Genetic differentiation revealed by selective loci of drought-responding EST-SSRs between upland and lowland rice in China

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Xia, Hui ^a   Zheng, Xiaoguo ^a   Chen, Liang ^a   Gao, Huan ^a   Yang, Hua ^a   Long, Ping ^a   Rong, Jun ^b   Lu, Baorong ^c   Li, Jiajia ^a   Luo, Lijun ^a  

^a SHANGHAI AGROBIOLOGICAL GENE CENTER   (China)

^b NANCHANG UNIVERSITY   (China)

^c FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CHINA; CONTROLLED STUDY; CORRELATIONAL STUDY; DROUGHT RESISTANCE; ECOTYPE; EXPRESSED SEQUENCE TAG; FIELD EXPERIMENT; GENE EXPRESSION; GENE LOCUS; GENETIC DISTANCE; GENETIC VARIABILITY; LANDRACE; LOWLAND RICE; MOLECULAR EVOLUTION; MORPHOLOGICAL TRAIT; NONHUMAN; OSMOTIC STRESS; RICE; SIMPLE SEQUENCE REPEAT; UPLAND RICE; ANATOMY AND HISTOLOGY; CONFIDENCE INTERVAL; DROUGHT; GENETICS; MOLECULAR GENETICS; PHYLOGENY; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCUS;

MICROSATELLITE DNA;

ALLELES; CHINA; CONFIDENCE INTERVALS; DROUGHTS; ECOTYPE; EXPRESSED SEQUENCE TAGS; GENETIC VARIATION; GENETICS, POPULATION; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; ORYZA SATIVA; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCI;

EID: 84907702273     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106352     Document Type: Article

References (29)

1. Nosil P, Funk DJ, Ortiz-Barrientos D (2009) Divergent selection and heterogeneous genomic divergence. Mol Ecol 18: 375-402.
2. Shikano T, Ramadevi J, Merilä J (2010) Identification of local- and habitatdependent selection: scanning functionally important genes in nine-spined sticklebacks (Pungitius pungitius). Mol Biol Evol 27: 2775-2789.
3. Hübner S, Höfïken M, Oren E, Haseneyer G, Stein N, et al. (2009) Strong correlation of wild barley (.Hordeum spontaneum) population structure with temperature and precipitation variation. Mol Ecol 18: 1523-1536.
4. Whitehead A, Triant DA, Champlin D, Nacci D (2010) Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population. Mol Ecol 19: 5186-5203.
5. Xia H, Camus-Kulandaivelu L, Stephan W, Tellier A, Zhang ZW (2010) Nucleotide diversity patterns of local adaptation at drought-related candidate genes in wild tomatoes. Mol Ecol 19: 4144-4154.
6. Bernier J, Atlin GN, Serraj R, Kumar A, Spaner D (2008) Breeding upland rice for drought resistance. J Sci Food Agr 88: 927-939.
7. Farooq M, Wahid A, Lee DJ, Ito O, Siddique KH (2009) Advances in drought resistance of rice. Crit Rev Plant Sci 28: 199-217.
8. Luo LJ (2010) Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot 61: 3509-3517.
9. IRRI (International Rice Research Institute) (1986) Upland rice:A global perspective. Los Baiios, Philippines.
10. Yu LX, Nguyen HT (1994) Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.) Theor Appl Genet 87: 668-672.
11. Zhang DL, Zhang HL, Wang MX, Sun JL, et al. (2009) Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 119: 1105-1117.
12. Ishikawa R, Maeda K, Harada T, Niizeki M, Saito K (1992) Genotypic variation for 17 isozyme genes among Japanese upland varieties in rice. Japan J Breeding 42: 737-746.
13. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. TRENDS Biotech 23: 48-55.
14. Lan JS, Hu FS, Zhang JR (1990) The concept and statistical method of drought resistance index in crops. Acta Agriculturae Boreali-Sinica 5: 20-25 (in Chinese with English abstract)
15. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
16. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G (2008) LOSITAN: a workbench to detect molecular adaptation based on a Fst-oudier method. BMC Bioinformatics 9: 323.
17. Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180: 977-993.
18. Vitalis R, Dawson K, Boursot P, Belkhir K (2003) DetSel 1.0: a computer program to detect markers responding to selection. J Heredity 94: 429-4-31.
19. Miller JR, Wood BP, Hamilton MB (2008) FST and QST Under Neutrality. Genetics, 180, 1023-1037.
20. Martin MA, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers. Tree Genetics & Genomes 6: 735-744.
21. Zhang H, Mao X, Wu X, Wang C, Jing R (2011) An abiotic stress response gene TaSnRK2.7-B in wheat accessions: genetic diversity analysis and gene mapping based on SNPs. Gene 478: 28-34.
22. Steele KA, Edwards G, Zhu J, Witcombe JR (2004) Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding. Theor Appl Genet 109: 1247-1260.
23. Knight CA, Vogel H, Kroymann J, Shumate A, Witsenboer H, Mitchell-Olds T (2006) Expression profiling and local adaptation of Boechera holboellii populations for water use efficiency across a naturally occurring water stress gradient. Mol Ecol 15: 1229-1237.
24. Ross-Ibarra J, Morrell PL, Gaut BS (2007) Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci, USA 104: 8641-8648.
25. Lyu J, Zhang SL, Dong Y, et al. (2013) Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nature Communications, 4: 2138. doi: 10.1038/ncomms3138.
26. Yang HP, Matsubayashi Y, Nakamura K, Sakagami Y (1999) Oryza sativa PSK gene encodes a precursor pf phytosulfokine-α, a sulfated peptide growth factor found in plants. Proc Natl Acad Sci, USA 96: 13560-13565.
27. Huang JY, Wang YE, Yang JS (2010) Over-expression of OsPSK3 increases chlorophyll content of leaves in rice. Hereditas 32: 1281-1289.
28. Ichitani K, Namigoshi K, Sato K, Taura S, Aoki M, et al. (2007) Fine mapping and allelic dosage effect of Hwcl a complementary hybrid weakness gene in rice. Theor Appl Genet 114: 1407-1415.
29. Gholizadeh A (2011) Heterologous expression of stress-responsive duf538 domain containing protein and its morpho-biochemical consequences. Prot J 30: 351-358.