作物学报 ›› 2024, Vol. 50 ›› Issue (2): 373-382.doi: 10.3724/SP.J.1006.2024.33021
杨静蕾1,**(), 吴冰杰1,**(), 王安洲1, 肖英杰1,2,*()
YANG Jing-Lei1,**(), WU Bing-Jie1,**(), WANG An-Zhou1, XIAO Ying-Jie1,2,*()
摘要:
基因组选择是利用覆盖基因组的高密度标记对未知表型进行预测并选择的技术。在植物中, 利用该技术可对不同作物性状进行早期选择, 保留优势个体, 节约田间管理和表型鉴定成本, 大大加快育种进程。本研究使用rrBLUP和LASSO两种统计模型, 基于基因组、转录组和代谢组数据对玉米的农艺性状和品质性状进行了基因组预测。研究发现, 对于不同组学数据而言, 其预测能力高低依次为基因组、转录组、代谢组数据。对于不同性状而言, 品质性状的预测能力高于农艺性状。对于rrBLUP和LASSO两种模型而言, 基于基因组数据预测时所有性状均是rrBLUP为最优预测模型; 基于转录组数据预测时有53种性状是以rrBLUP为最佳预测模型, 2种性状以LASSO为最佳预测模型; 基于代谢组数据, 有43种性状以rrBLUP为最佳预测模型, 12种性状以LASSO为最佳预测模型。此外, 还发现用不同系谱材料进行预测时, 热带玉米预测温带玉米, 其效果略优于温带玉米预测热带玉米。而对于品质性状, 不同系谱间材料的预测精度高于同一系谱内。本研究系统评估了各种组学数据和不同统计模型对玉米农艺及品质性状预测能力的差异, 为未来玉米重要性状的基因组育种提供了理论依据。
[1] |
He T H, Li C D. Harness the power of genomic selection and the potential of germplasm in crop breeding for global food security in the era with rapid climate change. Crop J, 2020, 8: 688-700.
doi: 10.1016/j.cj.2020.04.005 |
[2] |
Steinwand M A, Ronald P C. Crop biotechnology and the future of food. Nat Food, 2020, 1: 273-283.
doi: 10.1038/s43016-020-0072-3 |
[3] |
Hickey L T, Hafeez A N, Robinson H, Jackson S A, Leal-Bertioli S C M, Tester M, Gao C X, Godwin I D, Hayes Ben J, Wulff B B H. Breeding crops to feed 10 billion. Nat Biotechnol, 2019, 37: 744-754.
doi: 10.1038/s41587-019-0152-9 pmid: 31209375 |
[4] |
Borlaug N E. Contributions of conventional plant breeding to food production. Science, 1983, 219: 689-693.
doi: 10.1126/science.219.4585.689 pmid: 17814030 |
[5] |
Watson A, Ghosh S, Williams M J, Cubby W S, Simmonds J, Rey M D, Asyraf Md Hatta M, Hinchliffe A, Steed A, Reynolds D, Adamski N M, Breakspear A, Korolev A, Rayner T, Dixon L E, Riaz A, Martin W, Ryan M, Edwards D, Batley J, Raman H, Carter J, Rogers C, Domoney C, Moore G, Harwood W, Nicholson P, Dieters M J, DeLacy I H, Zhou J, Uauy C, Boden S A, Park R F, Wulff B B H, Hickey L T. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants, 2018, 4: 23-29.
doi: 10.1038/s41477-017-0083-8 pmid: 29292376 |
[6] |
Meuwissen T H E, Hayes B J, Goddard M E. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 2001, 157: 1819-1829.
doi: 10.1093/genetics/157.4.1819 pmid: 11290733 |
[7] |
Nakaya A, Isobe S N. Will genomic selection be a practical method for plant breeding? Ann Bot, 2012, 110: 1303-1316.
doi: 10.1093/aob/mcs109 |
[8] |
Farah M M, Swan A A, Fortes M R S, Fonseca R, Moore S S, Kelly M J. Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle. Anim Genet, 2016, 47: 3-11.
doi: 10.1111/age.12362 pmid: 26490440 |
[9] |
Kariuki C M, Brascamp E W, Komen H, Van Arendonk J A M. Economic evaluation of progeny-testing and genomic selection schemes for small-sized nucleus dairy cattle breeding programs in developing countries. J Dairy Sci, 2017, 100: 2258-2268.
doi: S0022-0302(17)30052-8 pmid: 28109609 |
[10] |
Schaeffer L R. Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet, 2006, 123: 218-223.
doi: 10.1111/j.1439-0388.2006.00595.x pmid: 16882088 |
[11] |
Lorenzana R E, Bernardo R. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet, 2009, 120: 151-161.
doi: 10.1007/s00122-009-1166-3 pmid: 19841887 |
[12] |
Zhang X C, Perez-Rodriguez P, Burgueno J, Olsen M, Buckler E, Atlin G, Prasanna B M, Vargas M, San Vicente F, Crossa J. Rapid cycling genomic selection in a multi-parental tropical maize population. G3: Gene Genome Genet, 2017, 7: 2315-2326.
doi: 10.1534/g3.117.043141 |
[13] |
Wang X, Li L, Yang Z, Zheng X, Yu S, Xu C, Hu Z. Predicting rice hybrid performance using univariate and multivariate GBLUP models based on North Carolina mating design II. Heredity, 2017, 118: 302-310.
doi: 10.1038/hdy.2016.87 pmid: 27649618 |
[14] | Ma Y S, Liu Z X, Wen Z X, Wei S H, Yang C M, Wang H C, Yang C Y, Lu W G, Xu R, Zhang W H, Wu J A, Hu G H, Luan X Y, Fu Y S, Wang S M, Han T F, Zhang M C, Zhang L, Yuan B, Guo Y, Reif J C, Jiang Y, Li W B, Wang D C, Qiu L J. Effect of population structure on prediction accuracy of soybean 100-seed weight by genomic selection. Crop J, 2018, 44: 43-52 (in Chinese with English abstract). |
[15] |
Charmet G, Storlie E, Oury F X, Laurent V, Beghin D, Chevarin L, Lapierre A, Perretant M R, Rolland B, Heumez E, Duchalais L, Goudemand E, Bordes J, Robert O. Genome-wide prediction of three important traits in bread wheat. Mol Breed, 2014, 34: 1843-1852.
doi: 10.1007/s11032-014-0143-y |
[16] |
Beyene Y, Semagn K, Mugo S, Tarekegne A, Babu R, Meisel B, Sehabiague P, Makumbi D, Magorokosho C, Oikeh S, Gakunga J, Vargas M, Olsen M, Prasanna B M, Banziger M, Crossa J. Genetic gains in grain yield through genomic selection in eight bi-parental maize populations under drought stress. Crop Sci, 2015, 55: 154-163.
doi: 10.2135/cropsci2014.07.0460 |
[17] |
Zhang X, Perez-Rodriguez P, Semagn K, Beyene Y, Babu R, Lopez-Cruz M A, Vicente F S, Olsen M, Buckler E, Jannink J L, Prasanna B M, Crossa J. Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs. Heredity, 2015, 114: 291-299.
doi: 10.1038/hdy.2014.99 pmid: 25407079 |
[18] | Cao S, Loladze A, Yuan Y B, Wu Y S, Zhang A, Chen J F, Huestis G, Cao J S, Chaikam V, Olsen M, Prasanna B M, San Vicente F, Zhang X C. Genome-wide analysis of Tar Spot Complex resistance in maize using genotyping-by-sequencing SNPs and whole-genome prediction. Plant Genome, 2017, 10: 1-14. |
[19] |
Zhang A, Wang H W, Beyene Y, Semagn K, Liu Y, B Cao S L, Cui Z H, Ruan Y Y, Burgueno J, San Vicente F, Olsen M, Prasanna B M, Crossa J, Yu H Q, Zhang X C. Effect of trait heritability, training population size and marker density on genomic prediction accuracy estimation in 22 bi-parental tropical maize populations. Front Plant Sci, 2017, 8: 1916.
doi: 10.3389/fpls.2017.01916 pmid: 29167677 |
[20] |
Guo Z G, Tucker D M, Lu J W, Kishore V, Gay G. Evaluation of genome-wide selection efficiency in maize nested association mapping populations. Theor Appl Genet, 2012, 124: 261-275.
doi: 10.1007/s00122-011-1702-9 pmid: 21938474 |
[21] |
Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, Sulpice R, Altmann T, Stitt M, Willmitzer L, Melchinger A E. Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet, 2012, 44: 217-220.
doi: 10.1038/ng.1033 pmid: 22246502 |
[22] |
Shikha M, Kanika A, Rao A R, Mallikarjuna M G, Gupta H S, Nepolean T. Genomic selection for drought tolerance using genome-wide SNPs in maize. Front Plant Sci, 2017, 8: 550.
doi: 10.3389/fpls.2017.00550 pmid: 28484471 |
[23] |
Crossa J, Perez-Rodriguez P, Cuevas J, Montesinos-Lopez O, Jarquín D, de los Campos G, Burgueno J, Camacho-Gonzalez J M, Perez-Elizalde S, Beyene Y, Dreisigacker S, Singh R, Zhang X C, Gowda M, Roorkiwal M, Rutkoski J, Varshney R K. Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci, 2017, 22: 961-975.
doi: S1360-1385(17)30184-X pmid: 28965742 |
[24] |
Azodi C B, Pardo J, VanBuren R, De Los Campos G, Shiu S H. Transcriptome-based prediction of complex traits in maize. Plant Cell, 2020, 32: 139-151.
doi: 10.1105/tpc.19.00332 |
[25] |
Bhering L L, Junqueira V S, Peixoto L A, Cruz C D, Laviola B G. Comparison of methods used to identify superior individuals in genomic selection in plant breeding. Genet Mol Res, 2015, 14: 10888-10896.
doi: 10.4238/2015.September.9.26 pmid: 26400316 |
[26] |
Yan H L, Guo H Y, Xu W X, Dai C H, Kimani W, Xie J Y, Zhang H F, Li T, Wang F, Yu Y J, Ma M, Hao Z F, He Z Y. GWAS-assisted genomic prediction of cadmium accumulation in maize kernel with machine learning and linear statistical methods. J Hazard Mater, 2023, 441: 129929.
doi: 10.1016/j.jhazmat.2022.129929 |
[27] | Tibshirani R. Regression shrinkage and selection via the lasso. J Roy Stat Soc B, 1996, 58: 267-288. |
[28] |
Ahmad I, Singh A, Fahad M, Waqas M M. Remote sensing-based framework to predict and assess the interannual variability of maize yields in Pakistan using Landsat imagery. Comput Electron Agric, 2020, 178: 105732-105732.
doi: 10.1016/j.compag.2020.105732 |
[29] |
Islam M S, Fang D D, Jenkins J N, Guo J, McCarty J C, Jones D C. Evaluation of genomic selection methods for predicting fiber quality traits in Upland cotton. Mol Genet Genom, 2020, 295: 67-79.
doi: 10.1007/s00438-019-01599-z |
[30] |
Tsai H Y, Janss L L, Andersen J R, Orabi J, Jensen J D, Jahoor A, Jensen J. Genomic prediction and GWAS of yield, quality and disease-related traits in spring barley and winter wheat. Sci Rep, 2020, 10: 1-15.
doi: 10.1038/s41598-019-56847-4 |
[31] |
Zhang F, Wu J F, Sade N, Wu S, Egbaria A, Fernie A R, Yan J B, Qin F, Wei C, Brotman Y, Dai M Q. Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biol, 2021, 22: 260-260.
doi: 10.1186/s13059-021-02481-1 pmid: 34488839 |
[32] |
Qin S, Xu Y, Nie Z, Liu H, Gao W, Li C, Zhao P. Metabolomic and antioxidant enzyme activity changes in response to cadmium stress under boron application of wheat (Triticum aestivum). Environ Sci Pollut Res Int, 2022, 29: 34701-34713.
doi: 10.1007/s11356-021-17123-z |
[33] |
Hu X H, Xie W B, Wu C C, Xu S Z. A directed learning strategy integrating multiple omic data improves genomic prediction. Plant Biotechnol J, 2019, 17: 2011-2020.
doi: 10.1111/pbi.13117 pmid: 30950198 |
[34] |
Li H, Peng Z Y, Yang X H, Wang W D, Fu J J, Wang J H, Han Y J, Chai Y C, Guo T T, Yang N, Liu J, Warburton M L, Cheng Y B, Hao X M, Zhang P, Zhao J Y, Liu Y J, Wang G Y, Li J S, Yan J B. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet, 2013, 45: 43-50.
doi: 10.1038/ng.2484 pmid: 23242369 |
[35] |
Yang N, Lu Y L, Yang X H, Huang J, Zhou Y, Ali F, Wen W W, Liu J, Li J S, Yan J B. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet, 2014, 10: e1004573.
doi: 10.1371/journal.pgen.1004573 |
[36] |
Wang H, Xu S T, Fan Y M, Liu N N, Zhan W, Liu H J, Xiao Y J, Li K, Pan Q C, Li W Q, Deng M, Liu J, Jin M, Yang X H, Li J S, Li Q, Yan J B. Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses. Plant Biotechnol J, 2018, 16: 1464-1475.
doi: 10.1111/pbi.12889 pmid: 29356296 |
[37] |
Deng M, Li D Q, Luo J Y, Xiao Y J, Liu H J, Pan Q C, Zhang X H, Jin M L, Zhao M C, Yan J B. The genetic architecture of amino acids dissection by association and linkage analysis in maize. Plant Biotechnol J, 2017, 15: 1250-1263.
doi: 10.1111/pbi.12712 pmid: 28218981 |
[38] | Wen W W, Li D, Li X, Gao Y Q, Li W Q, Li H H, Liu J, Liu H J, Chen W, Luo J, Yan J B. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun, 2014, 5: 1-10. |
[39] |
Endelman J B. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome, 2011, 4: 250-255.
doi: 10.3835/plantgenome2011.08.0024 |
[40] |
Zheng L W, Ma S J, Shen D D, Fu H, Wang Y, Liu Y, Shah K, Yue C P, Huang J Y. Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses. BMC Plant Biol, 2021, 21: 543.
doi: 10.1186/s12870-021-03332-8 pmid: 34800975 |
[41] |
De Los Campos G, Hickey J M, Pong-Wong R, Daetwyler H D, Calus M P. Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics, 2013, 193: 327-345.
doi: 10.1534/genetics.112.143313 pmid: 22745228 |
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