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Identification of candidate genes for panicle length in Oryza sativa L. ssp. japonica via genome-wide association study and linkage mapping

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Abstract

Panicle length is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Two populations were used to identify QTLs associated with panicle length. Based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs), twenty eight lead SNPs significantly associated with panicle length in 2018 and 2019 were detected on chromosomes 1, 2, 3, 4, 6, 7, 9, 10 and 11 in the natural population consisting of 295 japonica rice varieties collected from Northeast Asia. Eight QTLs for panicle length in 2018 and 2019 were detected on chromosomes 1, 2, 3, 6, 7 and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Kongyu131 (short panicle) and Xiaobaijingzi (long panicle). Interestingly, Chr6_7539486 identified by GWAS in both years, was located within the same region as qPL6 identified by the linkage mapping. According to LD decay of the whole genome, a 218-kb region on chromosome 6 was selected for further analysis. After haplotype analysis, quantitative real-time PCR and sequence analysis, LOC_Os06g14200 and LOC_Os06g14370 were initially considered as the candidate genes. Moreover, LOC_Os06g14200 encoding a C3HC4 type zinc finger protein containing RING finger domain plays an important role in the growth and development of plants, which was most likely involved in the regulation of panicle length in rice. This study provides resources for breeding aimed at improving rice high yield potential.

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References

  • Ashikari M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    Article  CAS  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  Google Scholar 

  • Famoso AN, Zhao K, Clark RT, Tung C, Wright MH, Bustamante C, Kochian LV, Mccouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa L.) determined through genome-wide association analysis and QTL mapping. Plos Genet 7:747–757

    Article  Google Scholar 

  • FAO (2017) Food and agricultural organization. Online interactive database on agriculture, FAOSTAT. www.fao.org

  • Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang J, Zheng KL, Liu G, Wang GC, Sidhu JS (2003) Identification of QTL for growth and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107:679–690

    Article  Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler E, Qian Q, Zhang Q, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967

    Article  CAS  Google Scholar 

  • Ikeda K, Sunohara H, Nagato Y (2004) Developmental course of inflorescence and spikelet in rice. Breed Sci 54:147–156

    Article  Google Scholar 

  • Jan A, Kitano H, Matsumoto H, Komatsu S (2006) The rice OsGAE1 is a novel gibberellin-regulated gene and involved in rice growth. Plant Mol Biol 62:439–452

    Article  CAS  Google Scholar 

  • Jiang GH, Xu CG, Li XH, He YQ (2004) Characterization of the genetic basis for yield and its component traits of rice revealed by doubled haploid population. Acta Genet Sin 31:63

    PubMed  Google Scholar 

  • Kawahara Y, Bastide M, Hamilton J, Kanamori H, McCombie W, Ouyang S, Schwartz D, Tanaka T, Wu J, Zhou S, Childs K, Davidson R, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee S, Kim J, Numa H, Itoh T, Buell C, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4

    Article  Google Scholar 

  • Kobayashi S, Fukuta Y, Sato T, Osaki M, Khush GS (2003) Molecular marker dissection of rice (Oryza sativa L.) plant architecture under temperate and tropical climates. Theor Appl Genet 107:1350–1356

    Article  CAS  Google Scholar 

  • Koiwai H, Tagiri A, Katoh S, Katoh E, Ichikawa H, Minami E, Nishizawa Y (2007) RING-H2 type ubiquitin ligase EL5 is involved in root development through the maintenance of cell viability in rice. Plant J 51:92–104

    Article  CAS  Google Scholar 

  • Li S, Qian Q, Fu Z, Zeng D, Meng X, Kyozuka J, Maekawa M, Zhu X, Zhang J, Li J (2009) Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. Plant J 58:592–605

    Article  CAS  Google Scholar 

  • Li M, Tang D, Wang K, Wu X, Lu L, Yu H, Gu M, Yan C, Cheng Z (2011a) Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnol J 9:1002–1013

    Article  CAS  Google Scholar 

  • Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011b) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269

    Article  CAS  Google Scholar 

  • Li M, Yeung J, Cherny S, Sham P (2012) Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet 131:747–756

    Article  CAS  Google Scholar 

  • Li N, Zheng H, Cui J, Wang J, Liu H, Sun J, Liu T, Zhao H, Lai Y, Zou D (2019) Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage. Rice 12:24

    Article  Google Scholar 

  • Liu H, Hedley P, Cardle L, Wright KM, Hein I, Marshall D, Waugh R (2005) Characterisation and functional analysis of two barley caleosins expressed during barley caryopsis development. Planta 221(4):513–522

    Article  CAS  Google Scholar 

  • Liu T, Li L, Zhang Y, Xu C, Li X, Xing Y (2011) Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. J Genet 90:377–382

    Article  Google Scholar 

  • Liu E, Liu Y, Wu G, Zeng S, Tran TTG, Liang L, Liang Y, Dong Z, She D, Wang H (2016) Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis. Front Plant Sci 7:596

    PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen T (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-△△Ct method. Methods 25:402–408

    Article  CAS  Google Scholar 

  • Lu S, Wei H, Wang Y, Wang H, Yang R, Zhang X, Tu J (2012) Overexpression of a transcription factor OsMADS15 modifies plant architecture and flowering time in rice (Oryza sativa L.). Plant Mol Biol Rep 30:1461–1469

    Article  CAS  Google Scholar 

  • McNellis TW, von Arnim AG, Deng XW (1994) Overexpression of Arabidopsis COP1 results in partial suppression of light-mediated development: evidence for a light-inactivable repressor of photo-morphogenesis. Plant Cell 6:1391–1400

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mei H, Li Z, Shu Q, Guo L, Wang Y, Yu X, Ying CS, Luo L (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110:649–659

    Article  Google Scholar 

  • Piao R, Chu S, Jiang W, Yu Y, Jin Y, Woo M, Lee J, Kim SH, Koh H (2014) Isolation and characterization of a dominant dwarf gene, d-h, in rice. Plos One 9:e86210

    Article  Google Scholar 

  • Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, Mccouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432

    Article  CAS  Google Scholar 

  • Sun P, Zhang W, Wang Y, He Q, Shu F, Liu H, Wang J, Wang J, Yuan L, Deng H (2016) OsGRF4 controls grain shape, panicle length and seed shattering in rice. J Integr Plant Biol 58:836–847

    Article  CAS  Google Scholar 

  • Thomson MJ, Tai TH, Mcclung AM, Lai X, Hinga ME, Lobos KB, Xu Y, Martinez CP, Mccouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Article  CAS  Google Scholar 

  • Tsuge T, Inagaki N, Yoshizumi T, Shimada H, Kawamoto T, Matsuki R, Yamamoto N, Matsui M (2001) Phytochrome-mediated control of COP1 gene expression in rice plants. Mol Genet Genomics 265:43–50

    Article  CAS  Google Scholar 

  • Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374

    Article  CAS  Google Scholar 

  • Wang X, Liu G, Wang Z, Chen S, Xiao Y, Yu C (2019) Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa L.) through single-segment substitution lines. Plant Breed 138:299–308

    Article  CAS  Google Scholar 

  • Wei Z, Ma H, Ge X (2011) Phylogenetic analysis and drought-responsive expression of the rice caleosin gene family. Chin Sci Bull 56:1612–1621

    Article  Google Scholar 

  • Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209

    Article  CAS  Google Scholar 

  • Yadav SK, Pandey P, Kumar B, Suresh B (2011) Genetic architecture, inter-relationship and selection criteria for yield improvement in rice (Oryza sativa L.). Pak J Biol Sci 14:540–545

    Article  CAS  Google Scholar 

  • Yano K, Yamamoto E, Aya K, Takeuchi H, Lo P, Hu L, Yamasaki M, Yoshida S, Kitano H, Hirano K (2016) Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet 48:927–934

    Article  CAS  Google Scholar 

  • Zhang L, Wang J, Wang J, Wang L, He Z (2015) Quantitative trait locus analysis and fine mapping of the qPL6 locus for panicle length in rice. Theor Appl Genet 128:1151–1161

    Article  CAS  Google Scholar 

  • Zhao H, Li J, Yang L, Qin G, Xia C, Xu X, Su Y, Liu Y, Ming L, Chen L, Xiong L, Xie W (2021) An inferred functional impact map of genetic variants in rice. Mol Plant 14:1584–1599

    Article  CAS  Google Scholar 

  • Zhu Z, Li X, Wei Y, Guo S, Sha A (2018) Identification of a novel QTL for panicle length from wild rice (Oryza minuta) by specific locus amplified fragment sequencing and high density genetic mapping. Front Plant Sci 9:1492

    Article  Google Scholar 

  • Zhu X, Zhang S, Chen Y, Mou C, Huang Y, Liu X, Ji J, Yu J, Hao Q, Yang C, Cai M, Nguyen T, Song W, Wang P, Dong H, Liu S, Jiang L, Wan J (2021) Decreased grain size1, a C3HC4-type RING protein, influences grain size in rice (Oryza sativa L.). Plant Mol Biol 105:405–417

    Article  CAS  Google Scholar 

Download references

Funding

This research was supported by the Heilongjiang Provincial government Postdoctoral Foundation of China (LBH-Z16188), and the Natural Science Foundation Joint Guide Project of Heilongjiang (LH2019C035).

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Authors and Affiliations

  1. Heilongjiang Acamedy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, China

    Hongliang Zheng, Shichen Sun, Liangming Bai, Shukun Jiang, Guohua Ding & Tongtong Wang

  2. Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China

    Hongliang Zheng, Hongwei Zhao, Jingguo Wang, Hualong Liu, Luomiao Yang, Yan Jia, Xin Wei & Detang Zou

  3. Heilongjiang Acamedy of Agricultural Sciences, Harbin, 150086, China

    Yongcai Lai

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  1. Hongliang Zheng
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Correspondence to Yongcai Lai.

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Zheng, H., Sun, S., Bai, L. et al. Identification of candidate genes for panicle length in Oryza sativa L. ssp. japonica via genome-wide association study and linkage mapping. Euphytica 218, 16 (2022). https://doi.org/10.1007/s10681-022-02972-7

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