African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6941

Full Length Research Paper

Association mapping for flag leaf thickness in an indica rice population from South China

Chuanguang Liu
  • Chuanguang Liu
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Dagang Chen
  • Dagang Chen
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Xinqiao Zhou
  • Xinqiao Zhou
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Jie Guo
  • Jie Guo
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Juchang Li
  • Juchang Li
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Lijun Li
  • Lijun Li
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar
Youding Chen
  • Youding Chen
  • Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
  • Google Scholar


  •  Received: 19 December 2018
  •  Accepted: 04 March 2019
  •  Published: 20 June 2019

References

Agrama HA, Eizenga GC, Yan W (2007). Association mapping of yield and its components in rice cultivars. Molecular Breeding 19:341-356.
Crossref

 

Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch S R (2015). Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). PLoS One 10:e0119873.
Crossref

 

Breseghello F, Sorrells ME (2006a). Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165-1177.
Crossref

 

Breseghello F, Sorrells ME (2006b). Association analysis as a strategy for improvement of quantitative traits in plants. Crop Science 46:1323-1330.
Crossref

 

Che Z, Liu H, Yi F, Cheng H, Yang Y, Wang L, Du J, Zhan P, Wang J, Yu D (2017). Genome-wide association study reveals novel loci for SC7 resistance in a soybean mutant panel. Frontiers in Plant Science 8:1771.
Crossref

 

Chen YD, Zhou XQ, Chen DG, Li LJ, Li JC, Zhang X (2011). Studies on the differences of morphological characteristics for different high-yielding rice types in the late crop environmental condition. In: Chen Y D and Zhang X eds, Researches on dynamic plant type in indica rice. Shanghai Scientific & Technical Publishers, Shanghai, China, pp. 28-38.

 

Cui D, Xu C, Tang C, Yang C, Yu T, A X, Cao G, Xu F, Zhang J, Han L (2013). Genetic structure and association mapping of cold tolerance in improved japonica rice germplasm at the booting stage. Euphytica 193:369-382.
Crossref

 

Davila Olivas NH, Kruijer W, Gort G, Wijnen CL, Loon JJA, Dicke M (2017). Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in arabidopsis thaliana. New Phytologist 213:838-851.
Crossref

 

Dong Z, Li D, Hu X, Liang L, Wu G, Zeng S, Liu E, Wu Y, Wang H, Bhanbhro L B, Dang X, Hong D (2018). Mining of favorable marker alleles for flag leaf inclination in some rice (Oryza Sativa, l.) accessions by association mapping. Euphytica 214:117.
Crossref

 

Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.
Crossref

 

Excoffier L, Laval G, Schneider S (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1:47-50.
Crossref

 

Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008). NARROW LEAF 7 controls leaf shape mediated by auxin in rice. Molecular Genetics and Genomics 279:499-507.
Crossref

 

Fujino K, Obara M, Shimizu T, Koyanagi K O, Ikegaya T (2015). Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region. Breeding Science 65:403-410.
Crossref

 

Gladun IV, Karpov EA (1993). Distribution of assimilates from the flag leaf of rice during the reproductive period of development. Russian Journal of Plant Physiology 40:215-219.

 

Hardy OJ, Vekemans X (2002). SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2:618-620.
Crossref

 

Huang X, Han B (2018). Genome-wide association mapping of complex traits in rice. In: Sasaki T., Ashikari M. (eds), Rice genomics, genetics and breeding. Springer, Singapore, pp. 497-510.
Crossref

 

Jiang S, Zhang X, Wang J, Chen W, Xu Z (2010). Fine mapping of the quantitative trait locus qFLL9 controlling flag leaf length in rice. Euphytica 176:341-347.
Crossref

 

Jin F, Hua S, Xu H, Yang L, Jiang Y, Xu Z, Shao X (2018). Comparisons of plant-type properties and grain quality in filial generations of Indica×Japonica hybridization grown in different rice-growing areas of China. International Journal of Agriculture and Biological Sciences 20:959-965.

 

Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J (2010). Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theoretical and Applied Genetics 121:475-487.
Crossref

 

Kanbe T, Sasaki H, Aoki N, Yamagishi T, Ebitani T, Yano M, Ohsugi R (2008). Identification of QTLs for improvement of plant type in rice (Oryza sativa L.) using Koshihikari/Kasalath chromosome segment substitution lines and backcross progeny F2 population. Plant Production Science 11:447-456.
Crossref

 

Khowaja FS, Price AH (2008). QTL mapping rolling, stomatal conductance and dimension traits of excised leaves in the Bala×Azucena recombinant inbred population of rice. Field Crops Research 106:248-257.
Crossref

 

Kraakman ATW, Martínez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006). Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Molecular Breeding 17:41-58.
Crossref

 

Khush GS (1995). Breaking the yield frontier of rice. GeoJournal 35:329-332.
Crossref

 

Laza MR, Kondo M, Ideta O, Barlaan E, Imbe T (2006). Identification of quantitative trait loci for δ13C and productivity in irrigated lowland rice. Crop Science 46:763-773.
Crossref

 

Liu CG, Zhou XQ, Chen DG, Li LJ, Li JC, Chen YD (2014). Natural variation of leaf thickness and its association to yield traits in indica rice. Journal of Integrative Agriculture 13:316-325.
Crossref

 

Liu KJ, Muse SV (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
Crossref

 

Liu C, Zhang G (2010). Genetic diversity revealed by SSR markers and temporal trends of major commercial inbred indica rice cultivars in South China in 1949-2005. Acta Agronomica Sinica 36:1843-1852.
Crossref

 

Mackay I, Powell W (2007). Methods for linkage disequilibrium mapping in crops. Trends in Plant Science 12:57-63.
Crossref

 

Matsushima S (1976). High-yielding rice cultivation. University of Tokyo Press 

View

 

Nakagawa S (2004). A farewell to Bonferroni: the problems of low statistical power and publication bias. Behavioral Ecology 15:1044-1045
Crossref

 

Neumann K, Kobiljski B, Denčić S, Varshney RK, Börner A (2011). Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Molecular Breeding 27:37-58.
Crossref

 

Pace J, Gardner C, Romay C, Ganapathysubramanian B, Lübberstedt T (2015). Genome-wide association analysis of seedling root development in maize (zea mays l.). BMC Genomics 16:47.
Crossref

 

Panaud O, Chen X, McCouch SR (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L). Molecular Genetics and Genomics 252:597-607.
Crossref

 

Peng S (2000). Single-leaf and canopy photosynthesis of rice. In, Sheehy J E, Mitchell P L, Hardy B, eds. Redesigning Rice Photosynthesis to Increase Yield. IRRI, Los Bannos, Philipines pp. 213-228.
Crossref

 

Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155:945-959

 

Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008). Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiology 147:1947-1959.
Crossref

 

Qu M, Zheng G, Hamdani S, Essemine J, Song Q, Wang H, Chu C, Sirault X, Zhua X (2017). Leaf photosynthetic parameters related to biomass accumulation in a global rice diversity survey. Plant Physiology 175:248-258.
Crossref

 

Rode J, Ahlemeyer J, Friedt W, Ordon F (2012). Identification of marker-trait associations in the German winter barley breeding gene pool (Hordeum vulgare L.). Molecular Breeding 30:831-843.
Crossref

 

Sabiel SAI, Huang S, Hu X, Ren X, Fu C, Peng J, Sun D (2017). SNP-based association analysis for seedling traits in durum wheat (triticum turgiduml.durum(desf.)). Breeding Science 67:83-94.
Crossref

 

Sakamoto T, Morinaka Y, Ohnishi T, Sunohara H, Fujioka S, Ueguchi-Tanaka M, Mizutani M, Sakata K, Takatsuto S, Yoshida S, Tanaka H, Kitano H, Matsuoka M (2006). Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nature Biotechnology 24:105-109.
Crossref

 

Shen B, Yu WD, Zhu YJ, Fan YY, Zhuang JY (2012). Fine mapping of a major quantitative trait locus, qFLL6.2, controlling flag leaf length and yield traits in rice (Oryza sativa L.). Euphytica 184:57-64.
Crossref

 

Shinada H, Yamamoto T, Yamamoto E, Hori K, Yonemaru J, Matsuba S, Fujino K (2014). Historical changes in population structure during rice

 

breeding programs in the northern limits of rice cultivation. Theoretical and Applied Genetics 127:995-1004.

 

Takai T, Kondo M, Yano M, Yamamoto T (2010). A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice. Rice 3:172-180.
Crossref

 

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28:2731-2739.
Crossref

 

Wang P, Zhou G, Yu H, Yu S (2011). Fine mapping a major QTL for flag leaf size and yield-related traits in rice. Theoretical and Applied Genetics 123:1319-1330.
Crossref

 

Wang R, Leng Y, Ali S, Wang M, Zhong S (2017). Genome-wide association mapping of spot blotch resistance to three different pathotypes of Cochliobolus sativus, in the USDA barley core collection. Molecular Breeding 37:44.
Crossref

 

Wang S, Basten CJ, Zeng ZB (2007). Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. 

View

 

Xu Q, Yuan X, Wang S, Feng Y, Yu H, Wang Y, Yang Y, Wei X, Li X (2016). The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis. BMC Genetics 17:53.
Crossref

 

Yang SR, Zhang LB, Wang JM (1984). The theory and method of ideal plant morphology in rice breeding. Scientia Agricultura Sinica 17:6-13.

 

Yang X, Yan J, Shah T, Warburton M, Li Q, Li L, GaoY, Chai Y, Fu Z, Zhou Y, Xu S, Bai G, Meng Y, Zheng Y, Li J (2010). Genetic analysis and characterization of new maize association mapping panel for quantitative trait loci dissection. Current Science 121:417-431.
Crossref

 

Yu J, Buckler ES (2006). Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17:155-160.
Crossref

 

Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen M, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38:203-208.
Crossref

 

Yu P, Yuan X, Xu Q, Wang C, Yu H, Wang Y, Tang S, Wei X (2013). Genetic Structure and Indica/Japonica Component Changes in Major Inbred Rice Varieties in China. Rice Science 20:39-44.
Crossref

 

Yuan LP (1997). Hybrid rice breeding for super high yield. Hybrid Rice 12(6):1-6.

 

Zhai L, Zheng T, Wang X, Wang Y, Chen K, Wang S, Wang Y, Xu J, Li Z (2018). QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome-wide association study. Rice 11:13.
Crossref

 

Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y (2011). Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 6:e27565.
Crossref

 

Zhang P, Liu X, Tong H, Lu Y, Li, J (2014). Association mapping for important agronomic traits in core collection of rice (oryza sativa l.) with ssr markers. PLoS One 9:e111508.
Crossref

 

Zhao WG, Chung JW, Kwon SW, Lee JH, Ma KH, Park YJ (2013). Association analysis of physicochemical traits on eating quality in rice (Oryza sativa L.). Euphytica 191:9-21.
Crossref

 

Zhao X, Xu J, Zhao M, Lafitte R, Zhu L, Fu B, Gao Y, Li Z (2008). QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.). Plant Science 174:618-625.
Crossref

 

Zheng K, Huang N, Bennett J, Khush GS (1995). PCR-based marker-assisted selection in rice breeding. IRRI discussion paper series No.12. Manila: IRRI

 

Zhou Y, Fang YX, Zhu JY, Li SQ, Gu F, Gu MH, Liang GH (2010). Genetic analysis and gene fine mapping of a rolling leaf mutant (rl11(t)) in rice (Oryza sativa L.). Chinese Science Bulletin 55:1763-1769.
Crossref

 

Zhu C, Gore M, Buckler ES, Yu J (2008). Status and prospects of association mapping in plants. Plant Genome 1:5-20.
Crossref

 

Zhu G, Peng S, Huang J, Cui K, Nie L, Wang F (2016). Genetic Improvements in Rice Yield and Concomitant Increases in Radiation- and Nitrogen-Use Efficiency in Middle Reaches of Yangtze River. Scientific Reports 6:21049.
Crossref