Welcome to Acta Agronomica Sinica，

Acta Agron Sin ›› 2011, Vol. 37 ›› Issue (01): 87-94.doi: 10.3724/SP.J.1006.2011.00087

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

Development of Exon-Targeted Intron-Exon Splicing Conjunction (ET-ISJ) Marker and Establishment of Upland Cotton Genetic Map

LIN Gang,ZHANG Jian,ZHANG Ke,TENG Zhong-Hua,ZHANG Zheng-Sheng*   

  1. College of Agronomy and Biotechnology / Key Laboratory of Biotechnology & Crop Quality Improvement, Ministry of Agriculture, Southwest University, Chongqing 400716, China
  • Received:2010-04-16 Revised:2010-07-29 Online:2011-01-12 Published:2010-10-09
  • Contact: ZHANG Zheng-Sheng,E-mail:zhangzs@swu.edu.cn,Tel:13883608797

PDF

1960

Cited

1

Abstract: Cotton is the leading fiber crop in the world, and upland cotton contributes over 95% of cotton production. The genetic map of upland cotton is far from saturated, so it is necessary to develop new markers for it. ET-ISJ (exon targeted intron-exon splice conjunctions) maker primers were designed according to the conserved intron-exon splicing junction sequences. A total of 1 280 ET-ISJ primer combinations were used to screen polymorphism between upland cotton cultivar Yumian 1 and T586, and 69 of which showed polymorphism, accounting for 5.4% of total primer combinations. The 69 polymorphic ET-ISJ primer combinations were used to detect (Yumian 1 × T586) F2:7 recombinant inbred line population, and 70 ET-ISJ loci were obtained. Linkage analysis was conducted on 70 ET-ISJ loci, 523 SSR, 59 IT-ISJ, 29 SRAP and 8 morphological loci, and a linkage map including 59 linkage groups and 673 loci (68 ET-ISJ, 510 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) was established. The linkage map covered 3 216.7 cM, accounting for 72.3% of cotton genome, with an average interval of 4.8 cM between two markers. Sixty-eight ET-ISJ loci were located on 20 chromosomes.The present study demonstrated that ET-ISJ markers are stable, relatively-high polymorphic, and able to be effectively applied in genetic map construction of cotton and other plant’s.

Key words: Upland cotton (Gossypium hirsutum L.), ET-ISJ, Genetic map

[1]Chen Z J, Scheffler B E, Dennis E, Triplett B A, Zhang T Z, Guo W Z, Chen X Y, Stelly D M, Rabinowicz P D, Town C D, Arioli T, Brubaker C, Cantrell R G, Lacape J M, Ulloa M, Chee P, Gingle A R, Haigler C H, Percy R, Saha S, Wilkins T, Wright R J, Deynze A V, Zhu Y X, Yu S X, Abdurakhmonov I, Katageri I, Kumar P A, Rahman M, Zafar Y, Yu J Z, Kohel R J, Wendel J F, Paterson A H. Toward sequencing cotton (Gossypium) genomes. Plant Physiol, 2007, 145: 1303–1310
[2]Thanksley S D, Hewitt J. Use of molecular markers in breeding for soluble solids content in tomato-are-examination. Theor Appl Genet, 1998, 75: 811–823
[3]Rong J K, Abbey C, Bowers J E, Brubaker C L, Chang C, Chee P W, Delmonte T A, Ding X, Garza J J, Marler B S, Park C H, Pierce G J, Rainey K M, Rastogi V K, Schulze S R, Trolinder N L, Wendel J F, Wilkins T A, Williams-Coplin T D, Wing R A, Wright R J, Zhao X, Zhu L, Paterson A H. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics, 2004, 166: 389–417
[4]Guo W Z, Cai C P, Wang C B, Zhao L, Wang L, Zhang T Z. A preliminary analysis of genome structure and composition in Gossypium hirsutum. BMC Genomics, 2008, 9: 314
[5]Lacape J M, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E, Viot C. A new interspecific, Gossypium hirsutum & Gossypium barbadense, RIL population: Towards a unified consensus linkage map of tetraploid cotton. Theor Appl Genet, 2009, 119: 281–292
[6]Ulloa M, Meredith W R. Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci, 2000, 4: 161–170
[7]Ulloa M, Meredith W R, Shappley Z W, Kahler A L. RFLP genetic linkage maps from four F2:3 populations and a joinmap of Gossypium hirsutum L. Theor Appl Genet, 2002, 104: 200–208
[8]Zhang Z S, Hu M C, Zhang J, Liu D J, Zhang K, Wang W, Wan Q. Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in (Gossypium hirsutum L.). Mol Breed, 2009, 24: 49–61
[9]Lin Z X, He D H, Zhang X L, Nie Y C, Feng C D, Stewart J M. Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breed, 2005, 124: 180–187
[10]Zheng J, Zhang Z S, Chen L, Wan Q, Hu M C, Wang W, Zhang K, Liu D J, Chen X, Wei X Q. Intron-targeted intron-exon splice conjunction (IT-ISJ) marker and its application in construction of upland cotton linkage map. Agric Sci China, 2008, 7: 1172–1180
[11]Wan Q, Zhang Z S, Hu M C, Chen L, Liu D J, Chen X, Wang W, Zheng J. T1 locus in cotton is the candidate gene affecting lint percentage, fiber quality and spiny bollworm (Earias spp.) resistance. Euphytica, 2007, 158: 241–247
[12]Zhang Z S, Xiao Y H, Luo M, Li X B, Luo X Y, Hou L, Li D M，Pei Y. Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica, 2005, 144: 91–99
[13]Van Ooijen J W, Voorrips R E. JoinMap 3.0, Software for the Calculation of Genetic Linkage Maps. Plant Research International, Wageningen, the Netherlands, 2001
[14]Voorrips R E. MapChart 2.2: Software for the Graphical Presentation of Linkage Maps and QTLs. Plant Research International, Wageningen, The Netherlands, 2006
[15]Reinisch A J, Dong J M, Brubaker C L, Stelly D M, Wendel J F, Paterson A H. A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: Chromosome organization and evolution in a disomic polyploid genome. Genetics, 1994, 38: 829–847
[16]Weining S, Langridge P. Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor Appl Genet, 1991, 82: 209–216
[17]Hawkins J D. A survey on intron and exon length. Nucl Acids Res, 1998, 16: 9893–9905
[18]Li G, Quiros C F. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: Its application to mapping and gene tagging in Brassica. Theor Appl Genet, 2001, 103: 455–461
[1] JIANG Shu-Kun,WANG Li-Zhi,YANG Xian-Li,LI Bo,MU Wei-Jie,DONG Shi-Chen,CHE Wei-Cai,LI Zhong-Jie,CHI Li-Yong,LI Ming-Xian,ZHANG Xi-Juan,JIANG Hui,LI Rui,ZHAO Qian,LI Wen-Hua. Detection of QTLs controlling cold tolerance at bud bursting stage by using a high-density SNP linkage map in japonica rice [J]. Acta Agronomica Sinica, 2020, 46(8): 1174-1184.
[2] ZENG Xin-Ying,GUO Jian-Bin,ZHAO Jiao-Jiao,CHEN Wei-Gang,QIU Xi-Ke,HUANG Li,LUO Huai-Yong,ZHOU Xiao-Jing,JIANG Hui-Fang,HUANG Jia-Quan. Identification of QTL related to seed size in peanut (Arachis hypogaea L.) [J]. Acta Agronomica Sinica, 2019, 45(8): 1200-1207.
[3] Qiang PENG,Jia-Li LI,Da-Shuang ZHANG,Xue JIANG,Ru-Yue DENG,Jian-Qiang WU,Su-Song ZHU. QTL Mapping for Rice Appearance Quality Traits Based on a High-density Genetic Map in Different Environments [J]. Acta Agronomica Sinica, 2018, 44(8): 1248-1255.
[4] DENG Zhao**,SHI Shao-Jie**,WANG Hui-Ying,SHANG-GUAN Xin-Xin,LIU Bing-Fang,JING Sheng-Li,DU Bo,CHEN Rong-Zhi,ZHU Li-Li,HE Guang-Cun*. Analysis of QTLs for Brown Planthopper Resistance in Indica Rice WD15515 [J]. Acta Agron Sin, 2016, 42(03): 353-360.
[5] GUO Jian-Bin,HUANG Li,CHENG Liang-Qiang1,CHEN Wei-Gang,REN Xiao-Ping,CHEN Yu-Ning,ZHOU Xiao-Jing,SHEN Jin-Xiong,JIANGHui-Fang. An Integrated Genetic Linkage Map from Three F2 Populations of Cultivated Peanut (ArachishypogaeaL.) [J]. Acta Agron Sin, 2016, 42(02): 159-169.
[6] QIN Wei-Wei,LI Yong-Xiang,LI Chun-Hui,CHEN Lin,WU Xun,BAI Na,SHI Yun-Su,SONG Yan-Chun,ZHANG Deng-Feng,WANG Tian-Yu,LI Yu. QTL Mapping for Kernel Related Traits Based on a High-Density Genetic Map [J]. Acta Agron Sin, 2015, 41(10): 1510-1518.
[7] LI Zhen-Dong, LI Xin-Ping, HUANG Li, REN Xiao-Ping, CHENG Yu-Ning, ZHOU Xiao-Jing, LIAO Bo-Shou, JIANG Hui-Fang. Mapping of QTLs for Pod Size Related Traits in Cultivated Peanut (Arachis hypogaea L.) [J]. Acta Agron Sin, 2015, 41(09): 1313-1323.
[8] LI Xin,XIAO Lu,DU De-Zhi. Fine Mapping and Map Integration of Brsc1 Gene in Dahuang Rape (Brassica rapa L.) [J]. Acta Agron Sin, 2015, 41(07): 1039-1046.
[9] CHENG Liang-Qiang,TANG Mei,REN Xiao-Ping,HUANG Li,CHEN Wei-Gang,LI Zhen-Dong,ZHOU Xiao-Jing,CHEN Yu-Ning,LIAO Bo-Shou,JIANG Hui-Fang*. Construction of Genetic Map and QTL Analysis for Mainstem Height and Total Branch Number in Peanut (Arachis hypogaea L.) [J]. Acta Agron Sin, 2015, 41(06): 979-987.
[10] ZHAO Hui-Yan,XIAO Lu,ZHAO Zhi,DU De-Zhi*. Development of Molecular Markers and Map Integration for Seed Color Traits in Dahuang Rape (Brassica rapa L.) [J]. Acta Agron Sin, 2014, 40(06): 965-972.
[11] XIAO Bing-Guang,QIU Jie,CAO Pei-Jian,GUI Yi-Jie,LU Xiu-Ping,LI Yong-Ping,FAN Long-Jiang. Development and Genetic Mapping of SNP Markers via Genome Complexity Reduction in Tobacco [J]. Acta Agron Sin, 2014, 40(03): 397-404.
[12] CHEN Feng,LI Xiang-Nan,CAO Ying-Ying,SUN Jian-Xi,ZHANG Fu-Yan,DONG Zhong-Dong,CUI Dang-Qun. Analysis of Association of puroindoline b-2 Alleles with Yield-Related Traits in Bread Wheat [J]. Acta Agron Sin, 2014, 40(01): 17-21.
[13] ZHANG Rui-Qi,WANG Xiu-E,CHEN Pei-Du. Inheritance and Mapping of Gene Controlling Four-Rowed Spike in Tetraploid Wheat (Triticum turgidum L.) [J]. Acta Agron Sin, 2013, 39(01): 29-33.
[14] HI Cui-Lan,ZHENG Fei-Fei,CHEN Jian-Sheng,HAN Shu-Xiao,WANG Yong-Rui,TIAN Ji-Chun. Construction of Genetic Map and Analysis of QTLs for Grain Weight Using a RIL Population Derived from Shannong 01-35 × Gaocheng 9411 [J]. Acta Agron Sin, 2012, 38(08): 1369-1377.
[15] HONG Xue-Juan, HOU Jin-Feng, DING Hui, LI Yong-Chun, GAI Jun-Yi, GENG Han. Comparison of Two Genetic Maps of Soybean constructed by RIL Populations Derived from Combinations of Peking×7605 under Two Ecological Sites [J]. Acta Agron Sin, 2012, 38(04): 614-623.
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