Welcome to Acta Agronomica Sinica，

Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (1): 36-46.doi: 10.3724/SP.J.1006.2010.00036

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Density-Enhanced Genetic Linkage Map of RIL Population NJRIKY and Its Impacts on Mapping Genes and QTLs and QTLs in Soybean

ZHOU Bin1,XING Han1,CHEN Shou-Yi2,GAI Jun-Yi1,*   

  1. 1Soybean Research Institute of Nanjing Agricultural University/National Center for Soybean Improvemet/State Key Laboratory of Crop Genetics and Germplasm Enhancement， Nanjing 210095，China；2 State Key Laboratory of Plant Gemomics，Institute of Genetics and developmental Biology,Chinese Academy of Sciences,Being 100101,China
  • Received:2009-05-08 Revised:2009-10-02 Online:2010-01-12 Published:2009-11-17
  • Contact: Gai Jun-Yi, E-mail: sri@njau.edu.cn; Tel: 025-84395405

PDF

1839

Cited

14

Abstract:

A high-density genetic linkage map with informative markers is essential for plant genome analysis, including gene mapping, identification of quantitative trait locus (QTL), map-based cloning, and physical map construction. Though four genetic linkage maps for the recombinant inbred line population NJRIKY derived from (Kefeng 1×Nannong 1138-2) have been established already, there are still problems of precision and accuracy in mapping genes and QTLs due to insufficiency of genetic information and number of markers. A total of 401 polymorphic SSR markers were screened out from 967 ones for density-enhancement of the previous maps. Along with other marker data, a new genetic linkage map was constructed by using Mapmaker/Exp 3.0b, with 553 markers, including 316 SSR, 197 RFLP, 39 EST and one morphologic markers, spanning 25 linkage groups, covering total length 2 071.6 cM of the soybean genome, with an average marker interval distance of 3.70 cM. In comparison with the old map, the number of gaps larger than 20 cM decreased from forty-two to two on the enhanced map. Using this map to relocate the seven SMV resistant genes, Rsc-3, Rsc-7, Rsc-9, Rsc-13, Rsa, Rn1 and Rn3 were mapped on LG D1b again with distances to the flanking markers all less than 6 cM, among them, Rsc-9, Rn1 and Rsa less than 1 cM and Rsc-13 co-segregating with EST-SSR marker GMKF168a. After re-mapping the QTLs for eight agronomic traits, 42 QTLs were detected on 12 linkage groups, with 20 of them accounted for more than 10% of the total variation, respectively, and their marker intervals obviously shortened.

Key words: Soybean, Genetic linkage map, SSR markers, QTL

[1] Klos K L E, Paz M M, Marek L F, Cregan P B, Shoemaker R C. Molecular markers useful for detecting resistance to brown stem rot in soybean. Crop Sci, 2000, 40: 1445-1452

[2] Akkaya M S, Bhagwat A A, Cregan P B. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics, 1992, 132: 1131-1139

[3] Cregan P B, Jarvik T, Bush A L, Shoemaker R C, Lark K G, Kahler A L, Kaya N, VanToai T T, Lohnes D G, Chung J, Specht J E. An integrated genetic linkage map of the soybean genome. Crop Sci, 1999, 39: 1464-1490

[4] Song Q J, Marek L F, Shoemaker R C, Lark K G, Concibido V C, Delannay X, Specht J E, Cregan P B. A new integrated genetic linkage map of the soybean. Theor Appl Genet, 2004, 109: 122-128

[5] Zhang D-S(张德水), Chen S-Y(陈受宜). DNA molecular markers, genome mapping and their applications for plant breeding. Biotechnol Bull (生物技术通报), 1998, 5: 15-22 (in Chinese with English abstract)

[6] Wu X-L(吴晓雷), He C-Y(贺超英), Wang Y-J(王永军), Zhang Z-Y(张志永), Dong-Fang Y(东方阳), Zhang J-S(张劲松), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). Construction and analysis of a genetic linkage map of soybean. Acta Genet Sin (遗传学报), 2001, 28(11): 1051-1061 (in Chinese with English abstract)

[7] Wang Y-J(王永军), Wu X-L(吴晓雷), He C-Y(贺超英), Zhang J-S(张劲松), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). A soybean genetic linkage map constructed after the mapping population being tested and adjusted. Sci Agric Sin (中国农业科学), 2003, 36(11): 1254-1260 (in Chinese with English abstract)

[8] Zhang W K, Wang Y J, Luo G Z, Zhang J S, He C Y, Wu X L, Gai J Y, Chen S Y. QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet, 2004, 108: 1131-1139

[9] Fu S X, Zhan Y, Zhi H J, Gai J Y, Yu D Y. Mapping of SMV resistance gene Rsc-7 by SSR markers in soybean. Genetica, 2006, 128: 63-69

[10] Wang C-E(王春娥), Gai J-Y(盖钧镒), Fu S-X(付三雄), Yu D-Y(喻德跃), Chen S-Y(陈受宜). Inheritance and QTL mapping of Tofu and soymilk output in soybean. Sci Agric Sin (中国农业科学), 2008, 41(5): 1274-1282 (in Chinese with English abstract)

[11] Wang F(王芳), Zhao T-J(赵团结), Yu D-Y(喻德跃), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). Inheritance and QTL analysis of submergence tolerance at seedling stage in soybean (Glycine max L. Merr.). Acta Agron Sin (作物学报), 2008, 34(5): 748-753 (in Chinese with English abstract)

[12] Gai J, Liu Y, Lv H, Xing H, Zhao T, Yu D, Chen S. Identification, inheritance and QTL mapping of root traits related to tolerance to rhizo-spheric stresses in soybean (G. max L. Merr.). Frontiers Agric China, 2007, 1: 119-128

[13] Qi B, Kiror P, Zhao T, Yu D, Chen S, Gai J. Mapping quantitative trait loci associated with aluminum toxin tolerance in NJRIKY recombinant inbred line population of soybean (Glycine max). J Integr Plant Biol, 2008, 50: 1089-1095

[14] Xing G-N(邢光南), Zhou B(周斌), Zhao T-J(赵团结), Yu D-Y(喻德跃), Xing H(邢邯), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). Mapping QTL of resistance to Megacota cribraria (fabricius) in soybean. Acta Agron Sin (作物学报), 2008, 34(3): 361-368 (in Chinese with English abstract)

[15] Geng L-Y(耿雷跃), Cui S-Y(崔士友), Zhang D(张丹), Xing H(邢邯), Gai J-Y(盖钧镒), Yu D-Y(喻德跃). QTL mapping and epistasis analysis for P-efficiency in soybean. Soybean Sci (大豆科学), 2007, 26(4): 460-466 (in Chinese with English abstract)

[16] Huang Z-W(黄中文), Zhao T-J(赵团结), Yu D-Y(喻德跃), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). Lodging resistance indices and related QTL in soybean. Acta Agron Sin (作物学报), 2008, 34(04): 605-611 (in Chinese with English abstract)

[17] Huang Z-W(黄中文), Zhao T-J(赵团结), Yu D-Y(喻德跃), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). Correlation and QTL mapping of biomass accumulation, apparent harvest index, and yield in soybean. Acta Agron Sin (作物学报), 2008, 34(6): 944-951 (in Chinese with English abstract)

[18] Cui S-Y(崔世友), Chen H-T(陈华涛), Yu D-Y(喻德跃). Mapping of QTL associated with leaf senescence in soybean. Sci Agric Sin (中国农业科学), 2007, 40(9): 2103-2108 (in Chinese with English abstract)

[19] Senior M L, Murphy J P, Goodman M M, Stuber C.W. Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci, 1998, 38: 1088-1098

[20] Poland J A. Mapping of Aegilops tauschii derived leaf rust resistance genes in common wheat. J Nat Resour Life Sci Edu, 2003, 32: 8-11

[21] Zhang Z-Y(张志永), Chen S-Y(陈受宜), Gai J-Y(盖钧镒). The molecular marker of gene Rsa resistant to SMV. Chin Sci Bull (科学通报), 1998, 43(20): 2197-2202 (in Chinese)

[22] Guo D-Q(郭东全), Wang Y-W(王延伟), Zhi H-J(智海剑), Gai J-Y(盖钧镒), Li H-C(李海朝), Li K(李凯). Inheritance and gene mapping of resistance to SMV strain group SC-13 in soybean. Soybean Sci (大豆科学), 2007, 26(1): 21-24 (in Chinese with English abstract)

[23] Wang Y-J(王永军), Dong-Fang Y(东方阳), Wang X-Q(王修强), Yang Y-L(杨雅麟), Yu D-Y(喻德跃), Gai J-Y(盖钧镒), Wu X-L(吴晓雷), He C-Y(贺超英), Zhang J-S(张劲松), Chen S-Y(陈受宜). Mapping of five genes resistant to SMV strains in soybean. Acta Genet Sin (遗传学报), 2004, 31(1): 87-90 (in Chinese with English abstract)

[24] Lincoln S E, Lander S L. "Mapmaker/Exp 3.0b and Mapmaker/QTL 1.1" Whitehead Institute of Medical Research, Cambridge, Mass., 1993

[25] Wang S, Basten C J, Zeng Z B. "Windows QTL Cartographer 2.5" Department of Statistics, North Carolina State University, Raleigh, NC, 2007

[26] Hyten D L, Song Q J, Zhu Y L, Choi I Y, Nelson R L, Costa J M, Specht J E, Shoemaker R C, Cregan P B. Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA, 2006, 103: 16666-16671
[27] Orf J H, Chase K, Jarvik T, Mansur L M, Cregan P B, Adler F R, Lark K G. Genetics of soybean agronomic traits. I. Comparison of three related recombinant inbred populations. Crop Sci, 1999, 39: 1642-1651
[1] CHEN Ling-Ling, LI Zhan, LIU Ting-Xuan, GU Yong-Zhe, SONG Jian, WANG Jun, QIU Li-Juan. Genome wide association analysis of petiole angle based on 783 soybean resources (Glycine max L.) [J]. Acta Agronomica Sinica, 2022, 48(6): 1333-1345.
[2] HU Wen-Jing, LI Dong-Sheng, YI Xin, ZHANG Chun-Mei, ZHANG Yong. Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat [J]. Acta Agronomica Sinica, 2022, 48(6): 1346-1356.
[3] YANG Huan, ZHOU Ying, CHEN Ping, DU Qing, ZHENG Ben-Chuan, PU Tian, WEN Jing, YANG Wen-Yu, YONG Tai-Wen. Effects of nutrient uptake and utilization on yield of maize-legume strip intercropping system [J]. Acta Agronomica Sinica, 2022, 48(6): 1476-1487.
[4] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[5] LI A-Li, FENG Ya-Nan, LI Ping, ZHANG Dong-Sheng, ZONG Yu-Zheng, LIN Wen, HAO Xing-Yu. Transcriptome analysis of leaves responses to elevated CO2 concentration, drought and interaction conditions in soybean [Glycine max (Linn.) Merr.] [J]. Acta Agronomica Sinica, 2022, 48(5): 1103-1118.
[6] PENG Xi-Hong, CHEN Ping, DU Qing, YANG Xue-Li, REN Jun-Bo, ZHENG Ben-Chuan, LUO Kai, XIE Chen, LEI Lu, YONG Tai-Wen, YANG Wen-Yu. Effects of reduced nitrogen application on soil aeration and root nodule growth of relay strip intercropping soybean [J]. Acta Agronomica Sinica, 2022, 48(5): 1199-1209.
[7] WANG Hao-Rang, ZHANG Yong, YU Chun-Miao, DONG Quan-Zhong, LI Wei-Wei, HU Kai-Feng, ZHANG Ming-Ming, XUE Hong, YANG Meng-Ping, SONG Ji-Ling, WANG Lei, YANG Xing-Yong, QIU Li-Juan. Fine mapping of yellow-green leaf gene (ygl2) in soybean (Glycine max L.) [J]. Acta Agronomica Sinica, 2022, 48(4): 791-800.
[8] LI Rui-Dong, YIN Yang-Yang, SONG Wen-Wen, WU Ting-Ting, SUN Shi, HAN Tian-Fu, XU Cai-Long, WU Cun-Xiang, HU Shui-Xiu. Effects of close planting densities on assimilate accumulation and yield of soybean with different plant branching types [J]. Acta Agronomica Sinica, 2022, 48(4): 942-951.
[9] DU Hao, CHENG Yu-Han, LI Tai, HOU Zhi-Hong, LI Yong-Li, NAN Hai-Yang, DONG Li-Dong, LIU Bao-Hui, CHENG Qun. Improving seed number per pod of soybean by molecular breeding based on Ln locus [J]. Acta Agronomica Sinica, 2022, 48(3): 565-571.
[10] ZHOU Yue, ZHAO Zhi-Hua, ZHANG Hong-Ning, KONG You-Bin. Cloning and functional analysis of the promoter of purple acid phosphatase gene GmPAP14 in soybean [J]. Acta Agronomica Sinica, 2022, 48(3): 590-596.
[11] WANG Juan, ZHANG Yan-Wei, JIAO Zhu-Jin, LIU Pan-Pan, CHANG Wei. Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean [J]. Acta Agronomica Sinica, 2022, 48(3): 635-643.
[12] HUANG Li, CHEN Yu-Ning, LUO Huai-Yong, ZHOU Xiao-Jing, LIU Nian, CHEN Wei-Gang, LEI Yong, LIAO Bo-Shou, JIANG Hui-Fang. Advances of QTL mapping for seed size related traits in peanut [J]. Acta Agronomica Sinica, 2022, 48(2): 280-291.
[13] ZHANG Yan-Bo, WANG Yuan, FENG Gan-Yu, DUAN Hui-Rong, LIU Hai-Ying. QTLs analysis of oil and three main fatty acid contents in cottonseeds [J]. Acta Agronomica Sinica, 2022, 48(2): 380-395.
[14] ZHANG Guo-Wei, LI Kai, LI Si-Jia, WANG Xiao-Jing, YANG Chang-Qin, LIU Rui-Xian. Effects of sink-limiting treatments on leaf carbon metabolism in soybean [J]. Acta Agronomica Sinica, 2022, 48(2): 529-537.
[15] SONG Li-Jun, NIE Xiao-Yu, HE Lei-Lei, KUAI Jie, YANG Hua, GUO An-Guo, HUANG Jun-Sheng, FU Ting-Dong, WANG Bo, ZHOU Guang-Sheng. Screening and comprehensive evaluation of shade tolerance of forage soybean varieties [J]. Acta Agronomica Sinica, 2021, 47(9): 1741-1752.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd