Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning

Liu, Yao-Guang; Li, Hongmei; Chen, Letian; Qiu, Weihua; Zhang, Qunyu; Wu, Hao; Yang, Chang Yeol; Su, Jing; Wang, Zhonghua; Tian, Dong; Mei, Mantong

doi:10.1016/s0378-1119(01)00849-6

Cited by 45 publications

(37 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the pLYTAC27 TAC vector tolerates a much larger insert size (Liu et al 2002) and was successfully used to clone Pi36-3 (.16 kb). We were then able to transfer the target fragment into a modified form of pCAMBIA1300 for the complementation study.…”

Section: Discussionmentioning

confidence: 99%

The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus

et al. 2007

View full text Add to dashboard Cite

The indica rice variety Kasalath carries Pi36, a gene that determines resistance to Chinese isolates of rice blast and that has been located to a 17-kb interval on chromosome 8. The genomic sequence of the reference japonica variety Nipponbare was used for an in silico prediction of the resistance (R) gene content of the interval and hence for the identification of candidate gene(s) for Pi36. Three such sequences, which all had both a nucleotide-binding site and a leucine-rich repeat motif, were present. The three candidate genes were amplified from the genomic DNA of a number of varieties by long-range PCR, and the resulting amplicons were inserted into pCAMBIA1300 and/or pYLTAC27 vectors to determine sequence polymorphisms correlated to the resistance phenotype and to perform transgenic complementation tests. Constructs containing each candidate gene were transformed into the blast-susceptible variety Q1063, which allowed the identification of Pi36-3 as the functional gene, with the other two candidates being probable pseudogenes. The Pi36-encoded protein is composed of 1056 amino acids, with a single substitution event (Asp to Ser) at residue 590 associated with the resistant phenotype. Pi36 is a single-copy gene in rice and is more closely related to the barley powdery mildew resistance genes Mla1 and Mla6 than to the rice blast R genes Pita, Pib, Pi9, and Piz-t. An RT-PCR analysis showed that Pi36 is constitutively expressed in Kasalath.

show abstract

Section: Discussionmentioning

confidence: 99%

The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Regarding wild rice, many studies have constructed large-insert genomic libraries, including 12 BAC libraries representing 10 genomes of Oryza species (Wing et al, 2005;Ammiraju et al, 2006), a BIBAC library of O. officinalis (He, 2003), TAC libraries of cultivated rice (Liu et al, 2002) and O. officinalis (unpublished data), and a BAC library of O. rufipogon (Li et al, 2008). These genomic libraries facilitate research into the comparative genetic mapping of Oryza species, gene cloning, and genome sequencing.…”

Section: Discussionmentioning

confidence: 99%

“…The direct transformation of BAC clones that carry a large insert of wild rice DNA to mine valuable genes is not possible, because a BAC vector has not been genetically modified for replication in A. tumefaciens. Both BIBAC and TAC vectors are capable of replicating in both Escherichia coli and A. tumefaciens, and can be used to transform a large insert of DNA directly into the plant genome by transgenic technology (Hamilton, 1997;Liu et al, 1999Liu et al, , 2002. He (2003) reported that a BIBAC clone with a 120-kb O. officinalis DNA insert was successfully transferred into the Japonica rice genome, but the stress responses of the transgenic plants were not tested.…”

Section: Discussionmentioning

confidence: 99%

“…The first genomic library of O. officinalis was constructed with a plant transformationcompetent binary bacterial artificial chromosome (BIBAC), and the candidate clones of target genes isolated from the library were directly used to transform Japonica rice variety H1493 by an Agrobacterium-mediated transformation method (He, 2003). Another transformation-competent artificial chromosome (TAC) vector (Liu et al, 2002) was used to construct an O. officinalis genomic library (unpublished data), and we have transferred several clones of this TAC library into indica and japonica rice varieties Liu et al, 2014). Both studies confirmed the feasibility of transferring agronomically important genes from wild rice species to cultivated rice by largefragment transformation.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone

Liu¹,

Zhang²,

Chen³

et al. 2015

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Oryza officinalis has proven to be a natural gene reservoir for the improvement of domesticated rice as it carries many desirable traits; however, the transfer of elite genes to cultivated rice by conventional hybridization has been a challenge for rice breeders. In this study, the conserved sequence of plant stress-related NAC transcription factors was selected as a probe to screen the O. officinalis genomic transformation-competent artificial chromosome library by Southern blot; 11 positive transformation-competent artificial chromosome clones were subsequently detected. By Agrobacterium-mediated transformation, an indica rice variety, Huajingxian 74 (HJX74), was transformed with a TAC clone harboring a NAC gene-positive genomic fragment from O. officinalis. Molecular analysis revealed that the O. officinalis genomic fragment was integrated into the genome of HJX74. The transgenic lines exhibited high tolerance to drought stress. Our results demonstrate that the introduction of stress-related transformation-competent artificial chromosome clones, coupled with a transgenic validation approach, is an 13667-13678 (2015) effective method of transferring agronomically important genes from O. officinalis to cultivated rice.

show abstract

“…Many BIBAC libraries have been constructed to date, such as those for rice (Liu et al 2002;Tao et al 2002) Three BAC libraries containing genomic DNA from maize inbred B73 have been constructed, each containing DNA digested with a different restriction enzyme , and they have been fingerprinted by two complementary methods (Nelson et al 2005). A large number of these clones have also been end sequenced .…”

mentioning

confidence: 99%

Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives

et al. 2013

View full text Add to dashboard Cite

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7-to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.M AIZE is one of the most important crops worldwide, already producing more tons of grain than any other plant species, and with continuing expansion of planted acreage in the developed and developing world. It is used as a staple food crop, but also for animal feed, biofuel, and various industrial by-products, such as starches, oil, sugars, sweeteners, beverages, and adhesives. It is also a key model species for research in genetics, epigenetics, genomics, development, physiology, and evolution (Bennetzen and Hake 2009;Schnable et al. 2009;Walbot 2009). Maize was domesticated 10,000 years ago from an annual wild teosinte, Zea mays ssp. parviglumis, that originated in the balsas river lowland in Mexico (Doebley et al. 2006;van Heerwaarden et al. 2011). One feature of contemporary maize is that it is probably the most genetically diverse of all crop species. Analyses of haplotypes; sequences around the bz, z1C1, and adh1 loci; and sequences of large genomic regions all showed striking structural diversity in maize inbred lines (Fu and Dooner 2002;Song et al. 2002;Song and Messing 2003;Jung et al. 2004;Brunner et al. 2005;Wang and Dooner 2006;Gore et al. 2009;Chia et al. 2012). It also has been shown that the two ancestral progenitors of maize and the progenitor of sorghum split 11.9 MYA and the progenitors of maize hybridized 4.8 MYA to form allotetraploid maize . Hybridization resulted in broken and fused chromosomes with the reduced set of today's 10 chromosomes (Wei et al. 2007 Divergence of the two homologous chromosomal regions contin...

show abstract

Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning

Cited by 45 publications

References 21 publications

The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus

The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus

Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone

Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives

Contact Info

Product

Resources

About