欢迎访问作物学报,今天是

作物学报 ›› 2015, Vol. 41 ›› Issue (10): 1463-1471.doi: 10.3724/SP.J.1006.2015.01463

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

大豆胞囊线虫主效抗病基因Rhg4(GmSHMT)的CAPS/dCAPS标记开发和利用

史学晖1,李英慧1,*,于佰双2,郭勇1,王家军2,邱丽娟1,*   

  1. 1农作物基因资源与基因改良国家重大科学工程/农业部北京大豆生物学重点实验室/中国农业科学院作物科学研究所,北京100081;2黑龙江省农业科学院大豆研究所,黑龙江哈尔滨150086
  • 收稿日期:2015-03-20 修回日期:2015-06-01 出版日期:2015-10-12 网络出版日期:2015-06-29
  • 通讯作者: 李英慧, E-mail: liyinghui@caas.cn; 邱丽娟, E-mail: qiulijuan@caas.cn
  • 基金资助:

    本研究由国家自然科学基金项目(31171575)和中国农业科学院科技创新工程(作物分子标记技术及其应用)项目资助。

Development and Utilization of CAPS/dCAPS Markers Based on the SNPs Lying in Soybean Cyst Nematode Resistant Genes Rhg4

SHI Xue-Hui1,LI Ying-Hui1,*,YU Bai-Shuang2,GUO Yong1,WANG Jia-Jun2,QIU Li-Juan1,*   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Soybean Biology in Beijing, Agriculture of Ministry / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; 2 Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
  • Received:2015-03-20 Revised:2015-06-01 Published:2015-10-12 Published online:2015-06-29
  • Contact: 李英慧, E-mail: liyinghui@caas.cn; 邱丽娟, E-mail: qiulijuan@caas.cn

摘要:

大豆胞囊线虫(soybean cyst nematode,SCN)严重危害世界大豆生产,Rhg4 (resistance to Heterodera glycines 4)是控制大豆SCN抗性的2个主效位点之一。本研究针对Rhg4 (GmSHMT)上的2个单核苷酸多态性(single nucleotide polymorphisms, SNP)位点开发了快速、经济、简便易行的CAPS (Rhg4-389)和dCAPS标记(Rhg4-1165),并用开发的2个标记鉴定了以大豆胞囊线虫应用核心种质为主的193份代表性抗感种质。结果表明,Rhg4-389和Rhg4-1165位点间存在显著连锁不平衡(P=0.0001,r2=0.87),可形成4种单倍型。Rhg4-389-G/Rhg4-1165-T和Rhg4-389-C/Rhg4-1165-A为优势单倍型,稀有单倍型Rhg4-389-G/Rhg4-1165-A和Rhg4-389-C/Rhg4-1165-T是在中国抗源中新发现的单倍型。结合193份种质对SCN 3号小种抗性鉴定分析发现,Rhg4-389-G和Rhg4-1165-T主要存在于抗病种质,它们形成的单倍型对抗病种质鉴定效率可达94.1%。本研究开发了可用于辅助大豆SCN抗性鉴定且方便育种家利用的CAPS/dCAPS标记,且用其摸清了应用核心种质等重要抗源在Rhg4位点的“本底”,为育种家有效利用这些优异抗源提供了重要信息。

关键词: 大豆胞囊线虫, Rhg4, CAPS/dCAPS标记, 单倍型, 分子标记辅助选择

Abstract:

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most destructive diseases which largely suppressed soybean production worldwide. Rhg4 was one of two major resistant loci for SCN. In this study two nonsynonymous SNPs (Rhg4-389-G/C and Rhg4-1165-T/A) in GmSHMT were deduced to confer SCN resistance or susceptibility. One CAPS marker (Rhg4-389) and one dCAPS marker (Rhg4-1165) with the advantages of rapid, economic, simple and easy way to use were developed based on two nonsynonymous SNPs (Rhg4-389-G/C and Rhg4-1165-T/A), respectively. Then, a total of 193 soybean cultivars mainly from SCN-applied-core collection were genotyped by markers Rhg4-389 and Rhg4-1165. Linkage disequilibrium (LD) analysis indicated pairwise of Rhg4-389 and Rhg4-1165 was in significant LD (P-value = 0.0001) with r2 of 0.87. Among four haplotypes detected in this panel, Rhg4-389-G/Rhg4-1165-T and Rhg4-389-C/Rhg4-1165-A were predominant; while both Rhg4-389-G/Rhg4-1165-A and Rhg4-389-C/Rhg4-1165-T were rare, which only discovered in the resistant cultivars from China. Rhg4-389-G and Rhg4-1165-T alleles mainly occurred in resistant cultivars, and almost coincided with Rhg4-389-G/Rhg4-1165-T haplotype. Of 101 resistant cultivars with Rhg4-389-G/Rhg4-1165-T haplotype, 94.1% (95) were resistant to SCN. In this study, we not only developed convenient CAPS/dCAPS markers for marker assisted selection (MAS) breeding, but also dissected the genetic architecture of Rhg4 locus among SCN-applied-core collection. Hopefully, this study will provide helpful information for improving the utilization efficiency of resistant resources in soybean breeding.

Key words: Soybean cyst nematode, Rhg4, CAPS/dCAPS marker, Haplotype, Marker assisted selection

[1]Chen S Y, Porter P M, Reese C D, Stienstra W C. Crop sequence effects on soybean cyst nematode and soybean and corn yields. Crop Sci, 2001, 41: 1843–1849



[2]大豆种质抗胞囊线虫鉴定研究协作组. 大豆种质资源对大豆胞囊线虫1、3和4号生理小种的抗性鉴定. 大豆科学, 1993, 12: 91–99



Coordinative Group of Evaluation of SCN. Evaluation of soybean germplasm for resistance to race 1, 3 and 4 of the soybean cyst nematode. Soybean Sci, 1993, 12: 91–99



[3]Ma Y S, Wang W H, Wang L X, Ma F M, Wang P W, Chang R Z, Qiu L J. Characteristics of soybean genetic diversity and establishment of applied core collection for Chinese soybean cyst nematode resistance. J Integr Plant Biol, 2006, 48: 722–731



[4]袁翠平, 沈波, 董英山. 中国大豆抗(耐)胞囊线虫病品种及其系谱分析. 大豆科学, 2009, 28: 1049–1053



Yuan C P, Shen B, Dong Y S. Released soybean varieties resistant to cyst nematode in China and their resistance genetic derivation. Soybean Sci, 2009, 28(6): 1049–1053



[5]Liu S, Kandoth P K, Warren S D, Yeckel G, Heinz R, Alden J, Yang C L, Jamai A, Mellouki T E, Juvale P S, Hill J, Baum T J, Cianzio S, Whitham S A, Korkin D, Mitchum M G, Meksem K. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature, 2012, 492: 256–260



[6]Konieczny A, Ausubel F M. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J, 1993, 4: 403–410



[7]Michaels S D, Amasino R M. A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J, 1998, 14: 381–385



[8]Neff M M, Neff J D, Chory J, Pepper A E. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J, 1998, 14: 387–392



[9]Weiland J J, Yu M H. A cleaved amplified polymorphic sequence (CAPS) marker associated with root-knot nematode resistance in sugarbeet. Crop Sci, 2003, 43: 1814–1818



[10]Komori T, Nitta N. Utilization of the CAPS/dCAPS method to convert rice SNPs into PCR-based markers. Breed Sci, 2005, 55: 93–98



[11]Caranta C, Thabuis A, Palloix A. Development of a CAPS marker for the Pvr4 locus: a tool for pyramiding potyvirus resistance genes in pepper. Genome, 1999, 42: 1111–1116



[12]王立浩, 王萱, 张宝玺, 毛胜利, 郭家珍. 利用CAPS标记辅助辣椒PVY抗性基因PVr4转育的研究. 辣椒杂志, 2007, (4): 1–3



Wang L H, Wang X, Zhang B X, Mao S L, Guo J Z. Application of CAPS marker in assisting selection of PVY resistance PVr4 gene in pepper. J China Capsicum, 2007, (4): 1–3



[13]王立浩, 张宝玺, Caranta C, 毛胜利, Palloix A. 利用分子标记对辣椒抗马铃薯Y病毒的3个QTLs进行选择. 园艺学报, 2008, 35: 53–58



Wang L H, Zhang B X, Caranta C, Mao S L, Palloix A. Molecular markers assisted selection for three QTLs resistant to PVY in pepper. Acta Hort Sin, 2008, 35: 53–58



[14]Lee G A, Koh H J, Chung H K, Dixit A, Chung J W, Ma K H, Lee S Y, Lee J R, Lee G S, Gwag H G, Kim T S, Park Y J. Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice. Mol Breed, 2009, 24: 93–101



[15]Jun T H, Mian M A R, Kang S T, Michel A P. Genetic mapping of the powdery mildew resistance gene in soybean PI 567301B. Theor Appl Genet, 2012, 125: 1159–1168



[16]Stöckel J, Bennewitz S, Hein P, Oelmüller R. The evolutionarily conserved tetratrico peptide repeat protein pale yellow green7 is required for photosystem I accumulation in Arabidopsis and copurifies with the complex. Plant Physiol, 2006, 141: 870–878



[17]Zimmerl S, Lafferty J, Buerstmayr H. Assessing diversity in Triticum durum cultivars and breeding lines for high versus low cadmium content in seeds using the CAPS marker usw47. Plant Breed, 2014, 133: 712–717



[18]Chen Y W, Wang D C, Arelli P, Ebrahimi M, Nelson R L. Molecular marker diversity of SCN-resistant sources in soybean. Genome, 2006, 49: 938–949



[19]Riggs R D, Schmitt D P. Complete characterization of the race scheme for Heterodera glycines. J Nematol, 1988, 20(3): 392



[20]Golden A M. Terminology and identity of infraspecific forms of the soybean cyst nematode (Heterodera glyecines). Plant Dis Rep, 1970, 54: 544–546



[21]Schmitt D P, Shannon G. Differentiating soybean responses to Heterodera glycines races. Crop Sci, 1992, 32: 275–277



[22]Clarke K R, Gorley R N. Primer v5: User Manual/Tutorial. Primer-E Limited, 2001



[23]Woffelman C. DNAMAN for Windows, version 2.6. Lynon Biosoft, Institute of Molecular Plant Sciences, Leiden University, the Netherlands, 1994



[24]Weir B S. Genetic Data Analysis II. Sunderland, Massachusetts, Sinauer Associates, 1996



[25]Fisher R A. The mathematical distribution used in the common tests of significance. Econometrica, 1935, 98: 39–54



[26]梁青山. Excel统计函数在卡方检验中的应用. 职业与健康, 2004, 20(5): 105–105



Liang Q S. Excel statistical function in the application of the chi-square test. Occup Health, 2004, 20(5):105–105



[27]Young N D. A cautiously optimistic vision for marker-assisted breeding. Mol Breed, 1999, 5: 505–510



[28]Mudge J, Cregan P B, Kenworthy J P, Kenworthy W J, Orf J H, Young N D. Two microsatellite markers that flank the major soybean cyst nematode resistance locus. Crop Sci, 1997, 37: 1611–1615



[29]Cregan P B, Mudge J, Fickus E W, Danesh D, Denny R, Young N D. Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet, 1999, 99: 811–818



[30]王文辉, 邱丽娟, 常汝镇, 马凤鸣, 谢华, 林凡云. 中国大豆种质抗SCN基因rhg1位点SSR标记等位变异特点分析. 大豆科学, 2003, 22: 246–250



Wang W H, Qiu L J, Chang R Z, Ma F M, Xie H, Lin F Y. Characteristics of alleles at Satt309 locus associated with rhg1 gene resistant to SCN of Chinese soybean germplasm. Soybean Sci, 2003, 22: 246–250



[31]李英慧, 袁翠平, 张辰, 李伟, 南海洋, 常汝镇, 邱丽娟. 基于大豆胞囊线虫病抗性候选基因的SNP位点遗传变异分析. 遗传, 2009, 12: 1259–1264



Li Y H, Yuan C P, Zhang C, Li W, Nan H Y Chang R Z, Qiu L J. Genetic variation of SNP loci based on candidate gene for resistance to soybean cyst nematode. Hereditas(Beijing), 2009, 12: 1259–1264 (in Chinese with English abstract)



[32]南海洋, 李英慧, 常汝镇, 邱丽娟. 基于大豆胞囊线虫病抗性候选基因rhg1的InDel标记开发与鉴定. 作物学报, 2009, 35: 1236–1243



Nan H Y, Li Y H, Chang R Z, Qiu L J. Development and identification of InDel markers based on rhg1 gene for resistance to soybean cyst nematode(Heterodera glycines Ichinohe). Acta Agron Sin, 2009, 35: 1236–1243 (in Chinese with English abstract)



[33]Meksem K, Pantazopoulos P, Njiti V N, Hyten L D, Arelli P R, Lightfoot D A. ’Forrest’resistance to the soybean cyst nematode is bigenic: saturation mapping of the Rhg1 and Rhg4 loci. Theor Appl Genet, 2001, 103: 710–717



[34]Brucker E, Carlson S, Wright E, Niblack T, Diers B. Rhg1 alleles from soybean PI 437654 and PI 88788 respond differentially to isolates of Heterodera glycines in the greenhouse. Theor Appl Genet, 2005, 111: 44–49



[35]Cook D E, Lee T G, Guo X, Melito S, Wang K, Bayless A M, Wang J, Hughes T J, Willis D K, Clemente T E, Diers B W, Jiang J, Hudson M E, Bent A F. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science, 2012, 338: 1206–1209



[36]Li Y H, Zhao S C, Ma J X, Li D, Yan L, Li J, Qi X T, Guo X, Zhang L, He W, Chang R Z, Liang Q, Guo Y, Ye C, Wang X B, Tao Y, Guan R, Wang J Y, Liu Y L, Jin L G, Zhang X, Liu Z, Zhang L, Chen J, Wang K J, Nielsen R, Li R Q, Chen P Y, Li W B, Reif J C, Purugganan M, Wang J, Zhang M C, Wang J, Qiu L J. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genom, 2013, 14: 579



[37]Lam H M, Xu X, Liu X, Chen W B, Yang G H, Wong F L, Li M W, He W M, Qin N, Wang B, Li J, Jian M, Wang J, Shao G H, Wang J, Sun S S, Zhang G Y. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet, 2010, 42: 1053–1059



[38]Li Y H, Zhou G Y, Ma J X, Jiang W K, Jin L G, Zhang Z H, Guo Y, Zhang J B, Sui Y, Zheng L T, Zhang S S, Zuo Q, Shi X H, Li Y F, Zhang W K, Hu Y, Kong G, Hong H L, Liu Z X, Wang Y, Ruan H, Yeung C K L, Liu J, Wang H, Zhang L, Guan R, Wang K J, Li W B, Chen S Y, Chang R Z, Jiang Z, Jackson S A, Li R Q, Qiu L J. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol, 2014, 32: 1045–1052



[39]Smith S M, Maughan P J. SNP Genotyping Using KASPar Assays. Plant Genotyping, 2015: 243–256



[40]Li Y H, Zhang C, Gao Z S, Smulders M J M, Ma Z L, Liu Z X, Nan H Y, Chang R Z and Qiu L J. Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean. Mol Breed, 2009, 24: 63–76



[41]Hiremath P J, Kumar A, Penmetsa R V, Farmer A, Schlueter J A, Chamarthi S K, Whaley A M, Carrasquilla-Garcia N, Gaur P M, Upadhyaya H D, Kavi K P B, Shah T M, Cook D R, Varshney R K. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J, 2012, 10: 716–732

[1] 彭佳泺, 李颖, 李丹丹, 杨军宁, 郭学峰, 张文姣, 俞晓雪, 周亚荣, 王振玉, 王彩香, 马雄风, 宿俊吉. 陆地棉I类LBD家族成员鉴定及GhLBD6调控开花期的功能和单倍型分析[J]. 作物学报, 2026, 52(6): 1682-1697.
[2] 唐宽强, 李公允, 宋美毅, 赵雪, 常春玲. 大豆株高性状全基因组关联分析及预测模型构建[J]. 作物学报, 2026, 52(6): 1743-1756.
[3] 张献丰, 郭利建, 李康春, 孔斌雪, 刘玉芳, 车卓, 杨德龙. 小麦ABHD6基因家族鉴定与粒重功能标记开发[J]. 作物学报, 2026, 52(6): 1711-1727.
[4] 李诗晴, 王茜, 王素华, 张耀文, 王丽侠. 绿豆种质资源苗期耐盐性鉴定及相关基因发掘[J]. 作物学报, 2026, 52(2): 376-388.
[5] 李璐琪, 程宇坤, 白斌, 雷斌, 耿洪伟. 小麦叶片气孔相关性状全基因组关联分析[J]. 作物学报, 2025, 51(9): 2266-2284.
[6] 杨海洋, 吴林宣, 李博纹, 石翰峰, 袁禧龙, 刘金朝, 蔡海荣, 陈诗怡, 郭涛, 王慧. 基于QTL定位发现的OsWRI3调控水稻种子的落粒性[J]. 作物学报, 2025, 51(7): 1712-1724.
[7] 刘建国, 陈冬东, 陈玉玉, 易琴琴, 李清, 徐正进, 钱前, 沈兰. 水稻MKKs家族基因成员OsMKK4的不同等位基因型及自然变异对籽粒的影响[J]. 作物学报, 2025, 51(3): 598-608.
[8] 徐林珊, 郜耿东, 王宇, 王家星, 杨吉招, 武亚瑞, 张宵寒, 常影, 李真, 谢雄泽, 龚德平, 王晶, 葛贤宏. 甘蓝型油菜漆酶基因家族成员表达模式及与茎秆抗折力的关联分析[J]. 作物学报, 2025, 51(1): 134-148.
[9] 裴法敬, 张文轩, 张晓, 王昕钰, 彭少兵, 米甲明. 长粒香型的超短生育期水稻新品系创制[J]. 作物学报, 2024, 50(7): 1684-1698.
[10] 范子培, 李龙, 史雨刚, 孙黛珍, 李超男, 景蕊莲. 小麦TabHLH112-2B基因克隆及每穗小穗数相关功能标记开发[J]. 作物学报, 2024, 50(2): 403-413.
[11] 阳世杰, 王华智, 潘怡敏, 黄蕊, 侯森, 秦慧彬, 穆志新, 王海岗. 山西谷子种质资源株高全基因组关联分析[J]. 作物学报, 2024, 50(12): 2984-2997.
[12] 胡艳娟, 薛丹, 耿嫡, 朱末, 王天穹, 王晓雪. 水稻OsCDF1基因突变效应及其基因组变异分析[J]. 作物学报, 2023, 49(9): 2362-2372.
[13] 李刚, 周彦辰, 熊亚俊, 陈伊洁, 郭庆元, 高杰, 宋健, 王俊, 李英慧, 邱丽娟. 大豆叶型调控基因Ln及其同源基因单倍型分析[J]. 作物学报, 2023, 49(8): 2051-2063.
[14] 朱治, 李龙, 李超男, 毛新国, 郝晨阳, 朱婷, 王景一, 常建忠, 景蕊莲. 小麦转录因子TaMYB5-3B与株高和千粒重相关[J]. 作物学报, 2023, 49(4): 906-916.
[15] 王睿, 任毅, 程宇坤, 王伟, 张志辉, 耿洪伟. 小麦旗叶形态相关性状全基因组关联分析[J]. 作物学报, 2023, 49(11): 2886-2901.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!