Unbiased genomic distribution of genes related to cell morphogenesis in cotton by chromosome mapping

Liu, Chuanxiang; Lin, Zhongxu; Zhang, Xianlong

doi:10.1007/s11240-011-0059-8

Cited by 7 publications

(5 citation statements)

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“…The polymorphic loci were integrated into the interspecific BC 1 linkage map [18], [19], [20], [21], and QTL mapping was performed based on newly improved linkage map. Both map construction and QTL mapping were carried out according to the methods described by Li et al [19].…”

Section: Methodsmentioning

confidence: 99%

“…A high-density linkage map including 2316 loci and enriched by new markers has been constructed in our laboratory [18], [19], [20], [21], and traits related to fiber quality have been explored. In this study, markers were developed from genes specifically or preferentially expressed during cotton fiber development to (i) understand their genomic distribution, (ii) determine their relationship to QTLs involved in fiber quality, and (iii) explore expression differences between G. hirsutum and G. barbadense .…”

Section: Introductionmentioning

confidence: 99%

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Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton

Yuan

Zhang

et al. 2013

PLoS ONE

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Cotton fiber is an ideal model to study cell elongation and cell wall construction in plants. During fiber development, some genes and proteins have been reported to be specifically or preferentially expressed. Mapping of them will reveal the genomic distribution of these genes, and will facilitate selection in cotton breeding. Based on previous reports, we designed 331 gene primers and 164 protein primers, and used single-strand conformation polymorphism (SSCP) to map and integrate them into our interspecific BC1 linkage map. This resulted in the mapping of 57 loci representing 51 genes or proteins on 22 chromosomes. For those three markers which were tightly linked with quantitative trait loci (QTLs), the QTL functions obtained in this study and gene functions reported in previous reports were consistent. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of 52 polymorphic functional primers showed that 21 gene primers and 17 protein primers had differential expression between Emian22 (Gossypium hirsutum) and 3–79 (G. barbadense). Both RT-PCR and quantitative real-time PCR (qRT-PCR) analyses of the three markers tightly linked with QTLs were consistent with QTL analysis and field experiments. Gene Ontology (GO) categorization revealed that almost all 51 mapped genes belonged to multiple categories that contribute to fiber development, indicating that fiber development is a complex process regulated by various genes. These 51 genes were all specifically or preferentially expressed during fiber cell elongation and secondary wall biosynthesis. Therefore, these functional gene-related markers would be beneficial for the genetic improvement of cotton fiber length and strength.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton

Yuan

Zhang

et al. 2013

PLoS ONE

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“…After linkage analysis, 9 of the 13 polymorphic loci of pre-miRNAs were mapped on 7 cotton chromosomes (Chr01, Chr04, Chr13, Chr15, Chr16, Chr23 and Chr26) based on SSCP analysis which can discover minor sequence mutations and reveal more polymorphisms to map genes [ 35 ]. For miRNA-based SRAP markers, 54 of the 59 polymorphic loci were mapped on 23 cotton chromosomes, except for Chr01, Chr22, and Chr24.…”

Section: Resultsmentioning

confidence: 99%

Linkage mapping and expression analysis of miRNAs and their target genes during fiber development in cotton

Gao

Zhang

et al. 2013

BMC Genomics

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BackgroundMicroRNAs (miRNAs) are small, endogenously expressed, non-coding RNA molecules involved in gene transcription and expression that combine with specific mRNA site of target genes to inhibit protein synthesis or degrade mRNA. Since the first plant miRNA was reported in 2002, numerous new miRNAs and their targets have been discovered via high-throughput sequencing and computational approaches. However, the genetic variation of miRNA genes is poorly understood due to the lack of miRNA-specific DNA markers.ResultsTo study the genetic variation and map miRNAs and their putative target genes in cotton, we designed specific primers based on pre-miRNAs and published putative target genes. A total of 83 pre-miRNA primers and 1,255 putative target gene primers were surveyed, and 9 pre-miRNA polymorphic loci were mapped on 7 of the 26 tetraploid cotton chromosomes. Furthermore, 156 polymorphic loci of the target genes were mapped on the cotton genome. To map more miRNA loci, miRNA-based SRAP (sequence-related amplified polymorphism) markers were used to map an additional 54 polymorphic loci on the cotton genome with the exception of Chr01, Chr22, and Chr24. Finally, a network between miRNAs and their targets was constructed. All pre-miRNAs and 98 putative target genes were selected for RT-PCR analysis, revealing unique expression patterns across different fiber development stages between the mapping parents.ConclusionsOur data provide an overview of miRNAs, their putative targets, and their network in cotton as well as comparative expression analyses between Gossypium hirsutum and G. barbadense. These data provide a foundation for understanding miRNA regulation during cotton fiber development.

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“…hirsutum TFs in an analysis of polymorphisms and revealed polymorphism ratios of 1.6%, 2.1%, and 2.3% in the (Yumian 1×CCRI35) F 2:6 , (Yumian 1×T586) F 2:7 , and (Yumian 1×7235) F 2:6 populations, respectively. The higher rate of polymorphisms detected in the present study may have been caused by SSCP, which can detect minor difference between sequences [ 38 ]. This result may also be caused by differences between the interspecific and intraspecific populations.…”

Section: Discussionmentioning

confidence: 99%

Genetic Mapping and Comparative Expression Analysis of Transcription Factors in Cotton

Jin

Lin

2015

PLoS ONE

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Transcription factors (TFs) play an important role in the regulation of plant growth and development. The study of the structure and function of TFs represents a research frontier in plant molecular biology. The findings of these studies will provide significant information regarding genetic improvement traits in crops. Currently, a large number of TFs have been cloned, and their function has been verified. However, relatively few studies that genetically map TFs in cotton are available. To genetically map TFs in cotton in this study, specific primers were designed for TF genes that were published in the Plant Transcription Factor Database. A total of 977 TF primers were obtained, and 31 TF polymorphic loci were mapped on 15 cotton chromosomes. These polymorphic loci were clearly preferentially distributed on chromosomes 5, 11, 19 and 20; and TFs from the same family mapped to homologous cotton chromosomes. In-silico mapping verified that many mapped TFs were mapped on their corresponding chromosomes or their homologous chromosomes’ corresponding chromosomes in the diploid genomes. QTL mapping for fiber quality revealed that TF-Ghi005602-2 mapped on Chr19 was associated with fiber length. Eighty-five TF genes were selected for RT-PCR analysis, and 4 TFs were selected for qRT-PCR analysis, revealing unique expression patterns across different stages of fiber development between the mapping parents. Our data offer an overview of the chromosomal distribution of TFs in cotton, and the comparative expression analysis between Gossypium hirsutum and G. barbadense provides a rough understanding of the regulation of TFs during cotton fiber development.

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Unbiased genomic distribution of genes related to cell morphogenesis in cotton by chromosome mapping

Cited by 7 publications

References 35 publications

Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton

Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton

Linkage mapping and expression analysis of miRNAs and their target genes during fiber development in cotton

Genetic Mapping and Comparative Expression Analysis of Transcription Factors in Cotton

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