Rice molecular markers and genetic mapping: Current status and prospects

doi:10.1016/S2095-3119(16)61591-5

摘要/Abstract

Abstract: Dramatic changes in climatic conditions that supplement the biotic and abiotic stresses pose severe threat to the sustainable rice production and have made it a difficult task for rice molecular breeders to enhance production and productivity under these stress factors. The main focus of rice molecular breeders is to understand the fundamentals of molecular pathways involved in complex agronomic traits to increase the yield. The availability of complete rice genome sequence and recent improvements in rice genomics research has made it possible to detect and map accurately a large number of genes by using linkage to DNA markers. Linkage mapping is an effective approach to identify the genetic markers which are co-segregating with target traits within the family. The ideas of genetic diversity, quantitative trait locus (QTL) mapping, and marker-assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium (LD) also called association mapping and genomic selection (GS), respectively. The use of cost-effective DNA markers derived from the fine mapped position of the genes for important agronomic traits will provide opportunities for breeders to develop high-yielding, stress-resistant, and better quality rice cultivars. Here we focus on the progress of molecular marker technologies, their application in genetic mapping and evolution of association mapping techniques in rice.

Key words: genetic mapping , molecular markers , maker assisted selection , Oryza sativa L. , quantitative trait loci

. [J]. Journal of Integrative Agriculture, 2017, 16(09): 1879-1891.

Ghulam Shabir, Kashif Aslam, Abdul Rehman Khan, Muhammad Shahid, Hamid Manzoor, Sibgha Noreen, Mueen Alam Khan, Muhammad Baber, Muhammad Sabar, Shahid Masood Shah, Muhammad Arif. Rice molecular markers and genetic mapping: Current status and prospects[J]. Journal of Integrative Agriculture, 2017, 16(09): 1879-1891.

参考文献

Abdurakhmonov I Y, Abdukarimov A. 2008. Application of association mapping to understanding the genetic diversity of plant germplasm resources. International Journal of Plant Genomics, 2008, 1–18.

Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27, 617–631.

Agrama H, Eizenga G, Yan W. 2007. Association mapping of yield and its components in rice cultivars. Molecular Breeding, 19, 341–356.

Al-Shugeairy Z, Price A H, Robinson D. 2015. Genome wide association mapping for drought recovery trait in rice (Oryza sativa L.). International Journal of Applied Agricultural Sciences, 1, 11–18.

Anonymous. 2011. From 6 billion to 7 billion: How population growth is changing and challenging our world, Population Institute. [2017-01-16]. http://apo.org.au/node/26644

Aranzana M J, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C. 2005. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genetics, 1, e60.

Aslam K, Arif M. 2014. SSR analysis of chromosomes 3 and 7 of rice (Oryza staiva L.) associated with grain length. Pakistan Journal of Botany, 46, 1363–1372.

Bao J, Corke H, Sun M. 2006. Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theoretical and Applied Genetics, 113, 1185–1196.

Begum H, Spindel J E, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch S R. 2015. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa). PLOS ONE, 10, e0119873.

Biscarini F, Cozzi P, Casella L, Riccardi P, Vattari A, Orasen G, Perrini R, Tacconi G, Tondelli A, Biselli C. 2016. Genome-wide association study for traits related to plant and grain morphology, and root architecture in temperate rice accessions. PLOS ONE, 11, e0155425.

Borlaug N E. 2000. Ending world hunger. The promise of biotechnology and the threat of antiscience zealotry. Plant Physiology, 124, 487–490.

Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2635.

Breseghello F, Coelho A S G. 2013. Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.). Journal of Agricultural and Food Chemistry, 61, 8277–8286.

Collard B, Jahufer M, Brouwer J, Pang E. 2005. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica, 142, 169–196.

Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A. 2013. Genome-wide association mapping of root traits in a japonica rice panel. PLOS ONE, 8, e78037.

Cui D, Xu C Y Tang C F, Yang C G, Yu T Q, Xin X A, Cao G I Xu F R, Zhang J G Han L Z. 2013. Genetic structure and association mapping of cold tolerance in improved japonica rice germplasm at the booting stage. Euphytica, 193, 369–382.

Du J H, Fan Y Y, Wu J R, Zhuang J Y. 2008. Dissection of QTLs for yield traits on the short arm of rice chromosome. Agricultural Sciences in China, 7, 513–520.

Edwards D, Batley J. 2010. Plant genome sequencing: Applications for crop improvement. Plant Biotechnology Journal, 8, 2–9.

Ehrenreich I M, Hanzawa Y, Chou L, Roe J L, Kover P X, Purugganan M D. 2009. Candidate gene association mapping of Arabidopsis flowering time. Genetics, 183, 325–335.

Feng Y, Lu Q, Zhai R, Zhang M, Xu Q, Yang Y, Wang S, Yuan X, Yu H, Wang Y. 2016. Genome wide association mapping for grain shape traits in indica rice. Planta, 244, 1–12.

Garris A J, McCOUCH S R, Kresovich S. 2003. Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics, 165, 759–769.

Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K. 2004. Assessing genetic potential in germplasm collections of crop plants by marker-trait association: A case study for potatoes with quantitative variation of resistance to late blight and maturity type. Molecular Breeding, 13, 93–102.

Gonzaga Z J, Aslam K, Septiningsih E M, Collard B C. 2015. Evaluation of SSR and SNP markers for molecular breeding in rice. Plant Breeding and Biotechnology, 3, 139–152.

Gupta P K, Varshney R K. 2005. Cereal genomics: An overview. In: Cereal Genomics. Springer, The Netherlands. pp. 1–18.

Harjes C E, Rocheford T R, Bai L, Brutnell T P, Kandianis C B, Sowinski S G, Stapleton A E, Vallabhaneni R, Williams M, Wurtzel E T. 2008. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science, 319, 330–333.

Hayward A, Mason A, Dalton-Morgan J, Zander M, Edwards D, Batley J. 2012. SNP discovery and applications in Brassica napus. Plant Biotechnology, 39, 12.

Hong Z, Ueguchi-Tanaka M, Umemura K, Uozu S, Fujioka S, Takatsuto S, Yoshida S, Ashikari M, Kitano H, Matsuoka M. 2003. A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450. The Plant Cell, 15, 2900–2910.

Hossain M. 1997. Rice supply and demand in Asia: A socioeconomic and biophysical analysis. In: Applications of Systems Approaches at the Farm and Regional Levels. vol. 1. Springer, The Netherlands. pp. 263–279.

Hu G, Zhang D, Pan H, Li B, Wu J, Zhou X, Zhang Q, Zhou L, Yao G, Li J. 2011. Fine mapping of the awn gene on chromosome 4 in rice by association and linkage analyses. Chinese Science Bulletin, 56, 835–839.

Huang N, Courtois B, Khush G S, Lin H, Wang G, Wu P, Zheng K. 1996. Association of quantitative trait loci for plant height with major dwarfing genes in rice. Heredity, 77, 130–137.

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42, 961–967.

Van Inghelandt D, Melchinger A E, Lebreton C, Stich B. 2010. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theoretical and Applied Genetics, 120, 1289–1299.

Jain S M, Brar D S, Ahloowalia B. 2010. Molecular Techniques in Crop Improvement. Springer, The Netherlands.

Jia L, Yan W, Zhu C, Agrama H A, Jackson A, Yeater K, Li X, Huang B, Hu B, McClung A. 2012. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS ONE, 7, e32703.

Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J. 2010. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theoretical and Applied Genetics, 121, 475–487.

Jones N, Ougham H, Thomas H. 1997. Markers and mapping: We are all geneticists now. New Phytologist, 137, 165–177.

Kalia R K, Rai M K, Kalia S, Singh R, Dhawan A. 2011. Microsatellite markers: An overview of the recent progress in plants. Euphytica, 177, 309–334.

Kobayashi S, Fukuta Y, Sato T, Osaki M, Khush G. 2003. Molecular marker dissection of rice (Oryza sativa L.) plant architecture under temperate and tropical climates. Theoretical and Applied Genetics, 107, 1350–1356.

Kumar V, Singh A, Mithra S A, Krishnamurthy S, Parida S K, Jain S, Tiwari K K, Kumar P, Rao A R, Sharma S. 2015. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Research, 22, 133–145.

Leegood R C, Evans J R, Furbank R T. 2010. Food security requires genetic advances to increase farm yields. Nature, 464, 831–831.

Li X, Yan W, Agrama H, Jia L, Jackson A, Moldenhauer K, Yeater K, McClung A, Wu D. 2012. Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS ONE, 7, e29350.

Liu E, Liu X, Zeng S, Zhao K, Zhu C, Liu Y, Breria M C, Zhang B, Hong D. 2015. Time-course association mapping of the grain-filling rate in rice (Oryza sativa L.). PLOS ONE, 10, e0119959.

Lu Q, Zhang M, Niu X, Wang S, Xu Q, Feng Y, Wang C, Deng H, Yuan X, Yu H. 2015. Genetic variation and association mapping for 12 agronomic traits in indica rice. BMC Genomics, 16, 1.

Maloof J N. 2003. QTL for plant growth and morphology. Current Opinion in Plant Biology, 6, 85–90.

McCouch S R, Teytelman L, Xu Y, Lobos K B, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research, 9, 199–207.

McCouch S R, Wright M H, Tung C W, Maron L G, McNally K L, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P. 2016. Open access resources for genome-wide association mapping in rice. Nature Communications, 7, doi: 10.1038/ncomms10532

McNally K L, Childs K L, Bohnert R, Davidson R M, Zhao K, Ulat V J, Zeller G, Clark R M, Hoen D R, Bureau T E. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America, 106, 12273–12278.

Meng L, Zhao X, Ponce K, Ye G, Leung H. 2016. QTL mapping for agronomic traits using multi-parent advanced generation inter-cross (MAGIC) populations derived from diverse elite indica rice lines. Field Crops Research, 189, 19–42.

Mgonja E M, Balimponya E G, Kang H, Bellizzi M, Park C H, Li Y, Mabagala R, Sneller C, Correll J, Opiyo S. 2016. Genome-wide association mapping of rice resistance genes against Magnaporthe oryzae isolates from four African countries. Phytopathology, 106, 1359–1365.

Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y. 2002. Positional cloning of rice semidwarfing gene, sd-1: Rice “Green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Research, 9, 11–17.

de Oliveira B T, Brondani R, Breseghello F, Coelho A, Mendonca J, Rangel P, Brondani C. 2010. Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Genetics and Molecular Biology, 33, 515.

Olsen K M, Purugganan M D. 2002. Molecular evidence on the origin and evolution of glutinous rice. Genetics, 162, 941–950.

Ordonez S A, Silva J, Oard J H. 2010. Association mapping of grain quality and flowering time in elite japonica rice germplasm. Journal of Cereal Science, 51, 337–343.

Pandey G K, Pandey A, Prasad M, Böhmer M. 2016. Editorial: Abiotic stress signaling in plants: Functional genomic intervention. Frontiers in Plant Science, 7, 681.

Raboin L M, Ballini E, Tharreau D, Ramanantsoanirina A, Frouin J, Courtois B, Ahmadi N. 2016. Association mapping of resistance to rice blast in upland field conditions. Rice, 9, 59.

Sax K. 1923. The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics, 8, 552.

Shabir G, Naveed S A, Arif M. 2013. Estimation of phenotypic variability and mutual association of yield and its components in rice (Oryza sativa L.) germplasm using multivariate analysis. Pakistan Journal of Agricultural Research, 51, 361–377.

Shah S M, Arif M, Aslam K, Shabir G, Thomson M J. 2016. Genetic diversity analysis of Pakistan rice (Oryza sativa) germplasm using multiplexed single nucleotide polymorphism markers. Genetic Resources and Crop Evolution, 63, 1113–1126.

Shah S M, Aslam K, Shabir G, Khan A R, Abbasi B H, Shinwari Z K, Arif M. 2015a. Population structure and diversity of the AA genome of rice based on simple sequence repeats variation in organelle genome. Pakistan Journal of Botany, 47, 1773–1782.

Shah S M, Shabir G, Aslam K, Sabar M, Arif M. 2015b. Identification of SSR markers to find adulteration in elite basmati rice varieties. Environment and Plant Systems, 1, 4–15.

Shao Y, Jin L, Zhang G, Lu Y, Shen Y, Bao J. 2011. Association mapping of grain color, phenolic content, flavonoid content and antioxidant capacity in dehulled rice. Theoretical and Applied Genetics, 122, 1005–1016.

Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics, 40, 1023–1028.

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink J L, McCouch S R. 2015. Genomic selection and association mapping in rice (Oryza sativa): Effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLOS Genetics, 11, e1005350.

Stuber C W, Edwards M, Wendel J F. 1987. Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits. Crop Science, 27, 639–648.

Wang L, Wang A, Huang X, Zhao Q, Dong G, Qian Q, Sang T, Han B. 2011. Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theoretical and Applied Genetics, 122, 327–340.

Wang X, Jia M H, Ghai P, Lee F N, Jia Y. 2015. Genome-wide association of rice blast disease resistance and yield-related components of rice. Molecular Plant-Microbe Interactions, 28, 1383–1392.

Wang Y, Li J. 2005. The plant architecture of rice (Oryza sativa). Plant Molecular Biology, 59, 75–84.

Wen W, Mei H, Feng F, Yu S, Huang Z, Wu J, Chen L, Xu X, Luo L. 2009. Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theoretical and Applied Genetics, 119, 459–470.

Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X. 2008. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Research, 18, 1199–1209.

William S K, Michael R C. 1996. Essentials of Genetics. 2nd. Prentice-Hall Inc., Upper Saddle River, USA.

Yan J, Zhu J, He C, Benmoussa M, Wu P. 1999. Molecular marker-assisted dissection of genotype×environment interaction for plant type traits in rice (Oryza sativa L.). Crop Science, 39, 538–544.

Yan W G, Li Y, Agrama H A, Luo D, Gao F, Lu X, Ren G. 2009. Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molecular Breeding, 24, 277–292.

Yang X, Xu Y, Shah T, Li H, Han Z, Li J, Yan J. 2011. Comparison of SSRs and SNPs in assessment of genetic relatedness in maize. Genetica, 139, 1045–1054.

Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y. 2000. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. The Plant Cell, 12, 2473–2483.

Yao X Y, Wang J Y, Liu J, Wang W, Yang S L, Zhang Y, Xu Z J. 2016. Comparison and analysis of QTLs for grain and hull thickness related traits in two recombinant inbred line (RIL) populations in rice (Oryza sativa L.). Journal of Integrative Agriculture, 15, 2437–2450.

Yonemaru J I, Yamamoto T, Fukuoka S, Uga Y, Hori K, Yano M. 2010. Q-TARO: QTL annotation rice online database. Rice, 3, 194–203.

Yu J, Buckler E S. 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology, 17, 155–160.

Zhang P, Zhong K, Tong H, Shahid M Q, Li J. 2016. Association mapping for aluminum tolerance in a core collection of rice landraces. Frontiers in Plant Science, 7, doi: 10.3389/fpls.2016.01415

Zhao J, Paulo M J, Jamar D, Lou P, Van Eeuwijk F, Bonnema G, Vreugdenhil D, Koornneef M. 2007. Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa. Genome, 50, 963–973.

Zhao K, Aranzana M J, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P. 2007. An Arabidopsis example of association mapping in structured samples. PLoS Genetics, 3, e4.

Zhao K, Tung C W, Eizenga G C, Wright M H, Ali M L, Price A H, Norton G J, Islam M R, Reynolds A, Mezey J. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications, 2, 467.

Zhou J, You A, Ma Z, Zhu L, He G. 2012. Association analysis of important agronomic traits in japonica rice germplasm. African Journal of Biotechnology, 11, 2957–2970.

Zhu D, Kang H, Li Z, Liu M, Zhu X, Wang Y, Wang D, Wang Z, Liu W, Wang G L. 2016. A genome-wide association study of field resistance to Magnaporthe oryzae in rice. Rice, 9, 44.