering time and root development in rice. Plant Cell Reports, 2005, 24(2): 79-85.
[49]   黄琼华, 杨光伟. 农杆菌介导法将 FPF1 基因导入油菜的研究初报. 西南农业大学学报, 2002, 24(2): 124-127.
HUANG Q H, YANG G W. Preliminary study on Agrobacterium mediated transformation of FPF1 gene into Brassica napus L.. Journal of Southwest Agricultural University, 2002, 24(2): 124-127. (in Chinese)
[50]   CHENG F, SUN R, HOU X, ZHENG H K, ZHANG F L, ZHANG Y Y, LIU B, LIANG J L, ZHUANG M, LIU Y X, et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nature Genetics,2016, 48(10): 1218-1224.
[51]   KIM S, PLAGNOL V, HU T T, TOOMAJIAN C, CLARK R M, OSSOWSKI S, ECKER J R, WEIGEL D, NORDBORG M. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genetics, 2007, 39(9): 1151-1155.
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