基于EST-SSR标记甘薯连锁图谱构建及淀粉性状的QTL定位

doi:10.3864/j.issn.0578-1752.2016.23.003

摘要/Abstract

摘要： 【目的】利用分子标记技术，构建甘薯遗传连锁图谱，并分析甘薯淀粉含量性状的QTL位点，为高淀粉含量甘薯种质资源利用及甘薯分子标记辅助育种提供理论和实践依据。【方法】以高淀粉含量品种万薯5号为母本、低淀粉含量品种商丘52-7为父本建立杂交群体，利用EST-SSR标记，采用“双假测交”策略和运用JoinMap4.0软件，分别构建双亲遗传连锁图谱，并结合F₁（2012、2013年）群体表型数据采用区间作图法对淀粉含量性状进行QTL检测。【结果】利用1 679对EST-SSR引物筛选出的1 045对多态性引物检测F₁群体的标记基因型，获得了1 418个标记位点。分别对上述获得的父母本多态性标记进行遗传连锁分析，在LOD≥5.0情况下，分别构建父母本的连锁遗传图谱。采用642个标记的多态性位点构建母本连锁群74个，其中，215个标记位点位于连锁图谱上，占标记多态性位点总数的33.5%。每个连锁群上有2—11个标记位点，连锁群长度在0.6—129.4 cM,图谱总长为3 826.07 cM，标记间平均距离为17.80 cM。属于父本的776个标记位点构建了80个连锁群，共有252个标记位点构建在连锁图谱上，占标记总数的32.5%，每个连锁群上有2—24个标记位点，连锁群长度在2.0—156.8 cM，图谱总长为3 955.0 cM，标记间平均距离为15.7 cM。以F₁杂交群体构建的遗传连锁图谱，结合2012年、2013年2个环境，利用QTL作图软件MapQTL5.0，采用区间作图法进行分析，共检测到17个与淀粉含量性状相关的QTL，贡献率在8.4%—40.5%。其中qWsc-1、qWsc-2、qWsc-3 3个QTL位于母本万薯5号连锁群上，且在2年环境中均可检测到；14个QTL位于父本商丘52-7连锁群上，qSsc-1、qSsc-2、qSsc-3、qSsc-4、qSsc-8、qSsc-10、qSsc-11、qSsc-12是在2个环境均检测到的QTL。qSsc-5、qSsc-6、qSsc-7、qSsc-9、qSsc-13、qSsc-14是只在1个环境检测到的QTL。标记GDAAS0603在双亲中和2个环境中均同时检测到，这些环境稳定QTL可用于分子标记辅助选择。【结论】分别构建了亲本EST-SSR分子标记连锁群图谱，丰富了构建甘薯图谱的标记类型，定位了17个与淀粉含量相关的QTL位点。

关键词: 甘薯, 淀粉含量, EST-SSR, 连锁图谱, 数量性状

Abstract: 【Objective】To provide a theoretical and practical basis for utilization of germplasm resources of sweetpotato with high starch content and molecular marker-assisted selection in sweetpotato, a genetic linkage map was constructed by using molecular markers, and quantitative trait loci (QTLs) associated with starch content were identified. 【Method】 A F₁ hybrid population was developed from a cross between Wanshu 5, a sweetpotato cultivar with high starch content, as the female parent, and Shangqiu 52-7, a cultivar with low starch content, as the male parent. By using EST-SSR markers and the software of JoinMap4.0, the molecular genetic linkage maps of both parents were constructed based on the “double pseudo testcross” strategy, respectively. And QTLs for starch content trait were identified using composite interval mapping method based on the phenotypic data of F₁ population in two years (2012 and 2013).【Result】Among the 1 679 EST-SSR primer pairs primarily tested in F₁ lines, 1 045 polymorphic primer pairs were selected to screen in the population lines, and 1 418 polymorphic loci were obtained. The genetic linkage relationship of polymorphic loci were analyzed with the LOD≥5.0 as a threshold, and the genetic linkage map of female and male parents were constructed respectively. A total of 74 linkage groups for female parent were constructed based on 642 polymorphic loci, of which 215 (33.5%) loci were placed on the genetic linkage map. The number of markers in each linkage group ranged from 2 to 11. The length of linkage groups ranged from 2.0 to 156.8 cM, and the linkage map covered a total length of 3 826.07 cM, with an average distance between markers of 17.80 cM. A genetic linkage map for male Shangqiu52-7 was constructed by using 776 polymorphic loci, of which 250 (32.5%) loci distributed on 80 linkage groups. The number of markers in each linkage group ranged from 2 to 24. The length of linkage groups ranged from 2.0 to 156.8 cM, and the linkage map covered a whole length of 3 955.0 cM with an average interval of 15.7 cM between markers. Using QTL analysis software Map QTL 5.0 and Interval Mapping method, QTLs for starch content were identified based on the starch content measured in two years (2012 and 2013) and two environments. Seventeen QTLs for starch content were detected, explaining 8.4%-40.5% of the phenotypic variation. Three QTLs qWsc-1, qWsc-2, and qWsc-3 mapped on the linkage group of female Wanshu 5 were detected under two environments. Fourteen QTLs were detected on the linkage group of male Shangqiu52-7, of which qSsc-1, qSsc-2, qSsc-3, qSsc-4, qSsc-8, qSsc-10, qSsc-11, qSsc-12 were detected under two environments, and qSsc-5, qSsc-6, qSsc-7, qSsc-9, qSsc-13, qSsc-14 were only detected under one environment. Mark GDAAS 0603 was detected simultaneously on the linkage groups of both parents and two environments. Those QTLs for starch content could be used in molecular marker-assisted selection of sweetpotato. 【Conclusion】Two genetic linkage map were constructed based on EST-SSR markers, and 17 QTLs for starch content of sweetpotato were identified. Results of the study has enriched the types of molecular markers used for genetic linkage map construction in sweetpotato.

Key words: sweetpotato, starch content, EST-SSR, genetic linkage map, QTL

唐道彬，张凯，吕长文，谢德斌，傅体华，王季春. 基于EST-SSR标记甘薯连锁图谱构建及淀粉性状的QTL定位[J]. 中国农业科学, 2016, 49(23): 4488-4506.

TANG Dao-bin, ZHANG Kai, Lü Chang-wen, XIE De-bin, FU Ti-hua, WANG Ji-chun. Genetic Linkage Map Construction Based on EST-SSR and Analysis of QTLs for Starch Content in Sweetpotato (Ipomoea batatas (L.) lam.)[J]. Scientia Agricultura Sinica, 2016, 49(23): 4488-4506.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2016.23.003

https://www.chinaagrisci.com/CN/Y2016/V49/I23/4488

参考文献

[1] FAOSTAT, Food and agriculture organization of the United Nations, production statistics. 2011, [2016-03-25]. http://faostat3.fao.org/home/ index.html.
[2] Dhir S K, Oglesby J, Bhagsari A S. Plant regeneration via somatic embryogenesis and transient gene expression in sweet potato protoplasts. Plant Cell Report,1998, 17: 665-669. [3] Hemmat M, Weeden N F, Manganaris A G, LANSON D M. Molecular marker linkage map for apple. The Journal of Heredity, 1994, 85(1): 4-11.

[4] Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics,1994, 137: 1121-1137.

[5] Lodhi M A, Ye G N, Weeden N F, Reisch B I, Daly M J.A molecular marker based linkage map of vitis. Genome, 1995, 38(4): 786-794.
[6] Van Ooijen J W, Voorrips R E. JoinMap 4.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen,The Netherlands, 2006: 2-63.

[7] Arthur Q V, La Bonte D R. Variation in randomly amplified DNA markers and root yield in “Jewel” sweetpotato clones. Journal of the American Society for Horticultural Science, 1995, 120(5): 734-740.

[8] ARhur Q V, La Bonte D R. Genetic variation among sweet potatoes propagated through nodal and adventitious sprouts. Journal of the American Society for Horticultural Science, 1996, 121(2): 170-174.
[9] Thompson P G, Hong L L, Ukoskit K, Zhu Z. Genetic linkage of randomly amplified polymorphic DNA (RAPD) markers in sweet potato. Journal of the American Society for Horticultural Science, 1997, 122: 79-82.

[10] Ukoskit K T, Thompson P G, Watson J C E, LAWRENCE G W. Identifying a randomly amplified polymorphic DNA(RAPD) marker linked to a gene for root knot nematode resistance in sweet potato. Journal of American Society Horticultural Science, 1997, 122: 818-821.

[11] Kriegner A, Cervantes J C, Burg K, MWANGA ROM, ZHANG D P. A genetic linkage map of sweetpotato (Ipomoea batatas (L.) based on AFLP markers. Molecular Breeding, 2003, 11: 169-185.

[12] Lander E S, Bostein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics,1989, 121: 185-199.

[13] Cervantes-Flores J C, Yencho G C, Kriegner A, Pecota K V, Faulk M A, Mwanga R O M, Sosinski B R. Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multipledose AFLP markers. Molecular Breeding, 2008, 21: 511-532.

[14] Li A X, Liu Q C, Wang Q M, Zhang L M, Zhai H, Liu S Z. Establishment of molecular linkage maps using SRAP markers in sweetpotato.Acta Agronomica Sinica, 2010, 36: 1286-1295.

[15] Zhao N, Yu X X, Jie Q, Li H, Li H, Hu J, Zhai H, He S Z, Liu Q C. A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweet potato. Molecular Breeding,2013, 32: 807-820.

[16] 吴洁, 谭文芳, 何俊蓉, 蒲志刚, 王大一, 张正圣, 詹付凤, 阎文昭. 甘薯SRAP连锁图构建淀粉含量QTL检测. 分子植物育种, 2005, 3(6): 841-845.

Wu J, Tan W F, Yan W Z, He J R, PU Z G, WANG D Y, ZHANG Z S, ZHAN F F, YAN W Z. Construct on of SRAP linkage map and qtl mapping for starch content in sweet potato. Molecular Plant Breeding,2005, 3(6): 841-845. (in Chinese)

[17]蒲志刚, 王大一, 谭文芳, 吴洁, 阎文昭. 利用AFLP构建甘薯连锁图及淀粉含量QTL定位. 西南农业学报, 2010, 23(4): 1047-1050.

Pu Z G, Wang D Y, Tan W f, Wu J, Yan W Z. AFLP maps and QTL analysis of starch content of sweet potato. Southwest China Journal of Agricultural Sciences,2010, 23(4): 1047-1050. (in Chinese)

[18] 唐茜, 何凤发, 王季春, 王瑞娜. 甘薯SRAP遗传图谱构建及淀粉含量QTL初步定位, 西南大学学报(自然科学版), 2010, 32(6): 40-45.

Tang Q, He F F, Wang J C, Wang R N. Construction of a linkage map using SRAP markers and QTL mapping for starch content in sweet potato. Journal of Southwest University(Natural Science Edition), 2010, 32(6): 40-45. (in Chinese)

[19] Cervantes-Flores J C, Sosinski B, Pecota K V, Mwanga R O M, Catignani G L, Truong V D, Watkins R H, Ulmer M R, Yencho G C. Identification of quantitative trait loci for dry-matter, starch, and b-carotene content in sweet potato. Molecular Breeding, 2011, 28: 201-216.

[20] Yu X X, Zhao N, Jie Q, Zhai H, He S Z, Li Q, Liu Q C. Identifition of QTL for Starch Content in Sweetpotato (Ipomoea batatas(L.) Lam.). Journal of Integrative Agriculture, 2014, 13(2): 310-315.

[21] Ukoskit K, Thompson P G, Watson J C E, LAWRENCE G W. Identifying a randomly amplified polymorphic DNA(RAPD) marker linked to a gene for root knot nematode resistance in sweetpotato. Journal of American Society Horticultural Science, 1997, 122: 818- 821.

[22] Hu J J, Nakatani M, Mizuno K, Fujimura T. Development and characterization of microsatellite markers in sweet potato. Breeding Science, 2004, 54: 177-188.

[23] Wang Z Y, Fang B P, Chen J Y, Zhang X J, Luo Z X, Huang L F, Chen X L, Li Y J. De novo assembly and characterization of root transcriptome using illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics, 2010, 11: 726-739.

[24] Wang Z Y, Li j, Luo Z X, Huang L F, Chen X L, Fang B P, Li Y J, Chen J y, Zhang X J. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biology, 2011, 11: 139.

[25] Schafleitner R, Tincopa L, Palomino O, Rossel G, Robles R F, Alagon R, RIVERA C, QUISPE C, ROJAS L, PACHECO J A, GERMA D, KIM J Y, HOU J, SIMON R. A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics, 2010, 11: 604.

[26] Zhang K, Wu Z D, Tang D B, Lv C W, Luo K, Zhao Y, Liu X, Huang Y X, Wang J C. Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas (L.). Frontiers in Plant Science, 2016, 7: 223.

[27] Van Ooijen J W. Joinmap^®4.0, Software for the calculation of genetic linkage maps in experimental populations. Wageningen, The Netherlands, 2006: 2-63.

[28] Van Ooijen J W. MapQTL^®5.0, Software for the mapping quantitative trait loci in experimental populations. Wageningen, The Netherlands, 2004: 2-63.

[29] Voorrips R E. MapChart 2.2, Software for the graphical presentation of linkage maps and QTL. The Journal of Heredity, 2006, 93(1): 77-78.

[30] Jie Q, Li H, Zhai H, Wang YP, Li Q, Ma D F, Xie Y P, Liu Q Q. Development of AFLP markers linked to stem nematode resistance gene in sweet potato (Ipomoea batatas (L.) Lam.). Journal of Agricultural Biotechnology,2009,6: 97-101.

[31] Li H, Zhao N, Yu X X, Liu Y X, Zhai H, He S H, Li Q, Ma D F, Liu Q C. Identification of QTLs for storage root yield in sweet potato. Scientia Horticulturae, 2014, 170: 182-188.