Genome-wide identification and expression analysis of stress-associated proteins (SAPs) containing A20/AN1 zinc finger in cotton

Gao, Wei; Long, Lu; Tian, Xiaohui; Jin, Jingjing; Liu, Huili; Zhang, Hui; Xu, Fuchun; Song, Chun‐Peng

doi:10.1007/s00438-016-1252-6

Cited by 44 publications

(44 citation statements)

References 37 publications

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Section: Resultsmentioning

confidence: 99%

“…The high number of homoeologous segments present in the genome of the allotetraploid cotton results in the existence of two or more copies for most genes ( Wang et al, 2014 ; Gao et al, 2016a ). In order to obtain a functional mutant in cotton, it is imperative to edit homoeologous sequences simultaneously, and in most cases, it is possible to find highly conserved CRISPR target sequences in the homeolog genes ( Gao et al, 2016a ). To test whether simultaneous mutation of homoeologous genes is feasible in cotton we chose Chloroplastos alterados 1 ( GhCLA1 ) which is involved in chloroplast development and have two homoeologous sequences (D10G1640 from the sub-genome D and A10G2292 from the sub-genome A, Figure 4A ).…”

Section: Resultsmentioning

confidence: 99%

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Genome Editing in Cotton with the CRISPR/Cas9 System

et al. 2017

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Genome editing is an important tool for gene functional studies as well as crop improvement. The recent development of the CRISPR/Cas9 system using single guide RNA molecules (sgRNAs) to direct precise double strand breaks in the genome has the potential to revolutionize agriculture. Unfortunately, not all sgRNAs are equally efficient and it is difficult to predict their efficiency by bioinformatics. In crops such as cotton (Gossypium hirsutum L.), with labor-intensive and lengthy transformation procedures, it is essential to minimize the risk of using an ineffective sgRNA that could result in the production of transgenic plants without the desired CRISPR-induced mutations. In this study, we have developed a fast and efficient method to validate the functionality of sgRNAs in cotton using a transient expression system. We have used this method to validate target sites for three different genes GhPDS, GhCLA1, and GhEF1 and analyzed the nature of the CRISPR/Cas9-induced mutations. In our experiments, the most frequent type of mutations observed in cotton cotyledons were deletions (∼64%). We prove that the CRISPR/Cas9 system can effectively produce mutations in homeologous cotton genes, an important requisite in this allotetraploid crop. We also show that multiple gene targeting can be achieved in cotton with the simultaneous expression of several sgRNAs and have generated mutations in GhPDS and GhEF1 at two target sites. Additionally, we have used the CRISPR/Cas9 system to produce targeted gene fragment deletions in the GhPDS locus. Finally, we obtained transgenic cotton plants containing CRISPR/Cas9-induced gene editing mutations in the GhCLA1 gene. The mutation efficiency was very high, with 80.6% of the transgenic lines containing mutations in the GhCLA1 target site resulting in an intense albino phenotype due to interference with chloroplast biogenesis.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Genome Editing in Cotton with the CRISPR/Cas9 System

et al. 2017

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“…Besides Pv04, this study identified a SNP on Pv09 for quantitative resistance against race 503 in gene model Phvul.009G169600 that encodes a zinc finger protein. This gene model contains a CCCH domain and its involvement in plant disease resistance is well documented ( Deng et al, 2012 ; Gao W. et al, 2016 ; Cui et al, 2018 ). In the common bean genome only two NBS-LRR genes are located at distal end of Pv09 ( Richard et al, 2017 ) and identification of QTL against race 503 on Pv09 is interesting and warrants in silico identification of other plant disease resistance signatures such as zinc finger proteins from the common bean genomes.…”

Section: Discussionmentioning

confidence: 99%

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

et al. 2020

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Common bean ( Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum . The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.

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“…The SAP gene family members have two special ZF domains: the highly conserved A20 domain, which was first isolated in human umbilical vein endothelial cells with the characterization of a tumor necrosis factor (TNF)-α-inducible protein; and/or the AN1 domain, which is also highly conserved and first identified from Xenopus laevis animal hemisphere 1 (AN1) maternal RNA with the delineation of the ubiquitin-like protein [ 8 , 9 ]. The SAP proteins expressed in Arabidopsis thaliana (hereafter Arabidopsis ), rice ( Oryza sativa ), tomato ( Solanum lycopersicum ), and cotton ( Gossypium hirsutum ) have been classified into five groups (I through V) based on results from their phylogenetic analyses [ 10 , 11 ]. One significant feature of plant SAPs is the very frequent occurrence of intronless genes [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

“…One significant feature of plant SAPs is the very frequent occurrence of intronless genes [ 2 ]. For example, 11 rice SAP genes, 15 from desert poplar ( Populus euphratica ), and 30 from cotton lack introns and show a remarkably higher percentage of intronless genes [ 2 , 6 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

Dong

Duan

Zhao

et al. 2018

IJMS

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Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

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Genome-wide identification and expression analysis of stress-associated proteins (SAPs) containing A20/AN1 zinc finger in cotton

Cited by 44 publications

References 37 publications

Genome Editing in Cotton with the CRISPR/Cas9 System

Genome Editing in Cotton with the CRISPR/Cas9 System

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

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