Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

BMC Genetics

Selvadurai Dayanandan²  Mohammed Latif Khan¹  Baharul Islam Choudhury² 

[1] Department of Botany, Dr. Hari Singh Gour Central University, Sagar 470003, Madhya Pradesh, India;Québec Centre for Biodiversity Sciences, Montréal, QC, Canada

关键词: Trait specific genes;    Rice;    NE India;    Nucleotide diversity;    Indigenous;   

Others  :  866443
DOI  :  10.1186/1471-2156-15-71

 received in 2013-08-03, accepted in 2014-06-10,  发布年份 2014

【 摘 要 】

Background

During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus.

Results

No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (π_tot = 0.0053) than nonglutinous type varieties (π_tot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (π_tot = 0.0010) than in the colored apiculus varieties (π_tot = 0.0023).

Conclusions

The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.

【 授权许可】

   
2014 Choudhury et al.; licensee BioMed Central Ltd.

【 图 表 】

【 参考文献 】

• [1]Doebley JF, Gaut BS, Smith BD: The molecular genetics of crop domestication. Cell 2006, 127(7):1309-1321.
• [2]Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M: An SNP caused loss of seed shattering during rice domestication. Science 2006, 312(5778):1392-1396.
• [3]Li C, Zhou A, Sang T: Rice domestication by reducing shattering. Science 2006, 311(5769):1936-1939.
• [4]Sweeney MT, Thomson MJ, Pfeil BE, McCouch S: Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 2006, 18(2):283-294.
• [5]Yamanaka S, Nakamura I, Watanabe KN, Sato YI: Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet 2004, 108(7):1200-1204.
• [6]Bradbury LM, Fitzgerald TL, Henry RJ, Jin Q, Waters DL: The gene for fragrance in rice. Plant Biotechnol J 2005, 3(3):363-370.
• [7]Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M: Cytokinin oxidase regulates rice grain production. Science 2005, 309(5735):741-745.
• [8]Song XJ, Huang W, Shi M, Zhu MZ, Lin HX: A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 2007, 39(5):623-630.
• [9]Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS: Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci 1998, 95(8):4441-4446.
• [10]Tanksley SD, McCouch SR: Seed banks and molecular maps: unlocking genetic potential from the wild. Science 1997, 277(5329):1063-1066.
• [11]Simmonds NW: Evolution of Crop Plants. New York: Longman; 1976.
• [12]Buckler ES, Thornsberry JM, Kresovich S: Molecular diversity, structure and domestication of grasses. Genet Res 2001, 77(3):213-218.
• [13]Wang RL, Stec A, Hey J, Lukens L, Doebley J: The limits of selection during maize domestication. Nature 1999, 398(6724):236-239.
• [14]Tian F, Stevens NM, Buckler ES: Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10. Proc Natl Acad Sci 2009, 106:9979-9986.
• [15]Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD: Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 2006, 173(2):975-983.
• [16]Roder W, Keoboulapha B, Vannalath K, Phouaravanh B: Glutinous rice and its importance for hill farmers in Laos. Econ Bot 1996, 50(4):401-408.
• [17]Sano Y: Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 1984, 68(5):467-473.
• [18]Hirano HY, Eiguchi M, Sano Y: A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol Biol Evol 1998, 15(8):978-987.
• [19]Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K: A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J 1998, 15(1):133-138.
• [20]Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD: Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 1997, 94(6–7):773-781.
• [21]Wan YX, Deng QM, Wang SQ, Liu MW, Zhou HQ, Li P: Genetic polymorphism of Wx gene and its correlation with main grain quality characteristics in rice. Rice Sci 2007, 14(2):85-93.
• [22]Wang ZF, Zheng FQ, Shen GZ, Gao JP, Snusted DP, Li MG, Zhang JL, Hong MM: The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 1995, 7:613-622.
• [23]Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM: Aberrant splicing of intron 1 leads to the heterogeneous 5′ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 1998, 14(4):459-465.
• [24]Olsen KM, Purugganan MD: Molecular evidence on the origin and evolution of glutinous rice. Genetics 2002, 162(2):941-950.
• [25]Dooner HK, Robbins TP, Jorgensen RA: Genetic and developmental control of anthocyanin biosynthesis. Annu Rev Genet 1991, 25(1):173-199.
• [26]Koes RE, Quattrocchio F, Mol JN: The flavonoid biosynthetic pathway in plants: function and evolution. BioEssays 1994, 16(2):123-132.
• [27]Saitoh K, Onishi K, Mikami I, Thidar K, Sano Y: Allelic diversification at the C (OsC1) Locus of wild and cultivated rice nucleotide changes associated with phenotypes. Genetics 2004, 168(2):997-1007.
• [28]Doyle JJ, Doyle JL: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987, 19:11-15.
• [29]Dayanandan S, Bawa KS, Kesseli RV: Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 1997, 84:1658-1663.
• [30]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948.
• [31]Librado P, Rozas J: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25(11):1451-1452.
• [32]Watterson GA: On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975, 7(2):256-276.
• [33]Nei M: Molecular Evolutionary Genetics. New York: Columbia University Press; 1987.
• [34]Tajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123(3):585-595.
• [35]Fu YX, Li WH: Statistical tests of neutrality of mutations. Genetics 1993, 133(3):693-709.
• [36]McDonald JH, Kreitman M: Adaptive protein evolution at the Adh locus in Drosophila. Nature 1991, 351(6328):652-654.
• [37]Shu QY, Wu DX, Xia YW, Gao MW, Ayres NM, Larkin PD, Park WD: Microsatellites polymorphism on the waxy gene locus and their relationship to amylose content in indica and japonica rice, Oryza sativa L. Acta Genet Sin 1999, 26(4):350-358.
• [38]Bao JS, Corke H, Sun M: Microsatellites, single nucleotide polymorphisms and sequence tagged site in starchsynthesizing genes in relation to starch physiochemical properties in non-waxy rice (Oryza sativa L.). Theor Appl Genet 2006, 113:1185-1196.
• [39]Doebley J, Stec A, Wendel J, Edwards M: Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc Natl Acad Sci 1990, 87:9888-9892.
• [40]Zhu Y, Ellstrand NC, Lu BR: Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication. Ecol Evol 2012, 2(9):2106-2113.
• [41]Wei-Hua Q, You-Tao C, Rong-Sheng W, Xin W, Li-Rong C, Wan-Xia Z, Qing-Wen Y: Nucleotide diversity in gene and validation of single nucleotide polymorphism in relation to amylose content in Chinese microcore rice germplasm. Crop Sci 2012, 52(4):1689-1697.
• [42]Zhang D, Zhang H, Wang M, Sun J, Qi Y, Wang F, Li Z: Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 2009, 119(6):1105-1117.
• [43]Sigmon B, Vollbrecht E: Evidence of selection at the ramosa1 locus during maize domestication. Mol Ecol 2010, 19(7):1296-1311.
• [44]Inukai T, Sako A, Hirano HY, Sano Y: Analysis of intragenic recombination at wx in rice: correlation between the molecular and genetic maps within the locus. Genome 2000, 43(4):589-596.
• [45]Zeng M, Morris CF, Batey IL, Wrigley CW: Sources of variation for starch gelatinization, pasting, and gelation properties in wheat. Cereal Chem 1997, 74:63-71.
• [46]Kiswara G, Lee JH, Hur YJ, Cho JH, Lee JY, Kim SY, Kim KM: Genetic analysis and molecular mapping of low amylose gene du12 (t) in rice (Oryza sativa L.). Theor Appl Genet 2014, 127(1):51-57.
• [47]Teng B, Zhang Y, Wu J, Cong X, Wang R, Han Y, Luo Z: Association between allelic variation at the Waxy locus and starch physicochemical properties using single‒segment substitution lines in rice (Oryza sativa L.). Starch-Starke 2013, 65(11–12):1069-1077.
• [48]Xu F, Zhang G, Tong C, Sun X, Corke H, Sun M, Bao J: Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.). J Agric Food Chem 2013, 61(42):10110-10117.
• [49]Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y, Sano Y: Allelic diversification at the wx locus in landraces of Asian rice. Theor Appl Genet 2008, 116(7):979-989.
• [50]Liu A, Burke JM: Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 2006, 173(1):321-330.