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Xu Y.,Jiangsu Academy of Agricultural Sciences | Xu Y.,Key Laboratory of Cotton and Rapeseed Nanjing | Du J.,Chinese Academy of Sciences
Plant Journal | Year: 2014

Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination-suppressed heterochromatin regions, and that young elements are preferentially located in the gene-rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non-random distribution of LTR retrotransposons in tomato plants. © 2014 John Wiley & Sons Ltd. Source


Xu P.,Key Laboratory of Cotton and Rapeseed Nanjing | Xu P.,Jiangsu Academy of Agricultural Sciences | Cao Z.,Key Laboratory of Cotton and Rapeseed Nanjing | Cao Z.,Jiangsu Academy of Agricultural Sciences | And 6 more authors.
Crop Science | Year: 2014

Exotic Gossypium germplasms are rich sources of useful agronomic traits for cultivated cotton improvement programs. The efficient use of genetic variation available in the wild relatives depends on the ability to identify and introgress their desirable DNA segments from wild species into cultivated cotton. To introgress favorable genes from G. klotzschianum into G. hirsutum, a BC1F2 population derived from (Simian 2 × G. klotzschianum) × Simian 2 was constructed. Single marker analysis showed that the simple sequence repeat (SSR) markers BNL2652, NAU1201, and NAU1141 on chromosome 13 were significantly correlated with fiber length and micronaire value in a small BC1F2- derived population. To confirm the genetic effects of G. klotzschianum loci on fiber quality, the BC2F3 and BC2F4 populations (716 individuals/lines) were then developed by crossing BC1F2 individuals containing target segments of chromosome 13 from G. klotzschianum to the recurrent parent Simian 2. In total, 171 SSR markers from chromosome 13 and its homoeologous chromosome 18 were used to analyze the BC2F3 population. A total of 8 quantitative loci (QTL), 3 for fiber length, 2 for miconaire, and 3 for fiber strength, were detected on these two chromosomes. The fiber length QTL identified in the BC1F2 population, qFL-13-1, was confirmed in the BC2F3 and BC2F4 populations, which accounted for 7.3 and 7.0% of the phenotypic variance, respectively. The G. klotzschianum allele increased fiber length. The QTL for fiber micronaire detected in the BC1F2 population, qFMIC-13-1, was also confirmed in the BC2F3 and BC2F4 populations, which accounted for 11.2 and 7.2% of the phenotypic variance, respectively. The G. klotzschianum allele decreased the micronaire value. Two other QTL on chromosome 18 for fiber length (qFL-18-2) and micronaire (qFMIC-18-1) were also detected in both generations. Furthermore, a pair of putative homoeologous QTL for fiber length, qFL-13-1 and qFL-18-2, was identified. This study showed that some G. klotzschianum loci associated with fiber quality can be successfully transferred into upland cotton and display genetic stability. © Crop Science Society of America. Source


Zhai C.,Key Laboratory of Cotton and Rapeseed Nanjing | Zhai C.,Jiangsu Academy of Agricultural Sciences | Xu P.,Key Laboratory of Cotton and Rapeseed Nanjing | Xu P.,Jiangsu Academy of Agricultural Sciences | And 8 more authors.
Theoretical and Applied Genetics | Year: 2015

Key Message: We reported the first development ofGossypium anomalum-derived microsatellite markers and identification of recombination between sexually incompatible species by a synthesized hexaploid on genome level. Abstract: To continue to develop improved cotton varieties, it is essential to transfer desired characters from diploid wild cotton species such as Gossypium anomalum to cultivated allotetraploid cotton species. However, interspecific reproductive barriers limit gene transfer between species. In a previous study, we used colchicine treatment to produce a synthesized hexaploid derived from an interspecific hybrid between Gossypium hirsutum and G. anomalum and demonstrated its hybridity and doubled status using morphological, cytological and molecular marker methods. In the current study, to effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum-derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72 % of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48 % of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86 % of the recombination events on all chromosomes. Recombination hotspots were observed at marker intervals JAAS1148-NAU5100 on chromosome 1 and JAAS0426-NAU998 on chromosome 2. Therefore, all G. anomalum chromosomes are capable of recombining with At chromosomes in G. hirsutum. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum. © 2015, Springer-Verlag Berlin Heidelberg. Source


Xu P.,Key Laboratory of Cotton and Rapeseed Nanjing | Xu P.,Jiangsu Academy of Agricultural Sciences | Liu Z.,Key Laboratory of Cotton and Rapeseed Nanjing | Liu Z.,Jiangsu Academy of Agricultural Sciences | And 8 more authors.
Gene | Year: 2013

Salinity stress is one of the most serious factors that impede the growth and development of various crops. Wild Gossypium species, which are remarkably tolerant to salt water immersion, are valuable resources for understanding salt tolerance mechanisms of Gossypium and improving salinity resistance in upland cotton. To generate a broad survey of genes with altered expression during various stages of salt stress, a mixed RNA sample was prepared from the roots and leaves of Gossypium aridum plants subjected to salt stress. The transcripts were sequenced using the Illumina sequencing platform. After cleaning and quality checks, approximately 41.5. million clean reads were obtained. Finally, these reads were eventually assembled into 98,989 unigenes with a mean size of 452. bp. All unigenes were compared to known cluster of orthologous groups (COG) sequences to predict and classify the possible functions of these genes, which were classified into at least 25 molecular families. Variations in gene expression were then examined after exposing the plants to 200. mM NaCl for 3, 12, 72 or 144. h. Sequencing depths of approximately six million raw tags were achieved for each of the five stages of salt stress. There were 2634 (1513 up-regulated/1121 down-regulated), 2449 (1586 up-regulated/863 down-regulated), 2271 (946 up-regulated/1325 down-regulated) and 3352 (933 up-regulated/2419 down-regulated) genes that were differentially expressed after exposure to NaCl for 3, 12, 72 and 144. h, respectively. Digital gene expression analysis indicated that pathways involved in "transport", "response to hormone stimulus" and "signaling" play important roles during salt stress, while genes involved in "protein kinase activity" and "transporter activity" undergo major changes in expression during early and later stages of salt stress, respectively. © 2013 Elsevier B.V. Source

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