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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. Source


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). Source


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. Source


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. Source


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. Source

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