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Development of EST-SSR marker and genetic diversity analysis in Sorghum bicolor×Sorghum sudanenes

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  • 1. College of Agronomy, Inner Mongolia Agricultural University, Huhhot 010019, China 2. College of Ecology and Environment, Inner Mongolia Agricultural University, Huhhot 010019, China

Received date: 2012-10-04

  Revised date: 2012-12-26

  Online published: 2013-02-25

Abstract

A total of 57 498 non-redundant ESTs were identified from 210 878 ESTs of Sorghum in NCBI by sequence analysis. In all, 3 338 SSRs were distributed in 3 116 ESTs with an average frequency of one SSR per 11.28 kb, which included 215 SSR motifs. Analysis of SSR motifs revealed that the trinucleotides were major motifs, accounting for 68.33%.The dinucleotides motifs accounted for 17.97%. There were 1 694 sequences from 3 338 EST-SSR sequences could be designed into primers and the proportion was 50.75%. Fourteen primers were selected to amplify EST-SSR loci with 50 collections of Sorghum bicolor × S. sudanenes, 7 collections of S. bicolor and 3 collections of S. sudanenes. Seventy-two allele variations were detected and the frequency was 5.14 gene loci per primer. The polymorphism index of each primer was in the range of 0.54-0.93. The genetic distance ranged from 0.1646 to 0.6398. This showed abundant genetic diversity in the materials. The materials were divided into 5 groups with clustering analysis of EST-SSR data. Each group included the varieties with similar parents or similar regional distribution. Meanwhile, 4 specific molecular markers were found. Primer D1763 was specific in the registered variety GB-4-2 which was the progeny of S. bicolor 314A ×S. sudanenes White Skull. The marker was specific in justification of the germ difference. These results showed that the EST-SSR was an effective marker for genetic diversity analysis and specificity studies on S. bicolor × S. sudanenes.

Cite this article

WEN Ying LU Xiao-Ping REN Rui MI Fu-Gui HAN Ping-An XUE Chun-Lei . Development of EST-SSR marker and genetic diversity analysis in Sorghum bicolor×Sorghum sudanenes[J]. Hereditas(Beijing), 2013 , 35(2) : 225 -232 . DOI: 10.3724/SP.J.1005.2013.00225

References

[1] 詹秋文, 钱章强. 高粱与苏丹草杂种优势利用的研究. 作物学报, 2004, 30(1): 73-77.
[2] 张延明, 曲敏, 徐香玲, 李集临. 表达序列标签(EST)分析及其在小麦研究中的应用. 黑龙江农业科学, 2007, (1): 82-85.
[3] 李小白, 张明龙, 崔海瑞. 油菜EST-SSR标记的建立. 分子细胞生物学报, 2007, 40(2): 137-144.
[4] 陈全求, 詹先进, 蓝家祥, 黄云, 符家平. EST分子标记在基因组学中应用的研究进展. 中国农学通报, 2010, 26(3): 59-63.
[5] 晏慧君, 张颢, 谢吉容, 李树发, 蹇洪英, 邱显钦, 王其刚, 王继华, 唐开学. 基于差减cDNA文库EST信息的月季花香突变体SSR标记的开发. 遗传, 2009, 31(9): 962-966.
[6] Varshney RK, Sigmund R, Bömer A, Korzun V, Stein N, Sorrells ME, Langridge P, Gran A. Interspecific transfer-ability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 2005, 168(1): 195-202.
[7] 陈军方, 任正隆, 高丽锋, 贾继增. 从小麦EST序列中开发新的SSR引物. 作物学报, 2005, 31(2): 154-158.
[8] Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet, 2003, 106(3): 411-422.
[9] 杨新泉, 刘鹏, 韩宗福, 倪中福, 刘旺清, 孙其信. 普通小麦Genomic-SSR和EST-SSR分子标记遗传差异及其与系谱遗传距离的比较研究. 遗传学报, 2005, 32(4): 406-416.
[10] 金基强, 崔海瑞, 龚晓春, 陈文岳, 忻雅. 用EST-SSR标记对茶树种质资源的研究. 遗传, 2007, 29(1): 103-108.
[11] Lu XP, Yun JF, Gao CP, Acharya S. Quantitative trait loci analysis of economically important traits in Sorghum bicolor × S. sudanense hybrid. Can J Plant Sci, 2011, 91(1): 81-90.
[12] 逯晓萍, 云锦凤, 张雅慧, 薛春雷, 陈强. 高丹草重组自交系群体的遗传变异与高产种质的创新. 华北农学, 2009, 24(5): 90-95.
[13] 逯晓萍, 云锦凤, 米福贵, 陈强, 张雅慧, 薛春雷. 基于性状和分子标记的高丹草近等基因系的分离研究. 中国农业科学, 2010, 43(3): 468-473.
[14] 温莹, 逯晓萍, 米福贵, 薛春蕾, 杨凯. 高丹草单株产量主基因+多基因混合遗传模型及效应分析. 见: 北方遗传资源的保护与利用研讨会论文汇编. 北京: 中国遗传学会, 2010.
[15] 李永强, 李宏伟, 高丽锋, 何蓓如. 基于表达序列标签的微卫星标记(EST-SSRs)研究进展. 植物遗传资源学报, 2004, 5(1): 91-95.
[16] 谢皓, 陈学珍, 杨柳, 王建立. EST-SSR标记的发展和在植物遗传研究中的应用. 北京农学院学报, 2005, 20(4): 73-76.
[17] 肖木辑, 李明顺, 李新海, 张世煌. 东北地区主要玉米自交系的SSR遗传多样性分析. 华北农学报, 2006, 21(增刊): 23-27.
[18] Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 1978, 89(3): 583-590.
[19] 姜春芽, 廖娇, 徐小彪, 辜青青, 刘善军, 陈金印. 植物EST-SSR技术及其应用. 分子植物育种, 2009, 7(1): 125-129.
[20] Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol, 2008, 8: 97.
[21] Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R. Transfer-ability of the EST-SSRs developed on Nules Clementine (Citrus clementina Hort ex Tan) to other citrus species and their effectiveness for genetic mapping. BMC Genomics, 2008, 9: 287.
[22] Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krish-nakumar V, Singh L. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Pppl Genet, 2007, 114(2): 359-372.
[23] 包文斌, 陈国宏, 误信生, 徐琪, 吴圣龙, 束婧婷, Wei-gend S. 中国红原鸡和泰国红原鸡遗传多样性分析. 遗传, 2007, 29(5): 587-592.
[24] Wang LX, Guan Y, Guan RX, Li YH, Ma YS, Dong ZM, Liu X, Zhang HY, Zhang YQ, Liu ZX, Chang RZ, Xu HM, Li LH, Lin FY, Luan WJ, Yan Z, Ning XC, Zhu L, Cui YH, Piao RH, Liu Y, Chen PY, Qiu LJ. Establishment of Chi-nese soybean Glycine max core collections with agronomic traits and SSR markers. Euphytica, 2006, 151(2): 215-223.
[25] 李丽华, 魏昕, 潘光堂, 唐保军, 丁勇, 赵发欣. 新选优良玉米自交系SSR遗传多样性分析. 玉米科学, 2009, 17(4): 24-28.
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