CIMBL55: a repository for maize drought resistance alleles
Tian Tian, Feng Qin
CIMBL55: a repository for maize drought resistance alleles
Droughts threaten crop yields worldwide. Compared to other major staple cereal crops, maize (Zea mays) is especially sensitive to drought, which can cause dramatic fluctuations in its yield potential. Natural maize populations contain many superior alleles that can enhance drought resistance through complex regulatory mechanisms. We recently de novo assembled the genome of a prominent drought-resistant maize germplasm, CIMBL55, and systematically dissected the genetic basis for its drought resistance on the genome, transcriptome, and epigenome levels. These analyses revealed 65 favorable drought resistance alleles in CIMBL55. Subsequently, we genetically verified the functions of the drought resistance genes ZmABF4, ZmNAC075, and ZmRtn16 and unraveled the function of ZmRtn16 on a molecular level.
Maize / Drought resistance / Genome assembly / Genetic variants
[1] |
Al Abdallat AM, Ayad JY, Abu Elenein JM, Al Ajlouni Z, Harwood WA (2014) Overexpression of the transcription factor HvSNAC1 improves drought tolerance in barley (Hordeum vulgare L.). Mol Breeding 33:401–414. https://doi.org/10.1007/s11032-013-9958-1
|
[2] |
Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS et al (2022) Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat Gen 54:1736. https://doi.org/10.1038/s41588-022-01184-y
|
[3] |
Hirt H, Al-Babili S, Almeida-Trapp M, Antoine M, Aranda M, Bartels D, Bennett M, Blilou I, Boer D, Boulouis A et al (2023) PlantACT! - how to tackle the climate crisis. Trends Plant Sci 28:537. https://doi.org/10.1016/j.tplants.2023.01.005
|
[4] |
Huang Y, Wang H, Zhu Y, Huang X, Li S, Wu X, Zhao Y, Bao Z, Qin L, Jin Y et al (2022) THP9 enhances seed protein content and nitrogen-use efficiency in maize. Nature 2022(612):292. https://doi.org/10.1038/s41586-022-05441-2
|
[5] |
Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y et al (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373:655–662. https://doi.org/10.1126/science.abg5289
|
[6] |
Li C, Xiang X, Huang Y, Zhou Y, An D, Dong J, Zhao C, Liu H, Li Y, Wang Q et al (2020) Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize. Nat Commun 11:17. https://doi.org/10.1038/s41467-019-14023-2
|
[7] |
Liang Y, Liu HJ, Yan J, Tian F (2021) Natural variation in crops: realized understanding, continuing promise. Annu Rev Plant Biol 72:357–385. https://doi.org/10.1146/annurev-arplant-080720-090632
|
[8] |
Lin G, He C, Zheng J, Koo DH, Le H, Zheng H, Tamang TM, Lin J, Liu Y, Zhao M et al (2021) Chromosome-level genome assembly of a regenerable maize inbred line A188. Genome Biol 22:175. https://doi.org/10.1186/s13059-021-02396-x
|
[9] |
Liu S, Li C, Wang H, Wang S, Yang S, Liu X, Yan J, Li B, Beatty M, Zastrow-Hayes G et al (2020) Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol 21:163. https://doi.org/10.1186/s13059-020-02069-1
|
[10] |
Madan Babu M, Teichmann SA (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31:1234–1244. https://doi.org/10.1093/nar/gkg210
|
[11] |
Rodrigues J, Inze D, Nelissen H, Saibo NJM (2019) Source-sink regulation in crops under water deficit. Trends Plant Sci 24:652–663. https://doi.org/10.1016/j.tplants.2019.04.005
|
[12] |
Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X et al (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 50:1289–1295. https://doi.org/10.1038/s41588-018-0182-0
|
[13] |
Tian T, Wang S, Yang S, Yang Z, Liu S, Wang Y, Gao H, Zhang S, Yang X, Jiang C et al (2023) Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm. Nat Gen 55:496. https://doi.org/10.1038/s41588-023-01297-y
|
[14] |
Wang B, Hou M, Shi J, Ku L, Song W, Li C, Ning Q, Li X, Li C, Zhao B et al (2023) De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nat Genet 55:312–323. https://doi.org/10.1038/s41588-022-01283-w
|
[15] |
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. Nat Genet 48:1233–1241. https://doi.org/10.1038/ng.3636
|
[16] |
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H et al (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40:e49. https://doi.org/10.1093/nar/gkr1293
|
[17] |
Yang N, Liu J, Gao Q, Gui S, Chen L, Yang L, Huang J, Deng T, Luo J, He L et al (2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet 51:1052–1059. https://doi.org/10.1038/s41588-019-0427-6
|
[18] |
Yang Z, Qin F (2023) The battle of crops against drought: Genetic dissection and improvement. J Integr Plant Biol 65:496–525. https://doi.org/10.1111/jipb.13451
|
[19] |
Zhang X, Ding X, Marshall RS, Paez-Valencia J, Lacey P, Vierstra RD, Otegui MS (2020) Reticulon proteins modulate autophagy of the endoplasmic reticulum in maize endosperm. Elife 9:e51918. https://doi.org/10.7554/elife.51918
|
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