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Editorial | Open Access

Breeding by design for future rice: Genes and genome technologies

Jianlong Xua,bYongzhong XingcYunbi Xua,dJianmin Wana
National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56130, Mexico
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References

[1]

Q. Zhang, Strategies for developing Green Super Rice, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 16402-16409.

[2]

Y. Li, J. Xiao, L. Chen, X. Huang, Z. Cheng, B. Han, Q. Zhang, C. Wu, Rice functional genomics research: past decade and future, Mol. Plant 11 (2018) 359-380.

[3]

D.B. Lobell, W. Schlenker, J. Costa-Roberts, Climate trends and global crop production since 1980, Science 333 (2011) 616-620.

[4]

C.S. Michael, Adaptation of plants to salinity, Adv. Agron. 60 (1997) 75-120.

[5]

X.M. Li, D.Y. Chao, Y. Wu, X. Huang, K.e. Chen, L.G. Cui, L. Su, W.W. Ye, H. Chen, H.C. Chen, N.Q. Dong, T. Guo, M. Shi, Q.i. Feng, P. Zhang, B. Han, J.X. Shan, J.P. Gao, H.X. Lin, Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice, Nat. Genet. 47 (2015) 827-833.

[6]

N. Sreenivasulu, V.M. Butardo, G. Misra, R.P. Cuevas, R. Anacleto, P.B. Kavi Kishor, Designing climate-resilient rice with ideal grain quality suited for high-temperature stress, J. Exp. Bot. 66 (2015) 1737-1748.

[7]

A.Y.M. Nevame, R.M. Emon, M.A. Malek, M.M. Hasan, M.A. Alam, F.M. Muharam, F. Aslani, M.Y. Rafii, M.R. Ismail, Relationship between high temperature and formation of chalkiness and their effects on quality of rice, Biomed Res. Int. 2018 (2018) 1653721.

[8]

Y. Kan, H.X. Lin, Molecular regulation and genetic control of rice thermal response, Crop J. 9 (2021) 497-505.

[9]

T.X. Chen, S. Shabala, Y.N. Niu, Z.H. Chen, L. Shabala, H. Meinke, G. Venkataraman, A. Pareek, J.L. Xu, M.X. Zhou, Molecular mechanisms of salinity tolerance in rice, Crop J. 9 (2021) 506-520.

[10]
Z.K. Li, J.L. Xu, Breeding for drought and salt tolerant rice (Oryza sativa L.): progress and perspectives, in: M.A. Jenks, P.M. Hasegawa, S.M. Jain (Eds), Advances in Molecular Breeding toward Drought and Salt Tolerant Crops, Springer 2007, pp. 531–564.
[11]

J.D. Platten, J.A. Egdane, A.M. Ismail, Salinity tolerance, Na+ exclusion and allele mining of HKT1,5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism?, BMC Plant Biol 13 (2013) 32.

[12]

C.A. Solis, M.T. Yong, R. Vinarao, K. Jena, P. Holford, L. Shabala, M. Zhou, S. Shabala, Z.H. Chen, Back to the wild: on a quest for donors toward salinity tolerant rice, Front. Plant Sci. 11 (2020) 323.

[13]

J.S. Luo, Z.H. Zhang, Mechanisms of cadmium phytoremediation and detoxification in plants, Crop J. 9 (2021) 521-529.

[14]

G. Duan, G. Shao, Z. Tang, H. Chen, B. Wang, Z. Tang, Y. Yang, Y. Liu, F.J. Zhao, Genotypic and environmental variations in grain Cadmium and Arsenic concentrations among a panel of high yielding rice cultivars, Rice 10 (2017) 9.

[15]

L. Sun, X. Xu, Y. Jiang, Q. Zhu, F. Yang, J. Zhou, Y. Yang, Z. Huang, A. Li, L. Chen, W. Tang, G. Zhang, J. Wang, G. Xiao, D. Huang, C. Chen, Genetic diversity, rather than cultivar type, determines relative grain Cd accumulation in hybrid rice, Front. Plant Sci. 7 (2016) 1407.

[16]

Y. Ding, S. Gong, Y.i. Wang, F. Wang, H. Bao, J. Sun, C. Cai, K. Yi, Z. Chen, C. Zhu, MicroRNA166 modulates cadmium tolerance and accumulation in rice, Plant Physiol. 177 (2018) 1691-1703.

[17]

J.S. Luo, J. Huang, D.L. Zeng, J.S. Peng, G.B. Zhang, H.L. Ma, Y. Guan, H.Y. Yi, Y.L. Fu, B. Han, H.X. Lin, Q. Qian, J.M. Gong, A defensin-like protein drives cadmium efflux and allocation in rice, Nat. Commun. 9 (2018) 645.

[18]

B. Feng, K. Chen, Y.R. Cui, Z.C. Wu, T.Q. Zheng, Y.J. Zhu, J. Ali, B.B. Wang, J.L. Xu, W.Z. Zhang, Z.K. Li, Genetic dissection and simultaneous improvement of drought and low nitrogen tolerances by designed QTL pyramiding in rice, Front. Plant Sci. 9 (2018) 306.

[19]

M. Perchlik, M. Tegeder, Improving plant nitrogen use efficiency through alteration of amino acid transport processes, Plant Physiol. 175 (2017) 235-247.

[20]

N. Guo, S.N. Zhang, M.J. Gu, G.H. Xu, Function, transport and regulation of amino acids: what is missing in rice?, Crop J 9 (2021) 530-542.

[21]
S.H. Ou, Rice Disease, Commonwealth Mycological Institute, Kew, UK, 1985.
[22]

J.J. Yin, L.J. Zou, X.B. Zhu, Y.Y. Cao, M. He, X.W. Chen, Fighting the enemy: how rice survives the blast pathogen’s attack, Crop J. 9 (2021) 543-552.

[23]

L. Wang, H.T. Xie, X.Y. Zheng, J.S. Chen, S. Zhang, J.G. Wu, Recent advances and emerging trends in antiviral defense networking in rice, Crop J. 9 (2021) 553-563.

[24]

E. Shikata, Y. Kitagawa, Rice black-streaked dwarf virus: its properties, morphology and. intracellular localization, Virology 77 (1977) 826-842.

[25]

Z. Chen, L. Xie, Q. Lin, Preliminary reports on rice dwarf-like virus disease, Sci. Agric. Sin. 11 (1978) 79-83 (in Chinese with English abstract).

[26]

F. Sun, Q. Xu, Z. Cheng, Y. Fan, Y. Zhou, Advances in rice black-streaked dwarf disease in China, Jiangsu J. Agric. Sci. 29 (2013) 195-201 (in Chinese with English abstract).

[27]

Q. Liu, G. Lan, Y. Zhu, K. Chen, C. Shen, X. Zhao, F. Zhang, J. Xu, Z. Li, Genome-wide association study on resistance to rice black-streaked dwarf disease caused by rice black-streaked dwarf virus, Plant Dis. 105 (2021) 607-615.

[28]

S.D. Tanksley, S.R. McCouch, Seed banks and molecular maps: unlocking genetic potential from the wild, Science 277 (1997) 1063-1066.

[29]

R. Xu, C.Q. Sun, What happened during domestication of wild to cultivated rice, Crop J. 9 (2021) 564-576.

[30]

C.Q. Sun, X.K. Wang, Z.C. Li, A. Yoshimura, N. Iwata, Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers, Theor. Appl. Genet. 102 (2001) 157-162.

[31]

X. Li, L. Tan, Z. Zhu, H. Huang, Y. Liu, S. Hu, C. Sun, Patterns of nucleotide diversity in wild and cultivated rice, Plant Syst. Evol. 281 (2009) 97-106.

[32]

Y. Xing, Q. Zhang, Genetic and molecular bases of rice yield, Annu. Rev. Plant. Biol. 61 (2010) 421-442.

[33]
S. Yoshida, Fundamentals of Rice Crop Science, International Rice ResearchInstitute, Manila, Philippines, 1981.
[34]

Y. Wang, Y. Pang, K. Chen, L. Zhai, C. Shen, S. Wang, J. Xu, Genetic bases of source-, sink-, and yield-related traits revealed by genome-wide association study in Xian rice, Crop J. 8 (2020) 119-131.

[35]

G.M. Li, J.Y. Tang, J.K. Zheng, C.C. Chu, Exploration of rice yield potential: decoding agronomic and physiological traits, Crop J. 9 (2021) 577-589.

[36]

G.L. Li, H.L. Zhang, J.J. Li, Z.Y. Zhang, Z.C. Li, Genetic control of panicle architecture in rice, Crop J. 9 (2021) 590-597.

[37]
G.S. Khush, Prospects of and approaches to increasing the genetic yieldpotential of rice, in: R.E. Evenson, R.W. Herdt, M. Hossain (Eds.), Rice Researchin Asia: Progress and Priorities, CAB International, Wallingford, UK, and theInternational Rice Research Institute University Press, Manila, Philippines, 1996, pp. 59–71.
[38]

J.L. Xu, S.B. Yu, L.J. Luo, D.B. Zhong, H.W. Mei, Z.K. Li, Molecular dissection of the primary sink size and its related traits in rice, Plant Breed. 123 (2004) 43-50.

[39]
J.S. Bao, Nutraceutials properties and health benefits of rice, in: L.L. Yu, R. Tsao, F. Shahidi (Eds.), Cereals and Pulses: Nutraceutical Properties and Health Benefits, Wiley-Blackwell, John Wiley & Sons Inc., Chichester, West Sussex, UK, 2012, pp. 37–64.
[40]

T. Oikawa, H. Maeda, T. Oguchi, T. Yamaguchi, N. Tanabe, K. Ebana, M. Yano, T. Ebitani, T. Izawa, The birth of a black rice gene and its local spread by introgression, Plant Cell 27 (2015) 2401-2414.

[41]

W.D. Seo, J.Y. Kim, S.I. Han, J.E. Ra, J.H. Lee, Y.C. Song, M.J. Park, H.W. Kang, S.K. Oh, K.C. Jang, Relationship of radical scavenging activities and anthocyanin contents in the 12 colored rice varieties in Korea, J. Korean Soc. Appl. Biol. Chem. 54 (2011) 693-699.

[42]

D. Xia, H. Zhou, Y.O. Wang, P.B. Li, P. Fu, B. Wu, Y.Q. He, How rice organs are colored: the genetic basis of anthocyanin biosynthesis in rice, Crop J. 9 (2021) 598-608.

[43]

J. Liu, X. Wu, X. Yao, R. Yu, P.J. Larkin, C.M. Liu, Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and improved nutritional value in rice grains, Proc. Natl. Acad. Sci. U. S. A. 115 (2018) 11327-11332.

[44]

X. Ye, P. Beyer, Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm, Science 287 (2000) 303-305.

[45]

Y. Shao, F. Xu, X. Sun, J. Bao, T. Beta, Identification and quantification of phenolic acids and anthocyanins as antioxidants in bran, embryo and endosperm of white, red and black rice kernels (Oryza sativa L.), J. Cereal Sci. 59 (2014) 211-218.

[46]

Z.Y. Gao, S.C. Zhao, W.M. He, L.B. Guo, Y.L. Peng, J.J. Wang, X.S. Guo, X.M. Zhang, Y.C. Rao, C. Zhang, G.J. Dong, F.Y. Zheng, C.X. Lu, J. Hu, Q. Zhou, H.J. Liu, H.Y. Wu, J. Xu, P.X. Ni, D.L. Zeng, D.H. Liu, P. Tian, L.H. Gong, C. Ye, G.H. Zhang, J. Wang, F.K. Tian, D.W. Xue, Y. Liao, L. Zhu, M.S. Chen, J.Y. Li, S.H. Cheng, G.Y. Zhang, J. Wang, Q. Qian, Proc. Natl. Acad. Sci. U. S. A. 110 (2013) 14492-14497.

[47]

Q.J. Zhang, T. Zhu, E.H. Xia, C. Shi, Y.L. Liu, Y. Zhang, Y. Liu, W.K. Jiang, Y.J. Zhao, S.Y. Mao, L.P. Zhang, H. Huang, J.Y. Jiao, P.Z. Xu, Q.Y. Yao, F.C. Zeng, L.L. Yang, J. Gao, D.Y. Tao, Y.J. Wang, J.L. Bennetzen, L.Z. Gao, Rapid diversification of five Oryza AA genomes associated with rice adaptation, Proc. Natl. Acad. Sci. U. S. A. 111 (2014) E4954-E4962.

[48]

L. Jia, L.J. Xie, S.T. Lao, Q.H. Zhu, L.J. Fan, Rice bioinformatics in the genomic era: status and perspectives, Crop J. 9 (2021) 609-621.

[49]

C. Huang, Z. Chen, C.Z. Liang, Oryza pan-genomics: a new foundation for future rice research and improvement, Crop J. 9 (2021) 622-632.

[50]

W. Wang, R. Mauleon, Z. Hu, D. Chebotarov, S. Tai, Z. Wu, M. Li, T. Zheng, R.R. Fuentes, F. Zhang, L. Mansueto, D. Copetti, M. Sanciangco, K.C. Palis, J. Xu, C. Sun, B. Fu, H. Zhang, Y. Gao, X. Zhao, F. Shen, X. Cui, H. Yu, Z. Li, M. Chen, J. Detras, Y. Zhou, X. Zhang, Y. Zhao, D. Kudrna, C. Wang, R. Li, B. Jia, J. Lu, X. He, Z. Dong, J. Xu, Y. Li, M. Wang, J. Shi, J. Li, D. Zhang, S. Lee, W. Hu, A. Poliakov, I. Dubchak, V.J. Ulat, F.N. Borja, J.R. Mendoza, J. Ali, J. Li, Q. Gao, Y. Niu, Z. Yue, M.E.B. Naredo, J. Talag, X. Wang, J. Li, X. Fang, Y. Yin, J.C. Glaszmann, J. Zhang, J. Li, R.S. Hamilton, R.A. Wing, J. Ruan, G. Zhang, C. Wei, N. Alexandrov, K.L. McNally, Z. Li, H. Leung, Genomic variation in 3010 diverse accessions of Asian cultivated rice, Nature 557 (2018) 43-49.

[51]

Q. Zhao, Q. Feng, H. Lu, Y. Li, A. Wang, Q. Tian, Q. Zhan, Y. Lu, L. Zhang, T. Huang, Y. Wang, D. Fan, Y. Zhao, Z. Wang, C. Zhou, J. Chen, C. Zhu, W. Li, Q. Weng, Q. Xu, Z.X. Wang, X. Wei, B. Han, X. Huang, Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice, Nat. Genet. 50 (2018) 278-284.

[52]

X. Jin, P. Zarco-Tejada, U. Schmidhalter, M.P. Reynolds, M.J. Hawkesford, R.K. Varshney, T. Yang, C. Nie, Z. Li, B. Ming, Y. Xiao, Y. Xie, S. Li, High-throughput estimation of crop traits: a review of ground and aerial phenotyping platforms, IEEE Trans. Geosci. Remote Sens. 9 (2021) 200-231.

[53]

H. Feng, Z. Guo, W. Yang, C. Huang, G. Chen, W. Fang, X. Xiong, H. Zhang, G. Wang, L. Xiong, Q. Liu, An integrated hyperspectral imaging and genome-wide association analysis platform provides spectral and genetic insights into the natural variation in rice, Sci. Rep. 7 (2017) 4401.

[54]

P. Song, J.L. Wang, X.Y. Guo, W.N. Yang, C.J. Zhao, High-throughput phenotyping: breaking through the bottleneck in future crop breeding, Crop J. 9 (2021) 633-645.

[55]

Z.K. Li, F. Zhang, Rice breeding in the post-genomics era: from concept to practice, Curr. Opin. Plant Biol. 16 (2013) 261-269.

[56]

J. Ali, J.L. Xu, Y.M. Gao, X.F. Ma, L.J. Meng, Y. Wang, Y.L. Pang, Y.S. Guan, M.R. Xu, J.E. Revilleza, N.J. Franje, S.C. Zhou, Z.K. Li, F.A. Feltus, Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.), PLoS ONE 12 (2017) e0172515.

[57]

F. Zhang, Y.Y. Shi, J. Ali, J.L. Xu, Z.K. Li, Breeding by selective introgression: theory, practices, and lessons learned from rice, Crop J. 9 (2021) 646-657.

[58]

G.Q. Zhang, Target chromosome-segment substitution: a way to breeding by design in rice, Crop J. 9 (2021) 658-668.

[59]
R.W. Allard, Principles of Plant Breeding, John Willey and Sons, New York, USA, 1960.
[60]

Z.A. Desta, R. Ortiz, Genomic selection: genome-wide prediction in plant improvement, Trends Plant Sci. 19 (2014) 592-601.

[61]

Y. Xu, K.X. Ma, Y. Zhao, X. Wang, K. Zhou, G.N. Yu, C. Li, P.C. Li, Z.F. Yang, C.W. Xu, S.Z. Xu, Genomic selection: a breakthrough technology in rice breeding, Crop J. 9 (2021) 669-677.

[62]

S. Svitashev, C. Schwartz, B. Lenderts, J.K. Young, A.M. Cigan, Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes, Nat. Commun. 7 (2016) 13274.

[63]

Y. Huang, H.R. Dong, M.Q. Shang, K.J. Wang, CRISPR/Cas systems: the link between functional genes and genetic improvement, Crop J. 9 (2021) 678-687.

[64]

C. Wang, Q. Liu, Y. Shen, Y. Hua, J. Wang, J. Lin, M. Wu, T. Sun, Z. Cheng, R. Mercier, K. Wang, Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes, Nat. Biotechnol. 37 (2019) 283-286.

[65]
L.P. Yuan, Breeding of super hybrid rice, in: S. Peng, B. Hardy (Eds.), Rice Research for Food Security and Poverty Alleviation, International Rice Research Institute, Metro Manila, Philippines, 2001, pp. 143–149.
[66]

S.N. Zhang, X.H. Huang, B. Han, Understanding the genetic basis of rice heterosis: advances and prospects, Crop J. 9 (2021) 688-692.

[67]

X.H. Huang, S.H. Yang, J.Y. Gong, Y. Zhao, Q. Feng, H. Gong, W.J. Li, Q. Zhan, B. Cheng, J. Xia, B. Han, Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis, Nat. Commun. 6 (2015) 6258.

[68]

C.C. Liao, W. Ya, Z.F. Chen, G. Xie, X.W. Deng, X.Y. Tang, Innovation and development of the third-generation hybrid rice technology, Crop J. 9 (2021) 693-701.

[69]

M.B. Espe, J.E. Hill, M. Leinfelder-Miles, L.A. Espino, R. Mutters, D. Mackill, C. van Kessel, B.A. Linquist, Rice yield improvements through plant breeding are offset by inherent yield declines over time, Field Crops Res. 222 (2018) 59-65.

[70]

X. Huo, S. Wu, Z. Zhu, F. Liu, Y. Fu, H. Cai, X. Sun, P. Gu, D. Xie, L. Tan, C. Sun, NOG1 increases grain production in rice, Nat. Commun. 8 (2017) e1497.

[71]

F. Zhang, C. Wang, M. Li, Y. Cui, Y. Shi, Z. Wu, Z. Hu, W. Wang, J. Xu, Z. Li, The landscape of gene-CDS-haplotype diversity in rice: properties, population organization, footprints of domestication and breeding, and implications for genetic improvement, Mol. Plant 14 (2021) 787-804.

[72]

X. Wei, J. Qiu, K. Yong, J. Fan, Q. Zhang, H. Hua, J. Liu, Q. Wang, K.M. Olsen, B. Han, X. Huang, A quantitative genomics map of rice provides genetic insights and guides breeding, Nat. Genet. 53 (2021) 243-253.

[73]

J. Gu, X.Y. Yin, T.J. Stomph, P.C. Struik, Can exploiting natural genetic variation in leaf photosynthesis contribute to increasing rice productivity? A simulation analysis, Plant Cell Environ. 37 (2014) 22-34.

[74]

Z. Shi, T.G. Chang, G.Y. Chen, Q.F. Song, Y.J. Wang, W. Zhou, M.Y. Wang, M.N. Qu, B.S. Wang, G. Zhua, Dissection of mechanisms for high yield in two elite rice cultivars, Field Crops Res. 241 (2019) 107563.

[75]

N. Guo, M. Gu, J. Hu, H. Qu, G. Xu, Rice OsLHT1 functions in leaf-to-panicle nitrogen allocation for grain yield and quality, Front. Plant Sci. 11 (2020) 1150.

[76]

B. Hu, W. Wang, S. Ou, J. Tang, H. Li, R. Che, Z. Zhang, X. Chai, H. Wang, Y. Wang, C. Liang, L. Liu, Z. Piao, Q. Deng, K. Deng, C. Xu, Y. Liang, L. Zhang, L. Li, C. Chu, Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies, Nat. Genet. 47 (2015) 834-838.

[77]

W. Yin, Y. Xiao, M. Niu, W. Meng, L. Li, X. Zhang, D. Liu, G. Zhang, Y. Qian, Z. Sun, R. Huang, S. Wang, C.M. Liu, C. Chu, H. Tong, ARGONAUTE2 enhances grain length and salt tolerance by activating BIG GRAIN3 to modulate cytokinin distribution in rice, Plant Cell 32 (2020) 2292-2306.

[78]

N. Dong, W. Yin, D. Liu, X. Zhang, Z. Yu, W. Huang, J. Liu, Y. Yang, W. Meng, M. Niu, H. Tong, Regulation of brassinosteroid signaling and salt resistance by SERK2 and potential utilization for crop improvement in rice, Front. Plant Sci. 11 (2020) 621859.

[79]

S.A. Atanda, M. Olsen, J. Burgueño, J. Crossa, D. Dzidzienyo, Y. Beyene, M. Gowda, K. Dreher, X. Zhang, B.M. Prasanna, P. Tongoona, E.Y. Danquah, G. Olaoye, K.R. Robbins, Maximizing efficiency of genomic selection in CIMMYT’s tropical maize breeding program, Theor. Appl. Genet. 134 (2021) 279-294.

The Crop Journal
Pages 491-496
Cite this article:
Xu J, Xing Y, Xu Y, et al. Breeding by design for future rice: Genes and genome technologies. The Crop Journal, 2021, 9(3): 491-496. https://doi.org/10.1016/j.cj.2021.05.001

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Published: 08 June 2021
© 2021 Crop Science Society of China and Institute of Crop Science, CAAS.

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