Welcome to Acta Agronomica Sinica，

Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (06): 918-931.doi: 10.3724/SP.J.1006.2010.00918

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

Analysis and Answers to Frequently Asked Questions in Quantitative Trait Locus Mapping

LI Hui-Hui,ZHANG Lu-Yan,WANG Jian-Kang*   

  1. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and genetic Improvement/CIMMYT China Office,Chinese Academy of Agricultural Sciences,Beijing 100081,China
  • Received:2010-01-18 Revised:2010-02-28 Online:2010-06-12 Published:2010-04-20
  • Contact: WANG Jian-Kang,E-mail:wangjk@caas.net.cn;jkwang@cgiar.org;Tel:010-82105846 E-mail:lihuihui@caas.net.cn; Tel: 010-82106038

PDF

3613

Cited

60

Abstract:

QTL mapping is an important step in gene fine mapping, map-based cloning, and the efficient use of gene information in molecular breeding. Questions are frequently met and asked in the application of QTL mapping in practical genetic populations. Questions related to statistical method of QTL mapping are: what does LOD score mean? What is the relationship between the reliability of detected QTL and the LOD threshold? How to evaluate different QTL mapping methods? How to improve the QTL detection power? Questions related to genetic parameter estimation are: how to calculate the phenotypic variance explained by each detected QTL? How to determine the source of favorable alleles at detected QTL? How efficient is the selective genotyping? Can composite traits be used in QTL mapping? Questions related to linkage map and mapping populations are: does the phenotype of a trait in interest have to follow a normal distribution? Does the increase in marker density greatly improve QTL mapping power? What effects will missing markers have in QTL mapping? What effects will segregation distortion have in QTL mapping? Our objective in this paper was to give an analysis and answer to each of the 12 frequently asked questions, based on our studies in past several years.

Key words: Quantitative trait, QTL mapping, Inclusive composite interval mapping, Likelihood ratio test, Power analysis

[1]Lynch M, Walsh B. Genetic and Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates, 1998
[2]Doerge R W. Mapping and analysis of quantitative trait loci in experiment populations. Nat Rev Genet, 2002, 3: 43-52
[3]Zhai H-Q (翟虎渠), Wang J-K (王建康). Applied Quantitative Genetics (应用数量遗传). Beijing: China Agricultural Science and Technology Press, 2007 (in Chinese)
[4]Wang J-K (王建康). Inclusive composite interval mapping of quantitative trait genes
[J].Acta Agron Sin(作物学报.2009, 35(2):239-245
[5]Lander E S, Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 1989, 121: 185-199
[6]Zeng Z B. Precision mapping of quantitative trait loci. Genetics, 1994, 136: 1457-1468
[7]Li H, Ye G, Wang J. A modified algorithm for the improvement of composite interval mapping. Genetics, 2007, 175: 361-374
[8]Li H, Ribaut J M, Li Z, Wang J. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations
[J].Theor Appl Genet
[9]Zhang L, Li H, Li Z, Wang J. Interactions between markers can be caused by the dominance effect of QTL
[J].Genetics
[10]Goffinet P, Loisel B, Lawrent B. Testing in normal mixture models when the proportions are known
[J].Biometrika
[11]Churchill G A, Doerge R W. Empirical threshold values for quantitative trait mapping. Genetics, 1994, 138: 963-971
[12]Chen L, Storey J D. Relaxed significance criteria for linkage analysis
[J].Genetics
[13]Li H.
[J].Hearne S, Bänziger M, Li Z, Wang J. Statistical properties of QTL linkage mapping in biparental genetic populations. Heredity
[14]Wang J, Wan X, Crossa J, Crouch J, Weng J, Zhai H, Wan J. QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet Res, 2006, 88: 93-104
[15]Wang J, Wan X, Li H, Pfeiffer W, Crouch J, Wan J. Application of identified QTL-marker associations in rice quality improvement through a design breeding approach
[J].Theor Appl Genet
[16]Tinker N A, Mather D E, Rossnagel B G, Kasha K J, Kleinhofs A, Hayes P M, Falk D E, Ferguson T, Shugar L P, Legge W G, Irvine R B, Choo T M, Briggs K G, Ullrich S E, Franckowiak J D, Blake T K, Graf R J, Dofing S M, Saghai-Maroof M A, Scoles G J, Hoffman D, Dahleen L S, Kilian A, Chen F, Biyashev R M, Kudrna D A, Steffenson B J. Regions of the genome that affect agronomic performance in two-row barley
[J].Crop Sci
[17]Zhang L P, Lin G Y, Niño-Liu D, Foolad M R. Mapping QTLs conferring early blight (Alternaria solani) resistance in a Lycopersicon esculentum × L. hirsutum cross by selective genotyping. Mol Breed, 2003, 12: 3-19
[18]Wingbermuehle W J, Gustus C, Smith K P. Exploiting selective genotyping to study genetic diversity of resistance to Fusarium head blight in barley
[J].Theor Appl Genet
[19]Docherty S J, Butcher L M, Schalkwyk L C, Plomin R. Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genome wide association studies
[J].BMC Genomics
[20]Sun Y, Wang J, Crouch J H, Xu Y. Efficiency of selective genotyping for genetic analysis and crop improvement of complex traits. Mol Breed, 2010 (in press)Wang Y.
[J].Li H, Zhang L, Lü W, Wang J. On the use of composite traits in quantitative trait locus mapping. GeneticsZhang L, Wang S, Li H, Deng Q, Zheng A, Li S, Li P, Li Z, Wang J. Effects of missing markers and segregation distortion on QTL mapping in F2 populations. Theor Appl Genet, 2010 (submitted)
[1] WANG Jing-Tian, ZHANG Ya-Wen, DU Ying-Wen, REN Wen-Long, LI Hong-Fu, SUN Wen-Xian, GE Chao, ZHANG Yuan-Ming. SEA v2.0: an R software package for mixed major genes plus polygenes inheritance analysis of quantitative traits [J]. Acta Agronomica Sinica, 2022, 48(6): 1416-1424.
[2] WANG Xiao-Lei, LI Wei-Xing, OU-YANG Lin-Juan, XU Jie, CHEN Xiao-Rong, BIAN Jian-Min, HU Li-Fang, PENG Xiao-Song, HE Xiao-Peng, FU Jun-Ru, ZHOU Da-Hu, HE Hao-Hua, SUN Xiao-Tang, ZHU Chang-Lan. QTL mapping for plant architecture in rice based on chromosome segment substitution lines [J]. Acta Agronomica Sinica, 2022, 48(5): 1141-1151.
[3] 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.
[4] 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.
[5] ZHANG Bo, PEI Rui-Qing, YANG Wei-Feng, ZHU Hai-Tao, LIU Gui-Fu, ZHANG Gui-Quan, WANG Shao-Kui. Mapping and identification QTLs controlling grain size in rice (Oryza sativa L.) by using single segment substitution lines derived from IAPAR9 [J]. Acta Agronomica Sinica, 2021, 47(8): 1472-1480.
[6] ZHOU Xin-Tong, GUO Qing-Qing, CHEN Xue, LI Jia-Na, WANG Rui. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 587-598.
[7] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[8] SHEN Wen-Qiang, ZHAO Bing-Bing, YU Guo-Ling, LI Feng-Fei, ZHU Xiao-Yan, MA Fu-Ying, LI Yun-Feng, HE Guang-Hua, ZHAO Fang-Ming. Identification of an excellent rice chromosome segment substitution line Z746 and QTL mapping and verification of important agronomic traits [J]. Acta Agronomica Sinica, 2021, 47(3): 451-461.
[9] SUN Zhi-Guang, WANG Bao-Xiang, ZHOU Zhen-Ling, FANG Lei, CHI Ming, LI Jing-Fang, LIU Jin-Bo, Bello Babatunde Kazeem, XU Da-Yong. Screening of germplasm resources and QTL mapping for germinability under submerged condition in rice (Oryza sativa L.) [J]. Acta Agronomica Sinica, 2021, 47(1): 61-70.
[10] Dai-Ling LIU,Jun-Feng XIE,Qian-Rui HE,Si-Wei CHEN,Yue HU,Jia ZHOU,Yue-Hui SHE,Wei-Guo LIU,Wen-Yu YANG,Xiao-Ling WU. QTL analysis for relative contents of glycinin and β-conglycinin fractions from storage protein in soybean seeds under monoculture and relay intercropping [J]. Acta Agronomica Sinica, 2020, 46(3): 341-353.
[11] WU Hai-Tao, ZHANG Yong, SU Bo-Hong, Lamlom F Sobhi, QIU Li-Juan. Development of molecular markers and fine mapping of qBN-18 locus related to branch number in soybean (Glycine max L.) [J]. Acta Agronomica Sinica, 2020, 46(11): 1667-1677.
[12] WANG Xiao-Lei, LI Wei-Xing, ZENG Bo-Hong, SUN Xiao-Tang, OU-YANG Lin-Juan, CHEN Xiao-Rong, HE Hao-Hua, ZHU Chang-Lan. QTL detection and stability analysis of rice grain shape and thousand-grain weight based on chromosome segment substitution lines [J]. Acta Agronomica Sinica, 2020, 46(10): 1517-1525.
[13] WANG Cun-Hu,LIU Dong,XU Rui-Neng,YANG Yong-Qing,LIAO Hong. Mapping of QTLs for leafstalk angle in soybean [J]. Acta Agronomica Sinica, 2020, 46(01): 9-19.
[14] YANG Xiao-Meng, LI Xia, PU Xiao-Ying, DU Juan, Muhammad Kazim Ali, YANG Jia-Zhen, ZENG Ya-Wen, YANG Tao. QTL mapping for total grain anthocyanin content and 1000-kernel weight in barley recombinant inbred lines population [J]. Acta Agronomica Sinica, 2020, 46(01): 52-61.
[15] WANG Da-Chuan,WANG Hui,MA Fu-Ying,DU Jie,ZHANG Jia-Yu,XU Guang-Yi,HE Guang-Hua,LI Yun-Feng,LING Ying-Hua,ZHAO Fang-Ming. Identification of rice chromosome segment substitution Line Z747 with increased grain number and QTL mapping for related traits [J]. Acta Agronomica Sinica, 2020, 46(01): 140-146.
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