Advances in Cereal Crop Genomics for Resilience under Climate Change
Abstract
1. Introduction
2. De Novo Domestication of Crop Wild Relatives and Better Exploitation of Orphan Crop Species
3. Advances in DNA Sequencing Technologies Accelerating Traits Discovery and Decoding Crop Species’ Whole Genomes
Species Name | Ploid Level | Genome Size | Assembled Genome (%) | 1 Repeat Elements (%) | GC % | Genes | 2 Sequencing Strategy | 3 Public Year | References |
---|---|---|---|---|---|---|---|---|---|
Triticum aestivum | 2n = 6x = 42 (AABBDD) allopolyploid | ~17 Gb | 14.5 Gb (85.29) | 85.00 | 48.25 | 107,891 | De novo WGS + BAC assemblies | 2018 | [12,86,92] |
4 Triticum urartu | 2n = 6x = 42 (AABBDD) | 4.94 Gb | 3.92 Gb (79.35) | 66.88 | 46.00 | 34,879 | WGS + Illumina | 2013 | [12,93] |
Oryza sativa | 2n = 2x = 24 | 389 Mb | 370 Mb (95.12) | ~51.00 | ~43.58–43.73 | 35,679 | BAC PMs + Sanger seq. | 2005 | [12,35,82] |
Zea mays | 2n = 2x = 20 | 2.3 Gb | 2.048 Gb (89.04) | 85.00 | 46.91 | 47,800 | BAC PMs + BAC seq. | 2009 | [35,83,86] |
Secale cereale | 2n = 2x = 14, RR | 7.86 Gb | 7.74 Gb (98.47) | 90.31 | 45.89 | 45,596 | PacBio + short read Illumina + Hi-C + Bio-Nano | 2021 | [94] |
Pearl millet | 2n = 2x = 14 | ~1.79 Gb | 1.76 Gb (98.32) | 68.16 | 47.90 | 38,579 | WGS + BAC | 2017 | [73] |
Sorghum bicolor (v1) | 2n = 2x = 20 | ~730 Mb | 625.6 Mb (85.70) | ~63.00 | 44.50 | ~27,640 | WGS + BACs + Sanger | 2009 | [35,84] |
Sorghum bicolor (v3) | 2n = 2x = 20 | ~700 Mb | 655.2 Mb (93.60) | 62.70 | 44.50 | 34,211 | Deep WG short read seq. + Sanger + BAC PMs | 2018 | [90] |
Eleusine coracana | 2n = 4x = 36 (AABB) | 1.45 Gb | 1.19 Gb (82.31) | 49.92 | 44.80 | 85,243 | WGS + Illumina paired-end | 2017 | [12,95] |
Hordeum vulgare | 2n = 2x = 14 | 5.1 Gb | 4.56 Gb (89.41) | ~84.00 | 44.40 | 26,159 | WGS | 2012 | [35,96] |
Setaria italica | 2n = 2x = 18 | ~490 Mb | ~423 Mb (86.33) | ~46.30 | 46.17 | 38,801 | WGS + NGS | 2012 | [12,75] |
Setaria italica | 2n = 2x = 18 | ~510 Mb | ~400 Mb (78.43) | ~40.00 | 46.17 | 24,000– 29,000 | WGS + Sanger + Illumina + BAC end seq. | 2012 | [12,35,74] |
Eragrotis tef | 2C = 2n = 4x = 40 | 772 Mb | 672 Mb (87.05) | 22.40 | 45.50 | 28,113 | Illumina HighSeq 2000 single and paired-end | 2014 | [12,32] |
Digitaria exilis | 2n = 4x = 36 | 701.66 Mb | 655.72 Mb (91.5) | 49.00 | - | 57,021 | Deep seq. of short reads + Illumina paired-end + Hi-C + Bionano optical map | 2020 | [32,97] |
4. Approaches in Mapping of Genomic Regions Controlling Variation of Quantitatively Inherited Traits
5. Broadening Crop Genetic Diversity through Mutagenesis
6. Use of Sequence Specific Nucleases for Precise Gene Editing for Crop Improvements
7. Double Haploid Technique as a Tool for Accelerated Crop Breeding for Climate Resilience
8. The Integral Role of Crop Phenotyping in Complementing Crop Genotyping
9. Unlocking the Roles of Plant Long Non-Coding RNAs (lncRNAs) in Regulating Plant Stress Responses and Adaptation
10. Pan-Genomics, Transposable Elements, and Machine Learning Hold Promise for Crop Improvement Getting into the Future
10.1. Pan-Genomics Facilitating Better Understanding and Utilization of Broader Crop Genetic Diversity for Accelerated Crop Improvement
10.2. Transposable Elements as Research Target for Decoding Crop Genomes and Understanding Crop Responses to Biotic and Abiotic Stresses
10.3. Machine Learning as a Powerful Tool for Gene Function Prediction and High-Throughput Field and Stress Phenotyping
11. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species Name | Mutant Name | Parent | Mutant Development Type (and Mutation Induction Type Used) | 1 Trait Category | 2 Description of Specific Traits Improved | 3 Reg. Year | Country | References |
---|---|---|---|---|---|---|---|---|
Oryza sativa L. | Sinar 1 | Sintanur | Gamma irradiation | Y, QNR | Higher yield and higher aromatic value than parent | 2020 | Indonesia | [142] |
Oryza sativa L. | Sinar 2 | Sintanur | Gamma irradiation | Y, BST, QNR | High yield, higher aromatic value, and higher disease resistance to BLB diseases | 2020 | Indonesia | [142] |
Oryza sativa L. | Zhefu 802 | Simei No. 2 | Gamma irradiation | BST, Y, A, QNR | Higher rice blast resistance, higher yield, early maturity, good grain quality | 1990 | China | [139,141,142] |
Triticum aestivum L. | Akebono-mochi | Kanto No. 107 | Hybridization with mutant obtained by EMS chemical treatment | QNR | Amylose free, lower pasting temperature, higher peak viscosity, and higher breakdown than for non-waxy wheat | 2000 | Japan | [142,143] |
Triticum aestivum L. | Binagom-1 | L-880 (NIAB, Pakhistan) | Direct use of an induced mutant | AST, Y | Has higher salinity tolerance, higher yield | 2016 | Bangladesh | [142] |
Triticum aestivum L. | Darkhan-172 | Darkhan-95 | Chemical mutageneis using sodium azide | Y, A | Higher yield, early maturity | 2018 | Mongolia | [142] |
Hordeum vulgare L. | Centenario | Buenavista | Gamma irradiation (333 Gy) | A | Altered maturity, seed production traits | 2006 | Peru | [142] |
Hordeum vulgare L. | Cruiser | Valticky, Diamant | Hybridization with mutant variety Diamant obtained by irradiation of seeds with X-rays (100 Gy) | A | Improved growth habit (erectoid type) | 2001 | Germany | [142] |
Hordeum vulgare L. | Phenix | Kharkivskiy 99 (mutant) | Hybridization with mutant Kharkivskiy 99 | AST | Improved drought tolerance | 2000 | Ukraine | [142] |
Zea mays L. | Kneja 627 | PCM4658 | Hybridization with mutant (from the cross PCM4658 × Mo17) | Y, A | Improved grain (seed) yield, late maturity | 2009 | Bulgaria | [142] |
Zea mays L. | P26 | F1 P1 3747 SC M3 | Treatment with fast neutrons (7.5 Gy) | A | Agronomic and botanic traits (combining ability) | 2001 | Hungary | [142] |
Zea mays L. | Longfuyu 3 | Fu2691 × 8008 | Direct use of an induced mutant | BST | Improved resistance to bacterial diseases | 2007 | China | [142] |
Setaria sp. | Jingu 21 | Jinfen 52 | Gamma irradiation (350 Gy) | Y, QNR | Improved grain (seed) yield, improved culinary quality | 2000 | China | [142] |
Panicum miliaceum L. | Cheget | Mutant parents not specified. | Hybridization with two chemo mutants | AST, BST | Improved drought tolerance, improved smut resistance | 1993 | Russia | [142] |
Sorghum bicolor L. | Fambe | CSM388 | Direct use of an induced mutant, gamma irradiation (300 Gy) | AST, Y | Resistance to lodging, high grain yield (increased number of grains per panicle) | 1998 | Mali | [142] |
Sorghum bicolor L. | PAHAT | - | Direct use of an induced mutant, gamma irradiation | Y, A, QNR | High yielding, semi dwarfness, early maturity, grain quality (protein, tannin, starch) | 2013 | Indonesia | [142,144] |
Sorghum bicolor L. | Samurai 1 | Zh-30 | Direct use of an induced mutant, gamma irradiation (0.3 Other) | Y, A, BST, QNR, AST | High yield, improved food processing quality, improved biomass, lodging resistance, resistance to midrib rot disease, large seed size | 2014 | Indonesia | [142] |
Crop Species | Delivery Mode 1 | Target Gene/s | DNA Repair Type 2 | sgRNA Promoter | Cas9 Promoter 3 | Vector Used | Trait Targeted for Improvement | References |
---|---|---|---|---|---|---|---|---|
Oryza sativa L. | EP | ERF922 | NHEJ | OsU6a | Ubi | C-ERF922 | Enhanced rice blast resistance | [196] |
AMT | ALS | HR | OsU3 | Ubi | pCXUN-Cas9-gRNA1-gRNA2-armed donor vector | Improved herbicides resistance | [197] | |
EP | SBEIIb | NHEJ | OsU3 | Ubi | pCXUN-Cas9 | High amylose content | [198] | |
EP, AMT | Gn1a, GS3, DEP1 | NHEJ | OsU6a | Ubi | pYLCRISPR/Cas9(I) | Improved grain number, larger grain size, and dense erect panicles | [199] | |
AMT | RR22 | NHEJ | OsU6a | Ubi | pYLCRSPR/Cas9 Pubi-H | Enhanced salt tolerance | [200] | |
AMT | PRX2 | NHEJ | OsPRX2 | - | pCAMBIA1301 | Improved potassium deficiency tolerance | [201] | |
Triticum aestivum L. | BMT | GW2 | NHEJ | TaU6 | Ubi | pET28a-Cas9-His | Increased grain weight and protein content | [202] |
BMT | EDR1 | NHEJ | TaU6 | Ubi | pJIT163-Ubi-Cas9 | Increased powdery mildew resistance | [203] | |
AMT | MLO | NHEJ | TaU6 | Ubi | pUC-T vector (CWBIO) | Increased mildew resistance | [204] | |
AMT | DREB2 and ERF3 | NHEJ | TaU6 | - | pJIT163-2NLSCas9 | Improved drought resistance | [193] | |
Zea mays L. | AMT | ARGOS8 | HR | ZmU6 | Ubi | sgRNA-Cas9 | Improved grain yield under drought stress tolerance | [194] |
AT | ALS2 | HR | ZmU1 | Ubi | UBI-Cas9 T-DNA vector | Improved resistance to herbicides | [205] | |
BMT | LIG1, M26, 45, ALS1 | HR | ZmU6 | Ubi | Cas9 DNA vector | Enhanced herbicide resistance and male sterility | [205] |
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Zenda, T.; Liu, S.; Dong, A.; Duan, H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life 2021, 11, 502. https://doi.org/10.3390/life11060502
Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life. 2021; 11(6):502. https://doi.org/10.3390/life11060502
Chicago/Turabian StyleZenda, Tinashe, Songtao Liu, Anyi Dong, and Huijun Duan. 2021. "Advances in Cereal Crop Genomics for Resilience under Climate Change" Life 11, no. 6: 502. https://doi.org/10.3390/life11060502
APA StyleZenda, T., Liu, S., Dong, A., & Duan, H. (2021). Advances in Cereal Crop Genomics for Resilience under Climate Change. Life, 11(6), 502. https://doi.org/10.3390/life11060502