|本期目录/Table of Contents|

[1]徐珍媚,邓光兵,张海莉,等.基于BSA分析定位控制西藏大麦侧小穗发育的基因[J].应用与环境生物学报,2018,24(06):1350-1358.[doi:10.19675/j.cnki.1006-687x.2018.03032]
 XU Zhenmei,et al..Mapping loci that control lateral spike development in Tibetan barley by bulked segregant analysis (BSA)[J].Chinese Journal of Applied & Environmental Biology,2018,24(06):1350-1358.[doi:10.19675/j.cnki.1006-687x.2018.03032]
点击复制

基于BSA分析定位控制西藏大麦侧小穗发育的基因
分享到:

《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
24卷
期数:
2018年06期
页码:
1350-1358
栏目:
研究论文
出版日期:
2018-12-25

文章信息/Info

Title:
Mapping loci that control lateral spike development in Tibetan barley by bulked segregant analysis (BSA)
作者:
徐珍媚 邓光兵 张海莉 梁俊俊 苏燕 李莉岚 龙海 余懋群
1中国科学院成都生物研究所 成都 610041 2中国科学院大学 北京 100049
Author(s):
XU Zhenmei et al.
1 Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu 610041, China 2 University of Chinese Academy of Sciences, Beijing 100049, China
关键词:
西藏大麦棱数性状集群分离法(BSA)基因定位
Keywords:
Tibetan barley row type bulked segregant analysis (BSA) gene mapping
分类号:
S512.303
DOI:
10.19675/j.cnki.1006-687x.2018.03032
摘要:
大麦侧小穗结实与否导致了二棱/六棱性状的分化,从而显著影响其籽粒产量,因此大麦二棱到六棱的变化具有显著驯化特征. 青藏高原野生和栽培大麦资源丰富,被认为是栽培大麦的驯化和遗传多样性中心之一. 为进一步了解大麦棱数调控的遗传基础以及西藏栽培大麦驯化的过程,以西藏野生二棱大麦和六棱大麦地方品种为亲本构建遗传分离群体,遗传分析发现二棱性状受单个显性基因位点控制. 通过集群分离法(Bulked segregant analysis,BSA)分别建立含有22个F2单株的二棱混池和六棱混池,基于SLAF-seq(Specific-locus amplified fragment sequencing)技术共获得456 691个SLAF标签,通过SNP-index和ED两种关联算法交集得到3个与棱数性状相关的侯选区域,总长度为53.84 Mb,包含536个基因,其中能分别被3个数据库GO、KEGG和COG注释的基因有413、189和160个基因. 上述研究实现了对控制西藏大麦侧小穗发育性状相关基因的初步定位,结果可为后续目标基因的精细定位和克隆提供理论参考. (图3 表7 参51)
Abstract:
Fertility of lateral spikelets determines the two-rowed or six-rowed spikes of barley (Hordeum vulgare L.), which results in significantly different grain yields. The change in row type from two-rowed to six-rowed shows remarkable domestication characteristics. The Qinghai-Tibet plateau has abundant resources of wild and cultivated barley, and is considered one of the centers of domestication and genetic diversity of cultivated barley. In order to obtain a primary understanding of the genetic basis of lateral spike development regulation and the domestication process in cultivated Tibetan barley, an F2 segregation population was constructed by crossing the two-rowed wild barley accession ZYM0083 with the six-rowed landraces Linzhiheiliuleng. Genetic analysis showed that the row type was controlled by a single gene. Using the specific-locus amplified fragment sequencing (SLAF-seq) technology and bulked segregant analysis (BSA), two DNA pools from 22 two-rowed spike individuals and 22 six-rowed spike individuals of the F2 population were constructed and sequenced. A total of 456 691 SLAF tags were obtained. By adopting the ED and SNP index for association analysis, three candidate regions with a 53.84-Mb interval and containing 536 genes were obtained. Four-hundred thirteen, 189, and 160 annotated genes were acquired by GO, KEGG, and COG libraries, respectively. Loci that control lateral spike development in Tibetan barley were primarily mapped by SLAF-seq, and the results presented in this study will facilitate the fine mapping and cloning of target genes.

参考文献/References:

1. Purugganan MD, Fuller DQ. The nature of selection during plant domestication [J]. Nature, 2009, 457 (7231): 843-848
2. van Bothmer R, Komatsuda T. Barley origin and related species [M]//Ullrich E. Barley: Production, Improvement, and Uses. Oxford: Wiley-Blackwell, 2010: 14-62
3. Zohary D, Hopf M, Weiss E. Domestication of Plants in the Old World: The Origin and Spread of Domesticated Plants in Southwest Asia, Europe, and the Mediterranean Basin [M]. Oxford: Oxford University, 2012
4. Harlan JR, Zohary D. Distribution of wild wheats and barley [J]. Science, 1966, 153 (3740): 1074-1080
5. Nevo E. "Evolution Canyon": a microcosm of life's evolution focusing on adaptation and speciation [J]. Isr J Ecol Evol, 2006, 52 (3): 501-506
6. Morrell PL, Clegg MT. Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent [J]. PNAS, 2007, 104 (9): 3289-3294
7. Nevo E. Genome evolution of wild cereal diversity and prospects for crop improvement [J]. Plant Genet Resour-C, 2007, 4 (1): 36-46
8. Zohary D. Monophyletic vs. polyphyletic origin of the crops on which agriculture was founded in the Near East [J]. Isr J Ecol Evol, 1999, 46 (2): 133-142
9. Azhaguvel P, Komatsuda T. A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley [J]. Ann Bot, 2007, 100 (5): 1009-1015
10. Dai F, Nevo E, Wu D, Comadran J, Zhou M, Qiu L, Chen Z, Beiles A, Chen G, Zhang G. Tibet is one of the centers of domestication of cultivated barley[J]. PNAS, 2012, 109 (42): 16969-16973
11. Dai F, Chen ZH, Wang X, LiZ, Jin G, Wu D, Cai S, Wang N, Wu F, Nevo E, Zhang G. Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley[J]. PNAS, 2014, 111 (37): 13403-13408
12. Molina-Cano JL, Russell JR, Moralejo MA, Escacena JL, Arias G, Powell W. Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley [J]. Theor Appl Genet, 2005, 110 (4): 613-619
13. 马得泉, 戴先凯, 洛桑更堆, 干志峰. 西藏栽培大麦的分类研究[J]. 中国农业科学, 1992, 25 (3): 44-49 [Ma DQ, Dai XK, LSGD, GAN ZF. The research on classification of cultivated barley in Tibet autonomous region (continued) [J]. Sci Agric Sin, 1992, 25 (3): 44-49]
14. 徐廷文. 中国栽培大麦的起源与进化[J]. 遗传学报, 1982, 9 (6): 440-446 [Xu TW. Origin and evolution of cultivated barley in China [J]. Acta Genet Sin, 1982, 9 (6): 440-446]
15. 张亚生, 金涛, 尼玛扎西, 关卫星, 李宝海, 拉巴. 西藏高原地区麦作农业起源几个问题的探讨[J]. 西藏农业科技, 1999, 21 (4): 4-11 [Zhang YS, Jin T, NMZX, Guan WX, L BH, LB. Discussion on the origin of wheat in the Tibetan Plateau region [J]. Xizang Agric Sci Technol, 1999, 21 (4): 4-11]
16. 邵启全, 李长森, 巴桑次仁. 栽培大麦的起源与进化——我国西藏和川西的野生大麦[J]. 遗传学报, 1975, 2 (2): 123-128+181-182 [Shao QQ, Li CS, BACR. Origin and evolution of the cultivated barley-wild barleys from south western part of China [J]. Acta Genet Sin, 1975, 2 (2): 123-128+181-182]
17. 马得泉, 徐廷文. 西藏栽培大麦的分类和起源研究[J]. 中国农业科学, 1988, (5): 7-14 [Ma DQ, Xu TW. The research on classification and origin of cultivated barley in Tibet autonomous region [J]. Sci Agric Sin, 1988, 21 (5): 7-14]
18. Ren X, Nevo E, Sun D, Sun G. Tibet as a potential domestication center of cultivated barley of China [J]. PLoS ONE, 2013, 8 (5): e62700
19. van Bothmer R, Jacobsen N. Origin, Taxonomy, and Related Species [M]//Rasmusson DC. Barley. Madison, Wisconsin: American Society of Agronomy, 1985: 19-56
20. Zohary D, Hopf M, Domestication of Plants in the Old World [M]. 3rd ed. New York: Oxford University Press, 2000
21. Bull H, Casao MC, Zwirek M, Flavell AJ, Thomas WTB, Guo W, Zhang R, Rapazote-Flores P, Kyriakidis S, Russell J, Druka A, McKim SM, Waugh R. Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility [J]. Nat Commun, 2017, 8 (1): 936
22. Lundqvist U. Scandinavian mutation research in barley - a historical review [J]. Hereditas, 2014, 151 (6): 123-131
23. Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, Korff M. Six-rowed spike3 (vrs3) is a histone demethylase that controls lateral spikelet development in barley [J]. Plant Physiol, 2017, 174 (4): 2397-2408
24. Youssef HM, Eggert K, Koppolu R, Alqudah AM, Poursarebani N, Fazeli A, Sakuma S, Tagiri A, Rutten T, Govind G, Lundqvist U, Graner A, Komatsuda T, Sreenivasulu N, Schnurbusch T. VRS2 regulates hormone-mediated inflorescence patterning in barley [J]. Nat Genet, 2017, 49 (1): 157-161
25. Lundqvist U, Franckowiak JD, Konishi T. New and revised descriptions of barley genes [J]. Barley Genetic Newsl, 1997, 26: 22-43
26. Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene [J]. PNAS, 2007, 104 (4): 1424-1429
27. Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M, Rutten T, Seiler C, Himmelbach A, Ariyadasa R, Youssef HM, Stein N, Sreenivasulu N, Komatsuda T, Schnurbusch T. Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley [J]. PNAS, 2013, 110 (32): 13198-131203
28. Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WT, Macaulay M, MacKenzie K, Simpson C, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer G J, Waugh R. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1 [J]. Nat Genet, 2011, 43 (2): 169-172
29. Youssef HM, Koppolu R, Schnurbusch T. Re-sequencing of vrs1 and int-c loci shows that labile barleys (Hordeum vulgare convar. labile) have a six-rowed genetic background [J]. Genet Resour Crop Evol, 2011, 59 (7): 1319-1328
30. Saisho D, Pourkheirandish M, Kanamori H, Matsumoto T, Komatsuda T. Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence [J]. Breeding Sci, 2009, 59 (5): 621-628
31. Doyle J, Doyle J. Isolation of plant dna from fresh tissue [J]. Focus, 1990, 12: 13-15
32. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. Special features of RAD Sequencing data: implications for genotyping [J]. Mol Ecol, 2013, 22 (11): 3151-3164
33. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform [J]. Appl Environ Microb, 2013, 79 (17): 5112-5120
34. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform [J]. Bioinformatics, 2010, 26 (5): 589-595
35. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data [J]. Genome Res, 2010, 20 (9): 1297-1303
36. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. The sequence alignment/map format and SAMtools [J]. Bioinformatics, 2009, 25 (16): 2078-2079
37. Hill JT, Demarest, BL, Bisgrove, BW, Gorsi, B, Su, YC, Yost, H. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq [J]. Genome Res, 2013, 23 (4): 687-697
38. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano L M, Kamoun S, Terauchi R. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations [J]. Plant J, 2013, 74 (1): 174-183
39. Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, Kanzaki H, Matsumura H, Saitoh H, Mitsuoka C, Utsushi H, Uemura A, Kanzaki E, Kosugi S, Yoshida K, Cano L, Kamoun S, Terauchi R. MutMap+: genetic mapping and mutant identification without crossing in rice [J]. PLoS ONE, 2013, 8 (7): e68529
40. Altschul SF, Madden TL, Sch?ffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Res, 1997, 25 (17): 3389-3402
41. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium [J]. Nat Genet, 2000, 25 (1): 25-29
42. Tatusov RL. The COG database: a tool for genome-scale analysis of protein functions and evolution [J]. Nucleic Acids Res, 2000, 28 (1): 33-36
43. Kanehisa M, Susumu G, Shuichi K, Yasushi O, Masahiro H. The KEGG resource for deciphering the genome [J]. Nucleic Acids Res, 2004, 32 : 277-288
44. Xia C, Chen Ll, Rong TZ, Li R, Xiang Y, Wang P, Liu CH, Dong XQ, Liu B, Zhao D, Wei RJ, Lan H. Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method [J]. Euphytica, 2014, 202 (1): 35-44
45. Han Y, Lv P, Hou S, Li S, Ji G, Ma X, Du R, Liu G. Combining next generation sequencing with bulked segregant analysis to fine map a stem moisture locus in sorghum (Sorghum bicolor L. Moench) [J]. PLoS ONE, 2015, 10 (5): 1-14
46. Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement [J]. Plant Biotechnol J, 2016, 14 (10): 1941-1955
47. Farkhari M, Krivanek A, Xu Y, Rong T, Naghavi MR, Samadi BY, Lu Y, Lübberstedt T. Root-lodging resistance in maize as an example for high-throughput genetic mapping via single nucleotide polymorphism-based selective genotyping [J]. Plant Breed, 2013, 132 (1): 90-98
48. Thyssen GN, Fang DD, Turley RB, Florane C, Li P, Naoumkina M. Next generation genetic mapping of the Ligon-lintless-2 (Li2) locus in upland cotton (Gossypium hirsutum L.) [J]. Theor Appl Genet, 2014, 127 (10): 2183-2192
49. International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N. A physical, genetic and functional sequence assembly of the barley genome [J]. Nature, 2012, 491 (7426): 711-716
50. International Rice Genome Sequencing Project. The map-based sequence of the rice genome [J]. Nature, 2005, 436 (7052): 793-800
51. The Arabidopsis Genome Initiative Project. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J]. Nature, 2000, 408: 796-815
52.

更新日期/Last Update: 2018-12-25