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Gu C.,Nanjing Agricultural University | Wu J.,Nanjing Agricultural University | Zhang S.-J.,Nanjing Agricultural University | Yang Y.-N.,Nanjing Agricultural University | And 4 more authors.
Tree Genetics and Genomes | Year: 2011

This study identified eight S-haplotype-specific F-box genes (SFB alleles) and one S-haplotype-specific F-box-like gene (SFB-like gene) from genomic DNA by PCR combined with cleaved amplified polymorphic sequence markers in Prunus pseudocerasus and Prunus speciosa. The unknown sequences of C-termini were obtained by thermal asymmetric interlaced PCR. The whole nucleotide sequences of these genes were submitted to the EMBL/GenBank database. The SFBs shared typical structural features with SFBs from other Prunus species exhibiting gametophytic self-incompatibility. The deduced amino acid identity ranged from 77.1% to 82.4% among the four PpsSFBs and from 70.4% to 80.2% among the four PspeSFBs. The typical structural features were also detected in the PpsFB, but the sequence polymorphism was lower. The nucleotide identities ranged from 71.3% to 90.3% among the eight introns of the SFBs, the length of these introns varied from 95 to 121 bp and showed few polymorphisms. The distance between these SFBs and the corresponding S-RNases (S-ribonucleases) varied from 33 to 956 bp. Moreover, sequence analysis showed that interspecific amino acid identities in comparison with some other Prunus species were often higher than intraspecific identities, similar to S-RNase alleles. In addition, a similarity comparison found that the deduced amino acid identities among SFB alleles were higher than among S-RNase alleles, and the similarity data showed that the relationships among SFB alleles differed among S-RNase alleles, suggesting that the S-RNase and SFB alleles were separated but correlated during the coevolutionary process. © 2011 Springer-Verlag.


Gu C.,Nanjing Agricultural University | Gu C.,CAS Wuhan Botanical Garden | Liu Q.-Z.,Pomological Institute of Shandong | Yang Y.-N.,Nanjing Agricultural University | And 5 more authors.
PLoS ONE | Year: 2013

The breakdown of self-incompatibility, which could result from the accumulation of non-functional S-haplotypes or competitive interaction between two different functional S-haplotypes, has been studied extensively at the molecular level in tetraploid Rosaceae species. In this study, two tetraploid Chinese cherry (Prunus pseudocerasus) cultivars and one diploid sweet cherry (Prunus avium) cultivar were used to investigate the ploidy of pollen grains and inheritance of pollen-S alleles. Genetic analysis of the S-genotypes of two intercross-pollinated progenies showed that the pollen grains derived from Chinese cherry cultivars were hetero-diploid, and that the two S-haplotypes were made up of every combination of two of the four possible S-haplotypes. Moreover, the distributions of single S-haplotypes expressed in self- and intercross-pollinated progenies were in disequilibrium. The number of individuals of the two different S-haplotypes was unequal in two self-pollinated and two intercross-pollinated progenies. Notably, the number of individuals containing two different S-haplotypes (S1- and S5-, S5- and S8-, S1- and S4-haplotype) was larger than that of other individuals in the two self-pollinated progenies, indicating that some of these hetero-diploid pollen grains may have the capability to inactivate stylar S-RNase inside the pollen tube and grow better into the ovaries. © 2013 Gu et al.


Fan L.,Nanjing Agricultural University | Zhang M.-Y.,Nanjing Agricultural University | Liu Q.-Z.,Pomological Institute of Shandong | Li L.-T.,Nanjing Agricultural University | And 4 more authors.
Plant Molecular Biology Reporter | Year: 2013

A set of 120 simple sequence repeats (SSRs) was developed from the newly assembled pear sequence and evaluated for polymorphisms in seven genotypes of pear from different genetic backgrounds. Of these, 67 (55.8 %) primer pairs produced polymorphic amplifications. Together, the 67 SSRs detected 277 alleles with an average of 4.13 per locus. Sequencing of the amplification products from randomly picked loci NAUPy31a and NAUpy53a verified the presence of the SSR loci. When the 67 primer pairs were tested on 96 individual members of eight species in the Rosaceae family, 61.2 % (41/67) of the tested SSRs successfully amplified a PCR product in at least one of the Rosaceae genera. The transferability from pear to different species varied from 58.2 % (apple) to 11.9 % (cherry). The ratio of transferability also reflected the closer relationships within Maloideae over Prunoideae. Two pear SSR markers, NAUpy43c and NAUpy55k, could distinguish the 20 different apple genotypes thoroughly, and UPGMA cluster analysis grouped them into three groups at the similarity level of 0.56. The high level of polymorphism and good transferability of pear SSRs to Rosaceae species indicate their promise for application to future molecular screening, map construction, and comparative genomic studies among pears and other Rosaceae species. © 2013 The Author(s).


Gu C.,Nanjing Agricultural University | Zhang S.-L.,Nanjing Agricultural University | Huang S.-X.,Nanjing Agricultural University | Heng W.,Nanjing Agricultural University | And 3 more authors.
Tree Genetics and Genomes | Year: 2010

Self-incompatibility has been studied extensively at the molecular level in Solanaceae, Rosaceae, and Scrophulariaceae, all of which exhibit gametophytic self-incompatibility. In the present study, we successfully isolated nine S-RNase alleles from cultivars of Chinese cherry by PCR amplification from genomic DNA and stylar cDNA combining with cleaved amplified polymorphic sequence marker. Analysis of amino acid sequences revealed five novel S-alleles, S2, S4, S6, S8, and S9, with respective accession numbers in the NCBI database of EF541168, EF541173, EF541172, FJ628598, and FJ628599. Results showed that "Dongtang" and "Yinzhu" contained six S-alleles (S1, S3, S5, S7, S8, and S9); "Taishanganying" contained four S-alleles (S1, S2, S4, and S6); "Daiba", "Dayingzui", and "Xiaomizi" contained four S-alleles (S1, S2, S5, and S8); "Laiyangduanzhi", "Shuangquanchangba", and "Daqingye" contained three S-alleles (S1, S2, and S8). It is interesting that different cultivars collected from the same place hold the same S-genotypes. Moreover, pollination tests and pollen tube growth assays showed that nine cultivars were self-compatible. Chinese cherry presented in this article are naturally polyploidy, which is a very useful material for the study of self-compatibility, and much of this information will be valuable for further work on self-(in)compatibility of fruit tree in Rosaceae. © 2010 Springer-Verlag.


Gu C.,Nanjing Agricultural University | Gu C.,CAS Wuhan Botanical Garden | Liu Q.-Z.,Pomological Institute of Shandong | Khan M.A.,International Potato Center | And 2 more authors.
Tree Genetics and Genomes | Year: 2014

Chinese cherry (Prunus pseudocerasus) has many natural tetraploid species within Prunus. The pollen grains of tetraploid Chinese cherry are hetero-diploid, the two S-haplotypes in the pollen are a combination of two of the four possible S-haplotypes. The abnormal segregation ratios of pollen-S indicate that a few hetero-diploid pollen grains could inactivate self-stylar S-RNase inside the pollen tube and grow better into the self-ovaries than to the others. In this study, three Chinese cherry cultivars, "Daiba" (S 1 S 2 S 5 S 8), "Taishanganying" (S 1 S 2 S 4 S 6), and "Laiyangduanzhi" (S 1 S 2 S 8 S x), were used to investigate the inheritance of hetero-diploid pollen-S alleles in non-self receptors. Genetic analysis showed that the distribution of S-haplotypes is unequally expressed in self- and cross-pollinated progenies. The S 2-haplotype, which is found with lowest frequency in all progeny plants, is a likely lethal mutation. Moreover, the number of individuals with two different S-haplotypes was also unequal in the two cross-pollinated progenies. Notably, the number of individuals with S 1 S 5 and S 1 S 8 genotypes was larger than other genotypes in the cross-pollinated progeny of "Laiyangduanzhi" × "Daiba", and the number of individuals with S 1 S 4, S 1 S 6, and S 4 S 6 genotypes was larger than S 2-haplotypes in the cross-pollinated progeny of "Laiyangduanzhi" × "Taishanganying". These results indicate that only a few genotypes of hetero-diploid pollen grains have the capability to grow into the ovaries of "Laiyangduanzhi". Interestingly, the pollen grains with S 5 S 8 genotypes, which is self-compatible, was incompatible with the styles of "Laiyangduanzhi", while the pollen grains with S 1 S 8, S 1 S 6 and S 4 S 6 genotypes, which are self-incompatible, were compatible with the styles of "Laiyangduanzhi". © 2014 Springer-Verlag Berlin Heidelberg.


Zhang M.-Y.,Nanjing Agricultural University | Fan L.,Nanjing Agricultural University | Liu Q.-Z.,Pomological Institute of Shandong | Song Y.,Nanjing Agricultural University | And 3 more authors.
Plant Molecular Biology Reporter | Year: 2014

Pear is a fruit species with worldwide distribution belonging to the Rosaceae family. In this study, transcriptomes of 12 different tissues of pear were newly assembled, with a total of 17,353 SSR loci identified. Within these, repetitive sequences with dinucleotide and trinucleotide motifs were more abundant than other types. We developed 194 EST-SSR makers from the assembled sequences to test on seven pear varieties from different genetic backgrounds, on which 132 EST-SSR primers had amplicons. There were 108 primers with dinucleotide and trinucleotide motifs detecting a total of 311 alleles, with an average per primer of 2.88 and 2.86, respectively. These had better quality than primers with tetranucleotides, pentanucleotides, and hexanucleotides. Fifty polymorphic markers divided 36 pear genotypes into two groups with a similarity coefficient of 0.62. Results showed that Japanese pears had a comparatively close relationship with Chinese pears, indicating the great potential of the novel EST-SSR makers in future evaluations of pear germplasm. Furthermore, 54 EST-SSR markers were selected to test transferability to 96 other Rosaceae cultivars from eight species, including Japanese apricot, plum, apricot, peach, cherry, apple, strawberry, and loquat. Seventeen EST-SSR primers had PCR amplification products in at least one of the 96 accessions, with the highest transferability was from pear to apple at 29.63 %. Transferability from pear to Japanese apricot, plum, apricot, peach, cherry, strawberry, and loquat was 9.26, 14.81, 11.11, 12.96, 5.56, 3.7, and 12.96 %, respectively. Therefore, the newly developed EST-SSR markers can contribute to exploring the genetic relationship, evolution and comparative genomics, and gene introgressions in the Rosaceae family. © 2013 Springer Science+Business Media New York.


Gu C.,CAS Wuhan Botanical Garden | Zong X.-J.,Pomological Institute of Shandong | Wang J.-W.,Pomological Institute of Shandong | Wei H.-R.,Pomological Institute of Shandong | Liu Q.-Z.,Pomological Institute of Shandong
Journal of Horticultural Science and Biotechnology | Year: 2013

Self-incompatibility (SI) in the genus Prunus is controlled by alleles of two genes at the S-locus, S-RNase and SFB. Both genes exhibit high levels of polymorphism and sequence diversity, characteristic of plant self-incompatibility systems. In this study, eight S-RNase alleles and five SFB alleles were isolated from five accessions of P. virginiana using PCR. These alleles were novel and have been submitted to GeneBank with the following Accession Numbers: S1-RNase - S8-RNase (JF907557 - JF907564), SFB1 (JF907565), SFB2 (JF907566), and SFB4 (JF907567).The Accession Numbers of SFB7 and SFB8 are the same as S7-RNase and S8-RNase, respectively. These S-RNase and SFB alleles shared the typical structural features of the equivalent alleles in other Prunus species. The identities of the deduced amino acid sequences range from 70.5 - 80.9% among the S-RNase alleles, and from 66.5 - 82.9% among the SFB alleles. The S-RNase and SFB genes were transcribed in opposite directions. The distances between pairs of alleles in these S-haplotypes varied from 325 - 1,789 bp. Sequence comparisons showed that the identities of the deduced amino acid sequences were 99.4% between Pvir-S3 and Pweb-S10, 99.0% between Pvir-S3 and Pd-S64, 97.1% between Pvir-S7 and Pps-S5, 98.2% between Pvir-S4 and Pa-S6, 98.2% between Pvir-S6 and Pspe-S3, 98.4% between Pvir-SFB4 and Pa- SFB6, and 97.4% between Pvir-SFB7 and Pps-SFB5. Moreover, the identity between the intergenic sequences of the S7-haplotype of P. virginian and the S5-haplotype of P. pseudocerasus was 99.7%, with only one nucleotide difference (C →T).These results show that these two S-haplotypes were the closest related lineages and further support the view that alleles at these two S-loci evolved before the divergence of Prunus species.


Liu Q.-Z.,Pomological Institute of Shandong | Gu C.,CAS Wuhan Botanical Garden | Zong X.-J.,Pomological Institute of Shandong | Wang J.-W.,Pomological Institute of Shandong
Journal of Horticultural Science and Biotechnology | Year: 2012

Self-incompatibility (SI) has been studied extensively at the molecular level in many members of the Solanaceae, Rosaceae, and Scrophulariaceae, all of which exhibit gametophytic self-incompatibility (GSI). In this study, we analysed 66 new accessions of Chinese cherry (Prunus pseudocerasus) collected in Shandong, Henan, Anhui, Jiangsu, Zhejiang, and Sichuan Provinces. Their S-genotypes were identified using PCR with two conserved or four allele-specific primers. No novel S-alleles were found in these accessions. The frequencies and distributions of the S-alleles were significantly unequal. The frequencies of S 1 and S 8 were the highest, and those of S 4 and S 6 were the lowest. The unequal frequencies and distributions of S-alleles could be associated with different climates and/or habitats, or caused by other factors such as natural selection, which would accelerate the evolution of S-alleles. Understanding the frequency and distribution of S-alleles would help to develop informed orchard management strategies for Chinese cherry cultivars.

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