Please wait a minute...
Journal of Integrative Agriculture  2017, Vol. 16 Issue (12): 2674-2685    DOI: 10.1016/S2095-3119(17)61813-6
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Genomics-assisted breeding - A revolutionary strategy for crop improvement
LENG Peng-fei1, Thomas Lübberstedt2, XU Ming-liang1
1 National Maize Improvement Center of China, China Agricultural University, Beijing 100193, P.R.China
2 Department of Agronomy, Iowa State University, Ames 50011, USA
Download:  PDF (279KB) ( )  
Export:  BibTeX | EndNote (RIS)      
Abstract  Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses.  With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding.  High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits.  Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding (GAB).  With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.  
Keywords:  germplasm        genotyping technology        phenotyping platform        genomics-assisted breeding  
Received: 20 July 2017   Accepted:
Corresponding Authors:  Correspondence XU Ming-liang, Tel: +86-10-62733166, E-mail: mxu@cau.edu.cn   
About author:  LENG Peng-fei, Tel: +86-10-62731135, E-mail: pfleng@163.com

Cite this article: 

LENG Peng-fei, Thomas Lübberstedt, XU Ming-liang. 2017. Genomics-assisted breeding - A revolutionary strategy for crop improvement. Journal of Integrative Agriculture, 16(12): 2674-2685.

Andrade-Sanchez P, Gore M A, Heun J T, Thorp K R, Carmo-Silva A E, French A N, Salvucci M E, White J W. 2014. Development and evaluation of a field-based high-throughput phenotyping platform. Functional Plant Biology, 41, 68–79.

Azevedo C, Sadanandom A, Kitagawa K, Freialdenhoven A, Shirasu K, Schulze-Lefert P. 2002. The RAR1 interactor SGT1, an essential component of R gene-triggered disease resistance. Science, 295, 2073–2076.

Bergelson J, Roux F. 2010. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nature Reviews Genetics, 11, 867–879.

Bevan M W, Uauy C, Wulff B B H, Zhou J, Krasileva K, Clark M D. 2017. Genomic innovation for crop improvement. Nature, 543, 346–354.

Bomblies K, Doebley J F. 2006. Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication. Genetics, 172, 519–531.

Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A. 2002. The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proceedings of the National Academy of the United States of America, 99, 9328–9333.

Buckler E S, Holland J B, Bradbury P J, Acharya C B, Brown P J, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Goodman M M, Harjes C, Guill K, Kroon D E, Larsson S, Lepak N K, Li H, Mitchell S E, Pressoir G, Peiffer J A, Rosas M O, et al.

2009. The genetic architecture of maize flowering time. Science, 325, 714–718.

Burr B, Burr F A, Thompson K H, Albertson M C, Stuber C W. 1988. Gene mapping with recombinant inbreds in maize. Genetics, 118, 519–526.

Chen W, Gao Y, Xie W, Gong L, Lu K, Wang W, Li Y, Liu X, Zhang H, Dong H, Zhang W, Zhang L, Yu S, Wang G, Lian X, Luo J. 2014. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nature Genetics, 46, 714–721.

Chin C S, Peluso P, Sedlazeck F J, Nattestad M, Concepcion G T, Clum A, Dunn C, O’Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer G R, Delledonne M, Luo C, Ecker J R, Cantu D, Rank D R, Schatz M C. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods, 13, 1050–1054.

Colasanti J, Yuan Z, Sundaresan V. 1998. The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell, 93, 593–603.

Collard B C Y, Mackill D J. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society (B: Biological Sciences), 363, 557–572.

Cooper M, Messina C D, Podlich D, Totir L R, Baumgarten A, Hausmann N J, Wright D, Graham G. 2014. Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction. Crop and Pasture Science, 65, 311–336.

Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de Los Campos G, Burgueño J, González-Camacho J M, Pérez-Elizalde S, Beyene Y, Dreisigacker S, Singh R, Zhang X, Gowda M, Roorkiwal M, Rutkoski J, Varshney R K. 2017. Genomic selection in plant breeding: Methods, models, and perspectives. Trends in Plant Science, 22, 961–975.

Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, Wang X, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z. 2017. Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science, 355, 962–965.

Doebley J, Stec A, Gustus C. 1995. Teosinte branched1 and the origin of maize: Evidence for epistasis and the evolution of dominance. Genetics, 141, 333–346.

Eathington S R, Crosbie T M, Edwards M D, Reiter R S, Bull J K. 2007. Molecular markers in a commercial breeding program. Crop Science, 47, S154–S163.

Elshire R J, Glaubitz J C, Sun Q, Poland J A, Kawamoto K, Buckler E S, Mitchell S E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One, 6, e19379.

Emebiri L C, Tan M K, El-Bouhssini M, Wildman O, Jighly A, Tadesse W, Ogbonnaya F C. 2017. QTL mapping identifies a major locus for resistance in wheat to Sunn pest (Eurygaster integriceps) feeding at the vegetative growth stage. Theoretical and Applied Genetics, 130, 309–318.

Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 112, 1164–1171.

Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B. 2003. Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proceedings of the National Academy of the United States of America, 100, 15253–15258.

Frankel O H. 1984. Genetic perspectives of germplasm conservation. In: Arber W, Illmensee K, Peacock W J, Starlinger P, eds., Genetic Manipulation: Impact on Man and Society. Cambridge University Press, Cambridge, UK. pp. 161–170.

Fu D, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen X, Sela H, Fahima T, Dubcovsky J. 2009. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science, 323, 1357–1360.

Fukatsu T, Watanabe T, Hu H, Yoichi H, Hirafuji M. 2012. Field monitoring support system for the occurrence of Leptocorisa chinensis Dallas (Hemiptera: Alydidae) using synthetic attractants, Field Servers, and image analysis. Computers and Electronics in Agriculture, 80, 8–16.

Ganal M W, Durstewitz G, Polley A, Bérard A, Buckler E S, Charcosset A, Clarke J D, Graner E M, Hansen M, Joets J, Le Paslier M C, McMullen M D, Montalent P, Rose M, Schön C C, Sun Q, Walter H, Martin O C, Falque M. 2011. A large maize (Zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One, 6, e28334.

Gore M A, Chia J M, Elshire R J, Sun Q, Ersoz E S, Hurwitz B L, Peiffer J A, McMullen M D, Grills G S, Ross-Ibarra J, Ware D H, Buckler E S. 2009. A first-generation haplotype map of maize. Science, 326, 1115–1117.

Gou J Y, Li K, Wu K, Wang X, Lin H, Cantu D, Uauy C, Dobon-Alonso A, Midorikawa T, Inoue K, Sánchez J, Fu D, Blechl A, Wallington E, Fahima T, Meeta M, Epstein L, Dubcovsky J. 2015. Wheat stripe rust resistance protein WKS1 reduces the ability of the thylakoid-associated ascorbate peroxidase to detoxify reactive oxygen species. The Plant Cell, 27, 1755–1770.

Guo Q, Wu F, Pang S, Zhao X, Chen L, Liu J, Xue B, Xu G, Li L, Jing H, Chu C. 2017. Crop 3D - A LiDAR based platform for 3D high-throughput crop phenotyping. Science China (Life Sciences), doi: 10.1007/s11427-017-9056-0

Gupta P K, Langridge P, Mir R R. 2010. Marker-assisted wheat breeding: Present status and future possibilities. Molecular Breeding, 26, 145–161.

He C, Holme J, Anthony J. 2014. SNP genotyping: The KASP assay. Crop Breeding: Methods and Protocols, 1145, 75–86.

Holbrook C C, Anderson W F. 1995. Evaluation of a core collection to identify resistance to late leafspot in peanut. Crop Science, 35, 1700–1702.

Hospital F, Chevalet C, Mulsant P. 1992. Using markers in gene introgression breeding programs. Genetics, 231, 1199–1210.

Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H, Shi Z, Pan J, Zhang D, Kang S, Zhu L, Dong G, Guo L, Zeng D, Zhang G, Xie L, Xiong G, Li J, Qian Q. 2015. A rare allele of GS2 enhances grain size and grain yield in rice. Molecular Plant, 8, 1455–1465.

Jansen M, Gilmer F, Biskup B, Nagel K A, Rascher U, Fischbach A, Briem S, Dreissen G, Tittmann S, Braun S, Jaeger I D, Metzlaff M, Schurr U, Scharr H, Walter A. 2009. Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants. Functional Plant Biology, 36, 902–914.

Jia J, Li H, Zhang X, Li Z, Qiu L. 2017. Genomics-based plant germplasm research (GPGR). The Crop Journal, 5, 166–174.

Jia Y, Jannink J L. 2012. Multiple-trait genomic selection methods increase genetic value prediction accuracy. Genetics, 192,1513–1522.

Jiang Y, Schulthess A W, Rodemann B, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Ganal M W, Röder M S, Reif J C. 2017. Validating the prediction accuracies of marker-assisted and genomic selection of Fusarium head blight resistance in wheat using an independent sample. Theoretical and Applied Genetics, 130, 471–482.

Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W, Zhang M, Xie S, Lai J. 2012. Genome-wide genetic changes during modern breeding of maize. Nature Genetics, 44, 812–815.

Johal G S, Briggs S P. 1992. Reductase activity encoded by the HM1 disease resistance gene in maize. Science, 258, 985–987.

Kelliher T, Starr D, Richbourg L, Chintamanani S, Delzer B, Nuccio M L, Green J, Chen Z, McCuiston J, Wang W, Liebler T, Bullock P, Martin B. 2017. MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction. Nature, 542, 105–109.

Kobayashi F, Tanaka T, Kanamori H, Wu J Z, Katayose Y, Handa H. 2016. Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotyping-by-sequencing. Breeding Science, 66, 213–225.

Konlasuk S, Xing Y, Zhang N, Zuo W, Zhang B, Tan G, Xu M. 2015. ZmWAK, a quantitative resistance gene to head smut in maize, improves yield performance by reducing the endophytic pathogen Sporisorium reiliana. Molecular Breeding, 35, 1–10.

Kump K L, Bradbury P J, Wisser R J, Buckler E S, Belcher A R, Oropeza-Rosas M A, Zwonitzer J C, Kresovich S, McMullen M D, Ware D, Balint-Kurti P J, Holland J B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics, 43, 163–168.

Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, et al. 2010. Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics, 42, 1027–1030.

Lee M. 1995. DNA markers and plant breeding programs. Advances in Agronomy, 55, 265–344.

De Leeuw M, Martinant J P, Duborjal H, Laffaire J B, Beugnot R. 2009. High throughput SNP discovery in wheat using methylation-sensitive digestion and next-generation sequencing. In: INRA (Institut National de la Recherche Agronomique), ed., 19th International Triticeae Mapping Initiative Meeting. Clermont-Ferrand, France.

Li H, Peng Z, Yang X, Wang W, Fu J, Wang J, Han Y, Chai Y, Guo T, Yang N, Liu J, Warburton M L, Cheng Y, Hao X, Zhang P, Zhao J, Liu Y, Wang G, Li J, Yan J. 2013. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nature Genetics, 45, 43–50.

Li J Y, Wang J, Zeigler R S. 2014. The 3,000 rice genomes project: Nw opportunities and challenges for future rice research. Giga Science, 3, 7.

Li K, Bao J, Corke H, Sun M. 2017. Association analysis of markers derived from starch biosynthesis related genes with starch physicochemical properties in the USDA rice mini-core collection. Frontiers in Plant Science, 8, 424.

Li W, Zhu Z, Chern M, Yin J, Yang C, Ran L, Cheng M, He M, Wang K, Wang J, Zhou X, Zhu X, Chen Z, Wang J, Zhao W, Ma B, Qin P, Chen W, Wang Y, Liu J, et al. 2017. A natural allele of a transcription factor in rice confers broad-spectrum blast resistance. Cell, 170, 114–126.

Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 43, 1266–1269.

Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y. 2014. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nature Genetics, 46, 398–404.

Liu M, Lei L, Miao F, Powers C, Zhang X, Deng J, Tadege M, Carver B F, Yan L. 2017. The STENOFOLIA gene from Medicago alters leaf width, flowering time and chlorophyll content in transgenic wheat. Plant Biotechnology Journal, doi: 10.1111/pbi.12759

Liu Q, Yang T, Yu T, Zhang S, Mao X, Zhao J, Wang X, Dong J, Liu B. 2017. Integrating small RNA sequencing with QTL mapping for identification of mirnas and their target genes associated with heat tolerance at the flowering stage in rice. Frontiers in Plant Science, 8, 43.

Long Y M, Chao W S, Ma G J, Xu S S, Qi L L. 2017. An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theoretical and Applied Genetics, 130, 597–607.

de Los Campos G, Naya H, Gianola D, Crossa J, Legarra A, Manfredi E, Weigel K, Cotes J M. 2009. Predicting quantitative traits with regression models for dense molecular markers and pedigree. Genetics, 182, 375–385.

Lu Y, Hao Z, Xie C, Crossa J, Arausa J L, Gao S, Vivek B S, Magorokosho C, Mugo S, Makumbi D, Taba S, Pan G, Li X, Rong T, Zhang S, Xu Y. 2011. Large-scale screening for maize drought resistance using multiple selection criteria evaluated under water-stressed and well-watered environments. Field Crops Research, 124, 37–45.

Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, Xiao J, Guo X, Xu S, Niu Y, Jin J, Zhang H, Xu X, Li L, Wang W, Qian Q, et al. 2015. COLD1 confers chilling tolerance in rice. Cell, 160, 1209–1221.

Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo M C, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y, Ayliffe M A, Bariana H, Park R F, McIntosh R, Dole?el J, Bergès H, Spielmeyer W, Lagudah E S, Ellis J G, et al. 2015. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. Nature Plants, 1, 15186.

Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S. 2012. SNP markers and their impact on plant breeding. International Journal of Plant Genomics, 2012, 728398.

Massonnet C, Vile D, Fabre J, Hannah M A, Caldana C, Lisec J, Beemster G T, Meyer R C, Messerli G, Gronlund J T, Perkovic J, Wigmore E, May S, Bevan M W, Meyer C, Rubio-Díaz S, Weigel D, Micol J L, Buchanan-Wollaston V, Fiorani F, et al. 2010. Probing the reproducibility of leaf growth and molecular phenotypes: A comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiology, 152, 2142–2157.

Meng X, Muszynski M G, Danilevskaya O N. 2011. The FT-like ZCN8 gene functions as a floral activator and is involved in photoperiod sensitivity in maize. The Plant Cell, 23, 942–960.

Meuwissen T H E, Hayes B J, Goddard M E. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819–1829.

Miller T A, Muslin E H, Dorweiler J E. 2008. A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods. Planta, 227, 1377–1388.

Montes J M, Technow F, Dhillon B S, Mauch F, Melchinger A E. 2011. High-throughput non-destructive biomass determination during early plant development in maize under field conditions. Field Crops Research, 121, 268–273.

Muraya M M, Chu J, Zhao Y, Junker A, Klukas C, Reif J C, Altmann T. 2016. Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non-invasive phenotyping. The Plant Journal, 89, 366–380.

Muszynski M G, Dam T, Li B, Shirbroun D M, Hou Z, Bruggemann E, Archibald R, Ananiev E V, Danilevskaya O N. 2006. Delayed flowering1 encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize. Plant Physiology, 142, 1523–1536.

Onogi A, Watanabe M, Mochizuki T, Hayashi T, Nakagawa H, Hasegawa T, Iwata H. 2016. Toward integration of genomic selection with crop modelling: The development of an integrated approach to predicting rice heading dates. Theoretical and Applied Genetics, 129, 805–817.

Pan A, Hayes P M, Chen F, Chen T, Blake T, Wright S, Karsai I, Bedo Z. 1994. Genetic analysis of the components of winter hardiness in barley (Hordeum vulgare L.). Theoretical and Applied Genetics, 89, 900–910.

Patil G, Do T, Vuong T D, Valliyodan B, Lee J D, Chaudhary J, Shannon J G, Nguyen H T. 2016. Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean. Scientific Reports, 6, 19199.

Qin L, Hao C, Hou J, Wang Y, Li T, Wang L, Ma Z, Zhang X. 2014. Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2. BMC Plant Biology, 14, 107.

Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang G L. 2006. The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics, 172, 1901–1914.

Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney R K, and He Z. 2017. Crop breeding chips and genotyping platforms: Progress, challenges and perspectives. Molecular Plant, 10, 1047–1064.

Reynolds M, Langridge P. 2016. Physiological breeding. Current Opinion in Plant Biology, 31, 162–171. 

Rodríguez-Leal D, Lemmon Z H, Man J, Bartlett M, Lippman Z. 2017. Engineering quantitative trait variation for crop improvement by genome editing. Cell, 171, 470–480.

Saint Pierre C, Burgueño J, Crossa J, Fuentes Dávila G, Figueroa López P, Solís Moya E, Ireta Moreno J, Hernández Muela V M, Zamora Villa V M, Vikram P, Mathews K, Sansaloni C, Sehgal D, Jarquin D, Wenzl P, Singh S. 2016. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones. Scientific Reports, 6, 27312.

Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler K A, Meeley R, Ananiev E V, Svitashev S, Bruggemann E, Li B, Hainey C F, Radovic S, Zaina G, Rafalski J A, Tingey S V, Miao G H, Phillips R L, Tuberosa R. 2007. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proceedings of the National Academy of Sciences of the United States of America, 104, 11376–11381.

Schläppi M R, Jackson A K, Eizenga G C, Wang A, Chu C, Shi Y, Shimoyama N, Boykin D L. 2017. Assessment of five chilling tolerance traits and gwas mapping in rice using the USDA mini-core collection. Frontiers in Plant Science, 8, 957.

Schmidt R J, Ketudat M, Aukerman M J, Hoschek G. 1992. Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. The Plant Cell, 4, 689–700.

Semagn K, Babu R, Hearne S, Olsen M. 2014. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): Overview of the technology and its application in crop improvement. Molecular Breeding, 33, 1–14.

Shen H, Zhong X, Zhao F, Wang Y, Yan B, Li Q, Chen G, Mao B, Wang J, Li Y, Xiao G, He Y, Xiao H, Li J, He Z. 2015. Overexpression of receptor-like kinase ERECTA improves thermotolerance in rice and tomato. Nature Biotechnology, 33, 996–1003.

Shirasu K, Lahaye T, Tan M W, Zhou F, Azevedo C, Schulze-Lefert P. 1999. A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell, 99, 355–366.

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.

Song W Y, Wang G L, Chen L L, Kim H S, Pi L Y, Holsten T, Gardner J, Wang B, Zhai W X, Zhu L H, Fauquet C, Ronald P. 1995. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science, 270, 1804–1806.

Song X J, Huang W, Shi M, Zhu M Z, Lin H X. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics, 39, 623–630.

Spindel J E, Begum H, Akdemir D, Collard B, Redoña E, Jannink J L, McCouch S. 2016. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity, 116, 395–408.

Sundaram R M, Naveenkumar B, Biradar S K, Balachandran S M, Mishra B, IlyasAhmed M, Viraktamath B C, Ramesha M S, Sarma N P. 2008. Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica, 163, 215–224.

Takahagi K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K, Mochida K, Saisho D. 2016. Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Scientific Reports, 6, 33199.

Tian F, Bradbury P J, Brown P J, Hung H, Sun Q, Flint-Garcia S, Rocheford T R, McMullen M D, Holland J B, Buckler E S. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nature Genetics, 43, 159–162.

Trachsel S, Kaeppler S M, Brown K M, Lynch J P. 2011. Shovelomics: High throughput phenotyping of maize (Zea mays L.) root architecture in the field. Plant and Soil, 341, 75–87.

Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J. 2006. A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science, 314, 1298–1301.

Valliyodan B, Ye H, Song L, Murphy M, Shannon J G, Nguyen H T. 2016. Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. Journal of Experimental Botany, 68, 1835–1849.

Van K, McHale L K. 2017. Meta-analyses of QTLs associated with protein and oil contents and compositions in soybean [Glycine max (L.) Merr.] seed. International Journal of Molecular Sciences, 18, 1180.

Wang C, Ren H, Shen J, Zhao X, Cao S, Wang Z. 2016. Molecular evaluation of Guizhou local maize genetic diversity and construction of Core Collection. Southwest China Journal of Agricultural Sciences, 29, 1018–1022. (in Chinese)

Wang D, Qin B, Li X, Tang D, Zhang Y, Cheng Z, Xue Y. 2016. Nucleolar DEAD-Box RNA helicase TOGR1 regulates thermotolerant growth as a pre-rRNA chaperone in rice. PLoS Genetics, 12, e1005844.

Wang Q, Liu Y, He J, Zheng X, Hu J, Liu Y, Dai H, Zhang Y, Wang B, Wu W, Gao H, Zhang Y, Tao X, Deng H, Yuan D, Jiang L, Zhang X, Guo X, Cheng X, Wu C, et al. 2014. STV11 encodes a sulphotransferase and confers durable resistance to rice stripe virus. Nature Communications, 5, 4768.

Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics, 44, 950–954.

Wang X, Wang H, Liu S, Ferjani A, Li J, Yan J, Yang X, Qin F. 2016. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nature Genetics, 48, 1233–1241.

Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W. 2015. Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nature Genetics, 47, 944–948.

Wasson A P, Richards R A, Chatrath R, Misra S C, Prasad S V, Rebetzke G J, Kirkegaard J A, Christopher J, Watt M. 2012. Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops. Journal of Experimental Botany, 63, 3485–3498.

Williams J G K, Kubelik A R, Livak K J, Rafalski J A, Tingey S V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531–6535.

Wu X, Li Y, Shi Y, Song Y, Zhang D, Li C, Buckler E S, Li Y, Zhang Z, Wang T. 2016. Joint-linkage mapping and GWAS reveal extensive genetic loci that regulate male inflorescence size in maize. Plant Biotechnology Journal, 14, 1551–1562.

Xu D, Duan X, Wang B, Hong B, Ho T H D, Wu R. 1996. Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiology, 110, 249–257.

Xu Y, Crouch J H. 2008. Marker-assisted selection in plant breeding: From publications to practice. Crop Science, 48, 391–407.

Xu Y, Lu Y, Xie C, Gao S, Wan J, Prasanna B M. 2012. Whole-genome strategies for marker-assisted plant breeding. Molecular Breeding, 29, 833–854.

Yan J, Warburton M, Crouch J. 2011. Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Science, 51, 433–449.

Yang H, Jian J, Li X, Renshaw D, Clements J, Sweetingham M W, Li C. 2015. Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC Genomics, 16, 1.

Yang Q, He Y, Kabahuma M, Chaya T, Kelly A, Borrego E, Bian Y, El Kasmi F, Yang L, Teixeira P, Kolkman J, Nelson R, Kolomiets M, L Dangl J, Wisser R, Caplan J, Li X, Lauter N, Balint-Kurti P. 2017. A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nature Genetics, 49, 1364–1372.

Yang Q, Li Z, Li W, Ku L, Wang C, Ye J, Li K, Yang N, Li Y, Zhong T, Li J, Chen Y, Yan J, Yang X, Xu M. 2013. CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proceedings of the National Academy of Sciences of the United States of America, 110, 16969–16974.

Zamir D. 2001. OPINION: Improving plant breeding with exotic genetic libraries. Nature Reviews Genetics, 2, 983.

Zhang D, Wu S, An X, Xie K, Zhou Y, Xu L, Fang W, Liu S, Liu S, Zhu T, Li J, Rao L, Zhao J, Wan X. 2017. Construction of a multi-control sterility system for a maize male-sterile line and hybrid seed production based on the ZmMs7 gene encoding a PHD-finger transcription factor. Plant Biotechnology Journal, doi: 10.1111/pbi.12786

Zhang X, Huang C, Wu D, Qiao F, Li W, Duan L, Wang K, Xiao Y, Chen G, Liu Q, Xiong L, Yang W, Yan J. 2017. High-throughput phenotyping and QTL mapping reveals the genetic architecture of maize plant growth. Plant Physiology, 173, 1554–1564.

Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, Qiu J L, Gao CX. 2016. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature Communications, 7, 12617.

Zhao B, Lin X, Poland J, Trick H, Leach J, Hulbert S. 2005. A maize resistance gene functions against bacterial streak disease in rice. Proceedings of the National Academy of Sciences of the United States of America, 102, 15383–15388.

Zhao X, Tan G, Xing Y, Wei L, Chao Q, Zuo W, Lübberstedt T, Xu M. 2012. Marker-assisted introgression of qHSR1 to improve maize resistance to head smut. Molecular Breeding, 30, 1077–1088.

Zhao Y, Gowda M, Liu W, Würschum T, Maurer H P, Longin F H, Ranc N, Reif J C. 2012. Accuracy of genomic selection in European maize elite breeding populations. Theoretical and Applied Genetics, 124, 769–776.

Zhou B, Qu S, Liu G, Dolan M, Sakai H, Lu G, Bellizzi M, Wang G L. 2006. The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Molecular Plant-Microbe Interactions, 19, 1216–1228.

Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, et al. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnology, 33, 408–414.

Zuo W, Chao Q, Zhang N, Ye J, Tan G, Li B, Xing Y, Zhang B, Liu H, Fengler K A, Zhao J, Zhao X, Chen Y, Lai J, Yan J, Xu M. 2015. A maize wall-associated kinase confers quantitative resistance to head smut. Nature Genetics, 47, 151–157.
[1] GU Xiao-zhen, CAO Ya-cong, ZHANG Zheng-hai, ZHANG Bao-xi, ZHAO Hong, ZHANG Xiao-min, WANG Hai-ping, LI Xi-xiang, WANG Li-hao. Genetic diversity and population structure analysis of Capsicum germplasm accessions[J]. >Journal of Integrative Agriculture, 2019, 18(6): 1312-1320.
No Suggested Reading articles found!